Starting phenix.real_space_refine
on Sun Aug 24 00:15:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e76_27936/08_2025/8e76_27936.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e76_27936/08_2025/8e76_27936.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e76_27936/08_2025/8e76_27936.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e76_27936/08_2025/8e76_27936.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e76_27936/08_2025/8e76_27936.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e76_27936/08_2025/8e76_27936.cif"
  }
  resolution = 2.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      84      5.16       5
     C   10208      2.51       5
     N    2724      2.21       5
     O    2912      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15928
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3982
          Classifications: {'peptide': 506}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 480}
          Chain breaks: 2
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 3.77, per 1000 atoms: 0.24
  Number of scatterers: 15928
  At special positions: 0
  Unit cell: (132.08, 135.2, 78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      84     16.00
     O    2912      8.00
     N    2724      7.00
     C   10208      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: 1.37
  Conformation dependent library (CDL) restraints added in 763.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3728

  Finding SS restraints...
    Secondary structure from input PDB file:
      108 helices and 12 sheets defined
      54.3% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 8
      removed outlier: 4.184A  pdb=" N   THR A   6 " --> pdb=" O   GLY A   2 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG A   7 " --> pdb=" O   TYR A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 17
    Processing helix  chain 'A' and resid 18 through 25
    Processing helix  chain 'A' and resid 37 through 50
    Processing helix  chain 'A' and resid 54 through 69
    Processing helix  chain 'A' and resid 69 through 79
    Processing helix  chain 'A' and resid 80 through 89
      Proline residue:  A  86  - end of helix
    Processing helix  chain 'A' and resid 91 through 99
      removed outlier: 3.599A  pdb=" N   LEU A  95 " --> pdb=" O   PRO A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 117
      No H-bonds generated for 'chain 'A' and resid 115 through 117'
    Processing helix  chain 'A' and resid 119 through 126
    Processing helix  chain 'A' and resid 154 through 169
    Processing helix  chain 'A' and resid 171 through 173
      No H-bonds generated for 'chain 'A' and resid 171 through 173'
    Processing helix  chain 'A' and resid 186 through 192
    Processing helix  chain 'A' and resid 207 through 224
    Processing helix  chain 'A' and resid 235 through 247
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 3.610A  pdb=" N   ILE A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 282
    Processing helix  chain 'A' and resid 291 through 307
      removed outlier: 4.160A  pdb=" N   GLY A 295 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 317
    Processing helix  chain 'A' and resid 405 through 411
    Processing helix  chain 'A' and resid 440 through 443
    Processing helix  chain 'A' and resid 444 through 456
    Processing helix  chain 'A' and resid 461 through 476
      removed outlier: 3.884A  pdb=" N   PHE A 465 " --> pdb=" O   PRO A 461 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   VAL A 476 " --> pdb=" O   ILE A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 489 through 491
      No H-bonds generated for 'chain 'A' and resid 489 through 491'
    Processing helix  chain 'A' and resid 492 through 511
    Processing helix  chain 'A' and resid 522 through 529
    Processing helix  chain 'B' and resid 2 through 8
      removed outlier: 4.185A  pdb=" N   THR B   6 " --> pdb=" O   GLY B   2 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ARG B   7 " --> pdb=" O   TYR B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 17
    Processing helix  chain 'B' and resid 18 through 25
    Processing helix  chain 'B' and resid 37 through 50
    Processing helix  chain 'B' and resid 54 through 69
    Processing helix  chain 'B' and resid 69 through 79
    Processing helix  chain 'B' and resid 80 through 89
      Proline residue:  B  86  - end of helix
    Processing helix  chain 'B' and resid 91 through 99
      removed outlier: 3.598A  pdb=" N   LEU B  95 " --> pdb=" O   PRO B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 117
      No H-bonds generated for 'chain 'B' and resid 115 through 117'
    Processing helix  chain 'B' and resid 119 through 126
    Processing helix  chain 'B' and resid 154 through 169
    Processing helix  chain 'B' and resid 171 through 173
      No H-bonds generated for 'chain 'B' and resid 171 through 173'
    Processing helix  chain 'B' and resid 186 through 192
    Processing helix  chain 'B' and resid 207 through 224
    Processing helix  chain 'B' and resid 235 through 247
    Processing helix  chain 'B' and resid 257 through 276
      removed outlier: 3.610A  pdb=" N   ILE B 274 " --> pdb=" O   ALA B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 282
    Processing helix  chain 'B' and resid 291 through 307
      removed outlier: 4.161A  pdb=" N   GLY B 295 " --> pdb=" O   GLU B 291 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE B 296 " --> pdb=" O   ALA B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 317
    Processing helix  chain 'B' and resid 405 through 411
    Processing helix  chain 'B' and resid 440 through 443
    Processing helix  chain 'B' and resid 444 through 456
    Processing helix  chain 'B' and resid 461 through 476
      removed outlier: 3.883A  pdb=" N   PHE B 465 " --> pdb=" O   PRO B 461 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL B 476 " --> pdb=" O   ILE B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 482
    Processing helix  chain 'B' and resid 489 through 491
      No H-bonds generated for 'chain 'B' and resid 489 through 491'
    Processing helix  chain 'B' and resid 492 through 511
    Processing helix  chain 'B' and resid 522 through 529
    Processing helix  chain 'C' and resid 2 through 8
      removed outlier: 4.185A  pdb=" N   THR C   6 " --> pdb=" O   GLY C   2 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ARG C   7 " --> pdb=" O   TYR C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 17
    Processing helix  chain 'C' and resid 18 through 25
    Processing helix  chain 'C' and resid 37 through 50
    Processing helix  chain 'C' and resid 54 through 69
    Processing helix  chain 'C' and resid 69 through 79
    Processing helix  chain 'C' and resid 80 through 89
      Proline residue:  C  86  - end of helix
    Processing helix  chain 'C' and resid 91 through 99
      removed outlier: 3.599A  pdb=" N   LEU C  95 " --> pdb=" O   PRO C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 117
      No H-bonds generated for 'chain 'C' and resid 115 through 117'
    Processing helix  chain 'C' and resid 119 through 126
    Processing helix  chain 'C' and resid 154 through 169
    Processing helix  chain 'C' and resid 171 through 173
      No H-bonds generated for 'chain 'C' and resid 171 through 173'
    Processing helix  chain 'C' and resid 186 through 192
    Processing helix  chain 'C' and resid 207 through 224
    Processing helix  chain 'C' and resid 235 through 247
    Processing helix  chain 'C' and resid 257 through 276
      removed outlier: 3.610A  pdb=" N   ILE C 274 " --> pdb=" O   ALA C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 282
    Processing helix  chain 'C' and resid 291 through 307
      removed outlier: 4.160A  pdb=" N   GLY C 295 " --> pdb=" O   GLU C 291 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE C 296 " --> pdb=" O   ALA C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 310 through 317
