Starting phenix.real_space_refine
on Sun Aug 24 00:34:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sik_40508/08_2025/8sik_40508.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sik_40508/08_2025/8sik_40508.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sik_40508/08_2025/8sik_40508.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sik_40508/08_2025/8sik_40508.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sik_40508/08_2025/8sik_40508.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sik_40508/08_2025/8sik_40508.cif"
  }
  resolution = 2.9
  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=   0.002 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      8      9.91       5
     S      80      5.16       5
     C   10196      2.51       5
     N    2708      2.21       5
     O    2840      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 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: 15832
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "B"
      Number of atoms: 1108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1108
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 2848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2848
          Classifications: {'peptide': 352}
          Link IDs: {'PTRANS': 7, 'TRANS': 344}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 1108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1108
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 15
    Chain: "F"
      Number of atoms: 1108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1108
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 15
    Chain: "H"
      Number of atoms: 1108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1108
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 15
    Chain: "G"
      Number of atoms: 2848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2848
          Classifications: {'peptide': 352}
          Link IDs: {'PTRANS': 7, 'TRANS': 344}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2848
          Classifications: {'peptide': 352}
          Link IDs: {'PTRANS': 7, 'TRANS': 344}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 2848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2848
          Classifications: {'peptide': 352}
          Link IDs: {'PTRANS': 7, 'TRANS': 344}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb="CA    CA B 202 " occ=0.46
    residue:
      pdb="CA    CA F 201 " occ=0.45
    residue:
      pdb="CA    CA H 201 " occ=0.51
    residue:
      pdb="CA    CA H 203 " occ=0.49
  Time building chain proxies: 4.29, per 1000 atoms: 0.27
  Number of scatterers: 15832
  At special positions: 0
  Unit cell: (113.265, 113.265, 124.172, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      8     19.99
     S      80     16.00
     O    2840      8.00
     N    2708      7.00
     C   10196      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: 1.26
  Conformation dependent library (CDL) restraints added in 630.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3680

  Finding SS restraints...
    Secondary structure from input PDB file:
      104 helices and 4 sheets defined
      81.3% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 22
    Processing helix  chain 'B' and resid 29 through 41
    Processing helix  chain 'B' and resid 45 through 57
      removed outlier: 3.604A  pdb=" N   GLU B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL B  56 " --> pdb=" O   MET B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 74
    Processing helix  chain 'B' and resid 79 through 92
      removed outlier: 3.593A  pdb=" N   VAL B  92 " --> pdb=" O   GLU B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 113
    Processing helix  chain 'B' and resid 118 through 129
    Processing helix  chain 'B' and resid 139 through 149
      removed outlier: 3.745A  pdb=" N   LYS B 149 " --> pdb=" O   MET B 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 115
    Processing helix  chain 'A' and resid 120 through 144
      removed outlier: 3.783A  pdb=" N   THR A 144 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 178
      removed outlier: 3.539A  pdb=" N   PHE A 157 " --> pdb=" O   THR A 153 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   TRP A 158 " --> pdb=" O   GLY A 154 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   MET A 159 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 181
      No H-bonds generated for 'chain 'A' and resid 179 through 181'
    Processing helix  chain 'A' and resid 185 through 196
      removed outlier: 3.720A  pdb=" N   GLY A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LYS A 196 " --> pdb=" O   ARG A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 216
    Processing helix  chain 'A' and resid 224 through 237
      removed outlier: 4.179A  pdb=" N   ILE A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
      removed outlier: 3.527A  pdb=" N   VAL A 241 " --> pdb=" O   MET A 238 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASP A 242 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 238 through 242'
    Processing helix  chain 'A' and resid 245 through 258
      removed outlier: 3.607A  pdb=" N   VAL A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 284
    Processing helix  chain 'A' and resid 298 through 311
    Processing helix  chain 'A' and resid 322 through 358
      removed outlier: 3.863A  pdb=" N   ILE A 337 " --> pdb=" O   SER A 333 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   SER A 338 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   PHE A 339 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
    Processing helix  chain 'A' and resid 359 through 361
      No H-bonds generated for 'chain 'A' and resid 359 through 361'
    Processing helix  chain 'A' and resid 363 through 366
    Processing helix  chain 'A' and resid 367 through 384
    Processing helix  chain 'A' and resid 389 through 396
      removed outlier: 3.862A  pdb=" N   TRP A 392 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS A 393 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE A 394 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR A 395 " --> pdb=" O   TRP A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 533
      removed outlier: 4.024A  pdb=" N   THR A 513 " --> pdb=" O   HIS A 509 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 516 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG A 519 " --> pdb=" O   LYS A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 568
      removed outlier: 3.585A  pdb=" N   VAL A 541 " --> pdb=" O   ASP A 537 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 22
    Processing helix  chain 'D' and resid 29 through 41
    Processing helix  chain 'D' and resid 45 through 57
      removed outlier: 3.560A  pdb=" N   GLU D  55 " --> pdb=" O   ASP D  51 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL D  56 " --> pdb=" O   MET D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 74
    Processing helix  chain 'D' and resid 79 through 92
      removed outlier: 3.593A  pdb=" N   VAL D  92 " --> pdb=" O   GLU D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 113
    Processing helix  chain 'D' and resid 118 through 129
    Processing helix  chain 'D' and resid 139 through 149
      removed outlier: 3.525A  pdb=" N   VAL D 143 " --> pdb=" O   TYR D 139 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS D 149 " --> pdb=" O   MET D 145 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 7 through 22
    Processing helix  chain 'F' and resid 29 through 41
