Starting phenix.real_space_refine
on Wed Jun 18 16:38:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yij_33860/06_2025/7yij_33860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yij_33860/06_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_33860/06_2025/7yij_33860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yij_33860/06_2025/7yij_33860.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yij_33860/06_2025/7yij_33860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yij_33860/06_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): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.69, per 1000 atoms: 0.64
  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: 5.07
  Conformation dependent library (CDL) restraints added in 2.7 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: 1.85
  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: 5.67

  Time building geometry restraints manager: 6.00 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:             4.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.860
  Check model and map are aligned:         0.150
  Set scattering table:                    0.210
  Process input model:                     45.820
  Find NCS groups from input model:        1.190
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.200
-------------------------------------------------------------------------------
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  : 2.261 
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: 0.2658
  time to fit residues: 140.2082
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  : 2.402 
-------------------------------------------------------------------------------
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 = 39988.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.188068 restraints weight = 52911.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.184591 restraints weight = 40145.020|
|-----------------------------------------------------------------------------|
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  : 2.152 
Fit side-chains
REVERT: A  109 MET cc_start: 0.2006 (pmm) cc_final: 0.1797 (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: 0.7420 (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: 0.7404 (tmm) cc_final: 0.7158 (tmm)
REVERT: B  509 ILE cc_start: 0.8716 (pt) cc_final: 0.8401 (mm)
REVERT: B  513 TRP cc_start: 0.7427 (m-10) cc_final: 0.6909 (m-10)
REVERT: C  109 MET cc_start: 0.2001 (pmm) cc_final: 0.1797 (pmm)
REVERT: C  270 PHE cc_start: 0.7762 (t80) cc_final: 0.7491 (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: 0.1786 (pmm)
REVERT: D  270 PHE cc_start: 0.7758 (t80) cc_final: 0.7488 (t80)
REVERT: D  506 MET cc_start: 0.7404 (tmm) cc_final: 0.7155 (tmm)
REVERT: D  509 ILE cc_start: 0.8699 (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: 0.2838
  time to fit residues: 142.3625
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  : 2.539 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 56 optimal weight:    1.9990
   chunk 164 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   chunk 242 optimal weight:    5.9990
   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:    2.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 ** 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 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 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 477 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 = 0.4681 r_free = 0.4681 target = 0.223429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.183283 restraints weight = 38496.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.181325 restraints weight = 51102.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.177508 restraints weight = 38153.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100  21804  Z= 0.186
  Angle     :  0.796  19.270  29584  Z= 0.419
  Chirality :  0.048   0.276   3404
  Planarity :  0.005   0.056   3668
  Dihedral  :  6.241  49.952   2864
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  1.22 %
    Allowed  : 13.61 %
    Favored  : 85.17 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.28 %
    Favored  : 84.37 %
  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: -2.39 (0.16), residues: 2616
  helix:  0.14 (0.15), residues: 1180
  sheet: -1.99 (0.49), residues: 108
  loop : -3.36 (0.16), residues: 1328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D 618 
 HIS   0.005   0.001   HIS A 539 
 PHE   0.032   0.002   PHE C 676 
 TYR   0.018   0.002   TYR D  88 
 ARG   0.007   0.000   ARG D 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05355 (  756)
  hydrogen bonds       : angle       4.55637 ( 2184)
  covalent geometry    : bond        0.00412 (21804)
