Starting phenix.real_space_refine
on Wed Mar  4 15:34:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ud3_20731/03_2026/6ud3_20731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ud3_20731/03_2026/6ud3_20731.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ud3_20731/03_2026/6ud3_20731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ud3_20731/03_2026/6ud3_20731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ud3_20731/03_2026/6ud3_20731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ud3_20731/03_2026/6ud3_20731.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     100      5.16       5
     C    9350      2.51       5
     N    2315      2.21       5
     O    2581      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14346
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 2846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2846
          Classifications: {'peptide': 352}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 335}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 2846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2846
          Classifications: {'peptide': 352}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 335}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "E"
      Number of atoms: 2846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2846
          Classifications: {'peptide': 352}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 335}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 2846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2846
          Classifications: {'peptide': 352}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 335}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 2846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2846
          Classifications: {'peptide': 352}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 335}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 19
          Unusual residues: {'NAG': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Modifications used: {'COO': 1}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'RI5': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 19
          Unusual residues: {'NAG': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Modifications used: {'COO': 1}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 19
          Unusual residues: {'NAG': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Modifications used: {'COO': 1}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.69, per 1000 atoms: 0.26
  Number of scatterers: 14346
  At special positions: 0
  Unit cell: (91.16, 90.1, 131.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     100     16.00
     O    2581      8.00
     N    2315      7.00
     C    9350      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: 1.46
  Conformation dependent library (CDL) restraints added in 523.7 milliseconds
  

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3380

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 30 sheets defined
      38.0% alpha, 22.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 42
    Processing helix  chain 'A' and resid 245 through 251
    Processing helix  chain 'A' and resid 251 through 269
      removed outlier: 4.118A  pdb=" N   PHE A 266 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP A 267 " --> pdb=" O   TRP A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 294
    Processing helix  chain 'A' and resid 306 through 339
      removed outlier: 3.970A  pdb=" N   ALA A 312 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 441
      removed outlier: 3.638A  pdb=" N   ARG A 415 " --> pdb=" O   ASP A 411 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
      removed outlier: 3.882A  pdb=" N   PHE A 425 " --> pdb=" O   VAL A 421 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE A 436 " --> pdb=" O   THR A 432 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 42
    Processing helix  chain 'C' and resid 245 through 251
    Processing helix  chain 'C' and resid 251 through 269
      removed outlier: 4.119A  pdb=" N   PHE C 266 " --> pdb=" O   SER C 262 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   TRP C 267 " --> pdb=" O   TRP C 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 294
    Processing helix  chain 'C' and resid 306 through 339
      removed outlier: 3.971A  pdb=" N   ALA C 312 " --> pdb=" O   ASP C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 400 through 441
      removed outlier: 3.638A  pdb=" N   ARG C 415 " --> pdb=" O   ASP C 411 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL C 416 " --> pdb=" O   THR C 412 " (cutoff:3.500A)
      Proline residue:  C 419  - end of helix
      removed outlier: 3.881A  pdb=" N   PHE C 425 " --> pdb=" O   VAL C 421 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE C 436 " --> pdb=" O   THR C 432 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 33 through 42
    Processing helix  chain 'E' and resid 245 through 251
    Processing helix  chain 'E' and resid 251 through 269
      removed outlier: 4.118A  pdb=" N   PHE E 266 " --> pdb=" O   SER E 262 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP E 267 " --> pdb=" O   TRP E 263 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 273 through 294
    Processing helix  chain 'E' and resid 306 through 339
      removed outlier: 3.970A  pdb=" N   ALA E 312 " --> pdb=" O   ASP E 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 400 through 441
      removed outlier: 3.638A  pdb=" N   ARG E 415 " --> pdb=" O   ASP E 411 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL E 416 " --> pdb=" O   THR E 412 " (cutoff:3.500A)
      Proline residue:  E 419  - end of helix
      removed outlier: 3.881A  pdb=" N   PHE E 425 " --> pdb=" O   VAL E 421 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE E 436 " --> pdb=" O   THR E 432 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 33 through 42
    Processing helix  chain 'D' and resid 245 through 251
    Processing helix  chain 'D' and resid 251 through 269
      removed outlier: 4.119A  pdb=" N   PHE D 266 " --> pdb=" O   SER D 262 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP D 267 " --> pdb=" O   TRP D 263 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 273 through 294
    Processing helix  chain 'D' and resid 306 through 339
      removed outlier: 3.970A  pdb=" N   ALA D 312 " --> pdb=" O   ASP D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 400 through 441
      removed outlier: 3.637A  pdb=" N   ARG D 415 " --> pdb=" O   ASP D 411 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL D 416 " --> pdb=" O   THR D 412 " (cutoff:3.500A)
      Proline residue:  D 419  - end of helix
      removed outlier: 3.881A  pdb=" N   PHE D 425 " --> pdb=" O   VAL D 421 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE D 436 " --> pdb=" O   THR D 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 42
    Processing helix  chain 'B' and resid 245 through 251
    Processing helix  chain 'B' and resid 251 through 269
      removed outlier: 4.118A  pdb=" N   PHE B 266 " --> pdb=" O   SER B 262 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   TRP B 267 " --> pdb=" O   TRP B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 294