    Processing helix  chain 'F' and resid 45 through 57
      removed outlier: 3.571A  pdb=" N   GLU F  55 " --> pdb=" O   ASP F  51 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL F  56 " --> pdb=" O   MET F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 65 through 74
    Processing helix  chain 'F' and resid 79 through 92
      removed outlier: 3.589A  pdb=" N   VAL F  92 " --> pdb=" O   GLU F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 103 through 113
    Processing helix  chain 'F' and resid 118 through 129
    Processing helix  chain 'F' and resid 139 through 147
    Processing helix  chain 'H' and resid 7 through 22
    Processing helix  chain 'H' and resid 29 through 41
    Processing helix  chain 'H' and resid 45 through 57
      removed outlier: 3.564A  pdb=" N   GLU H  55 " --> pdb=" O   ASP H  51 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   VAL H  56 " --> pdb=" O   MET H  52 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 65 through 74
    Processing helix  chain 'H' and resid 79 through 92
      removed outlier: 3.616A  pdb=" N   VAL H  92 " --> pdb=" O   GLU H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 113
    Processing helix  chain 'H' and resid 118 through 129
    Processing helix  chain 'H' and resid 139 through 149
      removed outlier: 3.839A  pdb=" N   LYS H 149 " --> pdb=" O   MET H 145 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 105 through 115
    Processing helix  chain 'G' and resid 120 through 145
      removed outlier: 3.830A  pdb=" N   THR G 144 " --> pdb=" O   SER G 140 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ILE G 145 " --> pdb=" O   VAL G 141 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 148 through 178
      removed outlier: 3.541A  pdb=" N   PHE G 157 " --> pdb=" O   THR G 153 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   TRP G 158 " --> pdb=" O   GLY G 154 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 179 through 181
      No H-bonds generated for 'chain 'G' and resid 179 through 181'
    Processing helix  chain 'G' and resid 185 through 194
      removed outlier: 3.646A  pdb=" N   GLY G 189 " --> pdb=" O   VAL G 185 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 196 through 216
    Processing helix  chain 'G' and resid 224 through 237
      removed outlier: 4.338A  pdb=" N   ILE G 230 " --> pdb=" O   ALA G 226 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 238 through 242
      removed outlier: 3.562A  pdb=" N   VAL G 241 " --> pdb=" O   MET G 238 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP G 242 " --> pdb=" O   LEU G 239 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 238 through 242'
    Processing helix  chain 'G' and resid 245 through 258
      removed outlier: 3.609A  pdb=" N   VAL G 254 " --> pdb=" O   LEU G 250 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 258 through 284
    Processing helix  chain 'G' and resid 298 through 311
    Processing helix  chain 'G' and resid 322 through 358
      removed outlier: 3.838A  pdb=" N   ILE G 337 " --> pdb=" O   SER G 333 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   SER G 338 " --> pdb=" O   VAL G 334 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   PHE G 339 " --> pdb=" O   PHE G 335 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE G 340 " --> pdb=" O   ALA G 336 " (cutoff:3.500A)
      Proline residue:  G 343  - end of helix
    Processing helix  chain 'G' and resid 359 through 361
      No H-bonds generated for 'chain 'G' and resid 359 through 361'
    Processing helix  chain 'G' and resid 363 through 366
    Processing helix  chain 'G' and resid 367 through 384
    Processing helix  chain 'G' and resid 389 through 396
      removed outlier: 3.911A  pdb=" N   TRP G 392 " --> pdb=" O   SER G 389 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LYS G 393 " --> pdb=" O   SER G 390 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE G 394 " --> pdb=" O   THR G 391 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TYR G 395 " --> pdb=" O   TRP G 392 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 509 through 533
      removed outlier: 4.185A  pdb=" N   THR G 513 " --> pdb=" O   HIS G 509 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL G 516 " --> pdb=" O   ALA G 512 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG G 519 " --> pdb=" O   LYS G 515 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ARG G 533 " --> pdb=" O   PHE G 529 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 537 through 568
      removed outlier: 3.572A  pdb=" N   VAL G 541 " --> pdb=" O   ASP G 537 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 115
    Processing helix  chain 'C' and resid 120 through 145
      removed outlier: 3.702A  pdb=" N   THR C 144 " --> pdb=" O   SER C 140 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 178
      removed outlier: 3.593A  pdb=" N   PHE C 157 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   TRP C 158 " --> pdb=" O   GLY C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 181
      No H-bonds generated for 'chain 'C' and resid 179 through 181'
    Processing helix  chain 'C' and resid 185 through 195
      removed outlier: 3.654A  pdb=" N   GLY C 189 " --> pdb=" O   VAL C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 216
    Processing helix  chain 'C' and resid 224 through 237
      removed outlier: 4.236A  pdb=" N   ILE C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 242
      removed outlier: 3.593A  pdb=" N   ASP C 242 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 258
      removed outlier: 3.604A  pdb=" N   VAL C 254 " --> pdb=" O   LEU C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 284
    Processing helix  chain 'C' and resid 298 through 311
    Processing helix  chain 'C' and resid 322 through 358
      removed outlier: 3.891A  pdb=" N   ILE C 337 " --> pdb=" O   SER C 333 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   SER C 338 " --> pdb=" O   VAL C 334 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   PHE C 339 " --> pdb=" O   PHE C 335 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE C 340 " --> pdb=" O   ALA C 336 " (cutoff:3.500A)
      Proline residue:  C 343  - end of helix
    Processing helix  chain 'C' and resid 359 through 361
      No H-bonds generated for 'chain 'C' and resid 359 through 361'
    Processing helix  chain 'C' and resid 363 through 366
    Processing helix  chain 'C' and resid 367 through 384
    Processing helix  chain 'C' and resid 389 through 396
      removed outlier: 3.876A  pdb=" N   TRP C 392 " --> pdb=" O   SER C 389 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS C 393 " --> pdb=" O   SER C 390 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE C 394 " --> pdb=" O   THR C 391 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TYR C 395 " --> pdb=" O   TRP C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 509 through 533
      removed outlier: 4.337A  pdb=" N   THR C 513 " --> pdb=" O   HIS C 509 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL C 516 " --> pdb=" O   ALA C 512 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG C 519 " --> pdb=" O   LYS C 515 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 537 through 568
      removed outlier: 3.587A  pdb=" N   VAL C 541 " --> pdb=" O   ASP C 537 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 105 through 115
    Processing helix  chain 'E' and resid 120 through 145