    Processing helix  chain 'C' and resid 405 through 411
    Processing helix  chain 'C' and resid 440 through 443
    Processing helix  chain 'C' and resid 444 through 456
    Processing helix  chain 'C' and resid 461 through 476
      removed outlier: 3.884A  pdb=" N   PHE C 465 " --> pdb=" O   PRO C 461 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   VAL C 476 " --> pdb=" O   ILE C 472 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 477 through 482
    Processing helix  chain 'C' and resid 489 through 491
      No H-bonds generated for 'chain 'C' and resid 489 through 491'
    Processing helix  chain 'C' and resid 492 through 511
    Processing helix  chain 'C' and resid 522 through 529
    Processing helix  chain 'D' and resid 2 through 8
      removed outlier: 4.185A  pdb=" N   THR D   6 " --> pdb=" O   GLY D   2 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ARG D   7 " --> pdb=" O   TYR D   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 17
    Processing helix  chain 'D' and resid 18 through 25
    Processing helix  chain 'D' and resid 37 through 50
    Processing helix  chain 'D' and resid 54 through 69
    Processing helix  chain 'D' and resid 69 through 79
    Processing helix  chain 'D' and resid 80 through 89
      Proline residue:  D  86  - end of helix
    Processing helix  chain 'D' and resid 91 through 99
      removed outlier: 3.599A  pdb=" N   LEU D  95 " --> pdb=" O   PRO D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 117
      No H-bonds generated for 'chain 'D' and resid 115 through 117'
    Processing helix  chain 'D' and resid 119 through 126
    Processing helix  chain 'D' and resid 154 through 169
    Processing helix  chain 'D' and resid 171 through 173
      No H-bonds generated for 'chain 'D' and resid 171 through 173'
    Processing helix  chain 'D' and resid 186 through 192
    Processing helix  chain 'D' and resid 207 through 224
    Processing helix  chain 'D' and resid 235 through 247
    Processing helix  chain 'D' and resid 257 through 276
      removed outlier: 3.610A  pdb=" N   ILE D 274 " --> pdb=" O   ALA D 270 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 278 through 282
    Processing helix  chain 'D' and resid 291 through 307
      removed outlier: 4.160A  pdb=" N   GLY D 295 " --> pdb=" O   GLU D 291 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE D 296 " --> pdb=" O   ALA D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 310 through 317
    Processing helix  chain 'D' and resid 405 through 411
    Processing helix  chain 'D' and resid 440 through 443
    Processing helix  chain 'D' and resid 444 through 456
    Processing helix  chain 'D' and resid 461 through 476
      removed outlier: 3.884A  pdb=" N   PHE D 465 " --> pdb=" O   PRO D 461 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   VAL D 476 " --> pdb=" O   ILE D 472 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 477 through 482
    Processing helix  chain 'D' and resid 489 through 491
      No H-bonds generated for 'chain 'D' and resid 489 through 491'
    Processing helix  chain 'D' and resid 492 through 511
    Processing helix  chain 'D' and resid 522 through 529
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36
      removed outlier: 7.075A  pdb=" N   PHE A  35 " --> pdb=" O   GLN B 554 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113
      removed outlier: 6.383A  pdb=" N   LEU A 110 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   ASP A 181 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE A 112 " --> pdb=" O   ASP A 181 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ALA A 134 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   VAL A 178 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL A 136 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   LEU A 180 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   THR A 138 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 320
      removed outlier: 6.557A  pdb=" N   PHE A 284 " --> pdb=" O   TRP A 319 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   VAL A 285 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   GLY A 437 " --> pdb=" O   PHE A 417 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   SER A 419 " --> pdb=" O   GLY A 437 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 554
    Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 113
      removed outlier: 6.383A  pdb=" N   LEU B 110 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   ASP B 181 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ILE B 112 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ALA B 134 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   VAL B 178 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL B 136 " --> pdb=" O   VAL B 178 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   LEU B 180 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   THR B 138 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 320
      removed outlier: 6.557A  pdb=" N   PHE B 284 " --> pdb=" O   TRP B 319 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   VAL B 285 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   GLY B 437 " --> pdb=" O   PHE B 417 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER B 419 " --> pdb=" O   GLY B 437 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 36
      removed outlier: 7.075A  pdb=" N   PHE C  35 " --> pdb=" O   GLN D 554 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 113
      removed outlier: 6.384A  pdb=" N   LEU C 110 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   ASP C 181 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE C 112 " --> pdb=" O   ASP C 181 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ALA C 134 " --> pdb=" O   LEU C 176 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   VAL C 178 " --> pdb=" O   ALA C 134 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   VAL C 136 " --> pdb=" O   VAL C 178 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   LEU C 180 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR C 138 " --> pdb=" O   LEU C 180 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 318 through 320
      removed outlier: 6.558A  pdb=" N   PHE C 284 " --> pdb=" O   TRP C 319 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   VAL C 285 " --> pdb=" O   ILE C 364 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   GLY C 437 " --> pdb=" O   PHE C 417 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER C 419 " --> pdb=" O   GLY C 437 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 553 through 554
    Processing sheet with id=AB2, first strand: chain 'D' and resid 110 through 113
      removed outlier: 6.383A  pdb=" N   LEU D 110 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   ASP D 181 " --> pdb=" O   LEU D 110 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE D 112 " --> pdb=" O   ASP D 181 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ALA D 134 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   VAL D 178 " --> pdb=" O   ALA D 134 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL D 136 " --> pdb=" O   VAL D 178 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   LEU D 180 " --> pdb=" O   VAL D 136 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR D 138 " --> pdb=" O   LEU D 180 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 318 through 320
      removed outlier: 6.558A  pdb=" N   PHE D 284 " --> pdb=" O   TRP D 319 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   VAL D 285 " --> pdb=" O   ILE D 364 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   GLY D 437 " --> pdb=" O   PHE D 417 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER D 419 " --> pdb=" O   GLY D 437 " (cutoff:3.500A)

    690 hydrogen bonds defined for protein.
    2010 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: 2.86