    Processing helix  chain 'B' and resid 306 through 339
      removed outlier: 3.970A  pdb=" N   ALA B 312 " --> pdb=" O   ASP B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 441
      removed outlier: 3.638A  pdb=" N   ARG B 415 " --> pdb=" O   ASP B 411 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL B 416 " --> pdb=" O   THR B 412 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
      removed outlier: 3.881A  pdb=" N   PHE B 425 " --> pdb=" O   VAL B 421 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE B 436 " --> pdb=" O   THR B 432 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91
      removed outlier: 5.751A  pdb=" N   VAL A  63 " --> pdb=" O   GLU A 193 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91
      removed outlier: 8.331A  pdb=" N   GLN A 201 " --> pdb=" O   CYS A  65 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ILE A  67 " --> pdb=" O   GLN A 201 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 86
      removed outlier: 3.841A  pdb=" N   VAL A 159 " --> pdb=" O   LYS A 128 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 108
    Processing sheet with id=AA5, first strand: chain 'A' and resid 123 through 124
      removed outlier: 4.182A  pdb=" N   GLU A 241 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 123 through 124
      removed outlier: 4.081A  pdb=" N   CYS A 233 " --> pdb=" O   CYS A 222 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91
      removed outlier: 5.750A  pdb=" N   VAL C  63 " --> pdb=" O   GLU C 193 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 91
      removed outlier: 8.332A  pdb=" N   GLN C 201 " --> pdb=" O   CYS C  65 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ILE C  67 " --> pdb=" O   GLN C 201 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 81 through 86
      removed outlier: 3.841A  pdb=" N   VAL C 159 " --> pdb=" O   LYS C 128 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 108
    Processing sheet with id=AB2, first strand: chain 'C' and resid 123 through 124
      removed outlier: 4.182A  pdb=" N   GLU C 241 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 123 through 124
      removed outlier: 4.080A  pdb=" N   CYS C 233 " --> pdb=" O   CYS C 222 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 89 through 91
      removed outlier: 5.751A  pdb=" N   VAL E  63 " --> pdb=" O   GLU E 193 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 89 through 91
      removed outlier: 8.330A  pdb=" N   GLN E 201 " --> pdb=" O   CYS E  65 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ILE E  67 " --> pdb=" O   GLN E 201 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 81 through 86
      removed outlier: 3.841A  pdb=" N   VAL E 159 " --> pdb=" O   LYS E 128 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 106 through 108
    Processing sheet with id=AB8, first strand: chain 'E' and resid 123 through 124
      removed outlier: 4.182A  pdb=" N   GLU E 241 " --> pdb=" O   ILE E 212 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 123 through 124
      removed outlier: 4.081A  pdb=" N   CYS E 233 " --> pdb=" O   CYS E 222 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 89 through 91
      removed outlier: 5.751A  pdb=" N   VAL D  63 " --> pdb=" O   GLU D 193 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 89 through 91
      removed outlier: 8.331A  pdb=" N   GLN D 201 " --> pdb=" O   CYS D  65 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ILE D  67 " --> pdb=" O   GLN D 201 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 81 through 86
      removed outlier: 3.841A  pdb=" N   VAL D 159 " --> pdb=" O   LYS D 128 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 106 through 108
    Processing sheet with id=AC5, first strand: chain 'D' and resid 123 through 124
      removed outlier: 4.182A  pdb=" N   GLU D 241 " --> pdb=" O   ILE D 212 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 123 through 124
      removed outlier: 4.081A  pdb=" N   CYS D 233 " --> pdb=" O   CYS D 222 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 89 through 91
      removed outlier: 5.750A  pdb=" N   VAL B  63 " --> pdb=" O   GLU B 193 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 89 through 91
      removed outlier: 8.331A  pdb=" N   GLN B 201 " --> pdb=" O   CYS B  65 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ILE B  67 " --> pdb=" O   GLN B 201 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 81 through 86
      removed outlier: 3.842A  pdb=" N   VAL B 159 " --> pdb=" O   LYS B 128 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 106 through 108
    Processing sheet with id=AD2, first strand: chain 'B' and resid 123 through 124
      removed outlier: 4.182A  pdb=" N   GLU B 241 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 123 through 124
      removed outlier: 4.081A  pdb=" N   CYS B 233 " --> pdb=" O   CYS B 222 " (cutoff:3.500A)

    705 hydrogen bonds defined for protein.
    2010 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.27

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        0.58 -     0.84: 1
        0.84 -     1.10: 1
        1.10 -     1.36: 4521
        1.36 -     1.62: 10001
        1.62 -     1.88: 176
  Bond restraints: 14700
  Sorted by residual:
  bond pdb=" C08 RI5 A 503 "
       pdb=" C13 RI5 A 503 "
    ideal  model  delta    sigma   weight residual
    1.554  0.584  0.970 2.00e-02 2.50e+03 2.35e+03
  bond pdb=" C07 RI5 A 503 "
       pdb=" C15 RI5 A 503 "
    ideal  model  delta    sigma   weight residual
    1.508  1.009  0.499 2.00e-02 2.50e+03 6.23e+02
  bond pdb=" C08 RI5 A 503 "
       pdb=" C09 RI5 A 503 "
    ideal  model  delta    sigma   weight residual
    1.551  1.167  0.384 2.00e-02 2.50e+03 3.69e+02
  bond pdb=" C07 RI5 A 503 "
       pdb=" C08 RI5 A 503 "
    ideal  model  delta    sigma   weight residual
    1.571  1.883 -0.312 2.00e-02 2.50e+03 2.44e+02
  bond pdb=" C05 RI5 A 503 "
       pdb=" O12 RI5 A 503 "
    ideal  model  delta    sigma   weight residual
    1.440  1.728 -0.288 2.00e-02 2.50e+03 2.08e+02
  ... (remaining 14695 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.70: 19779
        6.70 -    13.41: 153
       13.41 -    20.11: 12
       20.11 -    26.82: 0
       26.82 -    33.52: 2
  Bond angle restraints: 19946
  Sorted by residual:
  angle pdb=" C07 RI5 A 503 "
        pdb=" C15 RI5 A 503 "
        pdb=" O16 RI5 A 503 "
      ideal   model   delta    sigma   weight residual
     118.77  152.29  -33.52 3.00e+00 1.11e-01 1.25e+02
  angle pdb=" C13 RI5 A 503 "
        pdb=" C14 RI5 A 503 "
        pdb=" O16 RI5 A 503 "
      ideal   model   delta    sigma   weight residual
     113.55  145.85  -32.30 3.00e+00 1.11e-01 1.16e+02
  angle pdb=" NE  ARG B  89 "
        pdb=" CZ  ARG B  89 "
        pdb=" NH2 ARG B  89 "
      ideal   model   delta    sigma   weight residual
     119.20  126.33   -7.13 9.00e-01 1.23e+00 6.28e+01
  angle pdb=" NE  ARG A  89 "
        pdb=" CZ  ARG A  89 "
        pdb=" NH2 ARG A  89 "
      ideal   model   delta    sigma   weight residual
