Starting phenix.real_space_refine
on Wed Apr 30 20:06:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g14_29661/04_2025/8g14_29661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g14_29661/04_2025/8g14_29661.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g14_29661/04_2025/8g14_29661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g14_29661/04_2025/8g14_29661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g14_29661/04_2025/8g14_29661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g14_29661/04_2025/8g14_29661.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      48      5.16       5
     C    6332      2.51       5
     N    1728      2.21       5
     O    1912      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10020
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2505
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 4.77, per 1000 atoms: 0.48
  Number of scatterers: 10020
  At special positions: 0
  Unit cell: (96.025, 101.035, 91.015, 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      48     16.00
     O    1912      8.00
     N    1728      7.00
     C    6332      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: 2.28
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2408

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      39.2% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 26
    Processing helix  chain 'A' and resid 39 through 49
    Processing helix  chain 'A' and resid 81 through 85
      removed outlier: 3.699A  pdb=" N   ILE A  85 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.626A  pdb=" N   ALA A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 136 through 140
      removed outlier: 3.503A  pdb=" N   TYR A 140 " --> pdb=" O   HIS A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 169
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 3.907A  pdb=" N   GLY A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
      removed outlier: 3.522A  pdb=" N   ASN A 225 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 222 through 225'
    Processing helix  chain 'A' and resid 254 through 268
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.527A  pdb=" N   ASN A 287 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 335
      removed outlier: 3.581A  pdb=" N   SER A 321 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU A 335 " --> pdb=" O   MET A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 26
    Processing helix  chain 'B' and resid 39 through 49
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.699A  pdb=" N   ILE B  85 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
      removed outlier: 3.626A  pdb=" N   ALA B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 109
    Processing helix  chain 'B' and resid 110 through 113
    Processing helix  chain 'B' and resid 136 through 140
      removed outlier: 3.503A  pdb=" N   TYR B 140 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 169
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 195 through 200
    Processing helix  chain 'B' and resid 212 through 221
      removed outlier: 3.907A  pdb=" N   GLY B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
      removed outlier: 3.522A  pdb=" N   ASN B 225 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 222 through 225'
    Processing helix  chain 'B' and resid 254 through 268
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.527A  pdb=" N   ASN B 287 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 335
      removed outlier: 3.581A  pdb=" N   SER B 321 " --> pdb=" O   GLU B 317 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU B 335 " --> pdb=" O   MET B 331 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 26
    Processing helix  chain 'C' and resid 39 through 49
    Processing helix  chain 'C' and resid 81 through 85
      removed outlier: 3.700A  pdb=" N   ILE C  85 " --> pdb=" O   PRO C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 91
      removed outlier: 3.626A  pdb=" N   ALA C  90 " --> pdb=" O   LYS C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 110 through 113
    Processing helix  chain 'C' and resid 136 through 140
      removed outlier: 3.503A  pdb=" N   TYR C 140 " --> pdb=" O   HIS C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 169
      Proline residue:  C 159  - end of helix
    Processing helix  chain 'C' and resid 195 through 200
    Processing helix  chain 'C' and resid 212 through 221
      removed outlier: 3.907A  pdb=" N   GLY C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS C 219 " --> pdb=" O   LYS C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
      removed outlier: 3.522A  pdb=" N   ASN C 225 " --> pdb=" O   PRO C 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 222 through 225'
    Processing helix  chain 'C' and resid 254 through 268
    Processing helix  chain 'C' and resid 282 through 287
      removed outlier: 3.527A  pdb=" N   ASN C 287 " --> pdb=" O   SER C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 317 through 335
      removed outlier: 3.581A  pdb=" N   SER C 321 " --> pdb=" O   GLU C 317 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLU C 335 " --> pdb=" O   MET C 331 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 26
    Processing helix  chain 'D' and resid 39 through 49
    Processing helix  chain 'D' and resid 81 through 85