  Time building geometry restraints manager: 1.82 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: 5182
        1.34 -     1.45: 2603
        1.45 -     1.57: 8359
        1.57 -     1.69: 0
        1.69 -     1.81: 132
  Bond restraints: 16276
  Sorted by residual:
  bond pdb=" C   ASN A 395 "
       pdb=" N   PRO A 396 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.016 8.40e-03 1.42e+04 3.56e+00
  bond pdb=" C   ASN C 395 "
       pdb=" N   PRO C 396 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.016 8.40e-03 1.42e+04 3.54e+00
  bond pdb=" C   ASN D 395 "
       pdb=" N   PRO D 396 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.016 8.40e-03 1.42e+04 3.45e+00
  bond pdb=" C   ASN B 395 "
       pdb=" N   PRO B 396 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.016 8.40e-03 1.42e+04 3.43e+00
  bond pdb=" CB  ARG D 247 "
       pdb=" CG  ARG D 247 "
    ideal  model  delta    sigma   weight residual
    1.520  1.474  0.046 3.00e-02 1.11e+03 2.30e+00
  ... (remaining 16271 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 21363
        1.82 -     3.64: 588
        3.64 -     5.47: 77
        5.47 -     7.29: 16
        7.29 -     9.11: 4
  Bond angle restraints: 22048
  Sorted by residual:
  angle pdb=" N   GLU A 405 "
        pdb=" CA  GLU A 405 "
        pdb=" C   GLU A 405 "
      ideal   model   delta    sigma   weight residual
     113.43  106.93    6.50 1.26e+00 6.30e-01 2.66e+01
  angle pdb=" N   GLU B 405 "
        pdb=" CA  GLU B 405 "
        pdb=" C   GLU B 405 "
      ideal   model   delta    sigma   weight residual
     113.43  106.94    6.49 1.26e+00 6.30e-01 2.66e+01
  angle pdb=" N   GLU D 405 "
        pdb=" CA  GLU D 405 "
        pdb=" C   GLU D 405 "
      ideal   model   delta    sigma   weight residual
     113.43  106.94    6.49 1.26e+00 6.30e-01 2.66e+01
  angle pdb=" N   GLU C 405 "
        pdb=" CA  GLU C 405 "
        pdb=" C   GLU C 405 "
      ideal   model   delta    sigma   weight residual
     113.43  106.94    6.49 1.26e+00 6.30e-01 2.65e+01
  angle pdb=" N   ALA C 207 "
        pdb=" CA  ALA C 207 "
        pdb=" C   ALA C 207 "
      ideal   model   delta    sigma   weight residual
     113.43  109.30    4.13 1.26e+00 6.30e-01 1.07e+01
  ... (remaining 22043 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.18: 8613
       16.18 -    32.35: 871
       32.35 -    48.53: 192
       48.53 -    64.71: 44
       64.71 -    80.88: 24
  Dihedral angle restraints: 9744
    sinusoidal: 3912
      harmonic: 5832
  Sorted by residual:
  dihedral pdb=" CA  CYS D 151 "
           pdb=" C   CYS D 151 "
           pdb=" N   TYR D 152 "
           pdb=" CA  TYR D 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.38   22.62     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  CYS A 151 "
           pdb=" C   CYS A 151 "
           pdb=" N   TYR A 152 "
           pdb=" CA  TYR A 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.39   22.61     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  CYS B 151 "
           pdb=" C   CYS B 151 "
           pdb=" N   TYR B 152 "
           pdb=" CA  TYR B 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.39   22.61     0      5.00e+00 4.00e-02 2.04e+01
  ... (remaining 9741 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1247
       0.032 -    0.064: 843
       0.064 -    0.095: 242
       0.095 -    0.127: 112
       0.127 -    0.159: 20
  Chirality restraints: 2464
  Sorted by residual:
  chirality pdb=" CA  PHE B 445 "
            pdb=" N   PHE B 445 "
            pdb=" C   PHE B 445 "
            pdb=" CB  PHE B 445 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CA  PHE D 445 "
            pdb=" N   PHE D 445 "
            pdb=" C   PHE D 445 "
            pdb=" CB  PHE D 445 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.22e-01
  chirality pdb=" CA  PHE A 445 "
            pdb=" N   PHE A 445 "
            pdb=" C   PHE A 445 "
            pdb=" CB  PHE A 445 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.20e-01
  ... (remaining 2461 not shown)

  Planarity restraints: 2844
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 309 "   -0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO C 310 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO C 310 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 310 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 309 "    0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO A 310 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 310 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 310 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 309 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO B 310 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 310 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 310 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 2841 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 499
        2.70 -     3.25: 16453
        3.25 -     3.80: 28301
        3.80 -     4.35: 37030
        4.35 -     4.90: 58382
  Nonbonded interactions: 140665
  Sorted by model distance:
  nonbonded pdb=" O   GLY D 150 "
            pdb=" OH  TYR D 195 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   GLY B 150 "
            pdb=" OH  TYR B 195 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   GLY C 150 "
            pdb=" OH  TYR C 195 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" O   GLY A 150 "
            pdb=" OH  TYR A 195 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OD1 ASP A 213 "
            pdb=" OH  TYR A 246 "
     model   vdw
     2.192 3.040
  ... (remaining 140660 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     15.710
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  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:6.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6612
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      :  0.007   0.049  16276  Z= 0.317
  Angle     :  0.722   9.110  22048  Z= 0.396
  Chirality :  0.047   0.159   2464
  Planarity :  0.004   0.041   2844
  Dihedral  : 14.221  80.882   6016
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.28 (0.17), residues: 2000
  helix: -1.20 (0.15), residues: 944
  sheet: -0.49 (0.39), residues: 192
  loop : -2.03 (0.20), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 499 
 TYR   0.015   0.002   TYR A  74 
 PHE   0.019   0.002   PHE D  35 
 TRP   0.004   0.001   TRP D 127 
 HIS   0.004   0.001   HIS B 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00747 (16276)
  covalent geometry    : angle       0.72236 (22048)
  hydrogen bonds       : bond        0.16575 (  690)
  hydrogen bonds       : angle       8.23506 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 329
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  154 MET cc_start: 0.4035 (tpp) cc_final: 0.3754 (tpp)
REVERT: B  269 LEU cc_start: 0.7271 (mt) cc_final: 0.7049 (mt)
REVERT: C   63 MET cc_start: 0.5901 (mmp) cc_final: 0.5471 (mmt)
  outliers start: 0
  outliers final: 1
  residues processed: 329
  average time/residue: 0.5118
  time to fit residues: 190.1698
Evaluate side-chains
  187 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  430 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 98 optimal weight:    0.0570
   chunk 194 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    1.7504