  covalent geometry    : angle       0.79621 (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
  336 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 280
  time to evaluate  : 3.319 
Fit side-chains
REVERT: A  194 GLN cc_start: 0.4886 (mp10) cc_final: 0.4500 (mt0)
REVERT: A  509 ILE cc_start: 0.8730 (pt) cc_final: 0.8381 (mm)
REVERT: A  513 TRP cc_start: 0.7348 (m-10) cc_final: 0.6924 (m-10)
REVERT: A  560 ARG cc_start: 0.7254 (mtm180) cc_final: 0.6514 (mmt90)
REVERT: A  676 PHE cc_start: 0.4228 (p90) cc_final: 0.2895 (p90)
REVERT: B  194 GLN cc_start: 0.4883 (mp10) cc_final: 0.4497 (mt0)
REVERT: B  509 ILE cc_start: 0.8734 (pt) cc_final: 0.8386 (mm)
REVERT: B  513 TRP cc_start: 0.7359 (m-10) cc_final: 0.6933 (m-10)
REVERT: B  560 ARG cc_start: 0.7265 (mtm180) cc_final: 0.6528 (mmt90)
REVERT: B  676 PHE cc_start: 0.4238 (p90) cc_final: 0.2902 (p90)
REVERT: C  194 GLN cc_start: 0.4885 (mp10) cc_final: 0.4499 (mt0)
REVERT: C  509 ILE cc_start: 0.8726 (pt) cc_final: 0.8379 (mm)
REVERT: C  513 TRP cc_start: 0.7367 (m-10) cc_final: 0.6934 (m-10)
REVERT: C  560 ARG cc_start: 0.7284 (mtm180) cc_final: 0.6539 (mmt90)
REVERT: C  676 PHE cc_start: 0.4239 (p90) cc_final: 0.2898 (p90)
REVERT: D  194 GLN cc_start: 0.4897 (mp10) cc_final: 0.4506 (mt0)
REVERT: D  509 ILE cc_start: 0.8724 (pt) cc_final: 0.8377 (mm)
REVERT: D  513 TRP cc_start: 0.7354 (m-10) cc_final: 0.6923 (m-10)
REVERT: D  560 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6519 (mmt90)
REVERT: D  676 PHE cc_start: 0.4244 (p90) cc_final: 0.2901 (p90)
  outliers start: 56
  outliers final: 44
  residues processed: 312
  average time/residue: 0.3498
  time to fit residues: 186.7221
Evaluate side-chains
  300 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 256
  time to evaluate  : 3.192 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 166 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0970
   chunk 70 optimal weight:    9.9990
   chunk 139 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 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  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 HIS
** 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 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 = 0.4665 r_free = 0.4665 target = 0.221961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.180481 restraints weight = 38447.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.179625 restraints weight = 52368.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.176954 restraints weight = 38691.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100  21804  Z= 0.177
  Angle     :  0.762  19.697  29584  Z= 0.403
  Chirality :  0.047   0.264   3404
  Planarity :  0.005   0.057   3668
  Dihedral  :  6.040  48.324   2864
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 12.12 %
    Favored  : 86.51 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.97 %
    Favored  : 80.67 %
  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: -2.27 (0.16), residues: 2616
  helix:  0.23 (0.16), residues: 1160
  sheet: -1.94 (0.57), residues: 88
  loop : -3.22 (0.16), residues: 1368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D 618 
 HIS   0.004   0.001   HIS C 539 
 PHE   0.033   0.002   PHE D 676 
 TYR   0.019   0.001   TYR B  88 
 ARG   0.006   0.000   ARG B 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04902 (  756)
  hydrogen bonds       : angle       4.34202 ( 2184)
  covalent geometry    : bond        0.00392 (21804)
  covalent geometry    : angle       0.76210 (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
  360 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 280
  time to evaluate  : 2.434 
Fit side-chains
REVERT: A  509 ILE cc_start: 0.8613 (pt) cc_final: 0.8228 (mm)
REVERT: A  513 TRP cc_start: 0.7181 (m-10) cc_final: 0.6724 (m-10)
REVERT: B  474 MET cc_start: 0.3748 (OUTLIER) cc_final: 0.3514 (ttt)
REVERT: B  509 ILE cc_start: 0.8620 (pt) cc_final: 0.8232 (mm)
REVERT: B  513 TRP cc_start: 0.7190 (m-10) cc_final: 0.6736 (m-10)
REVERT: C  474 MET cc_start: 0.3712 (OUTLIER) cc_final: 0.3508 (ttt)
REVERT: C  509 ILE cc_start: 0.8622 (pt) cc_final: 0.8237 (mm)
REVERT: C  513 TRP cc_start: 0.7206 (m-10) cc_final: 0.6744 (m-10)
REVERT: D  509 ILE cc_start: 0.8618 (pt) cc_final: 0.8234 (mm)
REVERT: D  513 TRP cc_start: 0.7199 (m-10) cc_final: 0.6735 (m-10)
  outliers start: 80
  outliers final: 40
  residues processed: 332
  average time/residue: 0.2892
  time to fit residues: 155.3946
Evaluate side-chains
  288 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 246
  time to evaluate  : 2.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  260 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  240 THR
