Starting phenix.real_space_refine
on Wed May 21 12:45:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yij_33860/05_2025/7yij_33860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yij_33860/05_2025/7yij_33860.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yij_33860/05_2025/7yij_33860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yij_33860/05_2025/7yij_33860.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yij_33860/05_2025/7yij_33860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yij_33860/05_2025/7yij_33860.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     K       1      8.98       5
     S     128      5.16       5
     C   13796      2.51       5
     N    3544      2.21       5
     O    3844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 21313
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 660, 5328
          Classifications: {'peptide': 660}
          Link IDs: {'PTRANS': 19, 'TRANS': 640}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'  K': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 13.49, per 1000 atoms: 0.63
  Number of scatterers: 21313
  At special positions: 0
  Unit cell: (146.877, 146.877, 129.897, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       1     19.00
     S     128     16.00
     O    3844      8.00
     N    3544      7.00
     C   13796      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.28
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5048

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 8 sheets defined
      43.8% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.598A  pdb=" N   GLU A  79 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 154
      removed outlier: 4.142A  pdb=" N   THR A 153 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 178
    Processing helix  chain 'A' and resid 183 through 187
    Processing helix  chain 'A' and resid 211 through 238
      removed outlier: 3.500A  pdb=" N   THR A 215 " --> pdb=" O   CYS A 211 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
      Proline residue:  A 233  - end of helix
    Processing helix  chain 'A' and resid 245 through 265
      removed outlier: 3.523A  pdb=" N   VAL A 249 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ASP A 251 " --> pdb=" O   TRP A 247 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   SER A 252 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 300
      removed outlier: 3.959A  pdb=" N   PHE A 293 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   VAL A 294 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ILE A 295 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ASP A 296 " --> pdb=" O   TRP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
    Processing helix  chain 'A' and resid 327 through 330
    Processing helix  chain 'A' and resid 331 through 337
      removed outlier: 3.561A  pdb=" N   LYS A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 375
      removed outlier: 4.061A  pdb=" N   VAL A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 397
      removed outlier: 3.608A  pdb=" N   GLN A 391 " --> pdb=" O   SER A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 431
    Processing helix  chain 'A' and resid 442 through 463
      removed outlier: 3.860A  pdb=" N   LYS A 446 " --> pdb=" O   THR A 442 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA A 451 " --> pdb=" O   MET A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 494
      removed outlier: 4.170A  pdb=" N   THR A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
      removed outlier: 3.847A  pdb=" N   SER A 502 " --> pdb=" O   PRO A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 528
      removed outlier: 3.790A  pdb=" N   ILE A 527 " --> pdb=" O   VAL A 524 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   CYS A 528 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 524 through 528'
    Processing helix  chain 'A' and resid 529 through 542
      removed outlier: 3.895A  pdb=" N   ASN A 541 " --> pdb=" O   CYS A 537 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ARG A 542 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 563
    Processing helix  chain 'A' and resid 643 through 653
      removed outlier: 3.961A  pdb=" N   LYS A 648 " --> pdb=" O   GLU A 644 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   VAL A 649 " --> pdb=" O   ALA A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 658
      removed outlier: 3.799A  pdb=" N   ASN A 658 " --> pdb=" O   ALA A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 691
      removed outlier: 3.715A  pdb=" N   ARG A 691 " --> pdb=" O   GLU A 687 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 79
      removed outlier: 3.598A  pdb=" N   GLU B  79 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 154
      removed outlier: 4.142A  pdb=" N   THR B 153 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 178
    Processing helix  chain 'B' and resid 183 through 187
    Processing helix  chain 'B' and resid 211 through 238
      removed outlier: 3.500A  pdb=" N   THR B 215 " --> pdb=" O   CYS B 211 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR B 216 " --> pdb=" O   ALA B 212 " (cutoff:3.500A)
      Proline residue:  B 233  - end of helix
    Processing helix  chain 'B' and resid 245 through 265
      removed outlier: 3.523A  pdb=" N   VAL B 249 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ASP B 251 " --> pdb=" O   TRP B 247 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   SER B 252 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 300
      removed outlier: 3.959A  pdb=" N   PHE B 293 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   VAL B 294 " --> pdb=" O   LYS B 290 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ILE B 295 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ASP B 296 " --> pdb=" O   TRP B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 326
    Processing helix  chain 'B' and resid 327 through 330
    Processing helix  chain 'B' and resid 331 through 337
      removed outlier: 3.561A  pdb=" N   LYS B 337 " --> pdb=" O   ARG B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 375
      removed outlier: 4.061A  pdb=" N   VAL B 353 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 397
      removed outlier: 3.608A  pdb=" N   GLN B 391 " --> pdb=" O   SER B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 431
    Processing helix  chain 'B' and resid 442 through 463
      removed outlier: 3.860A  pdb=" N   LYS B 446 " --> pdb=" O   THR B 442 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA B 451 " --> pdb=" O   MET B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 494
      removed outlier: 4.171A  pdb=" N   THR B 469 " --> pdb=" O   GLY B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 514
      removed outlier: 3.847A  pdb=" N   SER B 502 " --> pdb=" O   PRO B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 528
      removed outlier: 3.790A  pdb=" N   ILE B 527 " --> pdb=" O   VAL B 524 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   CYS B 528 " --> pdb=" O   LEU B 525 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 524 through 528'
    Processing helix  chain 'B' and resid 529 through 542
      removed outlier: 3.895A  pdb=" N   ASN B 541 " --> pdb=" O   CYS B 537 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ARG B 542 " --> pdb=" O   VAL B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 563
    Processing helix  chain 'B' and resid 643 through 653
      removed outlier: 3.961A  pdb=" N   LYS B 648 " --> pdb=" O   GLU B 644 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   VAL B 649 " --> pdb=" O   ALA B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 658
      removed outlier: 3.799A  pdb=" N   ASN B 658 " --> pdb=" O   ALA B 655 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 681 through 691
      removed outlier: 3.715A  pdb=" N   ARG B 691 " --> pdb=" O   GLU B 687 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 79
      removed outlier: 3.598A  pdb=" N   GLU C  79 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 154
      removed outlier: 4.142A  pdb=" N   THR C 153 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 178
    Processing helix  chain 'C' and resid 183 through 187
    Processing helix  chain 'C' and resid 211 through 238
      removed outlier: 3.500A  pdb=" N   THR C 215 " --> pdb=" O   CYS C 211 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR C 216 " --> pdb=" O   ALA C 212 " (cutoff:3.500A)