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

Flipped N/Q/H residues before XYZ refinement:
A  28 HIS
A  41 GLN
A  66 GLN
A 115 HIS
A 174 GLN
A 281 ASN
A 459 HIS
A 480 HIS
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 GLN
B  66 GLN
B 115 HIS
B 174 GLN
B 217 GLN
B 281 ASN
B 459 HIS
B 480 HIS
C  41 GLN
C  66 GLN
C 174 GLN
** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 ASN
C 459 HIS
C 480 HIS
D  28 HIS
D  41 GLN
D  66 GLN
D  99 HIS
D 115 HIS
D 174 GLN
D 459 HIS
** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 29

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.085507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.067605 restraints weight = 45679.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 3.49
r_work: 0.3071 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  16276  Z= 0.193
  Angle     :  0.697   8.741  22048  Z= 0.360
  Chirality :  0.044   0.196   2464
  Planarity :  0.005   0.053   2844
  Dihedral  :  5.031  21.750   2210
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.52 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.18), residues: 2000
  helix:  0.11 (0.16), residues: 956
  sheet: -0.13 (0.41), residues: 188
  loop : -1.61 (0.20), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 409 
 TYR   0.026   0.002   TYR D 487 
 PHE   0.022   0.002   PHE B 434 
 TRP   0.009   0.001   TRP D 319 
 HIS   0.011   0.001   HIS B 298 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (16276)
  covalent geometry    : angle       0.69713 (22048)
  hydrogen bonds       : bond        0.04504 (  690)
  hydrogen bonds       : angle       5.54936 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 187
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 TYR cc_start: 0.6640 (t80) cc_final: 0.6373 (t80)
REVERT: A  407 CYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9006 (p)
REVERT: B   46 MET cc_start: 0.8848 (mmm) cc_final: 0.8640 (mmm)
REVERT: B  302 MET cc_start: 0.9162 (mtp) cc_final: 0.8891 (mtp)
REVERT: B  395 ASN cc_start: 0.8790 (p0) cc_final: 0.8259 (p0)
REVERT: B  406 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6017 (mttt)
REVERT: B  408 TYR cc_start: 0.7181 (m-80) cc_final: 0.6919 (m-80)
REVERT: B  490 LEU cc_start: 0.8872 (mt) cc_final: 0.8605 (mt)
REVERT: C   63 MET cc_start: 0.9056 (mmp) cc_final: 0.8674 (mmt)
REVERT: C   84 PHE cc_start: 0.8467 (m-80) cc_final: 0.8234 (m-80)
REVERT: C  282 HIS cc_start: 0.6797 (m90) cc_final: 0.6470 (m90)
REVERT: C  302 MET cc_start: 0.8091 (mmm) cc_final: 0.7737 (mtp)
REVERT: C  320 MET cc_start: 0.7461 (pmm) cc_final: 0.6620 (mtt)
REVERT: D   67 ASP cc_start: 0.8142 (p0) cc_final: 0.7231 (p0)
REVERT: D  260 THR cc_start: 0.9370 (m) cc_final: 0.9116 (p)
REVERT: D  294 MET cc_start: 0.8884 (mmm) cc_final: 0.8662 (mmm)
REVERT: D  304 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8735 (mm)
REVERT: D  306 LYS cc_start: 0.9401 (tptp) cc_final: 0.9200 (tppp)
  outliers start: 35
  outliers final: 8
  residues processed: 210
  average time/residue: 0.4544
  time to fit residues: 110.0645
Evaluate side-chains
  172 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 161
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  406 LYS
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain C residue  284 PHE
Chi-restraints excluded: chain C residue  498 LEU
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  490 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 3 optimal weight:    0.0980
   chunk 157 optimal weight:    0.9990
   chunk 154 optimal weight:    1.9990
   chunk 106 optimal weight:    8.9990
   chunk 86 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 142 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 131 optimal weight:    5.9990
   chunk 82 optimal weight:    9.9990
   overall best weight:    2.4188