     119.20  126.33   -7.13 9.00e-01 1.23e+00 6.27e+01
  angle pdb=" NE  ARG E  89 "
        pdb=" CZ  ARG E  89 "
        pdb=" NH2 ARG E  89 "
      ideal   model   delta    sigma   weight residual
     119.20  126.31   -7.11 9.00e-01 1.23e+00 6.25e+01
  ... (remaining 19941 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.43: 8053
       15.43 -    30.85: 683
       30.85 -    46.28: 119
       46.28 -    61.71: 23
       61.71 -    77.13: 10
  Dihedral angle restraints: 8888
    sinusoidal: 3683
      harmonic: 5205
  Sorted by residual:
  dihedral pdb=" CA  THR D 137 "
           pdb=" C   THR D 137 "
           pdb=" N   ASP D 138 "
           pdb=" CA  ASP D 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.42   19.58     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  THR B 137 "
           pdb=" C   THR B 137 "
           pdb=" N   ASP B 138 "
           pdb=" CA  ASP B 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.42   19.58     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  THR C 137 "
           pdb=" C   THR C 137 "
           pdb=" N   ASP C 138 "
           pdb=" CA  ASP C 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.43   19.57     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 8885 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.440: 2243
       0.440 -    0.879: 12
       0.879 -    1.319: 1
       1.319 -    1.759: 0
       1.759 -    2.198: 1
  Chirality restraints: 2257
  Sorted by residual:
  chirality pdb=" C08 RI5 A 503 "
            pdb=" C07 RI5 A 503 "
            pdb=" C09 RI5 A 503 "
            pdb=" C13 RI5 A 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.99    0.79    2.20 2.00e-01 2.50e+01 1.21e+02
  chirality pdb=" C14 RI5 A 503 "
            pdb=" C13 RI5 A 503 "
            pdb=" C15 RI5 A 503 "
            pdb=" O16 RI5 A 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.42    1.19    1.24 2.00e-01 2.50e+01 3.83e+01
  chirality pdb=" CB  ILE B 424 "
            pdb=" CA  ILE B 424 "
            pdb=" CG1 ILE B 424 "
            pdb=" CG2 ILE B 424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.95    0.70 2.00e-01 2.50e+01 1.21e+01
  ... (remaining 2254 not shown)

  Planarity restraints: 2483
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 502 "   -0.032 2.00e-02 2.50e+03   6.19e-02 3.83e+01
        pdb=" C   GLY A 502 "    0.107 2.00e-02 2.50e+03
        pdb=" O   GLY A 502 "   -0.038 2.00e-02 2.50e+03
        pdb=" OXT GLY A 502 "   -0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D 501 "   -0.032 2.00e-02 2.50e+03   6.18e-02 3.82e+01
        pdb=" C   GLY D 501 "    0.107 2.00e-02 2.50e+03
        pdb=" O   GLY D 501 "   -0.038 2.00e-02 2.50e+03
        pdb=" OXT GLY D 501 "   -0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 502 "   -0.032 2.00e-02 2.50e+03   6.17e-02 3.81e+01
        pdb=" C   GLY C 502 "    0.107 2.00e-02 2.50e+03
        pdb=" O   GLY C 502 "   -0.038 2.00e-02 2.50e+03
        pdb=" OXT GLY C 502 "   -0.037 2.00e-02 2.50e+03
  ... (remaining 2480 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3770
        2.81 -     3.34: 12890
        3.34 -     3.86: 23604
        3.86 -     4.38: 25383
        4.38 -     4.90: 45243
  Nonbonded interactions: 110890
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 279 "
            pdb=" OG1 THR A 283 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   LEU D 279 "
            pdb=" OG1 THR D 283 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   LEU E 279 "
            pdb=" OG1 THR E 283 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   LEU C 279 "
            pdb=" OG1 THR C 283 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   LEU B 279 "
            pdb=" OG1 THR B 283 "
     model   vdw
     2.294 3.040
  ... (remaining 110885 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 31 through 441 or resid 502))
  selection = (chain 'B' and resid 31 through 501)
  selection = (chain 'C' and (resid 31 through 441 or resid 502))
  selection = (chain 'D' and resid 31 through 501)
  selection = (chain 'E' and (resid 31 through 441 or resid 502))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.390
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.030
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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      :  0.018   0.970  14700  Z= 0.801
  Angle     :  1.600  33.524  19946  Z= 0.888
  Chirality :  0.112   2.198   2257
  Planarity :  0.011   0.062   2483
  Dihedral  : 12.054  77.132   5508
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  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 are not related in a simple way.
  whole: -1.90 (0.19), residues: 1740
  helix:  0.11 (0.21), residues: 640
  sheet: -2.11 (0.27), residues: 340
  loop : -2.00 (0.19), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  89 
 TYR   0.053   0.006   TYR A 325 
 PHE   0.081   0.005   PHE A 169 
 TRP   0.022   0.004   TRP E 263 
 HIS   0.006   0.002   HIS E 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.01779 (14700)
  covalent geometry    : angle       1.60028 (19946)
  hydrogen bonds       : bond        0.16487 (  635)
  hydrogen bonds       : angle       7.27235 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 411
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 CYS cc_start: 0.8418 (m) cc_final: 0.7936 (m)
REVERT: A  263 TRP cc_start: 0.8433 (m-10) cc_final: 0.7736 (m-10)
REVERT: C  176 CYS cc_start: 0.8377 (m) cc_final: 0.8084 (m)
REVERT: C  263 TRP cc_start: 0.8431 (m-10) cc_final: 0.7771 (m-10)
REVERT: E  114 LEU cc_start: 0.8239 (mt) cc_final: 0.7672 (pt)
REVERT: D  114 LEU cc_start: 0.8269 (mt) cc_final: 0.7718 (pt)
REVERT: D  179 GLN cc_start: 0.8623 (mt0) cc_final: 0.8366 (mt0)
REVERT: D  263 TRP cc_start: 0.8411 (m-10) cc_final: 0.7804 (m-10)
REVERT: B  114 LEU cc_start: 0.8301 (mt) cc_final: 0.7720 (pt)
REVERT: B  187 MET cc_start: 0.7905 (tpp) cc_final: 0.7091 (mmt)
REVERT: B  256 LEU cc_start: 0.9053 (tp) cc_final: 0.8746 (tt)
REVERT: B  263 TRP cc_start: 0.8424 (m-10) cc_final: 0.7751 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 411
  average time/residue: 0.1243
  time to fit residues: 74.3425
Evaluate side-chains
  216 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
C 290 GLN
E 335 HIS
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.092363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.078961 restraints weight = 45961.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.081689 restraints weight = 22950.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.083516 restraints weight = 13982.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.084688 restraints weight = 9729.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.085558 restraints weight = 7486.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14700  Z= 0.150
  Angle     :  0.679   9.287  19946  Z= 0.340
  Chirality :  0.045   0.188   2257
  Planarity :  0.004   0.039   2483
  Dihedral  :  5.189  35.706   2078
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.24 %
    Favored  : 82.67 %
  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 are not related in a simple way.