      Proline residue:  C 233  - end of helix
    Processing helix  chain 'C' and resid 245 through 265
      removed outlier: 3.523A  pdb=" N   VAL C 249 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ASP C 251 " --> pdb=" O   TRP C 247 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   SER C 252 " --> pdb=" O   LEU C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 300
      removed outlier: 3.959A  pdb=" N   PHE C 293 " --> pdb=" O   LEU C 289 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   VAL C 294 " --> pdb=" O   LYS C 290 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ILE C 295 " --> pdb=" O   THR C 291 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ASP C 296 " --> pdb=" O   TRP C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 326
    Processing helix  chain 'C' and resid 327 through 330
    Processing helix  chain 'C' and resid 331 through 337
      removed outlier: 3.561A  pdb=" N   LYS C 337 " --> pdb=" O   ARG C 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 375
      removed outlier: 4.061A  pdb=" N   VAL C 353 " --> pdb=" O   LEU C 349 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 397
      removed outlier: 3.608A  pdb=" N   GLN C 391 " --> pdb=" O   SER C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 414 through 431
    Processing helix  chain 'C' and resid 442 through 463
      removed outlier: 3.860A  pdb=" N   LYS C 446 " --> pdb=" O   THR C 442 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA C 451 " --> pdb=" O   MET C 447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 464 through 494
      removed outlier: 4.171A  pdb=" N   THR C 469 " --> pdb=" O   GLY C 465 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 498 through 514
      removed outlier: 3.847A  pdb=" N   SER C 502 " --> pdb=" O   PRO C 498 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 524 through 528
      removed outlier: 3.790A  pdb=" N   ILE C 527 " --> pdb=" O   VAL C 524 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   CYS C 528 " --> pdb=" O   LEU C 525 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 524 through 528'
    Processing helix  chain 'C' and resid 529 through 542
      removed outlier: 3.895A  pdb=" N   ASN C 541 " --> pdb=" O   CYS C 537 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ARG C 542 " --> pdb=" O   VAL C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 557 through 563
    Processing helix  chain 'C' and resid 643 through 653
      removed outlier: 3.961A  pdb=" N   LYS C 648 " --> pdb=" O   GLU C 644 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   VAL C 649 " --> pdb=" O   ALA C 645 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 654 through 658
      removed outlier: 3.799A  pdb=" N   ASN C 658 " --> pdb=" O   ALA C 655 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 681 through 691
      removed outlier: 3.715A  pdb=" N   ARG C 691 " --> pdb=" O   GLU C 687 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 79
      removed outlier: 3.597A  pdb=" N   GLU D  79 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 154
      removed outlier: 4.142A  pdb=" N   THR D 153 " --> pdb=" O   ALA D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 178
    Processing helix  chain 'D' and resid 183 through 187
    Processing helix  chain 'D' and resid 211 through 238
      removed outlier: 3.500A  pdb=" N   THR D 215 " --> pdb=" O   CYS D 211 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR D 216 " --> pdb=" O   ALA D 212 " (cutoff:3.500A)
      Proline residue:  D 233  - end of helix
    Processing helix  chain 'D' and resid 245 through 265
      removed outlier: 3.523A  pdb=" N   VAL D 249 " --> pdb=" O   ILE D 245 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ASP D 251 " --> pdb=" O   TRP D 247 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   SER D 252 " --> pdb=" O   LEU D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 282 through 300
      removed outlier: 3.959A  pdb=" N   PHE D 293 " --> pdb=" O   LEU D 289 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   VAL D 294 " --> pdb=" O   LYS D 290 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ILE D 295 " --> pdb=" O   THR D 291 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ASP D 296 " --> pdb=" O   TRP D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 326
    Processing helix  chain 'D' and resid 327 through 330
    Processing helix  chain 'D' and resid 331 through 337
      removed outlier: 3.561A  pdb=" N   LYS D 337 " --> pdb=" O   ARG D 333 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 375
      removed outlier: 4.061A  pdb=" N   VAL D 353 " --> pdb=" O   LEU D 349 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 387 through 397
      removed outlier: 3.608A  pdb=" N   GLN D 391 " --> pdb=" O   SER D 387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 431
    Processing helix  chain 'D' and resid 442 through 463
      removed outlier: 3.860A  pdb=" N   LYS D 446 " --> pdb=" O   THR D 442 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA D 451 " --> pdb=" O   MET D 447 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 464 through 494
      removed outlier: 4.171A  pdb=" N   THR D 469 " --> pdb=" O   GLY D 465 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 498 through 514
      removed outlier: 3.847A  pdb=" N   SER D 502 " --> pdb=" O   PRO D 498 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 524 through 528
      removed outlier: 3.790A  pdb=" N   ILE D 527 " --> pdb=" O   VAL D 524 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   CYS D 528 " --> pdb=" O   LEU D 525 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 524 through 528'
    Processing helix  chain 'D' and resid 529 through 542
      removed outlier: 3.895A  pdb=" N   ASN D 541 " --> pdb=" O   CYS D 537 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ARG D 542 " --> pdb=" O   VAL D 538 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 557 through 563
    Processing helix  chain 'D' and resid 643 through 653
      removed outlier: 3.961A  pdb=" N   LYS D 648 " --> pdb=" O   GLU D 644 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   VAL D 649 " --> pdb=" O   ALA D 645 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 654 through 658
      removed outlier: 3.799A  pdb=" N   ASN D 658 " --> pdb=" O   ALA D 655 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 681 through 691
      removed outlier: 3.715A  pdb=" N   ARG D 691 " --> pdb=" O   GLU D 687 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 567 through 570
      removed outlier: 6.770A  pdb=" N   ASP A 637 " --> pdb=" O   VAL A 591 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE A 641 " --> pdb=" O   LEU A 587 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU A 587 " --> pdb=" O   ILE A 641 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 603 through 606
      removed outlier: 4.108A  pdb=" N   ALA A 605 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 567 through 570
      removed outlier: 6.770A  pdb=" N   ASP B 637 " --> pdb=" O   VAL B 591 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE B 641 " --> pdb=" O   LEU B 587 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU B 587 " --> pdb=" O   ILE B 641 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 603 through 606
      removed outlier: 4.108A  pdb=" N   ALA B 605 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 567 through 570
      removed outlier: 6.770A  pdb=" N   ASP C 637 " --> pdb=" O   VAL C 591 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE C 641 " --> pdb=" O   LEU C 587 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU C 587 " --> pdb=" O   ILE C 641 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 603 through 606
      removed outlier: 4.108A  pdb=" N   ALA C 605 " --> pdb=" O   VAL C 597 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 567 through 570
      removed outlier: 6.770A  pdb=" N   ASP D 637 " --> pdb=" O   VAL D 591 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE D 641 " --> pdb=" O   LEU D 587 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU D 587 " --> pdb=" O   ILE D 641 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 603 through 606
      removed outlier: 4.108A  pdb=" N   ALA D 605 " --> pdb=" O   VAL D 597 " (cutoff:3.500A)

    756 hydrogen bonds defined for protein.