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

Flipped N/Q/H residues before XYZ refinement:
A 281 ASN
C 119 HIS
C 230 GLN
C 281 ASN
** D 480 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 = 0.3453 r_free = 0.3453 target = 0.075928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.057434 restraints weight = 46048.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 3.38
r_work: 0.2835 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  16276  Z= 0.200
  Angle     :  0.662  10.075  22048  Z= 0.343
  Chirality :  0.045   0.181   2464
  Planarity :  0.005   0.091   2844
  Dihedral  :  4.743  21.041   2208
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.40 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.18), residues: 2000
  helix:  0.36 (0.17), residues: 960
  sheet: -0.31 (0.42), residues: 168
  loop : -1.35 (0.20), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 106 
 TYR   0.031   0.002   TYR D 164 
 PHE   0.021   0.002   PHE C 104 
 TRP   0.013   0.001   TRP C 319 
 HIS   0.012   0.001   HIS C 480 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (16276)
  covalent geometry    : angle       0.66241 (22048)
  hydrogen bonds       : bond        0.03953 (  690)
  hydrogen bonds       : angle       5.21097 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 160
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.9219 (mtm) cc_final: 0.8704 (mtt)
REVERT: A  100 TYR cc_start: 0.7333 (t80) cc_final: 0.6937 (t80)
REVERT: A  294 MET cc_start: 0.9227 (mmm) cc_final: 0.8870 (mmm)
REVERT: A  298 HIS cc_start: 0.9332 (m-70) cc_final: 0.9002 (m-70)
REVERT: A  416 ILE cc_start: 0.9024 (mt) cc_final: 0.8725 (mm)
REVERT: A  551 MET cc_start: 0.8709 (ptm) cc_final: 0.8185 (ptp)
REVERT: B   46 MET cc_start: 0.9190 (mmm) cc_final: 0.8956 (mmm)
REVERT: B  302 MET cc_start: 0.9279 (mtp) cc_final: 0.9073 (mtp)
REVERT: B  395 ASN cc_start: 0.8775 (p0) cc_final: 0.8191 (p0)
REVERT: B  406 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6537 (mttt)
REVERT: B  408 TYR cc_start: 0.7075 (m-80) cc_final: 0.6700 (m-80)
REVERT: C   80 ASP cc_start: 0.8593 (t0) cc_final: 0.8184 (t0)
REVERT: C   84 PHE cc_start: 0.8733 (m-80) cc_final: 0.8247 (m-80)
REVERT: C  230 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8486 (tm-30)
REVERT: C  282 HIS cc_start: 0.7182 (m90) cc_final: 0.6892 (m90)
REVERT: C  302 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8139 (mtp)
REVERT: C  405 GLU cc_start: 0.8307 (tt0) cc_final: 0.7314 (mm-30)
REVERT: D   63 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.9137 (mmp)
REVERT: D  100 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.6512 (m-80)
REVERT: D  294 MET cc_start: 0.9068 (mmm) cc_final: 0.8794 (mmm)
REVERT: D  298 HIS cc_start: 0.9168 (t-90) cc_final: 0.8871 (m-70)
REVERT: D  320 MET cc_start: 0.6894 (mtt) cc_final: 0.5817 (pp-130)
REVERT: D  524 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8583 (tm-30)
REVERT: D  551 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8493 (ttm)
  outliers start: 45
  outliers final: 6
  residues processed: 190
  average time/residue: 0.4572
  time to fit residues: 99.7233
Evaluate side-chains
  150 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  406 LYS
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue  230 GLN
Chi-restraints excluded: chain C residue  255 ASP
Chi-restraints excluded: chain C residue  302 MET
Chi-restraints excluded: chain D residue   63 MET
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain D residue  524 GLU
Chi-restraints excluded: chain D residue  551 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 162 optimal weight:    4.9990
   chunk 83 optimal weight:   30.0000
   chunk 31 optimal weight:    9.9990
   chunk 188 optimal weight:   20.0000
   chunk 137 optimal weight:    6.9990
   chunk 158 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 164 optimal weight:    9.9990
   chunk 104 optimal weight:    0.9980
   chunk 139 optimal weight:    6.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 ASN
C 480 HIS
** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 480 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 = 0.3292 r_free = 0.3292 target = 0.068031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.049676 restraints weight = 46666.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 3.25
r_work: 0.2655 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.6038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  16276  Z= 0.281
  Angle     :  0.682  11.032  22048  Z= 0.356
  Chirality :  0.046   0.218   2464
  Planarity :  0.005   0.088   2844
  Dihedral  :  4.705  20.892   2208
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.93 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.19), residues: 2000
  helix:  0.53 (0.17), residues: 964
  sheet: -0.35 (0.43), residues: 168
  loop : -1.18 (0.21), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG C 485 
 TYR   0.018   0.002   TYR C 164 
 PHE   0.030   0.002   PHE A 434 
 TRP   0.008   0.001   TRP C 319 
 HIS   0.035   0.002   HIS C 480 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 (16276)
  covalent geometry    : angle       0.68245 (22048)
  hydrogen bonds       : bond        0.04180 (  690)
  hydrogen bonds       : angle       5.22237 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 138
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.9365 (mtm) cc_final: 0.9135 (mtm)
REVERT: A  305 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8996 (mm-30)
REVERT: A  551 MET cc_start: 0.8966 (ptm) cc_final: 0.8397 (ptp)
REVERT: B   46 MET cc_start: 0.9413 (mmm) cc_final: 0.9133 (mmm)
REVERT: B  294 MET cc_start: 0.8636 (mmm) cc_final: 0.8433 (mmm)
REVERT: B  302 MET cc_start: 0.9356 (mtp) cc_final: 0.9046 (mtp)
REVERT: B  395 ASN cc_start: 0.8750 (p0) cc_final: 0.8188 (p0)
REVERT: B  408 TYR cc_start: 0.7574 (m-80) cc_final: 0.7177 (m-80)
REVERT: B  416 ILE cc_start: 0.8759 (mt) cc_final: 0.8436 (mm)
REVERT: C   80 ASP cc_start: 0.8885 (t0) cc_final: 0.8466 (t0)
REVERT: C  100 TYR cc_start: 0.7173 (t80) cc_final: 0.6903 (t80)
REVERT: C  274 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8738 (mp)
REVERT: C  282 HIS cc_start: 0.7694 (m90) cc_final: 0.7459 (m90)
REVERT: C  302 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8715 (mtp)
REVERT: C  389 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8860 (pp)
REVERT: C  405 GLU cc_start: 0.8643 (tt0) cc_final: 0.7779 (mm-30)
REVERT: C  416 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8512 (pp)
REVERT: C  480 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.7630 (t-170)
REVERT: D  100 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.6714 (m-80)
REVERT: D  294 MET cc_start: 0.9327 (mmm) cc_final: 0.9119 (mmm)
REVERT: D  299 LEU cc_start: 0.9526 (tp) cc_final: 0.9293 (tt)
REVERT: D  395 ASN cc_start: 0.8990 (m-40) cc_final: 0.8436 (p0)
REVERT: D  462 ASP cc_start: 0.9050 (m-30) cc_final: 0.8797 (m-30)
REVERT: D  537 ASP cc_start: 0.8365 (t0) cc_final: 0.8054 (t0)
REVERT: D  551 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8984 (ttm)
  outliers start: 42
  outliers final: 7
  residues processed: 170
  average time/residue: 0.4897
  time to fit residues: 95.3696
Evaluate side-chains
  129 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain C residue  274 ILE
Chi-restraints excluded: chain C residue  302 MET
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  389 ILE
Chi-restraints excluded: chain C residue  416 ILE
Chi-restraints excluded: chain C residue  480 HIS
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  285 VAL
Chi-restraints excluded: chain D residue  551 MET
Chi-restraints excluded: chain D residue  553 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 154 optimal weight:    4.9990
   chunk 169 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 196 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 190 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 298 HIS
B  28 HIS
C 440 ASN
C 480 HIS
** D 282 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 = 0.3298 r_free = 0.3298 target = 0.068408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.050463 restraints weight = 46744.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 3.18
r_work: 0.2664 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.6290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16276  Z= 0.152
  Angle     :  0.596  10.824  22048  Z= 0.305
  Chirality :  0.043   0.285   2464
  Planarity :  0.004   0.050   2844
  Dihedral  :  4.528  20.944   2208
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.57 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.19), residues: 2000
  helix:  0.74 (0.17), residues: 960
  sheet: -0.32 (0.43), residues: 168
  loop : -1.14 (0.21), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 485 
 TYR   0.016   0.001   TYR D 487 
 PHE   0.019   0.002   PHE B 445 
 TRP   0.007   0.001   TRP C 319 
 HIS   0.028   0.001   HIS C 480 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (16276)
  covalent geometry    : angle       0.59619 (22048)
  hydrogen bonds       : bond        0.03539 (  690)
  hydrogen bonds       : angle       4.98693 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.9433 (mtm) cc_final: 0.9167 (mtm)
REVERT: A  305 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9004 (mm-30)
REVERT: A  416 ILE cc_start: 0.9078 (mt) cc_final: 0.8829 (mm)
REVERT: A  551 MET cc_start: 0.8873 (ptm) cc_final: 0.8336 (ptp)
REVERT: B   46 MET cc_start: 0.9428 (mmm) cc_final: 0.9200 (mmm)
REVERT: B  294 MET cc_start: 0.8772 (mmm) cc_final: 0.8513 (mmm)
REVERT: B  302 MET cc_start: 0.9412 (mtp) cc_final: 0.9089 (mtp)
REVERT: B  395 ASN cc_start: 0.8692 (p0) cc_final: 0.8112 (p0)
REVERT: B  408 TYR cc_start: 0.7559 (m-80) cc_final: 0.7344 (m-80)
REVERT: B  416 ILE cc_start: 0.8888 (mt) cc_final: 0.8603 (mm)
REVERT: C   80 ASP cc_start: 0.8851 (t0) cc_final: 0.8492 (t0)
REVERT: C  232 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8875 (tp30)
REVERT: C  302 MET cc_start: 0.9082 (mmm) cc_final: 0.8832 (mtp)
REVERT: C  405 GLU cc_start: 0.8609 (tt0) cc_final: 0.7741 (mm-30)
REVERT: C  416 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8678 (pp)
REVERT: C  480 HIS cc_start: 0.8672 (OUTLIER) cc_final: 0.8373 (t-90)
REVERT: D  100 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.6619 (m-80)
REVERT: D  299 LEU cc_start: 0.9523 (tp) cc_final: 0.9302 (tt)
REVERT: D  305 GLU cc_start: 0.8606 (tp30) cc_final: 0.8207 (mm-30)
REVERT: D  395 ASN cc_start: 0.8980 (m-40) cc_final: 0.8453 (p0)
  outliers start: 30
  outliers final: 11
  residues processed: 141
  average time/residue: 0.4868
  time to fit residues: 78.0198
Evaluate side-chains
  127 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  416 ILE
Chi-restraints excluded: chain C residue  480 HIS
Chi-restraints excluded: chain C residue  485 ARG
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  163 LEU
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  492 THR
Chi-restraints excluded: chain D residue  553 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 162 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   chunk 112 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 175 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0770
   chunk 17 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 195 optimal weight:    8.9990
   overall best weight:    1.6144