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  474 MET
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  240 THR
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  260 VAL
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  474 MET
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  240 THR
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain D residue  260 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:    8.9990
   chunk 94 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0770
   chunk 166 optimal weight:    0.9980
   chunk 243 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 209 optimal weight:    0.9980
   chunk 115 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 261 optimal weight:    8.9990
   chunk 18 optimal weight:    0.1980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
** 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 158 ASN
B 473 GLN
B 477 ASN
** 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 158 ASN
C 473 GLN
C 477 ASN
C 546 ASN
** 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 158 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 = 0.4683 r_free = 0.4683 target = 0.224234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.182614 restraints weight = 39459.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.181179 restraints weight = 49982.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.176262 restraints weight = 39381.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6624
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  21804  Z= 0.147
  Angle     :  0.748  19.358  29584  Z= 0.390
  Chirality :  0.046   0.255   3404
  Planarity :  0.004   0.059   3668
  Dihedral  :  5.827  46.974   2864
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 12.00 %
    Favored  : 86.62 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 19.16 %
    Favored  : 78.82 %
  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: -2.05 (0.17), residues: 2616
  helix:  0.49 (0.16), residues: 1156
  sheet: -1.86 (0.59), residues: 88
  loop : -3.16 (0.16), residues: 1372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 618 
 HIS   0.003   0.001   HIS B 539 
 PHE   0.046   0.002   PHE A 676 
 TYR   0.016   0.001   TYR C  88 
 ARG   0.003   0.000   ARG C 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04506 (  756)
  hydrogen bonds       : angle       4.24940 ( 2184)
  covalent geometry    : bond        0.00307 (21804)
  covalent geometry    : angle       0.74826 (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
  320 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 272
  time to evaluate  : 2.495 
Fit side-chains
REVERT: A  109 MET cc_start: 0.2582 (pmm) cc_final: -0.1656 (ptt)
REVERT: A  513 TRP cc_start: 0.7186 (m-10) cc_final: 0.6736 (m-10)
REVERT: A  532 MET cc_start: 0.5494 (ppp) cc_final: 0.5011 (ppp)
REVERT: B  109 MET cc_start: 0.2598 (pmm) cc_final: -0.1659 (ptt)
REVERT: B  513 TRP cc_start: 0.7178 (m-10) cc_final: 0.6734 (m-10)
REVERT: B  532 MET cc_start: 0.5514 (ppp) cc_final: 0.5031 (ppp)
REVERT: C  109 MET cc_start: 0.2585 (pmm) cc_final: -0.1650 (ptt)
REVERT: C  513 TRP cc_start: 0.7206 (m-10) cc_final: 0.6749 (m-10)
REVERT: C  532 MET cc_start: 0.5482 (ppp) cc_final: 0.4995 (ppp)
REVERT: D  109 MET cc_start: 0.2585 (pmm) cc_final: -0.1663 (ptt)
REVERT: D  513 TRP cc_start: 0.7201 (m-10) cc_final: 0.6743 (m-10)
REVERT: D  532 MET cc_start: 0.5489 (ppp) cc_final: 0.5001 (ppp)
  outliers start: 48
  outliers final: 32
  residues processed: 306
  average time/residue: 0.2743
  time to fit residues: 139.5090
Evaluate side-chains
  280 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 248
  time to evaluate  : 2.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   94 GLU
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   94 GLU
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   94 GLU
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   94 GLU
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:    0.8980
   chunk 153 optimal weight:    0.7980
   chunk 127 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   chunk 161 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 194 GLN
A 546 ASN
** 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 194 GLN
B 473 GLN
B 477 ASN
B 546 ASN
** 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
C 473 GLN
C 477 ASN
** 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
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: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.222111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.181335 restraints weight = 38262.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.177192 restraints weight = 52540.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.176133 restraints weight = 39505.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  21804  Z= 0.153