      removed outlier: 3.699A  pdb=" N   ILE D  85 " --> pdb=" O   PRO D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 91
      removed outlier: 3.626A  pdb=" N   ALA D  90 " --> pdb=" O   LYS D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 109
    Processing helix  chain 'D' and resid 110 through 113
    Processing helix  chain 'D' and resid 136 through 140
      removed outlier: 3.503A  pdb=" N   TYR D 140 " --> pdb=" O   HIS D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 169
      Proline residue:  D 159  - end of helix
    Processing helix  chain 'D' and resid 195 through 200
    Processing helix  chain 'D' and resid 212 through 221
      removed outlier: 3.907A  pdb=" N   GLY D 218 " --> pdb=" O   ALA D 214 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS D 219 " --> pdb=" O   LYS D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
      removed outlier: 3.522A  pdb=" N   ASN D 225 " --> pdb=" O   PRO D 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 222 through 225'
    Processing helix  chain 'D' and resid 254 through 268
    Processing helix  chain 'D' and resid 282 through 287
      removed outlier: 3.527A  pdb=" N   ASN D 287 " --> pdb=" O   SER D 284 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 317 through 335
      removed outlier: 3.581A  pdb=" N   SER D 321 " --> pdb=" O   GLU D 317 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU D 335 " --> pdb=" O   MET D 331 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63
      removed outlier: 10.200A  pdb=" N   ASP A  29 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 10.002A  pdb=" N   THR A  75 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   VAL A  31 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   PHE A  77 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ILE A  33 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   VAL A   8 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ILE A  33 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL A  95 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 210
      removed outlier: 3.715A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 12.281A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 11.086A  pdb=" N   GLY A 300 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
      removed outlier: 10.882A  pdb=" N   LYS A 309 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 8.818A  pdb=" N   GLY A 298 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   ILE A 311 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63
      removed outlier: 10.200A  pdb=" N   ASP B  29 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 10.003A  pdb=" N   THR B  75 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   VAL B  31 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   PHE B  77 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ILE B  33 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   VAL B   8 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ILE B  33 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL B  95 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 207 through 210
      removed outlier: 3.715A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLU B 172 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 12.281A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 11.086A  pdb=" N   GLY B 300 " --> pdb=" O   PHE B 307 " (cutoff:3.500A)
      removed outlier: 10.882A  pdb=" N   LYS B 309 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 8.818A  pdb=" N   GLY B 298 " --> pdb=" O   LYS B 309 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   ILE B 311 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 63
      removed outlier: 10.200A  pdb=" N   ASP C  29 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 10.003A  pdb=" N   THR C  75 " --> pdb=" O   ASP C  29 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   VAL C  31 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   PHE C  77 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ILE C  33 " --> pdb=" O   PHE C  77 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   VAL C   8 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ILE C  33 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL C  95 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 210
      removed outlier: 3.715A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLU C 172 " --> pdb=" O   ARG C 248 " (cutoff:3.500A)
      removed outlier: 12.281A  pdb=" N   PHE C 307 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      removed outlier: 11.085A  pdb=" N   GLY C 300 " --> pdb=" O   PHE C 307 " (cutoff:3.500A)
      removed outlier: 10.882A  pdb=" N   LYS C 309 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
      removed outlier: 8.818A  pdb=" N   GLY C 298 " --> pdb=" O   LYS C 309 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   ILE C 311 " --> pdb=" O   ASP C 296 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63
      removed outlier: 10.200A  pdb=" N   ASP D  29 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      removed outlier: 10.002A  pdb=" N   THR D  75 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   VAL D  31 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   PHE D  77 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ILE D  33 " --> pdb=" O   PHE D  77 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   VAL D   8 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ILE D  33 " --> pdb=" O   VAL D   8 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL D  95 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 207 through 210