  whole: -0.80 (0.19), residues: 1740
  helix:  1.38 (0.19), residues: 660
  sheet: -1.31 (0.25), residues: 455
  loop : -1.98 (0.21), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 237 
 TYR   0.013   0.001   TYR E 433 
 PHE   0.019   0.001   PHE D 169 
 TRP   0.021   0.002   TRP A 118 
 HIS   0.005   0.001   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14700)
  covalent geometry    : angle       0.67891 (19946)
  hydrogen bonds       : bond        0.04076 (  635)
  hydrogen bonds       : angle       4.23979 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 220
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 TRP cc_start: 0.7996 (m-10) cc_final: 0.7351 (m100)
REVERT: A  319 PHE cc_start: 0.7897 (t80) cc_final: 0.7669 (t80)
REVERT: C  263 TRP cc_start: 0.8066 (m-10) cc_final: 0.7533 (m-10)
REVERT: E  171 MET cc_start: 0.8019 (mpp) cc_final: 0.7793 (mpp)
REVERT: E  187 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7391 (tpp)
REVERT: E  287 MET cc_start: 0.9120 (mmm) cc_final: 0.8825 (tpp)
REVERT: E  311 MET cc_start: 0.8161 (mmm) cc_final: 0.7927 (ttm)
REVERT: D  250 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8045 (tp40)
REVERT: D  263 TRP cc_start: 0.7914 (m-10) cc_final: 0.7409 (m-10)
REVERT: B  256 LEU cc_start: 0.9087 (tp) cc_final: 0.8741 (tt)
REVERT: B  263 TRP cc_start: 0.8085 (m-10) cc_final: 0.7802 (m-10)
REVERT: B  287 MET cc_start: 0.8940 (mmm) cc_final: 0.8698 (tpp)
  outliers start: 33
  outliers final: 17
  residues processed: 244
  average time/residue: 0.1019
  time to fit residues: 38.8060
Evaluate side-chains
  192 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 173
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  288 THR
Chi-restraints excluded: chain C residue  431 ILE
Chi-restraints excluded: chain E residue  187 MET
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  256 LEU
Chi-restraints excluded: chain E residue  288 THR
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  250 GLN
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  431 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 152 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0270
   chunk 66 optimal weight:    0.7980
   chunk 165 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
A 335 HIS
C 335 HIS
** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 335 HIS
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 335 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.089888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.075043 restraints weight = 47531.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.077788 restraints weight = 24196.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.079563 restraints weight = 15120.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.080764 restraints weight = 10793.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.081588 restraints weight = 8440.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14700  Z= 0.124
  Angle     :  0.617   7.278  19946  Z= 0.307
  Chirality :  0.043   0.146   2257
  Planarity :  0.003   0.034   2483
  Dihedral  :  4.857  32.755   2078
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.75 %
    Favored  : 81.08 %
  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 are not related in a simple way.
  whole: -0.21 (0.20), residues: 1740
  helix:  2.05 (0.19), residues: 660
  sheet: -0.96 (0.26), residues: 425
  loop : -1.89 (0.21), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 437 
 TYR   0.014   0.001   TYR D 429 
 PHE   0.012   0.001   PHE D 169 
 TRP   0.009   0.001   TRP A 118 
 HIS   0.004   0.001   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (14700)
  covalent geometry    : angle       0.61700 (19946)
  hydrogen bonds       : bond        0.03529 (  635)
  hydrogen bonds       : angle       3.79116 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 189
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.7366 (pmm) cc_final: 0.7142 (pmm)
REVERT: A  164 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8057 (ptm)
REVERT: A  263 TRP cc_start: 0.8047 (m-10) cc_final: 0.7787 (m-10)
REVERT: C  187 MET cc_start: 0.8624 (mmm) cc_final: 0.8336 (mmm)
REVERT: C  212 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8644 (pt)
REVERT: C  263 TRP cc_start: 0.8091 (m-10) cc_final: 0.7531 (m-10)
REVERT: E  171 MET cc_start: 0.7365 (mpp) cc_final: 0.7120 (mpp)
REVERT: E  287 MET cc_start: 0.9204 (mmm) cc_final: 0.8987 (tpp)
REVERT: E  437 ARG cc_start: 0.5143 (mtm180) cc_final: 0.4803 (ptp-170)
REVERT: D  250 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7896 (tm-30)
REVERT: D  263 TRP cc_start: 0.8050 (m-10) cc_final: 0.7472 (m-10)
REVERT: B  256 LEU cc_start: 0.9078 (tp) cc_final: 0.8735 (tt)
  outliers start: 50
  outliers final: 20
  residues processed: 220
  average time/residue: 0.1081
  time to fit residues: 36.7108
Evaluate side-chains
  181 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  288 THR
Chi-restraints excluded: chain C residue  431 ILE
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  288 THR
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  250 GLN
Chi-restraints excluded: chain D residue  264 VAL
Chi-restraints excluded: chain D residue  288 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  431 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 133 optimal weight:    0.0870
   chunk 50 optimal weight:    7.9990
   chunk 43 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 154 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 164 optimal weight:    2.9990
   chunk 138 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.1564

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 174 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 = 0.3681 r_free = 0.3681 target = 0.086587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.071690 restraints weight = 46949.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.074332 restraints weight = 24407.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.076129 restraints weight = 15539.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.077367 restraints weight = 11215.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.078232 restraints weight = 8827.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14700  Z= 0.143
  Angle     :  0.636   8.621  19946  Z= 0.319
  Chirality :  0.043   0.182   2257
  Planarity :  0.003   0.032   2483
  Dihedral  :  4.839  32.410   2078
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.89 %
    Favored  : 80.57 %
  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 are not related in a simple way.