  Angle     :  0.742  18.729  29584  Z= 0.388
  Chirality :  0.046   0.226   3404
  Planarity :  0.004   0.058   3668
  Dihedral  :  5.759  45.964   2864
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 12.08 %
    Favored  : 86.54 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.92 %
    Favored  : 77.31 %
  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: -2.01 (0.17), residues: 2616
  helix:  0.49 (0.16), residues: 1160
  sheet: -2.03 (0.47), residues: 116
  loop : -3.12 (0.16), residues: 1340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 618 
 HIS   0.004   0.001   HIS C 539 
 PHE   0.041   0.002   PHE B 676 
 TYR   0.015   0.001   TYR A  88 
 ARG   0.004   0.000   ARG B 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04481 (  756)
  hydrogen bonds       : angle       4.22057 ( 2184)
  covalent geometry    : bond        0.00323 (21804)
  covalent geometry    : angle       0.74181 (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
  348 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 282
  time to evaluate  : 2.271 
Fit side-chains
REVERT: A  109 MET cc_start: 0.3059 (pmm) cc_final: -0.1060 (ptt)
REVERT: A  513 TRP cc_start: 0.6971 (m-10) cc_final: 0.6610 (m-10)
REVERT: A  625 HIS cc_start: 0.6666 (m-70) cc_final: 0.6383 (m-70)
REVERT: B  109 MET cc_start: 0.3050 (pmm) cc_final: -0.1082 (ptt)
REVERT: B  513 TRP cc_start: 0.6981 (m-10) cc_final: 0.6619 (m-10)
REVERT: B  625 HIS cc_start: 0.6658 (m-70) cc_final: 0.6377 (m-70)
REVERT: C  109 MET cc_start: 0.3073 (pmm) cc_final: -0.1042 (ptt)
REVERT: C  513 TRP cc_start: 0.6997 (m-10) cc_final: 0.6627 (m-10)
REVERT: C  625 HIS cc_start: 0.6639 (m-70) cc_final: 0.6344 (m-70)
REVERT: D  109 MET cc_start: 0.3072 (pmm) cc_final: -0.1051 (ptt)
REVERT: D  474 MET cc_start: 0.3739 (ttt) cc_final: 0.3353 (ttt)
REVERT: D  513 TRP cc_start: 0.6991 (m-10) cc_final: 0.6626 (m-10)
REVERT: D  625 HIS cc_start: 0.6656 (m-70) cc_final: 0.6359 (m-70)
  outliers start: 66
  outliers final: 32
  residues processed: 336
  average time/residue: 0.2533
  time to fit residues: 144.6763
Evaluate side-chains
  298 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 266
  time to evaluate  : 2.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  257 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  257 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  257 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  566 PHE
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  257 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 152 optimal weight:    3.9990
   chunk 153 optimal weight:    0.5980
   chunk 151 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 116 optimal weight:    8.9990
   chunk 38 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 197 optimal weight:    6.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** 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 473 GLN
** 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 473 GLN
** 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 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 = 0.4663 r_free = 0.4663 target = 0.221871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.190258 restraints weight = 38396.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.186980 restraints weight = 48987.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.183387 restraints weight = 37619.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6427
moved from start:          0.4014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.097  21804  Z= 0.158
  Angle     :  0.755  18.526  29584  Z= 0.395
  Chirality :  0.046   0.213   3404
  Planarity :  0.004   0.059   3668
  Dihedral  :  5.657  45.477   2864
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 12.39 %
    Favored  : 86.24 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.97 %
    Favored  : 76.01 %
  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: -2.08 (0.17), residues: 2616
  helix:  0.46 (0.16), residues: 1160
  sheet: -1.91 (0.49), residues: 116
  loop : -3.20 (0.16), residues: 1340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 618 
 HIS   0.004   0.001   HIS A 539 
 PHE   0.034   0.002   PHE C 491 
 TYR   0.013   0.001   TYR A 508 
 ARG   0.004   0.000   ARG B 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04556 (  756)
  hydrogen bonds       : angle       4.24901 ( 2184)
  covalent geometry    : bond        0.00342 (21804)
  covalent geometry    : angle       0.75538 (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
  366 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 294