    2184 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: 5.76

  Time building geometry restraints manager: 6.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6668
        1.34 -     1.46: 5264
        1.46 -     1.58: 9680
        1.58 -     1.70: 0
        1.70 -     1.82: 192
  Bond restraints: 21804
  Sorted by residual:
  bond pdb=" CA  ASP C  37 "
       pdb=" C   ASP C  37 "
    ideal  model  delta    sigma   weight residual
    1.519  1.544 -0.025 1.01e-02 9.80e+03 6.04e+00
  bond pdb=" CA  ASP B  37 "
       pdb=" C   ASP B  37 "
    ideal  model  delta    sigma   weight residual
    1.519  1.544 -0.025 1.01e-02 9.80e+03 6.04e+00
  bond pdb=" CA  ASP D  37 "
       pdb=" C   ASP D  37 "
    ideal  model  delta    sigma   weight residual
    1.519  1.544 -0.025 1.01e-02 9.80e+03 6.04e+00
  bond pdb=" CA  ASP A  37 "
       pdb=" C   ASP A  37 "
    ideal  model  delta    sigma   weight residual
    1.519  1.544 -0.025 1.01e-02 9.80e+03 6.04e+00
  bond pdb=" CB  THR B 468 "
       pdb=" CG2 THR B 468 "
    ideal  model  delta    sigma   weight residual
    1.521  1.443  0.078 3.30e-02 9.18e+02 5.59e+00
  ... (remaining 21799 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 29004
        2.78 -     5.57: 496
        5.57 -     8.35: 60
        8.35 -    11.14: 16
       11.14 -    13.92: 8
  Bond angle restraints: 29584
  Sorted by residual:
  angle pdb=" CA  TRP C  38 "
        pdb=" CB  TRP C  38 "
        pdb=" CG  TRP C  38 "
      ideal   model   delta    sigma   weight residual
     113.60  125.80  -12.20 1.90e+00 2.77e-01 4.12e+01
  angle pdb=" CA  TRP D  38 "
        pdb=" CB  TRP D  38 "
        pdb=" CG  TRP D  38 "
      ideal   model   delta    sigma   weight residual
     113.60  125.80  -12.20 1.90e+00 2.77e-01 4.12e+01
  angle pdb=" CA  TRP A  38 "
        pdb=" CB  TRP A  38 "
        pdb=" CG  TRP A  38 "
      ideal   model   delta    sigma   weight residual
     113.60  125.80  -12.20 1.90e+00 2.77e-01 4.12e+01
  angle pdb=" CA  TRP B  38 "
        pdb=" CB  TRP B  38 "
        pdb=" CG  TRP B  38 "
      ideal   model   delta    sigma   weight residual
     113.60  125.80  -12.20 1.90e+00 2.77e-01 4.12e+01
  angle pdb=" C   GLU B 378 "
        pdb=" N   VAL B 379 "
        pdb=" CA  VAL B 379 "
      ideal   model   delta    sigma   weight residual
     121.97  132.45  -10.48 1.80e+00 3.09e-01 3.39e+01
  ... (remaining 29579 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 11310
       16.36 -    32.72: 1318
       32.72 -    49.08: 244
       49.08 -    65.43: 36
       65.43 -    81.79: 24
  Dihedral angle restraints: 12932
    sinusoidal: 5144
      harmonic: 7788
  Sorted by residual:
  dihedral pdb=" CA  GLN B  34 "
           pdb=" C   GLN B  34 "
           pdb=" N   ILE B  35 "
           pdb=" CA  ILE B  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.57  -46.43     0      5.00e+00 4.00e-02 8.62e+01
  dihedral pdb=" CA  GLN D  34 "
           pdb=" C   GLN D  34 "
           pdb=" N   ILE D  35 "
           pdb=" CA  ILE D  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -133.57  -46.43     0      5.00e+00 4.00e-02 8.62e+01
  dihedral pdb=" CA  GLN A  34 "
           pdb=" C   GLN A  34 "
           pdb=" N   ILE A  35 "
           pdb=" CA  ILE A  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.57  -46.43     0      5.00e+00 4.00e-02 8.62e+01
  ... (remaining 12929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 3144
       0.089 -    0.177: 212
       0.177 -    0.266: 40
       0.266 -    0.355: 4
       0.355 -    0.443: 4
  Chirality restraints: 3404
  Sorted by residual:
  chirality pdb=" CB  THR D 468 "
            pdb=" CA  THR D 468 "
            pdb=" OG1 THR D 468 "
            pdb=" CG2 THR D 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.11    0.44 2.00e-01 2.50e+01 4.91e+00
  chirality pdb=" CB  THR A 468 "
            pdb=" CA  THR A 468 "
            pdb=" OG1 THR A 468 "
            pdb=" CG2 THR A 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.11    0.44 2.00e-01 2.50e+01 4.91e+00
  chirality pdb=" CB  THR B 468 "
            pdb=" CA  THR B 468 "
            pdb=" OG1 THR B 468 "
            pdb=" CG2 THR B 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.11    0.44 2.00e-01 2.50e+01 4.91e+00
  ... (remaining 3401 not shown)

  Planarity restraints: 3668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 676 "    0.031 2.00e-02 2.50e+03   3.32e-02 1.92e+01
        pdb=" CG  PHE B 676 "   -0.076 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 676 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 676 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 676 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 676 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 676 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 676 "   -0.031 2.00e-02 2.50e+03   3.32e-02 1.92e+01
        pdb=" CG  PHE C 676 "    0.076 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 676 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 676 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 676 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 676 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 676 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 676 "   -0.031 2.00e-02 2.50e+03   3.31e-02 1.92e+01
        pdb=" CG  PHE D 676 "    0.076 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 676 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 676 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 676 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 676 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 676 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 3665 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.74: 1803
        2.74 -     3.34: 25854
        3.34 -     3.94: 39922
        3.94 -     4.54: 51246
        4.54 -     5.14: 78234
  Nonbonded interactions: 197059
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 465 "
            pdb=" OG1 THR A 468 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" O   GLY D 465 "
            pdb=" OG1 THR D 468 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   GLY C 465 "
            pdb=" OG1 THR C 468 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   GLY B 465 "
            pdb=" OG1 THR B 468 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   THR D 512 "
            pdb=" OG  SER D 516 "
     model   vdw
     2.144 3.040
  ... (remaining 197054 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 11 through 692)
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.270
  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:             0.030
  Extract box with map and model:          0.840
  Check model and map are aligned:         0.160
  Set scattering table:                    0.200
  Process input model:                     46.220
  Find NCS groups from input model:        1.490
  Set up NCS constraints:                  0.050
  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:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
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   0.078  21804  Z= 0.219
  Angle     :  0.925  13.920  29584  Z= 0.526
  Chirality :  0.054   0.443   3404
  Planarity :  0.006   0.068   3668
  Dihedral  : 14.448  81.792   7884
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 19.50
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 13.30 %
    Favored  : 85.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -2.71 (0.16), residues: 2616
  helix:  0.10 (0.16), residues: 1076
  sheet: -1.98 (0.58), residues: 88
  loop : -3.50 (0.14), residues: 1452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP C  38 
 HIS   0.008   0.001   HIS D 539 
 PHE   0.076   0.002   PHE C 676 
 TYR   0.038   0.002   TYR C 195 
 ARG   0.008   0.000   ARG B 677 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17041 (  756)
  hydrogen bonds       : angle       5.69413 ( 2184)
  covalent geometry    : bond        0.00441 (21804)
  covalent geometry    : angle       0.92458 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 2.260 
Fit side-chains
REVERT: A  376 ILE cc_start: 0.5143 (tt) cc_final: 0.4833 (mt)
REVERT: A  442 THR cc_start: 0.8832 (p) cc_final: 0.8562 (t)