  whole:  0.17 (0.20), residues: 1740
  helix:  2.39 (0.19), residues: 660
  sheet: -0.65 (0.26), residues: 425
  loop : -1.79 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 437 
 TYR   0.014   0.001   TYR A 429 
 PHE   0.011   0.001   PHE D 169 
 TRP   0.011   0.001   TRP B 263 
 HIS   0.003   0.000   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (14700)
  covalent geometry    : angle       0.63643 (19946)
  hydrogen bonds       : bond        0.03382 (  635)
  hydrogen bonds       : angle       3.60909 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 161
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.7723 (pmm) cc_final: 0.7461 (pmm)
REVERT: A  263 TRP cc_start: 0.8046 (m-10) cc_final: 0.7844 (m-10)
REVERT: A  311 MET cc_start: 0.8041 (mtp) cc_final: 0.7731 (ttm)
REVERT: C  244 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.7007 (mmm)
REVERT: C  263 TRP cc_start: 0.8068 (m-10) cc_final: 0.7822 (m-10)
REVERT: C  287 MET cc_start: 0.9106 (tpp) cc_final: 0.8810 (tpp)
REVERT: E  187 MET cc_start: 0.8541 (tpp) cc_final: 0.8320 (mmm)
REVERT: E  263 TRP cc_start: 0.8154 (m-10) cc_final: 0.7719 (m-10)
REVERT: E  308 ASP cc_start: 0.8497 (m-30) cc_final: 0.8256 (m-30)
REVERT: D  250 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7978 (tm-30)
REVERT: D  263 TRP cc_start: 0.8059 (m-10) cc_final: 0.7509 (m-10)
REVERT: B  256 LEU cc_start: 0.9113 (tp) cc_final: 0.8780 (tt)
REVERT: B  263 TRP cc_start: 0.8136 (m-10) cc_final: 0.7905 (m-10)
REVERT: B  311 MET cc_start: 0.8326 (mtp) cc_final: 0.7822 (ttm)
REVERT: B  400 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6921 (ptp90)
  outliers start: 40
  outliers final: 22
  residues processed: 188
  average time/residue: 0.1046
  time to fit residues: 30.3373
Evaluate side-chains
  175 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  244 MET
Chi-restraints excluded: chain C residue  288 THR
Chi-restraints excluded: chain C residue  431 ILE
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  256 LEU
Chi-restraints excluded: chain E residue  257 LEU
Chi-restraints excluded: chain E residue  288 THR
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain D residue   77 GLU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  250 GLN
Chi-restraints excluded: chain D residue  288 THR
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  400 ARG
Chi-restraints excluded: chain B residue  431 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 29 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 138 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 145 optimal weight:    6.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 290 GLN
** B 174 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 = 0.3524 r_free = 0.3524 target = 0.077598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.063489 restraints weight = 47392.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.065981 restraints weight = 25152.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.067643 restraints weight = 16169.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.068756 restraints weight = 11780.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.069567 restraints weight = 9424.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.5643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14700  Z= 0.208
  Angle     :  0.688   9.938  19946  Z= 0.350
  Chirality :  0.045   0.194   2257
  Planarity :  0.004   0.045   2483
  Dihedral  :  5.402  32.419   2078
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.27 %
    Favored  : 79.30 %
  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 are not related in a simple way.
  whole:  0.33 (0.20), residues: 1740
  helix:  2.44 (0.19), residues: 660
  sheet: -0.18 (0.28), residues: 400
  loop : -1.87 (0.22), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 437 
 TYR   0.019   0.002   TYR B 429 
 PHE   0.016   0.002   PHE D 169 
 TRP   0.010   0.002   TRP D 310 
 HIS   0.004   0.001   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (14700)
  covalent geometry    : angle       0.68802 (19946)
  hydrogen bonds       : bond        0.03785 (  635)
  hydrogen bonds       : angle       3.75694 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 146
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.7871 (pmm) cc_final: 0.7654 (pmm)
REVERT: A  187 MET cc_start: 0.8572 (tpp) cc_final: 0.7874 (mpp)
REVERT: A  221 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7767 (p90)
REVERT: A  263 TRP cc_start: 0.8102 (m-10) cc_final: 0.7840 (m-10)
REVERT: C  256 LEU cc_start: 0.9239 (tp) cc_final: 0.8852 (tt)
REVERT: C  263 TRP cc_start: 0.8171 (m-10) cc_final: 0.7920 (m-10)
REVERT: C  279 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7926 (tt)
REVERT: E  206 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7871 (pp)
REVERT: E  263 TRP cc_start: 0.8301 (m-10) cc_final: 0.7927 (m-10)
REVERT: E  287 MET cc_start: 0.9209 (tpp) cc_final: 0.8950 (tpp)
REVERT: E  308 ASP cc_start: 0.8504 (m-30) cc_final: 0.8231 (m-30)
REVERT: E  400 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7090 (ptp90)
REVERT: D  164 MET cc_start: 0.8862 (ptm) cc_final: 0.8580 (ptp)
REVERT: D  263 TRP cc_start: 0.8138 (m-10) cc_final: 0.7706 (m-10)
REVERT: D  285 LEU cc_start: 0.9193 (mt) cc_final: 0.8829 (tt)
REVERT: D  400 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7203 (ptp90)
REVERT: B  256 LEU cc_start: 0.9158 (tp) cc_final: 0.8846 (tt)
REVERT: B  263 TRP cc_start: 0.8250 (m-10) cc_final: 0.7833 (m-10)
REVERT: B  311 MET cc_start: 0.8501 (mtp) cc_final: 0.7942 (ttm)
REVERT: B  400 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6976 (ptp90)
  outliers start: 54
  outliers final: 32
  residues processed: 186
  average time/residue: 0.1094
  time to fit residues: 31.1166
Evaluate side-chains
  177 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 139