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

Flipped N/Q/H residues before XYZ refinement:
C 480 HIS
** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.068423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.050431 restraints weight = 46616.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 3.20
r_work: 0.2667 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.6466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  16276  Z= 0.142
  Angle     :  0.601  18.205  22048  Z= 0.302
  Chirality :  0.042   0.234   2464
  Planarity :  0.004   0.047   2844
  Dihedral  :  4.408  21.051   2208
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 16.33 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.19), residues: 2000
  helix:  0.78 (0.17), residues: 968
  sheet: -0.33 (0.43), residues: 168
  loop : -1.01 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.013   0.001   TYR D 487 
 PHE   0.019   0.002   PHE B 445 
 TRP   0.006   0.001   TRP C 319 
 HIS   0.008   0.001   HIS C 480 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (16276)
  covalent geometry    : angle       0.60090 (22048)
  hydrogen bonds       : bond        0.03380 (  690)
  hydrogen bonds       : angle       4.89383 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.9435 (mtm) cc_final: 0.9158 (mtm)
REVERT: A  305 GLU cc_start: 0.9317 (mm-30) cc_final: 0.9004 (mm-30)
REVERT: A  416 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8810 (mm)
REVERT: A  503 LYS cc_start: 0.9564 (mmtt) cc_final: 0.9349 (mmmm)
REVERT: A  551 MET cc_start: 0.8857 (ptm) cc_final: 0.8302 (ptp)
REVERT: B   46 MET cc_start: 0.9445 (mmm) cc_final: 0.9245 (mmm)
REVERT: B  294 MET cc_start: 0.8738 (mmm) cc_final: 0.8497 (mmm)
REVERT: B  302 MET cc_start: 0.9390 (mtp) cc_final: 0.9111 (mtp)
REVERT: B  395 ASN cc_start: 0.8691 (p0) cc_final: 0.8138 (p0)
REVERT: B  416 ILE cc_start: 0.8975 (mt) cc_final: 0.8728 (mm)
REVERT: C   15 MET cc_start: 0.9265 (mtm) cc_final: 0.8809 (mtt)
REVERT: C   80 ASP cc_start: 0.8849 (t0) cc_final: 0.7841 (t0)
REVERT: C   82 GLU cc_start: 0.9157 (tp30) cc_final: 0.8948 (pm20)
REVERT: C  232 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8840 (tp30)
REVERT: C  302 MET cc_start: 0.9078 (mmm) cc_final: 0.8855 (mtp)
REVERT: C  389 ILE cc_start: 0.9428 (pt) cc_final: 0.9139 (pp)
REVERT: C  405 GLU cc_start: 0.8627 (tt0) cc_final: 0.7735 (mm-30)
REVERT: C  480 HIS cc_start: 0.8725 (OUTLIER) cc_final: 0.8451 (t-90)
REVERT: D  100 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.6615 (m-80)
REVERT: D  305 GLU cc_start: 0.8662 (tp30) cc_final: 0.8257 (mm-30)
REVERT: D  395 ASN cc_start: 0.8965 (m-40) cc_final: 0.8432 (p0)
  outliers start: 24
  outliers final: 12
  residues processed: 137
  average time/residue: 0.5079
  time to fit residues: 79.3029
Evaluate side-chains
  125 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  416 ILE
Chi-restraints excluded: chain C residue  480 HIS
Chi-restraints excluded: chain C residue  485 ARG
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  163 LEU
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  553 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 64 optimal weight:    0.0980
   chunk 158 optimal weight:    1.9990
   chunk 165 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 135 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 177 optimal weight:    7.9990
   chunk 104 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    2.6188