      removed outlier: 3.715A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLU D 172 " --> pdb=" O   ARG D 248 " (cutoff:3.500A)
      removed outlier: 12.281A  pdb=" N   PHE D 307 " --> pdb=" O   GLY D 300 " (cutoff:3.500A)
      removed outlier: 11.086A  pdb=" N   GLY D 300 " --> pdb=" O   PHE D 307 " (cutoff:3.500A)
      removed outlier: 10.882A  pdb=" N   LYS D 309 " --> pdb=" O   GLY D 298 " (cutoff:3.500A)
      removed outlier: 8.818A  pdb=" N   GLY D 298 " --> pdb=" O   LYS D 309 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   ILE D 311 " --> pdb=" O   ASP D 296 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1248 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: 3.12

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3000
        1.34 -     1.45: 1534
        1.45 -     1.57: 5602
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 10220
  Sorted by residual:
  bond pdb=" N   ILE D 207 "
       pdb=" CA  ILE D 207 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 9.10e-03 1.21e+04 1.36e+01
  bond pdb=" N   ILE C 207 "
       pdb=" CA  ILE C 207 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 9.10e-03 1.21e+04 1.30e+01
  bond pdb=" N   ILE A 207 "
       pdb=" CA  ILE A 207 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 9.10e-03 1.21e+04 1.26e+01
  bond pdb=" N   ILE B 207 "
       pdb=" CA  ILE B 207 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 9.10e-03 1.21e+04 1.26e+01
  bond pdb=" N   ASN B 205 "
       pdb=" CA  ASN B 205 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.27e-02 6.20e+03 7.49e+00
  ... (remaining 10215 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 13180
        1.42 -     2.84: 539
        2.84 -     4.26: 97
        4.26 -     5.68: 27
        5.68 -     7.10: 17
  Bond angle restraints: 13860
  Sorted by residual:
  angle pdb=" C   ILE A 206 "
        pdb=" N   ILE A 207 "
        pdb=" CA  ILE A 207 "
      ideal   model   delta    sigma   weight residual
     123.02  118.09    4.93 1.04e+00 9.25e-01 2.24e+01
  angle pdb=" C   ILE C 206 "
        pdb=" N   ILE C 207 "
        pdb=" CA  ILE C 207 "
      ideal   model   delta    sigma   weight residual
     123.02  118.11    4.91 1.04e+00 9.25e-01 2.23e+01
  angle pdb=" C   ILE B 206 "
        pdb=" N   ILE B 207 "
        pdb=" CA  ILE B 207 "
      ideal   model   delta    sigma   weight residual
     123.02  118.11    4.91 1.04e+00 9.25e-01 2.23e+01
  angle pdb=" C   ILE D 206 "
        pdb=" N   ILE D 207 "
        pdb=" CA  ILE D 207 "
      ideal   model   delta    sigma   weight residual
     123.02  118.12    4.90 1.04e+00 9.25e-01 2.22e+01
  angle pdb=" N   ASN A 239 "
        pdb=" CA  ASN A 239 "
        pdb=" C   ASN A 239 "
      ideal   model   delta    sigma   weight residual
     110.80  117.80   -7.00 2.13e+00 2.20e-01 1.08e+01
  ... (remaining 13855 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 5336
       17.41 -    34.81: 508
       34.81 -    52.22: 160
       52.22 -    69.63: 24
       69.63 -    87.03: 12
  Dihedral angle restraints: 6040
    sinusoidal: 2264
      harmonic: 3776
  Sorted by residual:
  dihedral pdb=" CA  ALA A 238 "
           pdb=" C   ALA A 238 "
           pdb=" N   ASN A 239 "
           pdb=" CA  ASN A 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.42  -17.58     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  ALA B 238 "
           pdb=" C   ALA B 238 "
           pdb=" N   ASN B 239 "
           pdb=" CA  ASN B 239 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.46  -17.54     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  ALA D 238 "
           pdb=" C   ALA D 238 "
           pdb=" N   ASN D 239 "
           pdb=" CA  ASN D 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.46  -17.54     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 6037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1165
       0.054 -    0.107: 299
       0.107 -    0.161: 112
       0.161 -    0.215: 0
       0.215 -    0.268: 4
  Chirality restraints: 1580
  Sorted by residual:
  chirality pdb=" CA  ILE B 206 "
            pdb=" N   ILE B 206 "
            pdb=" C   ILE B 206 "
            pdb=" CB  ILE B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  ILE D 206 "
            pdb=" N   ILE D 206 "
            pdb=" C   ILE D 206 "
            pdb=" CB  ILE D 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  ILE A 206 "
            pdb=" N   ILE A 206 "
            pdb=" C   ILE A 206 "
            pdb=" CB  ILE A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 1577 not shown)

  Planarity restraints: 1800
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C 244 "    0.010 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" CG  ASP C 244 "   -0.036 2.00e-02 2.50e+03
        pdb=" OD1 ASP C 244 "    0.014 2.00e-02 2.50e+03
        pdb=" OD2 ASP C 244 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 244 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" CG  ASP A 244 "    0.036 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 244 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 244 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D 244 "    0.010 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" CG  ASP D 244 "   -0.036 2.00e-02 2.50e+03