  time to evaluate  : 2.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 PHE cc_start: -0.0028 (OUTLIER) cc_final: -0.0921 (m-80)
REVERT: A  109 MET cc_start: 0.3087 (pmm) cc_final: -0.0880 (ptt)
REVERT: A  513 TRP cc_start: 0.6582 (m-10) cc_final: 0.6315 (m-10)
REVERT: A  625 HIS cc_start: 0.6561 (m-70) cc_final: 0.6322 (m-70)
REVERT: B  107 PHE cc_start: -0.0015 (OUTLIER) cc_final: -0.0904 (m-80)
REVERT: B  109 MET cc_start: 0.3093 (pmm) cc_final: -0.0882 (ptt)
REVERT: B  513 TRP cc_start: 0.6585 (m-10) cc_final: 0.6316 (m-10)
REVERT: B  625 HIS cc_start: 0.6557 (m-70) cc_final: 0.6324 (m-70)
REVERT: C  107 PHE cc_start: -0.0051 (OUTLIER) cc_final: -0.0933 (m-80)
REVERT: C  109 MET cc_start: 0.3118 (pmm) cc_final: -0.0865 (ptt)
REVERT: C  513 TRP cc_start: 0.6607 (m-10) cc_final: 0.6328 (m-10)
REVERT: C  625 HIS cc_start: 0.6533 (m-70) cc_final: 0.6297 (m-70)
REVERT: D  107 PHE cc_start: -0.0028 (OUTLIER) cc_final: -0.0918 (m-80)
REVERT: D  109 MET cc_start: 0.3098 (pmm) cc_final: -0.0873 (ptt)
REVERT: D  513 TRP cc_start: 0.6621 (m-10) cc_final: 0.6318 (m-10)
REVERT: D  625 HIS cc_start: 0.6531 (m-70) cc_final: 0.6298 (m-70)
  outliers start: 72
  outliers final: 52
  residues processed: 348
  average time/residue: 0.2960
  time to fit residues: 168.0919
Evaluate side-chains
  328 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 272
  time to evaluate  : 2.226 
-------------------------------------------------------------------------------
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   94 GLU
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  257 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 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   94 GLU
Chi-restraints excluded: chain B residue  107 PHE
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  473 GLN
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 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   94 GLU
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  473 GLN
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 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   94 GLU
Chi-restraints excluded: chain D residue  107 PHE
Chi-restraints excluded: chain D residue  202 THR
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  257 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
Chi-restraints excluded: chain D residue  676 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 233 optimal weight:    0.4980
   chunk 188 optimal weight:    1.9990
   chunk 257 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 139 optimal weight:    4.9990
   chunk 234 optimal weight:    0.6980
   chunk 197 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 161 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 473 GLN
** 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 473 GLN
** 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 473 GLN
** 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 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.219252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.176503 restraints weight = 38673.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.168258 restraints weight = 46141.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.166262 restraints weight = 38846.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  21804  Z= 0.173
  Angle     :  0.764  18.029  29584  Z= 0.401
  Chirality :  0.047   0.241   3404
  Planarity :  0.004   0.059   3668
  Dihedral  :  5.610  42.589   2864
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 12.27 %
    Favored  : 86.35 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.68 %
    Favored  : 74.83 %
  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: -2.11 (0.17), residues: 2616
  helix:  0.43 (0.16), residues: 1160
  sheet: -1.97 (0.48), residues: 116
  loop : -3.20 (0.16), residues: 1340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP C 618 
 HIS   0.004   0.001   HIS D 539 
 PHE   0.025   0.002   PHE A 491 
 TYR   0.014   0.001   TYR B 419 
 ARG   0.004   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04747 (  756)
  hydrogen bonds       : angle       4.33734 ( 2184)
  covalent geometry    : bond        0.00377 (21804)
  covalent geometry    : angle       0.76371 (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
  364 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 281
  time to evaluate  : 2.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 PHE cc_start: -0.0492 (OUTLIER) cc_final: -0.1259 (m-80)
REVERT: A  109 MET cc_start: 0.2831 (pmm) cc_final: -0.0946 (ptt)
REVERT: A  503 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7256 (tm-30)
REVERT: A  513 TRP cc_start: 0.6929 (m-10) cc_final: 0.6611 (m-10)
REVERT: A  522 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6436 (pm20)