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  431 ILE
Chi-restraints excluded: chain E residue   36 GLU
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain E residue   77 GLU
Chi-restraints excluded: chain E residue  178 MET
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  256 LEU
Chi-restraints excluded: chain E residue  288 THR
Chi-restraints excluded: chain E residue  400 ARG
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain D residue   77 GLU
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  262 SER
Chi-restraints excluded: chain D residue  264 VAL
Chi-restraints excluded: chain D residue  288 THR
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain D residue  400 ARG
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  400 ARG
Chi-restraints excluded: chain B residue  431 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0060
   chunk 27 optimal weight:    0.0370
   chunk 135 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   chunk 171 optimal weight:    3.9990
   chunk 131 optimal weight:    0.0040
   chunk 139 optimal weight:    0.8980
   overall best weight:    0.3486

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

Flipped N/Q/H residues before XYZ refinement:
E 179 GLN
** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 179 GLN
** B 243 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 = 0.3615 r_free = 0.3615 target = 0.082031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.068030 restraints weight = 46897.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.070652 restraints weight = 24214.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.072398 restraints weight = 15387.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.073572 restraints weight = 11089.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.074362 restraints weight = 8712.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.5648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  14700  Z= 0.112
  Angle     :  0.642   9.243  19946  Z= 0.311
  Chirality :  0.043   0.185   2257
  Planarity :  0.003   0.031   2483
  Dihedral  :  4.839  32.935   2078
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.32 %
    Favored  : 77.52 %
  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 are not related in a simple way.
  whole:  0.53 (0.21), residues: 1740
  helix:  2.56 (0.19), residues: 660
  sheet:  0.12 (0.28), residues: 395
  loop : -1.83 (0.21), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 295 
 TYR   0.010   0.001   TYR B 247 
 PHE   0.008   0.001   PHE A 425 
 TRP   0.004   0.001   TRP B 194 
 HIS   0.002   0.000   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (14700)
  covalent geometry    : angle       0.64186 (19946)
  hydrogen bonds       : bond        0.03112 (  635)
  hydrogen bonds       : angle       3.50804 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 166
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 TRP cc_start: 0.8010 (m-10) cc_final: 0.7787 (m-10)
REVERT: A  311 MET cc_start: 0.7795 (mtp) cc_final: 0.7481 (ttm)
REVERT: C  251 MET cc_start: 0.8523 (mpp) cc_final: 0.8165 (mpp)
REVERT: C  257 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8805 (tp)
REVERT: C  263 TRP cc_start: 0.8082 (m-10) cc_final: 0.7828 (m-10)
REVERT: C  437 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.6773 (mtm180)
REVERT: E  170 PRO cc_start: 0.8973 (Cg_exo) cc_final: 0.8767 (Cg_endo)
REVERT: E  206 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7676 (pp)
REVERT: E  263 TRP cc_start: 0.8035 (m-10) cc_final: 0.7673 (m-10)
REVERT: E  308 ASP cc_start: 0.8515 (m-30) cc_final: 0.8275 (m-30)
REVERT: E  311 MET cc_start: 0.7841 (mtp) cc_final: 0.7439 (ttm)
REVERT: E  400 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7100 (ptp90)
REVERT: D  263 TRP cc_start: 0.8114 (m-10) cc_final: 0.7667 (m-10)
REVERT: D  437 ARG cc_start: 0.5430 (ptt-90) cc_final: 0.4972 (ptp-170)
REVERT: B  256 LEU cc_start: 0.9055 (tp) cc_final: 0.8721 (tt)
REVERT: B  263 TRP cc_start: 0.8177 (m-10) cc_final: 0.7901 (m-10)
  outliers start: 34
  outliers final: 23
  residues processed: 193
  average time/residue: 0.1097
  time to fit residues: 32.3268
Evaluate side-chains
  175 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  319 PHE
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  431 ILE
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  178 MET
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  288 THR
Chi-restraints excluded: chain E residue  400 ARG
Chi-restraints excluded: chain E residue  431 ILE
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  288 THR
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  431 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 142 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 120 optimal weight:    0.0980
   chunk 165 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 116 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 133 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.082229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.067988 restraints weight = 46474.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.070629 restraints weight = 24342.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.072355 restraints weight = 15414.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.073559 restraints weight = 11146.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.074341 restraints weight = 8761.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.5818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14700  Z= 0.122
  Angle     :  0.656  11.309  19946  Z= 0.315
  Chirality :  0.042   0.178   2257
  Planarity :  0.003   0.033   2483
  Dihedral  :  4.690  32.720   2078
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 21.71 %
    Favored  : 75.87 %
  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 are not related in a simple way.