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

Flipped N/Q/H residues before XYZ refinement:
C  28 HIS
** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 480 HIS
** D 282 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 = 0.3278 r_free = 0.3278 target = 0.067335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.049476 restraints weight = 46394.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 3.15
r_work: 0.2641 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.6724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  16276  Z= 0.179
  Angle     :  0.609  15.228  22048  Z= 0.307
  Chirality :  0.043   0.248   2464
  Planarity :  0.004   0.046   2844
  Dihedral  :  4.356  20.996   2208
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.80 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.19), residues: 2000
  helix:  0.94 (0.17), residues: 960
  sheet: -0.34 (0.43), residues: 168
  loop : -0.97 (0.21), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 106 
 TYR   0.013   0.001   TYR D 487 
 PHE   0.019   0.002   PHE C 104 
 TRP   0.006   0.001   TRP C 319 
 HIS   0.027   0.001   HIS C 480 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (16276)
  covalent geometry    : angle       0.60872 (22048)
  hydrogen bonds       : bond        0.03403 (  690)
  hydrogen bonds       : angle       4.88780 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.9462 (mtm) cc_final: 0.9197 (mtm)
REVERT: A  305 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9012 (mm-30)
REVERT: A  503 LYS cc_start: 0.9561 (mmtt) cc_final: 0.9349 (mmmm)
REVERT: A  551 MET cc_start: 0.8889 (ptm) cc_final: 0.8298 (ptp)
REVERT: B  294 MET cc_start: 0.8787 (mmm) cc_final: 0.8528 (mmm)
REVERT: B  302 MET cc_start: 0.9447 (mtp) cc_final: 0.9185 (mtp)
REVERT: B  395 ASN cc_start: 0.8646 (p0) cc_final: 0.8112 (p0)
REVERT: B  416 ILE cc_start: 0.9112 (mt) cc_final: 0.8885 (mm)
REVERT: C   15 MET cc_start: 0.9270 (mtm) cc_final: 0.8737 (mtt)
REVERT: C   80 ASP cc_start: 0.9009 (t0) cc_final: 0.8010 (t0)
REVERT: C  232 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.9021 (tp30)
REVERT: C  389 ILE cc_start: 0.9469 (pt) cc_final: 0.9169 (pp)
REVERT: C  405 GLU cc_start: 0.8720 (tt0) cc_final: 0.7830 (mm-30)
REVERT: C  480 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8377 (t-90)
REVERT: D  100 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6709 (m-80)
REVERT: D  305 GLU cc_start: 0.8695 (tp30) cc_final: 0.8277 (mm-30)
REVERT: D  395 ASN cc_start: 0.8931 (m-40) cc_final: 0.8434 (p0)
  outliers start: 26
  outliers final: 12
  residues processed: 133
  average time/residue: 0.4960
  time to fit residues: 74.8627
Evaluate side-chains
  121 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  416 ILE
Chi-restraints excluded: chain C residue  480 HIS
Chi-restraints excluded: chain C residue  485 ARG
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  163 LEU
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  553 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 147 optimal weight:    1.9990
   chunk 172 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 129 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 44 optimal weight:    9.9990
   chunk 183 optimal weight:    0.0370
   chunk 186 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.4066

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

Flipped N/Q/H residues before XYZ refinement:
** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 480 HIS
** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 298 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.067285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.049335 restraints weight = 46706.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 3.19
r_work: 0.2637 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.6918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  16276  Z= 0.169
  Angle     :  0.615  14.449  22048  Z= 0.308
  Chirality :  0.043   0.238   2464
  Planarity :  0.004   0.047   2844
  Dihedral  :  4.335  21.765   2208
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 17.33 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.19), residues: 2000
  helix:  0.95 (0.17), residues: 960
  sheet: -0.36 (0.43), residues: 168
  loop : -0.95 (0.21), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.013   0.001   TYR D 487 
 PHE   0.020   0.002   PHE C 104 
 TRP   0.006   0.001   TRP A 319 
 HIS   0.006   0.001   HIS A  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (16276)
  covalent geometry    : angle       0.61546 (22048)
  hydrogen bonds       : bond        0.03417 (  690)
  hydrogen bonds       : angle       4.88221 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.9482 (mtm) cc_final: 0.9207 (mtm)
REVERT: A  305 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9038 (mm-30)
REVERT: A  503 LYS cc_start: 0.9560 (mmtt) cc_final: 0.9349 (mmmm)
REVERT: A  551 MET cc_start: 0.8897 (ptm) cc_final: 0.8299 (ptp)
REVERT: B  294 MET cc_start: 0.8783 (mmm) cc_final: 0.8518 (mmm)
REVERT: B  302 MET cc_start: 0.9444 (mtp) cc_final: 0.9150 (mtp)
REVERT: B  395 ASN cc_start: 0.8713 (p0) cc_final: 0.8139 (p0)
REVERT: B  416 ILE cc_start: 0.9147 (mt) cc_final: 0.8919 (mm)
REVERT: C   80 ASP cc_start: 0.8718 (t0) cc_final: 0.8417 (t0)
REVERT: C  232 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.9015 (tp30)
REVERT: C  389 ILE cc_start: 0.9499 (pt) cc_final: 0.9179 (pp)
REVERT: C  405 GLU cc_start: 0.8773 (tt0) cc_final: 0.7845 (mm-30)
REVERT: C  480 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8439 (t-90)
REVERT: D  100 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6702 (m-80)
REVERT: D  305 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8316 (mm-30)
REVERT: D  320 MET cc_start: 0.7098 (mpt) cc_final: 0.6897 (mpp)
REVERT: D  395 ASN cc_start: 0.8905 (m-40) cc_final: 0.8458 (p0)
  outliers start: 22
  outliers final: 12
  residues processed: 130
  average time/residue: 0.5296
  time to fit residues: 77.3076
Evaluate side-chains
  123 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  416 ILE
Chi-restraints excluded: chain C residue  480 HIS
Chi-restraints excluded: chain C residue  485 ARG
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  163 LEU
Chi-restraints excluded: chain D residue  305 GLU
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  553 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 195 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 151 optimal weight:    0.9990
   chunk 187 optimal weight:   20.0000
   chunk 120 optimal weight:   10.0000
   chunk 196 optimal weight:    0.8980
   chunk 114 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 173 optimal weight:   10.0000
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 480 HIS
** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.067986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.050206 restraints weight = 46778.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 3.17
r_work: 0.2662 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.7029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16276  Z= 0.124
  Angle     :  0.604  14.406  22048  Z= 0.302
  Chirality :  0.042   0.228   2464
  Planarity :  0.004   0.049   2844
  Dihedral  :  4.288  22.302   2208
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 17.68 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.19), residues: 2000
  helix:  0.90 (0.17), residues: 968
  sheet: -0.36 (0.43), residues: 168
  loop : -0.91 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.012   0.001   TYR D 487 
 PHE   0.019   0.002   PHE B 445 
 TRP   0.005   0.001   TRP C 319 
 HIS   0.010   0.001   HIS C 480 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (16276)
  covalent geometry    : angle       0.60367 (22048)
  hydrogen bonds       : bond        0.03278 (  690)
  hydrogen bonds       : angle       4.82516 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.9469 (mtm) cc_final: 0.9173 (mtm)
REVERT: A  305 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8957 (mm-30)
REVERT: A  551 MET cc_start: 0.8795 (ptm) cc_final: 0.8183 (ptp)
REVERT: B   80 ASP cc_start: 0.8882 (t0) cc_final: 0.8596 (t0)
REVERT: B  294 MET cc_start: 0.8790 (mmm) cc_final: 0.8521 (mmm)
REVERT: B  302 MET cc_start: 0.9434 (mtp) cc_final: 0.9131 (mtp)
REVERT: B  395 ASN cc_start: 0.8669 (p0) cc_final: 0.8077 (p0)
REVERT: B  416 ILE cc_start: 0.9145 (mt) cc_final: 0.8922 (mm)
REVERT: C   80 ASP cc_start: 0.8665 (t0) cc_final: 0.8400 (t0)
REVERT: C  232 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8952 (tp30)
REVERT: C  389 ILE cc_start: 0.9504 (pt) cc_final: 0.9183 (pp)
REVERT: C  405 GLU cc_start: 0.8750 (tt0) cc_final: 0.7802 (mm-30)
REVERT: C  480 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.8370 (t-90)
REVERT: D  100 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6752 (m-80)
REVERT: D  305 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8292 (mm-30)
REVERT: D  395 ASN cc_start: 0.8858 (m-40) cc_final: 0.8459 (p0)
  outliers start: 18
  outliers final: 12
  residues processed: 125
  average time/residue: 0.5766
  time to fit residues: 81.0552
Evaluate side-chains
  121 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  416 ILE
Chi-restraints excluded: chain C residue  480 HIS
Chi-restraints excluded: chain C residue  485 ARG
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  305 GLU
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  553 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 150 optimal weight:    0.0980
   chunk 103 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 165 optimal weight:    0.7980
   chunk 88 optimal weight:    8.9990
   chunk 151 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 171 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
C  99 HIS
** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 480 HIS
** D 282 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 = 0.3307 r_free = 0.3307 target = 0.068515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.050612 restraints weight = 46384.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 3.24
r_work: 0.2674 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.7114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16276  Z= 0.115
  Angle     :  0.612  14.289  22048  Z= 0.303
  Chirality :  0.042   0.223   2464
  Planarity :  0.004   0.062   2844
  Dihedral  :  4.241  21.207   2208
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 17.97 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.19), residues: 2000
  helix:  0.90 (0.17), residues: 968
  sheet: -0.32 (0.43), residues: 168
  loop : -0.86 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG D 106 
 TYR   0.012   0.001   TYR D 487 
 PHE   0.019   0.001   PHE C 104 
 TRP   0.004   0.000   TRP A 319 
 HIS   0.016   0.001   HIS C 480 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (16276)
  covalent geometry    : angle       0.61213 (22048)
  hydrogen bonds       : bond        0.03196 (  690)
  hydrogen bonds       : angle       4.78368 ( 2010)