REVERT: A  625 HIS cc_start: 0.6751 (m-70) cc_final: 0.6403 (m-70)
REVERT: B  107 PHE cc_start: -0.0516 (OUTLIER) cc_final: -0.1274 (m-80)
REVERT: B  109 MET cc_start: 0.2828 (pmm) cc_final: -0.0940 (ptt)
REVERT: B  503 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7271 (tm-30)
REVERT: B  513 TRP cc_start: 0.6953 (m-10) cc_final: 0.6631 (m-10)
REVERT: B  522 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6425 (pm20)
REVERT: B  625 HIS cc_start: 0.6756 (m-70) cc_final: 0.6409 (m-70)
REVERT: C  107 PHE cc_start: -0.0517 (OUTLIER) cc_final: -0.1273 (m-80)
REVERT: C  109 MET cc_start: 0.2833 (pmm) cc_final: -0.0943 (ptt)
REVERT: C  503 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7257 (tm-30)
REVERT: C  513 TRP cc_start: 0.6946 (m-10) cc_final: 0.6621 (m-10)
REVERT: C  522 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6444 (pm20)
REVERT: C  625 HIS cc_start: 0.6740 (m-70) cc_final: 0.6455 (m-70)
REVERT: D  107 PHE cc_start: -0.0501 (OUTLIER) cc_final: -0.1267 (m-80)
REVERT: D  109 MET cc_start: 0.2826 (pmm) cc_final: -0.0934 (ptt)
REVERT: D  503 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: D  513 TRP cc_start: 0.6946 (m-10) cc_final: 0.6619 (m-10)
REVERT: D  522 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6446 (pm20)
REVERT: D  625 HIS cc_start: 0.6738 (m-70) cc_final: 0.6455 (m-70)
  outliers start: 83
  outliers final: 54
  residues processed: 344
  average time/residue: 0.2739
  time to fit residues: 155.0183
Evaluate side-chains
  332 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 274
  time to evaluate  : 2.303 
-------------------------------------------------------------------------------
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  230 ILE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  257 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   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  230 ILE
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  473 GLN
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   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  240 THR
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  379 VAL
Chi-restraints excluded: chain C residue  473 GLN
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   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  230 ILE
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  257 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 264
   random chunks:
   chunk 232 optimal weight:    0.1980
   chunk 11 optimal weight:    0.5980
   chunk 195 optimal weight:    0.0040
   chunk 13 optimal weight:    0.1980
   chunk 110 optimal weight:    7.9990
   chunk 239 optimal weight:    0.7980
   chunk 246 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 222 optimal weight:    0.9990
   chunk 128 optimal weight:    3.9990
   overall best weight:    0.3592

-------------------------------------------------------------------------------
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 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 HIS
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 639 HIS
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 473 GLN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 639 HIS
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 639 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.222642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.178773 restraints weight = 38563.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.173287 restraints weight = 52891.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.171347 restraints weight = 36052.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.4635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082  21804  Z= 0.142
  Angle     :  0.746  18.122  29584  Z= 0.391
  Chirality :  0.045   0.239   3404
  Planarity :  0.004   0.059   3668
  Dihedral  :  5.412  42.154   2864
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  : 11.12 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 23.28 %
    Favored  : 73.95 %
  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:  0.52 (0.16), residues: 1160
  sheet: -1.83 (0.50), residues: 116
  loop : -3.21 (0.16), residues: 1340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP D 618 
 HIS   0.005   0.001   HIS C 539 
 PHE   0.030   0.001   PHE A 491 
 TYR   0.015   0.001   TYR D 508 
 ARG   0.004   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04224 (  756)
  hydrogen bonds       : angle       4.21592 ( 2184)
  covalent geometry    : bond        0.00289 (21804)
  covalent geometry    : angle       0.74599 (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
  365 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 299