  whole:  0.53 (0.21), residues: 1740
  helix:  2.54 (0.19), residues: 660
  sheet:  0.17 (0.28), residues: 395
  loop : -1.85 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG E 437 
 TYR   0.011   0.001   TYR D 429 
 PHE   0.008   0.001   PHE C 266 
 TRP   0.007   0.001   TRP E 194 
 HIS   0.002   0.000   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (14700)
  covalent geometry    : angle       0.65590 (19946)
  hydrogen bonds       : bond        0.03088 (  635)
  hydrogen bonds       : angle       3.48825 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 TRP cc_start: 0.8087 (m-10) cc_final: 0.7853 (m-10)
REVERT: C  257 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8788 (tp)
REVERT: C  263 TRP cc_start: 0.8132 (m-10) cc_final: 0.7877 (m-10)
REVERT: E  206 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7678 (pp)
REVERT: E  263 TRP cc_start: 0.8160 (m-10) cc_final: 0.7788 (m-10)
REVERT: E  308 ASP cc_start: 0.8581 (m-30) cc_final: 0.8293 (m-30)
REVERT: E  311 MET cc_start: 0.8028 (mtp) cc_final: 0.7608 (ttm)
REVERT: E  400 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7164 (ptp90)
REVERT: D  263 TRP cc_start: 0.8160 (m-10) cc_final: 0.7697 (m-10)
REVERT: B  256 LEU cc_start: 0.9023 (tp) cc_final: 0.8707 (tt)
REVERT: B  263 TRP cc_start: 0.8230 (m-10) cc_final: 0.7930 (m-10)
REVERT: B  400 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7061 (ptp90)
  outliers start: 38
  outliers final: 25
  residues processed: 181
  average time/residue: 0.1050
  time to fit residues: 29.4406
Evaluate side-chains
  175 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  431 ILE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain E residue  178 MET
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  288 THR
Chi-restraints excluded: chain E residue  400 ARG
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain D residue   77 GLU
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  288 THR
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  400 ARG
Chi-restraints excluded: chain B residue  431 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   chunk 106 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 159 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 160 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.079420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.065344 restraints weight = 46622.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.067877 restraints weight = 24145.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.069562 restraints weight = 15317.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.070683 restraints weight = 11077.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.071439 restraints weight = 8754.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.6166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14700  Z= 0.177
  Angle     :  0.699  10.307  19946  Z= 0.341
  Chirality :  0.044   0.175   2257
  Planarity :  0.003   0.034   2483
  Dihedral  :  5.003  33.089   2078
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.46 %
    Favored  : 75.68 %
  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 are not related in a simple way.
  whole:  0.46 (0.21), residues: 1740
  helix:  2.44 (0.19), residues: 660
  sheet:  0.23 (0.28), residues: 395
  loop : -1.90 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 295 
 TYR   0.015   0.002   TYR B 429 
 PHE   0.012   0.001   PHE D 169 
 TRP   0.008   0.001   TRP C 310 
 HIS   0.003   0.000   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (14700)
  covalent geometry    : angle       0.69854 (19946)
  hydrogen bonds       : bond        0.03562 (  635)
  hydrogen bonds       : angle       3.66172 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 151
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.7663 (t0) cc_final: 0.7353 (t0)
REVERT: A  263 TRP cc_start: 0.8133 (m-10) cc_final: 0.7871 (m-10)
REVERT: C  263 TRP cc_start: 0.8166 (m-10) cc_final: 0.7911 (m-10)
REVERT: C  287 MET cc_start: 0.8967 (tpt) cc_final: 0.8609 (tpp)
REVERT: C  308 ASP cc_start: 0.8657 (m-30) cc_final: 0.8353 (m-30)
REVERT: E  206 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7954 (pp)
REVERT: E  263 TRP cc_start: 0.8237 (m-10) cc_final: 0.7853 (m-10)
REVERT: E  287 MET cc_start: 0.9133 (tpp) cc_final: 0.8866 (tpt)
REVERT: E  308 ASP cc_start: 0.8493 (m-30) cc_final: 0.8207 (m-30)
REVERT: E  400 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7135 (ptp90)
REVERT: D  263 TRP cc_start: 0.8157 (m-10) cc_final: 0.7707 (m-10)
REVERT: D  437 ARG cc_start: 0.5325 (ptt-90) cc_final: 0.4826 (ptp-170)
REVERT: B  256 LEU cc_start: 0.9105 (tp) cc_final: 0.8791 (tt)
REVERT: B  263 TRP cc_start: 0.8226 (m-10) cc_final: 0.7784 (m-10)
REVERT: B  400 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7207 (ptp90)
  outliers start: 45
  outliers final: 30
  residues processed: 186
  average time/residue: 0.1018
  time to fit residues: 29.6832
Evaluate side-chains
  181 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 148
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  288 THR
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain E residue  178 MET
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  212 ILE
Chi-restraints excluded: chain E residue  400 ARG
Chi-restraints excluded: chain D residue   77 GLU
Chi-restraints excluded: chain D residue  117 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  258 ILE
Chi-restraints excluded: chain D residue  288 THR
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  400 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 120 optimal weight:    0.9990
   chunk 137 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 79 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.083705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.068545 restraints weight = 47984.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.071223 restraints weight = 23987.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.072942 restraints weight = 15012.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.074106 restraints weight = 10770.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.074871 restraints weight = 8449.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.6225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14700  Z= 0.126
  Angle     :  0.673  10.762  19946  Z= 0.323
  Chirality :  0.043   0.166   2257
  Planarity :  0.003   0.033   2483
  Dihedral  :  4.822  35.397   2078
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 22.41 %
    Favored  : 75.17 %
  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 are not related in a simple way.