REVERT: A  513 TRP cc_start: 0.7390 (m-10) cc_final: 0.7139 (m-10)
REVERT: A  647 LEU cc_start: 0.8750 (pp) cc_final: 0.8478 (mt)
REVERT: A  658 ASN cc_start: 0.6591 (t0) cc_final: 0.6361 (t0)
REVERT: B  376 ILE cc_start: 0.5114 (tt) cc_final: 0.4811 (mt)
REVERT: B  442 THR cc_start: 0.8738 (p) cc_final: 0.8502 (t)
REVERT: B  513 TRP cc_start: 0.7396 (m-10) cc_final: 0.7142 (m-10)
REVERT: B  647 LEU cc_start: 0.8739 (pp) cc_final: 0.8471 (mt)
REVERT: B  658 ASN cc_start: 0.6599 (t0) cc_final: 0.6369 (t0)
REVERT: C  376 ILE cc_start: 0.5141 (tt) cc_final: 0.4840 (mt)
REVERT: C  442 THR cc_start: 0.8724 (p) cc_final: 0.8456 (t)
REVERT: C  513 TRP cc_start: 0.7408 (m-10) cc_final: 0.7154 (m-10)
REVERT: C  647 LEU cc_start: 0.8739 (pp) cc_final: 0.8472 (mt)
REVERT: C  658 ASN cc_start: 0.6583 (t0) cc_final: 0.6350 (t0)
REVERT: D  376 ILE cc_start: 0.5168 (tt) cc_final: 0.4858 (mt)
REVERT: D  442 THR cc_start: 0.8746 (p) cc_final: 0.8472 (t)
REVERT: D  513 TRP cc_start: 0.7407 (m-10) cc_final: 0.7152 (m-10)
REVERT: D  647 LEU cc_start: 0.8752 (pp) cc_final: 0.8482 (mt)
REVERT: D  658 ASN cc_start: 0.6579 (t0) cc_final: 0.6347 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 316
  average time/residue: 0.2700
  time to fit residues: 141.8075
Evaluate side-chains
  240 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 2.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 222 optimal weight:    0.8980
   chunk 200 optimal weight:    0.9980
   chunk 111 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   chunk 134 optimal weight:    0.9980
   chunk 106 optimal weight:    0.4980
   chunk 206 optimal weight:    0.7980
   chunk 80 optimal weight:    7.9990
   chunk 125 optimal weight:    0.1980
   chunk 154 optimal weight:    0.2980
   chunk 239 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
A  91 ASN
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 ASN
B  91 ASN
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 ASN
C  91 ASN
** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  32 ASN
D  91 ASN
** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.228464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.188829 restraints weight = 39988.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.188068 restraints weight = 52914.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.184595 restraints weight = 40145.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.4248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090  21804  Z= 0.164
  Angle     :  0.776  18.754  29584  Z= 0.412
  Chirality :  0.047   0.279   3404
  Planarity :  0.005   0.055   3668
  Dihedral  :  6.311  48.036   2864
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 12.69 %
    Favored  : 85.93 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  9.24 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -2.39 (0.16), residues: 2616
  helix:  0.28 (0.16), residues: 1132
  sheet: -1.68 (0.61), residues: 88
  loop : -3.39 (0.15), residues: 1396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP C  38 
 HIS   0.004   0.001   HIS B 579 
 PHE   0.046   0.002   PHE B 676 
 TYR   0.013   0.001   TYR C 195 
 ARG   0.007   0.001   ARG C 677 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05142 (  756)
  hydrogen bonds       : angle       4.70560 ( 2184)
  covalent geometry    : bond        0.00335 (21804)
  covalent geometry    : angle       0.77605 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 288
  time to evaluate  : 2.666 
Fit side-chains
REVERT: A  109 MET cc_start: 0.2007 (pmm) cc_final: 0.1798 (pmm)
REVERT: A  270 PHE cc_start: 0.7756 (t80) cc_final: 0.7489 (t80)
REVERT: A  506 MET cc_start: 0.7398 (tmm) cc_final: 0.7148 (tmm)
REVERT: A  509 ILE cc_start: 0.8709 (pt) cc_final: 0.8394 (mm)
REVERT: A  513 TRP cc_start: 0.7421 (m-10) cc_final: 0.6904 (m-10)
REVERT: B  109 MET cc_start: 0.1994 (pmm) cc_final: 0.1789 (pmm)
REVERT: B  270 PHE cc_start: 0.7751 (t80) cc_final: 0.7483 (t80)
REVERT: B  506 MET cc_start: 0.7403 (tmm) cc_final: 0.7157 (tmm)
REVERT: B  509 ILE cc_start: 0.8716 (pt) cc_final: 0.8401 (mm)
REVERT: B  513 TRP cc_start: 0.7426 (m-10) cc_final: 0.6909 (m-10)
REVERT: C  109 MET cc_start: 0.2002 (pmm) cc_final: 0.1798 (pmm)
REVERT: C  270 PHE cc_start: 0.7762 (t80) cc_final: 0.7492 (t80)
REVERT: C  506 MET cc_start: 0.7401 (tmm) cc_final: 0.7152 (tmm)
REVERT: C  509 ILE cc_start: 0.8714 (pt) cc_final: 0.8400 (mm)
REVERT: C  513 TRP cc_start: 0.7425 (m-10) cc_final: 0.6905 (m-10)
REVERT: D  109 MET cc_start: 0.1989 (pmm) cc_final: 0.1787 (pmm)
REVERT: D  270 PHE cc_start: 0.7758 (t80) cc_final: 0.7487 (t80)
REVERT: D  506 MET cc_start: 0.7403 (tmm) cc_final: 0.7154 (tmm)
REVERT: D  509 ILE cc_start: 0.8698 (pt) cc_final: 0.8389 (mm)
REVERT: D  513 TRP cc_start: 0.7404 (m-10) cc_final: 0.6889 (m-10)
  outliers start: 32
  outliers final: 28
  residues processed: 308
  average time/residue: 0.2779
  time to fit residues: 138.7993
Evaluate side-chains
  264 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 236
  time to evaluate  : 2.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 TRP
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  482 HIS
Chi-restraints excluded: chain A residue  558 CYS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain B residue   38 TRP
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  482 HIS
Chi-restraints excluded: chain B residue  558 CYS
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain C residue   38 TRP
Chi-restraints excluded: chain C residue  262 ILE
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  482 HIS
Chi-restraints excluded: chain C residue  558 CYS
Chi-restraints excluded: chain C residue  564 VAL
Chi-restraints excluded: chain D residue   38 TRP
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  482 HIS
Chi-restraints excluded: chain D residue  558 CYS
Chi-restraints excluded: chain D residue  564 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 157 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 164 optimal weight:    1.9990
   chunk 117 optimal weight:    0.0470
   chunk 242 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 167 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.6086

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.222665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.178927 restraints weight = 38491.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.170421 restraints weight = 46581.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.169511 restraints weight = 35176.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6794
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099  21804  Z= 0.197
  Angle     :  0.806  19.161  29584  Z= 0.424
  Chirality :  0.049   0.284   3404
  Planarity :  0.005   0.056   3668
  Dihedral  :  6.293  50.110   2864
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  1.22 %
    Allowed  : 13.61 %
    Favored  : 85.17 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.32 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.40 (0.16), residues: 2616
  helix:  0.21 (0.16), residues: 1156
  sheet: -2.01 (0.49), residues: 108
  loop : -3.38 (0.16), residues: 1352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D 618 
 HIS   0.006   0.001   HIS A 539 
 PHE   0.032   0.002   PHE C 676 
 TYR   0.020   0.002   TYR C  88 
 ARG   0.007   0.000   ARG C 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05445 (  756)
  hydrogen bonds       : angle       4.59773 ( 2184)
  covalent geometry    : bond        0.00441 (21804)
  covalent geometry    : angle       0.80595 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 264
  time to evaluate  : 2.538 
Fit side-chains
REVERT: A  194 GLN cc_start: 0.4919 (mp10) cc_final: 0.4500 (mt0)
REVERT: A  270 PHE cc_start: 0.7953 (t80) cc_final: 0.7749 (t80)
REVERT: A  506 MET cc_start: 0.7562 (tmm) cc_final: 0.7357 (tmm)
REVERT: A  509 ILE cc_start: 0.8789 (pt) cc_final: 0.8444 (mm)
REVERT: A  513 TRP cc_start: 0.7454 (m-10) cc_final: 0.7016 (m-10)
REVERT: A  676 PHE cc_start: 0.4365 (p90) cc_final: 0.2989 (p90)
REVERT: B  194 GLN cc_start: 0.4913 (mp10) cc_final: 0.4496 (mt0)
REVERT: B  270 PHE cc_start: 0.7949 (t80) cc_final: 0.7741 (t80)
REVERT: B  506 MET cc_start: 0.7570 (tmm) cc_final: 0.7365 (tmm)