        pdb=" OD1 ASP D 244 "    0.014 2.00e-02 2.50e+03
        pdb=" OD2 ASP D 244 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1797 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 3779
        2.90 -     3.40: 8808
        3.40 -     3.90: 16490
        3.90 -     4.40: 19454
        4.40 -     4.90: 33052
  Nonbonded interactions: 81583
  Sorted by model distance:
  nonbonded pdb=" N   ASP B 127 "
            pdb=" OD1 ASP B 127 "
     model   vdw
     2.404 3.120
  nonbonded pdb=" N   ASP C 127 "
            pdb=" OD1 ASP C 127 "
     model   vdw
     2.404 3.120
  nonbonded pdb=" N   ASP D 127 "
            pdb=" OD1 ASP D 127 "
     model   vdw
     2.404 3.120
  nonbonded pdb=" N   ASP A 127 "
            pdb=" OD1 ASP A 127 "
     model   vdw
     2.405 3.120
  nonbonded pdb=" OE2 GLU D  97 "
            pdb=" OG1 THR D  99 "
     model   vdw
     2.409 3.040
  ... (remaining 81578 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.650
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.800
  Find NCS groups from input model:        0.190
  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:16.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9165
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      :  0.005   0.040  10220  Z= 0.240
  Angle     :  0.720   7.100  13860  Z= 0.430
  Chirality :  0.056   0.268   1580
  Planarity :  0.006   0.050   1800
  Dihedral  : 15.717  87.035   3632
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 15.75 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.22), residues: 1328
  helix: -0.88 (0.23), residues: 360
  sheet: -0.03 (0.38), residues: 220
  loop : -0.68 (0.22), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  87 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.009   0.001   PHE D 295 
 TYR   0.017   0.002   TYR B 314 
 ARG   0.006   0.001   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18595 (  464)
  hydrogen bonds       : angle       7.62549 ( 1248)
  covalent geometry    : bond        0.00452 (10220)
  covalent geometry    : angle       0.72031 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 1.029 
Fit side-chains
  outliers start: 12
  outliers final: 16
  residues processed: 88
  average time/residue: 1.7073
  time to fit residues: 159.9296
Evaluate side-chains
  80 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  266 SER
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain C residue  335 GLU
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain D residue  266 SER
Chi-restraints excluded: chain D residue  335 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 62 optimal weight:    0.1980
   chunk 77 optimal weight:    6.9990
   chunk 119 optimal weight:    7.9990
   overall best weight:    2.8186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.061577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.048368 restraints weight = 19229.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.2576 rms_B_bonded: 2.37
r_work: 0.2442 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2319 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9217
moved from start:          0.0863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10220  Z= 0.187
  Angle     :  0.537   7.787  13860  Z= 0.301
  Chirality :  0.049   0.174   1580
  Planarity :  0.005   0.051   1800
  Dihedral  :  7.596 103.433   1436
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.09 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.24), residues: 1328
  helix:  0.91 (0.27), residues: 368
  sheet: -0.11 (0.35), residues: 276
  loop : -0.24 (0.25), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 313 
 HIS   0.003   0.001   HIS D  53 
 PHE   0.008   0.001   PHE D 286 
 TYR   0.012   0.001   TYR A 314 
 ARG   0.003   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04962 (  464)
  hydrogen bonds       : angle       5.94829 ( 1248)
  covalent geometry    : bond        0.00443 (10220)
  covalent geometry    : angle       0.53685 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 1.178 
Fit side-chains
  outliers start: 16
  outliers final: 4
  residues processed: 68
  average time/residue: 1.4349
  time to fit residues: 104.7821
Evaluate side-chains
  60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain D residue  244 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 116 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 101 optimal weight:    0.0020
   chunk 12 optimal weight:    0.3980
   chunk 89 optimal weight:    0.7980
   chunk 74 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.6390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.065508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.052397 restraints weight = 19334.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2670 rms_B_bonded: 2.41
r_work: 0.2545 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2427 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9141
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015  10220  Z= 0.078
  Angle     :  0.427   5.293  13860  Z= 0.237
  Chirality :  0.045   0.134   1580
  Planarity :  0.004   0.040   1800
  Dihedral  :  7.319 115.011   1416
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 15.57 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.24), residues: 1328
  helix:  1.39 (0.28), residues: 372
  sheet: -0.28 (0.33), residues: 288
  loop : -0.08 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 313 