      removed outlier: 3.804A  pdb=" N   THR E 144 " --> pdb=" O   SER E 140 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E 141 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 148 through 178
      removed outlier: 3.708A  pdb=" N   PHE E 157 " --> pdb=" O   THR E 153 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   TRP E 158 " --> pdb=" O   GLY E 154 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   MET E 159 " --> pdb=" O   THR E 155 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 181
      No H-bonds generated for 'chain 'E' and resid 179 through 181'
    Processing helix  chain 'E' and resid 185 through 194
      removed outlier: 3.626A  pdb=" N   GLY E 189 " --> pdb=" O   VAL E 185 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 216
    Processing helix  chain 'E' and resid 224 through 237
      removed outlier: 4.242A  pdb=" N   ILE E 230 " --> pdb=" O   ALA E 226 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 238 through 242
      removed outlier: 3.571A  pdb=" N   ASP E 242 " --> pdb=" O   LEU E 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 245 through 258
      removed outlier: 3.630A  pdb=" N   VAL E 254 " --> pdb=" O   LEU E 250 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 258 through 285
    Processing helix  chain 'E' and resid 298 through 311
    Processing helix  chain 'E' and resid 322 through 358
      removed outlier: 3.877A  pdb=" N   ILE E 337 " --> pdb=" O   SER E 333 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   SER E 338 " --> pdb=" O   VAL E 334 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   PHE E 339 " --> pdb=" O   PHE E 335 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE E 340 " --> pdb=" O   ALA E 336 " (cutoff:3.500A)
      Proline residue:  E 343  - end of helix
    Processing helix  chain 'E' and resid 359 through 361
      No H-bonds generated for 'chain 'E' and resid 359 through 361'
    Processing helix  chain 'E' and resid 363 through 366
    Processing helix  chain 'E' and resid 367 through 384
    Processing helix  chain 'E' and resid 389 through 396
      removed outlier: 3.856A  pdb=" N   TRP E 392 " --> pdb=" O   SER E 389 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS E 393 " --> pdb=" O   SER E 390 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE E 394 " --> pdb=" O   THR E 391 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR E 395 " --> pdb=" O   TRP E 392 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 509 through 533
      removed outlier: 4.267A  pdb=" N   THR E 513 " --> pdb=" O   HIS E 509 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL E 516 " --> pdb=" O   ALA E 512 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ARG E 519 " --> pdb=" O   LYS E 515 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 537 through 567
      removed outlier: 3.581A  pdb=" N   VAL E 541 " --> pdb=" O   ASP E 537 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102
    Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 102
    Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102
    Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102

    1112 hydrogen bonds defined for protein.
    3306 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: 1.83

  Time building geometry restraints manager: 1.72 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: 5098
        1.34 -     1.46: 2385
        1.46 -     1.57: 8533
        1.57 -     1.69: 0
        1.69 -     1.81: 136
  Bond restraints: 16152
  Sorted by residual:
  bond pdb=" C   ILE A 368 "
       pdb=" N   PRO A 369 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.36e-02 5.41e+03 3.13e+00
  bond pdb=" C   ILE C 368 "
       pdb=" N   PRO C 369 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.36e-02 5.41e+03 3.05e+00
  bond pdb=" C   GLY D  26 "
       pdb=" O   GLY D  26 "
    ideal  model  delta    sigma   weight residual
    1.239  1.222  0.017 1.09e-02 8.42e+03 2.44e+00
  bond pdb=" CA  LYS D  22 "
       pdb=" C   LYS D  22 "
    ideal  model  delta    sigma   weight residual
    1.523  1.541 -0.018 1.34e-02 5.57e+03 1.85e+00
  bond pdb=" CB  ILE B 131 "
       pdb=" CG1 ILE B 131 "
    ideal  model  delta    sigma   weight residual
    1.530  1.550 -0.020 2.00e-02 2.50e+03 1.00e+00
  ... (remaining 16147 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 21507
        1.74 -     3.47: 271
        3.47 -     5.21: 35
        5.21 -     6.94: 7
        6.94 -     8.68: 4
  Bond angle restraints: 21824
  Sorted by residual:
  angle pdb=" N   ILE A 227 "
        pdb=" CA  ILE A 227 "
        pdb=" C   ILE A 227 "
      ideal   model   delta    sigma   weight residual
     112.96  109.20    3.76 1.00e+00 1.00e+00 1.41e+01
  angle pdb=" CB  ILE B 131 "
        pdb=" CG1 ILE B 131 "
        pdb=" CD1 ILE B 131 "
      ideal   model   delta    sigma   weight residual
     113.80  120.89   -7.09 2.10e+00 2.27e-01 1.14e+01
  angle pdb=" N   GLY D  26 "
        pdb=" CA  GLY D  26 "
        pdb=" C   GLY D  26 "
      ideal   model   delta    sigma   weight residual
     114.95  110.49    4.46 1.41e+00 5.03e-01 1.00e+01
  angle pdb=" CG  ARG E 507 "
        pdb=" CD  ARG E 507 "
        pdb=" NE  ARG E 507 "
      ideal   model   delta    sigma   weight residual
     112.00  118.29   -6.29 2.20e+00 2.07e-01 8.17e+00
  angle pdb=" CA  GLU D  12 "
        pdb=" CB  GLU D  12 "
        pdb=" CG  GLU D  12 "
      ideal   model   delta    sigma   weight residual
     114.10  119.41   -5.31 2.00e+00 2.50e-01 7.04e+00
  ... (remaining 21819 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 8299
       17.48 -    34.96: 897
       34.96 -    52.44: 251
       52.44 -    69.93: 20
       69.93 -    87.41: 25
  Dihedral angle restraints: 9492
    sinusoidal: 3776
      harmonic: 5716
  Sorted by residual:
  dihedral pdb=" CA  GLN E 234 "
           pdb=" C   GLN E 234 "
           pdb=" N   ILE E 235 "
           pdb=" CA  ILE E 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.37   21.63     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CG  ARG G 109 "
           pdb=" CD  ARG G 109 "
           pdb=" NE  ARG G 109 "
           pdb=" CZ  ARG G 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.49  -44.49     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CB  GLU A 170 "
           pdb=" CG  GLU A 170 "
           pdb=" CD  GLU A 170 "
           pdb=" OE1 GLU A 170 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.93   86.93     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 9489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1972
       0.049 -    0.097: 406
       0.097 -    0.146: 60
       0.146 -    0.194: 1
       0.194 -    0.243: 5
  Chirality restraints: 2444
  Sorted by residual:
  chirality pdb=" CG  LEU G 191 "
            pdb=" CB  LEU G 191 "
            pdb=" CD1 LEU G 191 "
            pdb=" CD2 LEU G 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  ASN F  43 "
            pdb=" N   ASN F  43 "
            pdb=" C   ASN F  43 "
            pdb=" CB  ASN F  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CG  LEU E 191 "
            pdb=" CB  LEU E 191 "
            pdb=" CD1 LEU E 191 "
            pdb=" CD2 LEU E 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 2441 not shown)

  Planarity restraints: 2752
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D  21 "   -0.012 2.00e-02 2.50e+03   2.35e-02 5.54e+00
        pdb=" C   ASP D  21 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ASP D  21 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LYS D  22 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G 507 "    0.196 9.50e-02 1.11e+02   8.81e-02 5.33e+00