REVERT: B  509 ILE cc_start: 0.8784 (pt) cc_final: 0.8439 (mm)
REVERT: B  513 TRP cc_start: 0.7450 (m-10) cc_final: 0.7018 (m-10)
REVERT: B  676 PHE cc_start: 0.4332 (p90) cc_final: 0.2966 (p90)
REVERT: C  194 GLN cc_start: 0.4923 (mp10) cc_final: 0.4508 (mt0)
REVERT: C  270 PHE cc_start: 0.7960 (t80) cc_final: 0.7753 (t80)
REVERT: C  506 MET cc_start: 0.7553 (tmm) cc_final: 0.7346 (tmm)
REVERT: C  509 ILE cc_start: 0.8784 (pt) cc_final: 0.8434 (mm)
REVERT: C  513 TRP cc_start: 0.7461 (m-10) cc_final: 0.7026 (m-10)
REVERT: C  676 PHE cc_start: 0.4346 (p90) cc_final: 0.2977 (p90)
REVERT: D  194 GLN cc_start: 0.4918 (mp10) cc_final: 0.4507 (mt0)
REVERT: D  270 PHE cc_start: 0.7955 (t80) cc_final: 0.7748 (t80)
REVERT: D  506 MET cc_start: 0.7558 (tmm) cc_final: 0.7353 (tmm)
REVERT: D  509 ILE cc_start: 0.8787 (pt) cc_final: 0.8436 (mm)
REVERT: D  513 TRP cc_start: 0.7449 (m-10) cc_final: 0.7016 (m-10)
REVERT: D  676 PHE cc_start: 0.4349 (p90) cc_final: 0.2977 (p90)
  outliers start: 56
  outliers final: 44
  residues processed: 296
  average time/residue: 0.2651
  time to fit residues: 131.5151
Evaluate side-chains
  296 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 252
  time to evaluate  : 2.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  482 HIS
Chi-restraints excluded: chain A residue  558 CYS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  482 HIS
Chi-restraints excluded: chain B residue  558 CYS
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  612 VAL
Chi-restraints excluded: chain C residue   94 GLU
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  260 VAL
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  482 HIS
Chi-restraints excluded: chain C residue  558 CYS
Chi-restraints excluded: chain C residue  564 VAL
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain D residue   94 GLU
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  277 VAL
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  482 HIS
Chi-restraints excluded: chain D residue  558 CYS
Chi-restraints excluded: chain D residue  564 VAL
Chi-restraints excluded: chain D residue  612 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 203 optimal weight:    8.9990
   chunk 96 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 166 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 79 optimal weight:   10.0000
   chunk 65 optimal weight:    0.1980
   chunk 70 optimal weight:    8.9990
   chunk 139 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 209 HIS
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 209 HIS
** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 HIS
** C 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 209 HIS
** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.225426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.192096 restraints weight = 38660.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.189813 restraints weight = 51222.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.188341 restraints weight = 41750.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.4307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6307
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.100  21804  Z= 0.151
  Angle     :  0.729  19.560  29584  Z= 0.386
  Chirality :  0.046   0.258   3404
  Planarity :  0.004   0.057   3668
  Dihedral  :  5.920  48.693   2864
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 11.31 %
    Favored  : 87.31 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.84 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.18 (0.17), residues: 2616
  helix:  0.38 (0.16), residues: 1156
  sheet: -1.78 (0.50), residues: 108
  loop : -3.26 (0.16), residues: 1352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  38 
 HIS   0.004   0.001   HIS D 579 
 PHE   0.032   0.002   PHE D 676 
 TYR   0.016   0.001   TYR C  88 
 ARG   0.005   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04580 (  756)
  hydrogen bonds       : angle       4.24721 ( 2184)
  covalent geometry    : bond        0.00321 (21804)
  covalent geometry    : angle       0.72941 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 268
  time to evaluate  : 2.197 
Fit side-chains
REVERT: A  194 GLN cc_start: 0.4909 (mp10) cc_final: 0.4590 (mt0)
REVERT: A  509 ILE cc_start: 0.8423 (pt) cc_final: 0.8193 (mm)
REVERT: A  513 TRP cc_start: 0.6953 (m-10) cc_final: 0.6567 (m-10)
REVERT: A  560 ARG cc_start: 0.6846 (mtm180) cc_final: 0.6215 (mmt90)
REVERT: B  194 GLN cc_start: 0.4915 (mp10) cc_final: 0.4590 (mt0)
REVERT: B  509 ILE cc_start: 0.8421 (pt) cc_final: 0.8198 (mm)
REVERT: B  513 TRP cc_start: 0.6951 (m-10) cc_final: 0.6572 (m-10)
REVERT: B  560 ARG cc_start: 0.6838 (mtm180) cc_final: 0.6215 (mmt90)
REVERT: C  194 GLN cc_start: 0.4913 (mp10) cc_final: 0.4585 (mt0)
REVERT: C  509 ILE cc_start: 0.8416 (pt) cc_final: 0.8182 (mm)
REVERT: C  513 TRP cc_start: 0.6955 (m-10) cc_final: 0.6572 (m-10)
REVERT: C  560 ARG cc_start: 0.6842 (mtm180) cc_final: 0.6215 (mmt90)
REVERT: D  194 GLN cc_start: 0.4905 (mp10) cc_final: 0.4582 (mt0)
REVERT: D  509 ILE cc_start: 0.8422 (pt) cc_final: 0.8193 (mm)
REVERT: D  513 TRP cc_start: 0.6965 (m-10) cc_final: 0.6583 (m-10)
REVERT: D  560 ARG cc_start: 0.6846 (mtm180) cc_final: 0.6216 (mmt90)
  outliers start: 68
  outliers final: 28
  residues processed: 316
  average time/residue: 0.2942
  time to fit residues: 146.1140
Evaluate side-chains
  272 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 244
  time to evaluate  : 2.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  482 HIS
Chi-restraints excluded: chain A residue  558 CYS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  482 HIS
Chi-restraints excluded: chain B residue  558 CYS
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  612 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  482 HIS
Chi-restraints excluded: chain C residue  558 CYS
Chi-restraints excluded: chain C residue  564 VAL
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  482 HIS
Chi-restraints excluded: chain D residue  558 CYS
Chi-restraints excluded: chain D residue  564 VAL
Chi-restraints excluded: chain D residue  612 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 23 optimal weight:    0.4980
   chunk 166 optimal weight:    0.0060
   chunk 243 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 209 optimal weight:    0.7980
   chunk 115 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 261 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0370
   overall best weight:    0.4674

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 546 ASN
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 ASN
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 546 ASN
** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 158 ASN
** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 546 ASN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 158 ASN
** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 546 ASN
** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.225802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.185314 restraints weight = 39253.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.182606 restraints weight = 51881.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.180348 restraints weight = 39013.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6495
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  21804  Z= 0.143
  Angle     :  0.736  19.322  29584  Z= 0.384
  Chirality :  0.045   0.233   3404
  Planarity :  0.004   0.058   3668
  Dihedral  :  5.761  47.447   2864
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 11.93 %
    Favored  : 86.70 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 18.28 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.04 (0.17), residues: 2616
  helix:  0.55 (0.16), residues: 1156
  sheet: -1.69 (0.51), residues: 108
  loop : -3.24 (0.16), residues: 1352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP D 618 
 HIS   0.004   0.001   HIS C 539 
 PHE   0.048   0.002   PHE B 676 
 TYR   0.020   0.001   TYR C  88 
 ARG   0.004   0.000   ARG B 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04364 (  756)
  hydrogen bonds       : angle       4.16505 ( 2184)
  covalent geometry    : bond        0.00295 (21804)