  time to evaluate  : 2.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 PHE cc_start: -0.0632 (OUTLIER) cc_final: -0.1477 (m-80)
REVERT: A  109 MET cc_start: 0.2632 (pmm) cc_final: -0.1171 (ptt)
REVERT: A  513 TRP cc_start: 0.7091 (m-10) cc_final: 0.6884 (m-10)
REVERT: A  522 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7064 (tp30)
REVERT: A  533 ARG cc_start: 0.7660 (tmm-80) cc_final: 0.7342 (tpt-90)
REVERT: A  611 ASP cc_start: 0.6146 (m-30) cc_final: 0.5804 (m-30)
REVERT: B  107 PHE cc_start: -0.0652 (OUTLIER) cc_final: -0.1493 (m-80)
REVERT: B  109 MET cc_start: 0.2623 (pmm) cc_final: -0.1162 (ptt)
REVERT: B  513 TRP cc_start: 0.7066 (m-10) cc_final: 0.6865 (m-10)
REVERT: B  522 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7002 (tp30)
REVERT: B  533 ARG cc_start: 0.7644 (tmm-80) cc_final: 0.7341 (tpt-90)
REVERT: B  611 ASP cc_start: 0.6116 (m-30) cc_final: 0.5786 (m-30)
REVERT: C  107 PHE cc_start: -0.0707 (OUTLIER) cc_final: -0.1523 (m-80)
REVERT: C  109 MET cc_start: 0.2613 (pmm) cc_final: -0.1169 (ptt)
REVERT: C  513 TRP cc_start: 0.7056 (m-10) cc_final: 0.6843 (m-10)
REVERT: C  522 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7014 (tp30)
REVERT: C  533 ARG cc_start: 0.7657 (tmm-80) cc_final: 0.7341 (tpt-90)
REVERT: C  611 ASP cc_start: 0.6191 (m-30) cc_final: 0.5876 (m-30)
REVERT: D  107 PHE cc_start: -0.0690 (OUTLIER) cc_final: -0.1515 (m-80)
REVERT: D  109 MET cc_start: 0.2611 (pmm) cc_final: -0.1163 (ptt)
REVERT: D  513 TRP cc_start: 0.7081 (m-10) cc_final: 0.6867 (m-10)
REVERT: D  522 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7040 (tp30)
REVERT: D  533 ARG cc_start: 0.7648 (tmm-80) cc_final: 0.7331 (tpt-90)
REVERT: D  611 ASP cc_start: 0.6170 (m-30) cc_final: 0.5853 (m-30)
  outliers start: 66
  outliers final: 42
  residues processed: 345
  average time/residue: 0.2752
  time to fit residues: 156.9771
Evaluate side-chains
  316 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 270
  time to evaluate  : 2.545 
-------------------------------------------------------------------------------
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  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  473 GLN
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 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  473 GLN
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 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  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:    5.9990
   chunk 227 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 133 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 59 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 155 optimal weight:    7.9990
   overall best weight:    1.1788

-------------------------------------------------------------------------------
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 178 HIS
** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 178 HIS
** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 HIS
C 477 ASN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 178 HIS
D 473 GLN
** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.219135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.177589 restraints weight = 38173.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.168474 restraints weight = 52374.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.164611 restraints weight = 45973.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.4883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  21804  Z= 0.165
  Angle     :  0.802  17.766  29584  Z= 0.412
  Chirality :  0.046   0.202   3404
  Planarity :  0.005   0.059   3668
  Dihedral  :  5.449  40.114   2864
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  1.22 %
    Allowed  : 12.39 %
    Favored  : 86.39 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 24.20 %
    Favored  : 73.36 %
  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: -2.12 (0.17), residues: 2616
  helix:  0.41 (0.16), residues: 1156
  sheet: -1.81 (0.51), residues: 116
  loop : -3.21 (0.16), residues: 1344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP D 618 
 HIS   0.005   0.001   HIS C 539 
 PHE   0.027   0.002   PHE D 491 
 TYR   0.016   0.001   TYR B 508 
 ARG   0.004   0.000   ARG C 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04748 (  756)
  hydrogen bonds       : angle       4.32257 ( 2184)
  covalent geometry    : bond        0.00358 (21804)
  covalent geometry    : angle       0.80203 (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
  326 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 268
  time to evaluate  : 2.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 PHE cc_start: -0.0293 (OUTLIER) cc_final: -0.1215 (m-80)
REVERT: A  109 MET cc_start: 0.2619 (pmm) cc_final: -0.1126 (ptt)