        pdb=" NE  ARG G 507 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG G 507 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG G 507 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG G 507 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 131 "    0.007 2.00e-02 2.50e+03   1.46e-02 2.15e+00
        pdb=" C   ILE B 131 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ILE B 131 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP B 132 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2749 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1625
        2.74 -     3.28: 16120
        3.28 -     3.82: 26892
        3.82 -     4.36: 31323
        4.36 -     4.90: 55056
  Nonbonded interactions: 131016
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU H  68 "
            pdb="CA    CA H 203 "
     model   vdw
     2.206 2.510
  nonbonded pdb=" OE1 GLU H  55 "
            pdb=" NZ  LYS G 527 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OD1 ASN H  61 "
            pdb="CA    CA H 203 "
     model   vdw
     2.211 2.510
  nonbonded pdb=" OE1 GLU H 124 "
            pdb=" OG  SER G 390 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OE1 GLU B 124 "
            pdb=" OG  SER A 390 "
     model   vdw
     2.268 3.040
  ... (remaining 131011 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'B' and resid 6 through 201)
  selection = (chain 'D' and resid 6 through 201)
  selection = chain 'F'
  selection = (chain 'H' and resid 6 through 201)
}

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=0.45 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:             3.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     14.800
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
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      :  0.003   0.026  16152  Z= 0.130
  Angle     :  0.506   8.678  21824  Z= 0.296
  Chirality :  0.039   0.243   2444
  Planarity :  0.004   0.088   2752
  Dihedral  : 15.666  87.408   5812
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 19.64 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.43 (0.19), residues: 1952
  helix:  2.13 (0.13), residues: 1504
  sheet:  None (None), residues: 0
  loop : -0.12 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG G 507 
 TYR   0.017   0.001   TYR D 139 
 PHE   0.013   0.001   PHE E 332 
 TRP   0.023   0.002   TRP G 323 
 HIS   0.005   0.001   HIS E 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (16152)
  covalent geometry    : angle       0.50590 (21824)
  hydrogen bonds       : bond        0.09180 ( 1112)
  hydrogen bonds       : angle       4.47777 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 202
  time to evaluate  : 0.628 
Fit side-chains
REVERT: G  195 ARG cc_start: 0.6353 (mtp180) cc_final: 0.5956 (mtm110)
REVERT: C  191 LEU cc_start: 0.6722 (mp) cc_final: 0.6407 (mm)
  outliers start: 16
  outliers final: 12
  residues processed: 216
  average time/residue: 0.6263
  time to fit residues: 147.5418
Evaluate side-chains
  207 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 195
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain D residue   39 SER
Chi-restraints excluded: chain F residue   39 SER
Chi-restraints excluded: chain H residue   39 SER
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  310 VAL
Chi-restraints excluded: chain G residue  567 ILE
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  366 ARG
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  310 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 194 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 234 GLN
** E 234 GLN ** 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 = 0.4026 r_free = 0.4026 target = 0.181527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.147467 restraints weight = 15656.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.82
r_work: 0.3477 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.0509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  16152  Z= 0.139
  Angle     :  0.464   7.526  21824  Z= 0.257
  Chirality :  0.038   0.213   2444
  Planarity :  0.003   0.045   2752
  Dihedral  :  3.940  38.439   2182
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.20 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.50 (0.19), residues: 1952
  helix:  2.16 (0.13), residues: 1520
  sheet:  None (None), residues: 0
  loop : -0.10 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 507 
 TYR   0.013   0.002   TYR C 545 
 PHE   0.014   0.001   PHE C 332 
 TRP   0.015   0.001   TRP G 323 
 HIS   0.003   0.001   HIS E 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (16152)
  covalent geometry    : angle       0.46397 (21824)
  hydrogen bonds       : bond        0.04305 ( 1112)
  hydrogen bonds       : angle       3.78173 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 205
  time to evaluate  : 0.473 
Fit side-chains
REVERT: B  131 ILE cc_start: 0.4326 (OUTLIER) cc_final: 0.4036 (pp)
REVERT: A  191 LEU cc_start: 0.7121 (mp) cc_final: 0.6824 (mm)
REVERT: D   12 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6840 (pm20)
REVERT: D  112 ASN cc_start: 0.8608 (m-40) cc_final: 0.8397 (m-40)
REVERT: F   68 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7174 (mt-10)
REVERT: F  140 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6230 (mp0)
REVERT: H  112 ASN cc_start: 0.8641 (m-40) cc_final: 0.8421 (m-40)
REVERT: H  141 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7010 (pp20)
REVERT: G  195 ARG cc_start: 0.7253 (mtp180) cc_final: 0.6873 (mtm110)
REVERT: C  191 LEU cc_start: 0.7154 (mp) cc_final: 0.6804 (mm)
  outliers start: 57
  outliers final: 19
  residues processed: 246
  average time/residue: 0.6413
  time to fit residues: 172.0577
Evaluate side-chains
  223 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 199
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain D residue   12 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   68 GLU
Chi-restraints excluded: chain F residue  125 MET
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue  141 GLU
Chi-restraints excluded: chain G residue  172 VAL
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  310 VAL
Chi-restraints excluded: chain G residue  366 ARG
Chi-restraints excluded: chain C residue  172 VAL
Chi-restraints excluded: chain C residue  285 LYS
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  285 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 177 optimal weight:    0.5980
   chunk 87 optimal weight:    4.9990
   chunk 120 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9980
   chunk 147 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
D  42 GLN
** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 234 GLN ** 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 = 0.4053 r_free = 0.4053 target = 0.184136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.149579 restraints weight = 15837.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.87
r_work: 0.3486 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3333
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.0723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  16152  Z= 0.115
  Angle     :  0.436   6.978  21824  Z= 0.239
  Chirality :  0.037   0.227   2444
  Planarity :  0.003   0.029   2752
  Dihedral  :  3.434  23.349   2170
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.75 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.70 (0.19), residues: 1952
  helix:  2.31 (0.13), residues: 1520
  sheet:  None (None), residues: 0