  covalent geometry    : angle       0.73556 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 274
  time to evaluate  : 2.276 
Fit side-chains
REVERT: A  226 PHE cc_start: 0.8811 (t80) cc_final: 0.8445 (t80)
REVERT: A  513 TRP cc_start: 0.7135 (m-10) cc_final: 0.6670 (m-10)
REVERT: B  226 PHE cc_start: 0.8810 (t80) cc_final: 0.8444 (t80)
REVERT: B  513 TRP cc_start: 0.7139 (m-10) cc_final: 0.6674 (m-10)
REVERT: C  226 PHE cc_start: 0.8806 (t80) cc_final: 0.8443 (t80)
REVERT: C  513 TRP cc_start: 0.7145 (m-10) cc_final: 0.6676 (m-10)
REVERT: D  226 PHE cc_start: 0.8805 (t80) cc_final: 0.8442 (t80)
REVERT: D  513 TRP cc_start: 0.7145 (m-10) cc_final: 0.6678 (m-10)
  outliers start: 37
  outliers final: 28
  residues processed: 303
  average time/residue: 0.2570
  time to fit residues: 130.6360
Evaluate side-chains
  270 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 242
  time to evaluate  : 2.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  482 HIS
Chi-restraints excluded: chain A residue  558 CYS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  482 HIS
Chi-restraints excluded: chain B residue  558 CYS
Chi-restraints excluded: chain B residue  612 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  482 HIS
Chi-restraints excluded: chain C residue  558 CYS
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  482 HIS
Chi-restraints excluded: chain D residue  558 CYS
Chi-restraints excluded: chain D residue  612 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 153 optimal weight:    0.5980
   chunk 127 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 161 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   chunk 73 optimal weight:    0.3980
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 ASN
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 287 ASN
** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.224696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.183297 restraints weight = 38540.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.176215 restraints weight = 50449.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.172681 restraints weight = 42422.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  21804  Z= 0.146
  Angle     :  0.726  18.702  29584  Z= 0.381
  Chirality :  0.045   0.236   3404
  Planarity :  0.004   0.058   3668
  Dihedral  :  5.625  46.304   2864
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 11.62 %
    Favored  : 87.00 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 19.83 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.17), residues: 2616
  helix:  0.56 (0.16), residues: 1156
  sheet: -1.78 (0.50), residues: 116
  loop : -3.13 (0.16), residues: 1344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP C 618 
 HIS   0.005   0.001   HIS C 539 
 PHE   0.040   0.002   PHE C 676 
 TYR   0.017   0.001   TYR A  88 
 ARG   0.004   0.000   ARG A 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04354 (  756)
  hydrogen bonds       : angle       4.18484 ( 2184)
  covalent geometry    : bond        0.00308 (21804)
  covalent geometry    : angle       0.72600 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 284
  time to evaluate  : 2.787 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.6921 (tptt) cc_final: 0.6157 (tptt)
REVERT: A  109 MET cc_start: 0.2512 (pmm) cc_final: -0.1519 (ptt)
REVERT: A  296 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7167 (t70)
REVERT: A  513 TRP cc_start: 0.7141 (m-10) cc_final: 0.6751 (m-10)
REVERT: B   76 LYS cc_start: 0.6902 (tptt) cc_final: 0.6146 (tptt)
REVERT: B  109 MET cc_start: 0.2508 (pmm) cc_final: -0.1520 (ptt)
REVERT: B  296 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7159 (t70)
REVERT: B  513 TRP cc_start: 0.7136 (m-10) cc_final: 0.6748 (m-10)
REVERT: C   76 LYS cc_start: 0.6925 (tptt) cc_final: 0.6160 (tptt)
REVERT: C  109 MET cc_start: 0.2532 (pmm) cc_final: -0.1514 (ptt)
REVERT: C  296 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7148 (t70)
REVERT: C  513 TRP cc_start: 0.7138 (m-10) cc_final: 0.6751 (m-10)
REVERT: D   76 LYS cc_start: 0.6911 (tptt) cc_final: 0.6151 (tptt)
REVERT: D  109 MET cc_start: 0.2527 (pmm) cc_final: -0.1509 (ptt)
REVERT: D  296 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7153 (t70)
REVERT: D  513 TRP cc_start: 0.7127 (m-10) cc_final: 0.6742 (m-10)
  outliers start: 51
  outliers final: 24
  residues processed: 323
  average time/residue: 0.2653
  time to fit residues: 143.5635
Evaluate side-chains
  288 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 260
  time to evaluate  : 2.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  296 ASP
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  482 HIS
Chi-restraints excluded: chain A residue  558 CYS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  482 HIS
Chi-restraints excluded: chain B residue  558 CYS
Chi-restraints excluded: chain B residue  612 VAL
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  296 ASP
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  482 HIS
Chi-restraints excluded: chain C residue  558 CYS
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  296 ASP
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  482 HIS
Chi-restraints excluded: chain D residue  558 CYS
Chi-restraints excluded: chain D residue  612 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 152 optimal weight:    0.6980
   chunk 153 optimal weight:    0.5980
   chunk 151 optimal weight:   10.0000
   chunk 130 optimal weight:    6.9990
   chunk 116 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 197 optimal weight:    9.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 639 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 = 0.4686 r_free = 0.4686 target = 0.224262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.182964 restraints weight = 38373.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 106)---------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.171553 restraints weight = 49309.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.170111 restraints weight = 39003.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6750
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  21804  Z= 0.152
  Angle     :  0.740  18.646  29584  Z= 0.388
  Chirality :  0.046   0.312   3404
  Planarity :  0.004   0.058   3668
  Dihedral  :  5.618  45.758   2864
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 12.08 %
    Favored  : 86.54 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 20.76 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.00 (0.17), residues: 2616
  helix:  0.59 (0.16), residues: 1160
  sheet: -1.82 (0.49), residues: 116
  loop : -3.22 (0.16), residues: 1340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP D 618 
 HIS   0.005   0.001   HIS C 539 
 PHE   0.027   0.002   PHE B 491 
 TYR   0.012   0.001   TYR D 508 
 ARG   0.003   0.000   ARG B 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04487 (  756)
  hydrogen bonds       : angle       4.17057 ( 2184)
  covalent geometry    : bond        0.00326 (21804)
  covalent geometry    : angle       0.73971 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 264
  time to evaluate  : 2.371 
Fit side-chains
REVERT: A  109 MET cc_start: 0.2577 (pmm) cc_final: -0.1176 (ptt)
REVERT: A  513 TRP cc_start: 0.6959 (m-10) cc_final: 0.6623 (m-10)
REVERT: A  604 VAL cc_start: 0.4646 (m) cc_final: 0.4309 (t)
REVERT: B  109 MET cc_start: 0.2589 (pmm) cc_final: -0.1168 (ptt)
REVERT: B  513 TRP cc_start: 0.6945 (m-10) cc_final: 0.6617 (m-10)
REVERT: B  604 VAL cc_start: 0.4634 (m) cc_final: 0.4300 (t)
REVERT: C  109 MET cc_start: 0.2567 (pmm) cc_final: -0.1172 (ptt)
REVERT: C  513 TRP cc_start: 0.6954 (m-10) cc_final: 0.6622 (m-10)
REVERT: C  604 VAL cc_start: 0.4638 (m) cc_final: 0.4308 (t)
REVERT: D  109 MET cc_start: 0.2575 (pmm) cc_final: -0.1174 (ptt)
REVERT: D  513 TRP cc_start: 0.6959 (m-10) cc_final: 0.6627 (m-10)
REVERT: D  604 VAL cc_start: 0.4640 (m) cc_final: 0.4306 (t)
  outliers start: 51
  outliers final: 31
  residues processed: 307
  average time/residue: 0.2687
  time to fit residues: 135.3647
Evaluate side-chains
  283 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 252
  time to evaluate  : 2.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  482 HIS