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

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

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4000 Ramachandran restraints generated.
    2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.9433 (mtm) cc_final: 0.9135 (mtm)
REVERT: A   80 ASP cc_start: 0.9156 (t0) cc_final: 0.8558 (t0)
REVERT: A  305 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8941 (mm-30)
REVERT: A  320 MET cc_start: 0.7705 (mpp) cc_final: 0.6600 (pp-130)
REVERT: A  551 MET cc_start: 0.8791 (ptm) cc_final: 0.8171 (ptp)
REVERT: B   15 MET cc_start: 0.9260 (mtt) cc_final: 0.8640 (mtt)
REVERT: B  294 MET cc_start: 0.8813 (mmm) cc_final: 0.8546 (mmm)
REVERT: B  302 MET cc_start: 0.9423 (mtp) cc_final: 0.9134 (mtp)
REVERT: B  416 ILE cc_start: 0.9140 (mt) cc_final: 0.8924 (mm)
REVERT: C   80 ASP cc_start: 0.8669 (t0) cc_final: 0.8390 (t0)
REVERT: C  232 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8932 (tp30)
REVERT: C  389 ILE cc_start: 0.9503 (pt) cc_final: 0.9183 (pp)
REVERT: C  405 GLU cc_start: 0.8743 (tt0) cc_final: 0.7812 (mm-30)
REVERT: C  480 HIS cc_start: 0.8765 (OUTLIER) cc_final: 0.7822 (t-90)
REVERT: C  485 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8219 (mtm-85)
REVERT: D  100 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.6663 (m-80)
REVERT: D  305 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8377 (mm-30)
REVERT: D  320 MET cc_start: 0.7707 (mpp) cc_final: 0.6325 (pp-130)
REVERT: D  395 ASN cc_start: 0.8830 (m-40) cc_final: 0.8448 (p0)
  outliers start: 18
  outliers final: 10
  residues processed: 126
  average time/residue: 0.5217
  time to fit residues: 74.5016
Evaluate side-chains
  118 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  416 ILE
Chi-restraints excluded: chain C residue  480 HIS
Chi-restraints excluded: chain C residue  485 ARG
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  305 GLU
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  553 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 200
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 164 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0870
   chunk 140 optimal weight:    9.9990
   chunk 149 optimal weight:    5.9990
   chunk 79 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 182 optimal weight:   20.0000
   overall best weight:    3.4164

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

Flipped N/Q/H residues before XYZ refinement:
** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 480 HIS
** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.066357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.048238 restraints weight = 46762.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.2756 rms_B_bonded: 3.24
r_work: 0.2609 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.7297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  16276  Z= 0.218
  Angle     :  0.650  13.246  22048  Z= 0.324
  Chirality :  0.044   0.218   2464
  Planarity :  0.004   0.073   2844
  Dihedral  :  4.273  21.847   2208
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 18.21 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.19), residues: 2000
  helix:  1.03 (0.17), residues: 968
  sheet: -0.26 (0.43), residues: 168
  loop : -0.75 (0.22), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG D 106 
 TYR   0.014   0.001   TYR C  74 
 PHE   0.024   0.002   PHE B  84 
 TRP   0.003   0.001   TRP A 319 
 HIS   0.030   0.001   HIS C 480 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (16276)
  covalent geometry    : angle       0.64979 (22048)
  hydrogen bonds       : bond        0.03537 (  690)
  hydrogen bonds       : angle       4.88922 ( 2010)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4489.19 seconds
wall clock time: 77 minutes 44.65 seconds (4664.65 seconds total)