  loop : -0.07 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 109 
 TYR   0.011   0.001   TYR C 545 
 PHE   0.012   0.001   PHE E 332 
 TRP   0.014   0.001   TRP A 323 
 HIS   0.003   0.001   HIS G 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (16152)
  covalent geometry    : angle       0.43573 (21824)
  hydrogen bonds       : bond        0.03960 ( 1112)
  hydrogen bonds       : angle       3.63095 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 206
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A  557 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7408 (mtpt)
REVERT: D   68 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6917 (mt-10)
REVERT: D  112 ASN cc_start: 0.8563 (m-40) cc_final: 0.8318 (m-40)
REVERT: F   42 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.6840 (mp10)
REVERT: F   68 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7155 (mt-10)
REVERT: F  140 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6122 (mp0)
REVERT: H  112 ASN cc_start: 0.8581 (m-40) cc_final: 0.8328 (m-40)
REVERT: H  141 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6954 (pp20)
REVERT: G  195 ARG cc_start: 0.7188 (mtp180) cc_final: 0.6789 (mtm110)
REVERT: G  508 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6284 (mp0)
REVERT: C  533 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7567 (mtm180)
  outliers start: 48
  outliers final: 16
  residues processed: 241
  average time/residue: 0.6314
  time to fit residues: 165.2993
Evaluate side-chains
  221 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   39 SER
Chi-restraints excluded: chain F residue   42 GLN
Chi-restraints excluded: chain F residue   68 GLU
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain H residue   39 SER
Chi-restraints excluded: chain H residue  141 GLU
Chi-restraints excluded: chain G residue  163 LEU
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  508 GLU
Chi-restraints excluded: chain G residue  567 ILE
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  310 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 155 optimal weight:    0.9990
   chunk 130 optimal weight:    7.9990
   chunk 85 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 156 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 180 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 GLN
** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 234 GLN ** 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 = 0.4057 r_free = 0.4057 target = 0.184285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.149861 restraints weight = 15670.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 1.83
r_work: 0.3494 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3343
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3343
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.0786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16152  Z= 0.117
  Angle     :  0.434   6.256  21824  Z= 0.238
  Chirality :  0.037   0.250   2444
  Planarity :  0.003   0.029   2752
  Dihedral  :  3.344  17.440   2168
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.17 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.57 (0.19), residues: 1952
  helix:  2.21 (0.13), residues: 1544
  sheet:  None (None), residues: 0
  loop : -0.28 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 562 
 TYR   0.012   0.001   TYR C 545 
 PHE   0.012   0.001   PHE E 332 
 TRP   0.014   0.001   TRP G 323 
 HIS   0.003   0.001   HIS G 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (16152)
  covalent geometry    : angle       0.43418 (21824)
  hydrogen bonds       : bond        0.03925 ( 1112)
  hydrogen bonds       : angle       3.61021 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 207
  time to evaluate  : 0.613 
Fit side-chains
REVERT: B  141 GLU cc_start: 0.7460 (pt0) cc_final: 0.6992 (pp20)
REVERT: A  557 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7413 (mtpt)
REVERT: D   12 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6779 (pm20)
REVERT: D   68 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7020 (mt-10)
REVERT: D  112 ASN cc_start: 0.8559 (m-40) cc_final: 0.8308 (m-40)
REVERT: F   42 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.6863 (mp10)
REVERT: F   68 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7154 (mt-10)
REVERT: F  140 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6131 (mp0)
REVERT: H  112 ASN cc_start: 0.8578 (m-40) cc_final: 0.8338 (m-40)
REVERT: H  141 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6958 (pp20)
REVERT: G  195 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6759 (mtm110)
REVERT: C  533 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7524 (mtm180)
REVERT: E  560 GLN cc_start: 0.7373 (tp-100) cc_final: 0.6681 (mt0)
  outliers start: 46
  outliers final: 27
  residues processed: 239
  average time/residue: 0.6619
  time to fit residues: 172.0183
Evaluate side-chains
  240 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 206
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain D residue   12 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   39 SER
Chi-restraints excluded: chain F residue   42 GLN
Chi-restraints excluded: chain F residue   68 GLU
Chi-restraints excluded: chain F residue  131 ILE
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   39 SER
Chi-restraints excluded: chain H residue  141 GLU
Chi-restraints excluded: chain G residue  163 LEU
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  366 ARG
Chi-restraints excluded: chain G residue  567 ILE
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  285 LYS
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  366 ARG
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain E residue  163 LEU
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  312 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 173 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 166 optimal weight:    8.9990
   chunk 89 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 113 optimal weight:    0.8980
   chunk 176 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 234 GLN
** E 234 GLN ** 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 = 0.4056 r_free = 0.4056 target = 0.184155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.149812 restraints weight = 15699.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 1.83
r_work: 0.3490 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3331
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3331
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.0892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16152  Z= 0.121
  Angle     :  0.438   6.315  21824  Z= 0.240
  Chirality :  0.038   0.258   2444
  Planarity :  0.003   0.029   2752
  Dihedral  :  3.351  17.563   2168
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.45 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.57 (0.19), residues: 1952
  helix:  2.21 (0.13), residues: 1544
  sheet:  None (None), residues: 0
  loop : -0.27 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 109 
 TYR   0.012   0.001   TYR C 545 
 PHE   0.012   0.001   PHE E 332 
 TRP   0.015   0.001   TRP G 323 
 HIS   0.004   0.001   HIS G 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (16152)
  covalent geometry    : angle       0.43785 (21824)
  hydrogen bonds       : bond        0.03932 ( 1112)
  hydrogen bonds       : angle       3.60778 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 210
  time to evaluate  : 0.414 
Fit side-chains
REVERT: B  141 GLU cc_start: 0.7514 (pt0) cc_final: 0.7066 (pp20)