Chi-restraints excluded: chain A residue  558 CYS
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  482 HIS
Chi-restraints excluded: chain B residue  558 CYS
Chi-restraints excluded: chain B residue  566 PHE
Chi-restraints excluded: chain B residue  612 VAL
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  482 HIS
Chi-restraints excluded: chain C residue  558 CYS
Chi-restraints excluded: chain C residue  566 PHE
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  482 HIS
Chi-restraints excluded: chain D residue  558 CYS
Chi-restraints excluded: chain D residue  566 PHE
Chi-restraints excluded: chain D residue  612 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 233 optimal weight:    2.9990
   chunk 188 optimal weight:    6.9990
   chunk 257 optimal weight:    9.9990
   chunk 117 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0770
   chunk 139 optimal weight:    0.0000
   chunk 234 optimal weight:    0.9980
   chunk 197 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0980
   chunk 161 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    0.8344

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
A 473 GLN
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 625 HIS
A 639 HIS
B  32 ASN
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 625 HIS
B 639 HIS
C  32 ASN
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 625 HIS
C 639 HIS
D  32 ASN
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 625 HIS
** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.223075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.174376 restraints weight = 39080.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.167925 restraints weight = 42841.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.164618 restraints weight = 27526.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  21804  Z= 0.148
  Angle     :  0.730  18.282  29584  Z= 0.382
  Chirality :  0.046   0.215   3404
  Planarity :  0.004   0.058   3668
  Dihedral  :  5.501  44.333   2864
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 11.01 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.34 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.97 (0.17), residues: 2616
  helix:  0.63 (0.16), residues: 1156
  sheet: -1.84 (0.48), residues: 116
  loop : -3.21 (0.16), residues: 1344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 618 
 HIS   0.004   0.001   HIS B 539 
 PHE   0.026   0.002   PHE D 491 
 TYR   0.015   0.001   TYR A  88 
 ARG   0.003   0.000   ARG B 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04446 (  756)
  hydrogen bonds       : angle       4.26403 ( 2184)
  covalent geometry    : bond        0.00313 (21804)
  covalent geometry    : angle       0.73044 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 268
  time to evaluate  : 2.254 
Fit side-chains
REVERT: A  109 MET cc_start: 0.2536 (pmm) cc_final: -0.0895 (ptt)
REVERT: A  513 TRP cc_start: 0.7192 (m-10) cc_final: 0.6876 (m-10)
REVERT: B  109 MET cc_start: 0.2500 (pmm) cc_final: -0.0922 (ptt)
REVERT: B  513 TRP cc_start: 0.7159 (m-10) cc_final: 0.6840 (m-10)
REVERT: C  109 MET cc_start: 0.2543 (pmm) cc_final: -0.0900 (ptt)
REVERT: C  513 TRP cc_start: 0.7174 (m-10) cc_final: 0.6852 (m-10)
REVERT: D  109 MET cc_start: 0.2562 (pmm) cc_final: -0.0877 (ptt)
REVERT: D  513 TRP cc_start: 0.7194 (m-10) cc_final: 0.6873 (m-10)
  outliers start: 57
  outliers final: 48
  residues processed: 309
  average time/residue: 0.2653
  time to fit residues: 135.8964
Evaluate side-chains
  312 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 264
  time to evaluate  : 2.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  482 HIS
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  558 CYS
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  482 HIS
Chi-restraints excluded: chain B residue  521 THR
Chi-restraints excluded: chain B residue  558 CYS
Chi-restraints excluded: chain B residue  566 PHE
Chi-restraints excluded: chain B residue  612 VAL
Chi-restraints excluded: chain B residue  676 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   68 MET
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  482 HIS
Chi-restraints excluded: chain C residue  521 THR
Chi-restraints excluded: chain C residue  558 CYS
Chi-restraints excluded: chain C residue  566 PHE
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain C residue  676 PHE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  482 HIS
Chi-restraints excluded: chain D residue  521 THR
Chi-restraints excluded: chain D residue  558 CYS
Chi-restraints excluded: chain D residue  566 PHE
Chi-restraints excluded: chain D residue  612 VAL
Chi-restraints excluded: chain D residue  676 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 232 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 195 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0670
   chunk 110 optimal weight:    0.9990
   chunk 239 optimal weight:    0.6980
   chunk 246 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 222 optimal weight:    0.7980
   chunk 128 optimal weight:    7.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 HIS
B  32 ASN
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
** B 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 639 HIS
C  32 ASN
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 639 HIS
D  32 ASN
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.224436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.182911 restraints weight = 38791.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.170872 restraints weight = 47066.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.171083 restraints weight = 44508.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  21804  Z= 0.139
  Angle     :  0.722  18.022  29584  Z= 0.378
  Chirality :  0.045   0.205   3404
  Planarity :  0.004   0.058   3668
  Dihedral  :  5.352  42.627   2864
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 10.93 %
    Favored  : 87.69 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 22.44 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.17), residues: 2616
  helix:  0.61 (0.16), residues: 1160
  sheet: -1.68 (0.49), residues: 116
  loop : -3.21 (0.16), residues: 1340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 618 
 HIS   0.005   0.001   HIS B 539 
 PHE   0.024   0.002   PHE D 491 
 TYR   0.015   0.001   TYR A  88 
 ARG   0.005   0.000   ARG D 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  756)
  hydrogen bonds       : angle       4.27585 ( 2184)
  covalent geometry    : bond        0.00289 (21804)
  covalent geometry    : angle       0.72188 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 288
  time to evaluate  : 1.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 PHE cc_start: -0.0660 (OUTLIER) cc_final: -0.1320 (m-80)
REVERT: A  109 MET cc_start: 0.2892 (pmm) cc_final: -0.0759 (ptt)
REVERT: A  297 LEU cc_start: 0.8349 (tp) cc_final: 0.8147 (mp)
REVERT: A  513 TRP cc_start: 0.7026 (m-10) cc_final: 0.6806 (m-10)
REVERT: A  522 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6791 (tp30)
REVERT: B  107 PHE cc_start: -0.0675 (OUTLIER) cc_final: -0.1332 (m-80)
REVERT: B  109 MET cc_start: 0.2891 (pmm) cc_final: -0.0775 (ptt)
REVERT: B  513 TRP cc_start: 0.7012 (m-10) cc_final: 0.6798 (m-10)
REVERT: B  522 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6783 (tp30)
REVERT: C  107 PHE cc_start: -0.0664 (OUTLIER) cc_final: -0.1322 (m-80)
REVERT: C  109 MET cc_start: 0.2879 (pmm) cc_final: -0.0782 (ptt)
REVERT: C  297 LEU cc_start: 0.8363 (tp) cc_final: 0.8162 (mp)
REVERT: C  503 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7344 (tm-30)
REVERT: C  513 TRP cc_start: 0.7013 (m-10) cc_final: 0.6797 (m-10)
REVERT: C  522 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6788 (tp30)
REVERT: D  107 PHE cc_start: -0.0670 (OUTLIER) cc_final: -0.1324 (m-80)
REVERT: D  109 MET cc_start: 0.2879 (pmm) cc_final: -0.0768 (ptt)
REVERT: D  503 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7333 (tm-30)
REVERT: D  513 TRP cc_start: 0.7014 (m-10) cc_final: 0.6802 (m-10)
REVERT: D  522 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6805 (tp30)
  outliers start: 49
  outliers final: 44
  residues processed: 325