  whole:  0.56 (0.21), residues: 1740
  helix:  2.49 (0.20), residues: 660
  sheet:  0.38 (0.28), residues: 395
  loop : -1.88 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 437 
 TYR   0.011   0.001   TYR A 429 
 PHE   0.009   0.001   PHE C 266 
 TRP   0.005   0.001   TRP E 263 
 HIS   0.002   0.000   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (14700)
  covalent geometry    : angle       0.67260 (19946)
  hydrogen bonds       : bond        0.03177 (  635)
  hydrogen bonds       : angle       3.57249 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 157
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.7591 (t0) cc_final: 0.7269 (t0)
REVERT: A  263 TRP cc_start: 0.8099 (m-10) cc_final: 0.7860 (m-10)
REVERT: C  257 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8832 (tp)
REVERT: C  263 TRP cc_start: 0.8102 (m-10) cc_final: 0.7856 (m-10)
REVERT: C  287 MET cc_start: 0.8982 (tpt) cc_final: 0.8685 (tpp)
REVERT: C  308 ASP cc_start: 0.8664 (m-30) cc_final: 0.8420 (m-30)
REVERT: E  206 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7892 (pp)
REVERT: E  263 TRP cc_start: 0.8154 (m-10) cc_final: 0.7786 (m-10)
REVERT: E  287 MET cc_start: 0.9195 (tpp) cc_final: 0.8942 (tpt)
REVERT: E  308 ASP cc_start: 0.8490 (m-30) cc_final: 0.8223 (m-30)
REVERT: E  400 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7126 (ptp90)
REVERT: D  170 PRO cc_start: 0.8868 (Cg_exo) cc_final: 0.8644 (Cg_endo)
REVERT: D  263 TRP cc_start: 0.8149 (m-10) cc_final: 0.7726 (m-10)
REVERT: D  437 ARG cc_start: 0.5281 (ptt-90) cc_final: 0.4772 (ptp-170)
REVERT: B  256 LEU cc_start: 0.9053 (tp) cc_final: 0.8742 (tt)
REVERT: B  263 TRP cc_start: 0.8229 (m-10) cc_final: 0.7845 (m-10)
REVERT: B  311 MET cc_start: 0.8024 (mtp) cc_final: 0.7659 (ttp)
  outliers start: 38
  outliers final: 29
  residues processed: 188
  average time/residue: 0.1078
  time to fit residues: 31.3980
Evaluate side-chains
  181 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  288 THR
Chi-restraints excluded: chain C residue  323 LEU
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain E residue  178 MET
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  212 ILE
Chi-restraints excluded: chain E residue  323 LEU
Chi-restraints excluded: chain E residue  400 ARG
Chi-restraints excluded: chain D residue   77 GLU
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  258 ILE
Chi-restraints excluded: chain D residue  288 THR
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  323 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 149 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 159 optimal weight:    6.9990
   chunk 101 optimal weight:    7.9990
   chunk 131 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0270
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.7640

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

Flipped N/Q/H residues before XYZ refinement:
** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.085544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.070606 restraints weight = 46462.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.073235 restraints weight = 24550.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.075059 restraints weight = 15668.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.076297 restraints weight = 11331.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.077087 restraints weight = 8929.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.6307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14700  Z= 0.123
  Angle     :  0.689  10.737  19946  Z= 0.327
  Chirality :  0.043   0.166   2257
  Planarity :  0.003   0.032   2483
  Dihedral  :  4.698  33.594   2078
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.54 %
    Favored  : 75.37 %
  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 are not related in a simple way.
  whole:  0.59 (0.21), residues: 1740
  helix:  2.50 (0.20), residues: 660
  sheet:  0.45 (0.28), residues: 395
  loop : -1.89 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 437 
 TYR   0.011   0.001   TYR D 429 
 PHE   0.009   0.001   PHE C 266 
 TRP   0.005   0.001   TRP E 263 
 HIS   0.002   0.000   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (14700)
  covalent geometry    : angle       0.68934 (19946)
  hydrogen bonds       : bond        0.03110 (  635)
  hydrogen bonds       : angle       3.53107 ( 2010)

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

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

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3480 Ramachandran restraints generated.
    1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 157
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.7690 (t0) cc_final: 0.7312 (t0)
REVERT: A  263 TRP cc_start: 0.8158 (m-10) cc_final: 0.7940 (m-10)
REVERT: C  257 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8808 (tp)
REVERT: C  263 TRP cc_start: 0.8120 (m-10) cc_final: 0.7873 (m-10)
REVERT: C  287 MET cc_start: 0.9070 (tpt) cc_final: 0.8693 (tpp)
REVERT: C  308 ASP cc_start: 0.8718 (m-30) cc_final: 0.8456 (m-30)
REVERT: E  206 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7803 (pp)
REVERT: E  263 TRP cc_start: 0.8223 (m-10) cc_final: 0.7846 (m-10)
REVERT: E  308 ASP cc_start: 0.8573 (m-30) cc_final: 0.8296 (m-30)
REVERT: E  400 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7099 (ptp90)
REVERT: D  170 PRO cc_start: 0.8897 (Cg_exo) cc_final: 0.8679 (Cg_endo)
REVERT: D  263 TRP cc_start: 0.8177 (m-10) cc_final: 0.7719 (m-10)
REVERT: D  437 ARG cc_start: 0.5180 (ptt-90) cc_final: 0.4725 (ptp-170)
REVERT: B  256 LEU cc_start: 0.9022 (tp) cc_final: 0.8719 (tt)
REVERT: B  263 TRP cc_start: 0.8240 (m-10) cc_final: 0.7847 (m-10)
REVERT: B  311 MET cc_start: 0.8039 (mtp) cc_final: 0.7648 (ttp)
  outliers start: 33
  outliers final: 27
  residues processed: 183
  average time/residue: 0.1050
  time to fit residues: 30.0167
Evaluate side-chains
  183 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  258 ILE
Chi-restraints excluded: chain C residue  288 THR
Chi-restraints excluded: chain C residue  323 LEU
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain E residue  164 MET
Chi-restraints excluded: chain E residue  178 MET
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  212 ILE
Chi-restraints excluded: chain E residue  400 ARG
Chi-restraints excluded: chain D residue   77 GLU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  258 ILE
Chi-restraints excluded: chain D residue  288 THR
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  323 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 163 optimal weight:    0.3980
   chunk 93 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 98 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 148 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
B 290 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.083448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.070089 restraints weight = 47631.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.072578 restraints weight = 24317.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.074272 restraints weight = 15180.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.075385 restraints weight = 10823.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.076163 restraints weight = 8446.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.6459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14700  Z= 0.160
  Angle     :  0.715  10.770  19946  Z= 0.343
  Chirality :  0.043   0.167   2257
  Planarity :  0.003   0.037   2483
  Dihedral  :  4.853  36.108   2078
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 22.54 %
    Favored  : 75.05 %
  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 are not related in a simple way.
  whole:  0.56 (0.21), residues: 1740
  helix:  2.48 (0.20), residues: 660
  sheet:  0.44 (0.28), residues: 395
  loop : -1.92 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 437 
 TYR   0.013   0.001   TYR A 429 
 PHE   0.012   0.001   PHE D 169 
 TRP   0.008   0.001   TRP A  92 
 HIS   0.003   0.000   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (14700)
  covalent geometry    : angle       0.71485 (19946)
  hydrogen bonds       : bond        0.03340 (  635)
  hydrogen bonds       : angle       3.59227 ( 2010)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2111.15 seconds
wall clock time: 37 minutes 34.03 seconds (2254.03 seconds total)