REVERT: A  557 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7374 (mtpt)
REVERT: D   12 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6889 (pm20)
REVERT: D   68 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6911 (mt-10)
REVERT: D  112 ASN cc_start: 0.8536 (m-40) cc_final: 0.8277 (m-40)
REVERT: F   42 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.6886 (mp10)
REVERT: F   68 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7148 (mt-10)
REVERT: F  140 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6091 (mp0)
REVERT: H  112 ASN cc_start: 0.8551 (m-40) cc_final: 0.8288 (m-40)
REVERT: H  141 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6965 (pp20)
REVERT: G  195 ARG cc_start: 0.7157 (mtp180) cc_final: 0.6735 (mtm110)
REVERT: C  533 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7300 (mtm110)
REVERT: E  560 GLN cc_start: 0.7315 (tp-100) cc_final: 0.6666 (mt0)
  outliers start: 59
  outliers final: 32
  residues processed: 253
  average time/residue: 0.5938
  time to fit residues: 163.7433
Evaluate side-chains
  243 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 204
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain D residue   12 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   39 SER
Chi-restraints excluded: chain F residue   42 GLN
Chi-restraints excluded: chain F residue   68 GLU
Chi-restraints excluded: chain F residue  131 ILE
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   39 SER
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  141 GLU
Chi-restraints excluded: chain G residue  163 LEU
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  366 ARG
Chi-restraints excluded: chain G residue  567 ILE
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  172 VAL
Chi-restraints excluded: chain C residue  285 LYS
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  366 ARG
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain E residue  163 LEU
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  285 LYS
Chi-restraints excluded: chain E residue  310 VAL
Chi-restraints excluded: chain E residue  312 THR
Chi-restraints excluded: chain E residue  390 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 164 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 194 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0870
   chunk 171 optimal weight:    0.8980
   chunk 195 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 162 optimal weight:    1.9990
   overall best weight:    0.9562

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

Flipped N/Q/H residues before XYZ refinement:
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.183782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.149527 restraints weight = 15599.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 1.85
r_work: 0.3480 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.0922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  16152  Z= 0.126
  Angle     :  0.447   7.157  21824  Z= 0.244
  Chirality :  0.038   0.247   2444
  Planarity :  0.003   0.029   2752
  Dihedral  :  3.367  17.693   2168
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.23 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.56 (0.19), residues: 1952
  helix:  2.20 (0.13), residues: 1544
  sheet:  None (None), residues: 0
  loop : -0.26 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 109 
 TYR   0.013   0.001   TYR C 545 
 PHE   0.013   0.001   PHE E 332 
 TRP   0.016   0.001   TRP G 323 
 HIS   0.004   0.001   HIS G 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (16152)
  covalent geometry    : angle       0.44717 (21824)
  hydrogen bonds       : bond        0.03981 ( 1112)
  hydrogen bonds       : angle       3.61624 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 205
  time to evaluate  : 0.426 
Fit side-chains
REVERT: B  141 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7089 (pp20)
REVERT: A  557 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7378 (mtpt)
REVERT: D   12 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6888 (pm20)
REVERT: D   68 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7002 (mt-10)
REVERT: D  112 ASN cc_start: 0.8544 (m-40) cc_final: 0.8283 (m-40)
REVERT: F   42 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.6890 (mp10)
REVERT: F   68 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7149 (mt-10)
REVERT: H  112 ASN cc_start: 0.8558 (m-40) cc_final: 0.8288 (m-40)
REVERT: H  141 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6966 (pp20)
REVERT: G  195 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6829 (mtm110)
REVERT: G  508 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6300 (mp0)
REVERT: C  533 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7291 (mtm110)
  outliers start: 55
  outliers final: 33
  residues processed: 243
  average time/residue: 0.6524
  time to fit residues: 172.3940
Evaluate side-chains
  245 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 204
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain D residue   12 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   39 SER
Chi-restraints excluded: chain F residue   42 GLN
Chi-restraints excluded: chain F residue   68 GLU
Chi-restraints excluded: chain F residue  131 ILE
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   39 SER
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  141 GLU
Chi-restraints excluded: chain G residue  163 LEU
Chi-restraints excluded: chain G residue  172 VAL
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  366 ARG
Chi-restraints excluded: chain G residue  508 GLU
Chi-restraints excluded: chain G residue  567 ILE
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  172 VAL
Chi-restraints excluded: chain C residue  285 LYS
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  366 ARG
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain E residue  163 LEU
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  285 LYS
Chi-restraints excluded: chain E residue  310 VAL
Chi-restraints excluded: chain E residue  312 THR
Chi-restraints excluded: chain E residue  390 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 177 optimal weight:    0.7980
   chunk 138 optimal weight:    0.5980
   chunk 19 optimal weight:    0.1980
   chunk 45 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   chunk 168 optimal weight:    4.9990
   chunk 170 optimal weight:    4.9990
   chunk 131 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN
D  42 GLN
H  42 GLN
** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.185378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.151143 restraints weight = 15661.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 1.83
r_work: 0.3503 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  16152  Z= 0.105
  Angle     :  0.433   8.016  21824  Z= 0.235
  Chirality :  0.037   0.248   2444
  Planarity :  0.003   0.028   2752
  Dihedral  :  3.289  17.890   2168
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.77 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.71 (0.19), residues: 1952
  helix:  2.31 (0.13), residues: 1544
  sheet:  None (None), residues: 0
  loop : -0.20 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 109 
 TYR   0.011   0.001   TYR C 545 
 PHE   0.011   0.001   PHE E 332 
 TRP   0.016   0.001   TRP E 323 
 HIS   0.004   0.001   HIS G 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (16152)
  covalent geometry    : angle       0.43335 (21824)
  hydrogen bonds       : bond        0.03716 ( 1112)