REVERT: A  207 ILE cc_start: 0.8001 (mp) cc_final: 0.7688 (mm)
REVERT: A  377 ASP cc_start: 0.7076 (m-30) cc_final: 0.6560 (m-30)
REVERT: A  522 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6473 (pm20)
REVERT: B  107 PHE cc_start: -0.0288 (OUTLIER) cc_final: -0.1217 (m-80)
REVERT: B  109 MET cc_start: 0.2594 (pmm) cc_final: -0.1147 (ptt)
REVERT: B  207 ILE cc_start: 0.8006 (mp) cc_final: 0.7693 (mm)
REVERT: B  377 ASP cc_start: 0.7046 (m-30) cc_final: 0.6530 (m-30)
REVERT: B  513 TRP cc_start: 0.7032 (m-10) cc_final: 0.6831 (m-10)
REVERT: B  522 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6472 (pm20)
REVERT: C  107 PHE cc_start: -0.0271 (OUTLIER) cc_final: -0.1202 (m-80)
REVERT: C  109 MET cc_start: 0.2576 (pmm) cc_final: -0.1138 (ptt)
REVERT: C  207 ILE cc_start: 0.7980 (mp) cc_final: 0.7669 (mm)
REVERT: C  377 ASP cc_start: 0.7058 (m-30) cc_final: 0.6546 (m-30)
REVERT: C  513 TRP cc_start: 0.7056 (m-10) cc_final: 0.6853 (m-10)
REVERT: C  522 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6468 (pm20)
REVERT: D  107 PHE cc_start: -0.0250 (OUTLIER) cc_final: -0.1190 (m-80)
REVERT: D  109 MET cc_start: 0.2605 (pmm) cc_final: -0.1144 (ptt)
REVERT: D  207 ILE cc_start: 0.7998 (mp) cc_final: 0.7685 (mm)
REVERT: D  377 ASP cc_start: 0.7087 (m-30) cc_final: 0.6571 (m-30)
REVERT: D  522 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6460 (pm20)
  outliers start: 58
  outliers final: 41
  residues processed: 309
  average time/residue: 0.2806
  time to fit residues: 142.8262
Evaluate side-chains
  307 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 262
  time to evaluate  : 2.278 
-------------------------------------------------------------------------------
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  230 ILE
Chi-restraints excluded: chain A residue  260 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  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  260 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  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  260 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  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  260 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  566 PHE
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:    0.9990
   chunk 236 optimal weight:    0.8980
   chunk 164 optimal weight:    0.6980
   chunk 192 optimal weight:    3.9990
   chunk 127 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 154 optimal weight:    3.9990
   chunk 136 optimal weight:   10.0000
   chunk 73 optimal weight:    0.3980
   chunk 219 optimal weight:    0.7980
   chunk 144 optimal weight:    0.9980
   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 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 178 HIS
** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 625 HIS
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 178 HIS
B 473 GLN
** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 625 HIS
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 HIS
C 473 GLN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 625 HIS
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 178 HIS
** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 625 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.221045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.172784 restraints weight = 38134.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.160263 restraints weight = 40994.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.160862 restraints weight = 34730.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.5139

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= 0.148
  Angle     :  0.746  17.694  29584  Z= 0.388
  Chirality :  0.045   0.236   3404
  Planarity :  0.004   0.059   3668
  Dihedral  :  5.331  39.192   2864
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  1.19 %
    Allowed  : 12.46 %
    Favored  : 86.35 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 24.24 %
    Favored  : 73.53 %
  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:  0.50 (0.16), residues: 1156
  sheet: -1.88 (0.50), residues: 116
  loop : -3.18 (0.16), residues: 1344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 618 
 HIS   0.006   0.001   HIS D 625 
 PHE   0.033   0.002   PHE B 471 
 TYR   0.016   0.001   TYR B 508 
 ARG   0.004   0.000   ARG C 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04462 (  756)
  hydrogen bonds       : angle       4.27132 ( 2184)
  covalent geometry    : bond        0.00309 (21804)
  covalent geometry    : angle       0.74587 (29584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7466.54 seconds
wall clock time: 131 minutes 56.84 seconds (7916.84 seconds total)