  average time/residue: 0.2694
  time to fit residues: 145.2610
Evaluate side-chains
  316 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 268
  time to evaluate  : 2.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  482 HIS
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  558 CYS
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  107 PHE
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  482 HIS
Chi-restraints excluded: chain B residue  521 THR
Chi-restraints excluded: chain B residue  558 CYS
Chi-restraints excluded: chain B residue  566 PHE
Chi-restraints excluded: chain B residue  612 VAL
Chi-restraints excluded: chain B residue  676 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   68 MET
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  482 HIS
Chi-restraints excluded: chain C residue  521 THR
Chi-restraints excluded: chain C residue  558 CYS
Chi-restraints excluded: chain C residue  566 PHE
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain C residue  676 PHE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  107 PHE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  482 HIS
Chi-restraints excluded: chain D residue  521 THR
Chi-restraints excluded: chain D residue  558 CYS
Chi-restraints excluded: chain D residue  566 PHE
Chi-restraints excluded: chain D residue  612 VAL
Chi-restraints excluded: chain D residue  676 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 227 optimal weight:    0.0670
   chunk 8 optimal weight:    6.9990
   chunk 133 optimal weight:    7.9990
   chunk 109 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0770
   chunk 59 optimal weight:    2.9990
   chunk 16 optimal weight:   30.0000
   chunk 155 optimal weight:    8.9990
   overall best weight:    1.2282

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 118 HIS
** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  87 ASN
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 HIS
** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 ASN
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 HIS
C 473 GLN
** C 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  87 ASN
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 118 HIS
D 473 GLN
** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.220196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.174997 restraints weight = 38541.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.161256 restraints weight = 44949.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.160646 restraints weight = 33905.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.4830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  21804  Z= 0.168
  Angle     :  0.754  17.861  29584  Z= 0.396
  Chirality :  0.047   0.281   3404
  Planarity :  0.005   0.068   3668
  Dihedral  :  5.530  40.960   2864
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 12.23 %
    Favored  : 86.39 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 23.11 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.97 (0.17), residues: 2616
  helix:  0.56 (0.16), residues: 1160
  sheet: -1.42 (0.52), residues: 108
  loop : -3.20 (0.16), residues: 1348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 618 
 HIS   0.005   0.001   HIS D 539 
 PHE   0.020   0.002   PHE C 491 
 TYR   0.022   0.002   TYR A  88 
 ARG   0.005   0.000   ARG A 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04811 (  756)
  hydrogen bonds       : angle       4.37476 ( 2184)
  covalent geometry    : bond        0.00365 (21804)
  covalent geometry    : angle       0.75399 (29584)

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

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

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5232 Ramachandran restraints generated.
    2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 272
  time to evaluate  : 2.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 PHE cc_start: -0.1142 (OUTLIER) cc_final: -0.1750 (m-80)
REVERT: A  109 MET cc_start: 0.2671 (pmm) cc_final: -0.0612 (ptt)
REVERT: A  207 ILE cc_start: 0.8178 (mp) cc_final: 0.7869 (mm)
REVERT: A  522 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7068 (tp30)
REVERT: B  107 PHE cc_start: -0.1155 (OUTLIER) cc_final: -0.1755 (m-80)
REVERT: B  109 MET cc_start: 0.2682 (pmm) cc_final: -0.0599 (ptt)
REVERT: B  207 ILE cc_start: 0.8203 (mp) cc_final: 0.7890 (mm)
REVERT: B  522 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7049 (tp30)
REVERT: C  107 PHE cc_start: -0.1167 (OUTLIER) cc_final: -0.1761 (m-80)
REVERT: C  109 MET cc_start: 0.2673 (pmm) cc_final: -0.0591 (ptt)
REVERT: C  207 ILE cc_start: 0.8173 (mp) cc_final: 0.7863 (mm)
REVERT: C  522 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7030 (tp30)
REVERT: D  107 PHE cc_start: -0.1167 (OUTLIER) cc_final: -0.1772 (m-80)
REVERT: D  109 MET cc_start: 0.2675 (pmm) cc_final: -0.0610 (ptt)
REVERT: D  207 ILE cc_start: 0.8193 (mp) cc_final: 0.7886 (mm)
REVERT: D  522 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7055 (tp30)
  outliers start: 51
  outliers final: 40
  residues processed: 314
  average time/residue: 0.2720
  time to fit residues: 140.9400
Evaluate side-chains
  299 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 255
  time to evaluate  : 2.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  482 HIS
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  558 CYS
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  107 PHE
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  482 HIS
Chi-restraints excluded: chain B residue  521 THR
Chi-restraints excluded: chain B residue  558 CYS
Chi-restraints excluded: chain B residue  566 PHE
Chi-restraints excluded: chain B residue  612 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   68 MET
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  482 HIS
Chi-restraints excluded: chain C residue  521 THR
Chi-restraints excluded: chain C residue  558 CYS
Chi-restraints excluded: chain C residue  566 PHE
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  107 PHE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  482 HIS
Chi-restraints excluded: chain D residue  521 THR
Chi-restraints excluded: chain D residue  558 CYS
Chi-restraints excluded: chain D residue  612 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 236 optimal weight:    0.9990
   chunk 164 optimal weight:    1.9990
   chunk 192 optimal weight:    3.9990
   chunk 127 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 154 optimal weight:    2.9990
   chunk 136 optimal weight:    8.9990
   chunk 73 optimal weight:    3.9990
   chunk 219 optimal weight:    0.9980
   chunk 144 optimal weight:    9.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 ASN
** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.217375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.170215 restraints weight = 38428.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.157494 restraints weight = 45160.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.157142 restraints weight = 38732.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.5169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  21804  Z= 0.201
  Angle     :  0.792  17.616  29584  Z= 0.415
  Chirality :  0.048   0.256   3404
  Planarity :  0.005   0.064   3668
  Dihedral  :  5.754  39.291   2864
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 16.65
  Ramachandran Plot:
    Outliers :  1.07 %
    Allowed  : 12.92 %
    Favored  : 86.01 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 23.19 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.07 (0.17), residues: 2616
  helix:  0.48 (0.16), residues: 1148
  sheet: -1.41 (0.73), residues: 60
  loop : -3.18 (0.16), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D 618 
 HIS   0.006   0.001   HIS D 539 
 PHE   0.025   0.002   PHE C 491 
 TYR   0.055   0.002   TYR D 288 
 ARG   0.005   0.000   ARG C 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05142 (  756)
  hydrogen bonds       : angle       4.57602 ( 2184)
  covalent geometry    : bond        0.00440 (21804)
  covalent geometry    : angle       0.79165 (29584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7211.75 seconds
wall clock time: 127 minutes 58.38 seconds (7678.38 seconds total)