  hydrogen bonds       : angle       3.53040 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 210
  time to evaluate  : 0.408 
Fit side-chains
REVERT: B  141 GLU cc_start: 0.7524 (pt0) cc_final: 0.7085 (pp20)
REVERT: A  557 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7366 (mtpt)
REVERT: D   12 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6830 (pm20)
REVERT: D   68 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6931 (mt-10)
REVERT: D  112 ASN cc_start: 0.8505 (m-40) cc_final: 0.8257 (m-40)
REVERT: F   39 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.8210 (p)
REVERT: F   68 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7157 (mt-10)
REVERT: F  140 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6024 (mp0)
REVERT: H  112 ASN cc_start: 0.8519 (m-40) cc_final: 0.8277 (m-40)
REVERT: H  141 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6997 (pp20)
REVERT: H  145 MET cc_start: 0.7682 (pp-130) cc_final: 0.7430 (pp-130)
REVERT: G  195 ARG cc_start: 0.7126 (mtp180) cc_final: 0.6773 (mtm110)
REVERT: C  533 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7375 (mtm110)
REVERT: E  191 LEU cc_start: 0.7457 (mm) cc_final: 0.7225 (mp)
  outliers start: 48
  outliers final: 24
  residues processed: 250
  average time/residue: 0.6167
  time to fit residues: 167.9825
Evaluate side-chains
  240 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 209
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain D residue   12 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   39 SER
Chi-restraints excluded: chain F residue   68 GLU
Chi-restraints excluded: chain F residue  131 ILE
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   39 SER
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  141 GLU
Chi-restraints excluded: chain G residue  163 LEU
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  342 LEU
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  366 ARG
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  310 VAL
Chi-restraints excluded: chain E residue  312 THR
Chi-restraints excluded: chain E residue  390 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 145 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 176 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0980
   chunk 8 optimal weight:    0.5980
   chunk 139 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 182 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 177 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.185725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.151441 restraints weight = 15691.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.83
r_work: 0.3509 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3349
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  16152  Z= 0.106
  Angle     :  0.441   8.196  21824  Z= 0.238
  Chirality :  0.037   0.251   2444
  Planarity :  0.003   0.028   2752
  Dihedral  :  3.276  17.621   2168
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.13 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.73 (0.19), residues: 1952
  helix:  2.31 (0.13), residues: 1544
  sheet:  None (None), residues: 0
  loop : -0.15 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 109 
 TYR   0.011   0.001   TYR C 545 
 PHE   0.011   0.001   PHE E 332 
 TRP   0.017   0.001   TRP E 323 
 HIS   0.005   0.001   HIS G 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (16152)
  covalent geometry    : angle       0.44069 (21824)
  hydrogen bonds       : bond        0.03680 ( 1112)
  hydrogen bonds       : angle       3.50940 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 215
  time to evaluate  : 0.739 
Fit side-chains
REVERT: B  141 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7102 (pp20)
REVERT: A  557 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7400 (mtpt)
REVERT: D   12 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6853 (pm20)
REVERT: D   68 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7167 (mt-10)
REVERT: D  112 ASN cc_start: 0.8485 (m-40) cc_final: 0.8258 (m-40)
REVERT: F   39 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8229 (p)
REVERT: F   68 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7174 (mt-10)
REVERT: F  140 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6083 (mp0)
REVERT: H  112 ASN cc_start: 0.8514 (m-40) cc_final: 0.8274 (m-40)
REVERT: H  141 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6979 (pp20)
REVERT: G  191 LEU cc_start: 0.7585 (mm) cc_final: 0.7204 (mp)
REVERT: G  195 ARG cc_start: 0.7114 (mtp180) cc_final: 0.6773 (mtm110)
REVERT: C  533 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7325 (mtm110)
  outliers start: 39
  outliers final: 26
  residues processed: 245
  average time/residue: 0.6922
  time to fit residues: 185.1525
Evaluate side-chains
  245 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 211
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain D residue   12 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   39 SER
Chi-restraints excluded: chain F residue   68 GLU
Chi-restraints excluded: chain F residue  131 ILE
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   39 SER
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  141 GLU
Chi-restraints excluded: chain G residue  163 LEU
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  310 VAL
Chi-restraints excluded: chain G residue  342 LEU
Chi-restraints excluded: chain G residue  567 ILE
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  366 ARG
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  310 VAL
Chi-restraints excluded: chain E residue  312 THR
Chi-restraints excluded: chain E residue  390 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 109 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 145 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 119 optimal weight:    0.3980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B  43 ASN
D  42 GLN
G 234 GLN
** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 359 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.184284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.149990 restraints weight = 15645.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.81
r_work: 0.3495 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3333
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  16152  Z= 0.128
  Angle     :  0.471   8.597  21824  Z= 0.253
  Chirality :  0.038   0.265   2444
  Planarity :  0.003   0.029   2752
  Dihedral  :  3.360  17.342   2168
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.71 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.56 (0.19), residues: 1952
  helix:  2.20 (0.13), residues: 1544
  sheet:  None (None), residues: 0
  loop : -0.24 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 109 
 TYR   0.013   0.001   TYR C 545 
 PHE   0.014   0.001   PHE G 193 
 TRP   0.021   0.001   TRP G 323 
 HIS   0.006   0.001   HIS G 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (16152)
  covalent geometry    : angle       0.47078 (21824)
  hydrogen bonds       : bond        0.03937 ( 1112)
  hydrogen bonds       : angle       3.59347 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 209
  time to evaluate  : 0.570 
Fit side-chains
REVERT: B  141 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7086 (pp20)
REVERT: A  557 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7363 (mtpt)
REVERT: D   12 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6976 (pm20)
REVERT: D   68 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.7012 (mt-10)
REVERT: D  112 ASN cc_start: 0.8500 (m-40) cc_final: 0.8238 (m-40)
REVERT: F   39 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8222 (p)
REVERT: F   68 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7198 (mt-10)
REVERT: H  112 ASN cc_start: 0.8530 (m-40) cc_final: 0.8265 (m-40)
REVERT: H  141 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7030 (pp20)
REVERT: G  195 ARG cc_start: 0.7126 (mtp180) cc_final: 0.6789 (mtm110)
REVERT: G  508 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6300 (mp0)
REVERT: C  533 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7370 (mtm110)
REVERT: E  191 LEU cc_start: 0.7465 (mm) cc_final: 0.7236 (mp)
  outliers start: 48
  outliers final: 29
  residues processed: 246
  average time/residue: 0.6161
  time to fit residues: 165.4437
Evaluate side-chains
  245 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 208
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  145 MET
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain D residue   12 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   39 SER
Chi-restraints excluded: chain F residue   68 GLU
Chi-restraints excluded: chain F residue  131 ILE
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   39 SER
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  141 GLU
Chi-restraints excluded: chain G residue  163 LEU
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  310 VAL
Chi-restraints excluded: chain G residue  508 GLU
Chi-restraints excluded: chain G residue  567 ILE
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  366 ARG
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain E residue  163 LEU
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  285 LYS
Chi-restraints excluded: chain E residue  310 VAL
Chi-restraints excluded: chain E residue  312 THR
Chi-restraints excluded: chain E residue  390 SER
Chi-restraints excluded: chain E residue  567 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9980
   chunk 179 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 187 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN
** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 359 GLN
** E 234 GLN ** 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 = 0.4058 r_free = 0.4058 target = 0.184386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.150217 restraints weight = 15576.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 1.80
r_work: 0.3493 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3333
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  16152  Z= 0.128
  Angle     :  0.476   8.076  21824  Z= 0.257
  Chirality :  0.038   0.268   2444
  Planarity :  0.003   0.029   2752
  Dihedral  :  3.377  17.509   2168
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.31 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.53 (0.19), residues: 1952
  helix:  2.17 (0.13), residues: 1544
  sheet:  None (None), residues: 0
  loop : -0.26 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 109 
 TYR   0.013   0.001   TYR C 545 
 PHE   0.015   0.001   PHE G 193 
 TRP   0.023   0.002   TRP C 323 
 HIS   0.007   0.001   HIS G 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (16152)
  covalent geometry    : angle       0.47640 (21824)
  hydrogen bonds       : bond        0.03932 ( 1112)
  hydrogen bonds       : angle       3.59753 ( 3306)

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

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

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3904 Ramachandran restraints generated.
    1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 208
  time to evaluate  : 0.412 
Fit side-chains
REVERT: B  141 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7077 (pp20)
REVERT: A  557 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7356 (mtpt)
REVERT: D   12 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6965 (pm20)
REVERT: D   68 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6981 (mt-10)
REVERT: D  112 ASN cc_start: 0.8495 (m-40) cc_final: 0.8232 (m-40)
REVERT: F   39 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8213 (p)
REVERT: F   68 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7246 (mt-10)
REVERT: H  112 ASN cc_start: 0.8529 (m-40) cc_final: 0.8273 (m-40)
REVERT: H  141 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7032 (pp20)
REVERT: G  191 LEU cc_start: 0.7569 (mm) cc_final: 0.7183 (mp)
REVERT: G  195 ARG cc_start: 0.7147 (mtp180) cc_final: 0.6810 (mtm110)
REVERT: G  508 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6312 (mp0)
REVERT: C  533 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7394 (mtm110)
REVERT: E  191 LEU cc_start: 0.7428 (mm) cc_final: 0.7199 (mp)
  outliers start: 36
  outliers final: 26
  residues processed: 234
  average time/residue: 0.5978
  time to fit residues: 152.2348
Evaluate side-chains
  242 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 208
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  366 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  567 ILE
Chi-restraints excluded: chain D residue   12 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   39 SER
Chi-restraints excluded: chain F residue   68 GLU
Chi-restraints excluded: chain F residue  131 ILE
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   39 SER
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  141 GLU
Chi-restraints excluded: chain G residue  163 LEU
Chi-restraints excluded: chain G residue  230 ILE
Chi-restraints excluded: chain G residue  310 VAL
Chi-restraints excluded: chain G residue  508 GLU
Chi-restraints excluded: chain G residue  567 ILE
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  366 ARG
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain E residue  230 ILE
Chi-restraints excluded: chain E residue  285 LYS
Chi-restraints excluded: chain E residue  310 VAL
Chi-restraints excluded: chain E residue  312 THR
Chi-restraints excluded: chain E residue  390 SER
Chi-restraints excluded: chain E residue  567 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 178 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 167 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 180 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 131 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 357 GLN
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 359 GLN
** E 234 GLN ** 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 = 0.4062 r_free = 0.4062 target = 0.184934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.150723 restraints weight = 15600.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 1.81
r_work: 0.3498 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  16152  Z= 0.120
  Angle     :  0.471   7.892  21824  Z= 0.253
  Chirality :  0.038   0.256   2444
  Planarity :  0.003   0.029   2752
  Dihedral  :  3.353  17.645   2168
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.13 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.57 (0.19), residues: 1952
  helix:  2.21 (0.13), residues: 1544
  sheet:  None (None), residues: 0
  loop : -0.24 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 109 
 TYR   0.012   0.001   TYR C 545 
 PHE   0.014   0.001   PHE G 193 
 TRP   0.024   0.002   TRP C 323 
 HIS   0.007   0.001   HIS G 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (16152)
  covalent geometry    : angle       0.47088 (21824)
  hydrogen bonds       : bond        0.03835 ( 1112)
  hydrogen bonds       : angle       3.56356 ( 3306)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5499.21 seconds
wall clock time: 94 minutes 8.32 seconds (5648.32 seconds total)