 HIS   0.001   0.000   HIS C  53 
 PHE   0.004   0.001   PHE C 295 
 TYR   0.006   0.001   TYR A 314 
 ARG   0.001   0.000   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03064 (  464)
  hydrogen bonds       : angle       5.34101 ( 1248)
  covalent geometry    : bond        0.00161 (10220)
  covalent geometry    : angle       0.42680 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 1.020 
Fit side-chains
REVERT: A  318 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8662 (m-80)
REVERT: B  318 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8660 (m-80)
REVERT: D  318 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8663 (m-80)
  outliers start: 7
  outliers final: 0
  residues processed: 71
  average time/residue: 1.2690
  time to fit residues: 97.4264
Evaluate side-chains
  67 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 108 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 43 optimal weight:    0.3980
   chunk 126 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 131 optimal weight:    0.9990
   overall best weight:    2.4788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.062189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.048531 restraints weight = 19411.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2577 rms_B_bonded: 2.44
r_work: 0.2440 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2318 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9152
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  10220  Z= 0.161
  Angle     :  0.498   6.892  13860  Z= 0.277
  Chirality :  0.048   0.147   1580
  Planarity :  0.004   0.045   1800
  Dihedral  :  4.267  16.587   1408
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 0.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 15.47 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.24), residues: 1328
  helix:  1.54 (0.28), residues: 368
  sheet: -0.09 (0.33), residues: 276
  loop : -0.07 (0.25), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 313 
 HIS   0.003   0.000   HIS C  53 
 PHE   0.008   0.001   PHE A 286 
 TYR   0.012   0.001   TYR A 314 
 ARG   0.002   0.000   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  464)
  hydrogen bonds       : angle       5.43132 ( 1248)
  covalent geometry    : bond        0.00381 (10220)
  covalent geometry    : angle       0.49751 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 1.039 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8945 (mmmm)
REVERT: B   86 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8947 (mmmm)
REVERT: C   86 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8948 (mmmm)
REVERT: D   86 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8947 (mmmm)
  outliers start: 12
  outliers final: 0
  residues processed: 72
  average time/residue: 1.4166
  time to fit residues: 109.7852
Evaluate side-chains
  64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain D residue   86 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 36 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 96 optimal weight:    0.0980
   chunk 58 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 116 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 107 optimal weight:    9.9990
   overall best weight:    1.7584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.063044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.049477 restraints weight = 19302.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.2595 rms_B_bonded: 2.43
r_work: 0.2460 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2339 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9139
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  10220  Z= 0.123
  Angle     :  0.469   6.470  13860  Z= 0.261
  Chirality :  0.047   0.141   1580
  Planarity :  0.004   0.045   1800
  Dihedral  :  4.203  17.643   1408
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 0.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 16.60 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.24), residues: 1328
  helix:  1.59 (0.27), residues: 372
  sheet: -0.06 (0.32), residues: 276
  loop : -0.13 (0.26), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 313 
 HIS   0.002   0.000   HIS D  53 
 PHE   0.006   0.001   PHE C 295 
 TYR   0.010   0.001   TYR D 314 
 ARG   0.001   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03858 (  464)
  hydrogen bonds       : angle       5.29041 ( 1248)
  covalent geometry    : bond        0.00286 (10220)
  covalent geometry    : angle       0.46863 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 1.318 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8946 (mmmm)
REVERT: B   86 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8949 (mmmm)
REVERT: C   86 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8948 (mmmm)
REVERT: D   86 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8948 (mmmm)
  outliers start: 4
  outliers final: 0
  residues processed: 64
  average time/residue: 1.7132
  time to fit residues: 118.0996
Evaluate side-chains
  64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain D residue   86 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 100 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 120 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 108 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 118 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   overall best weight:    2.3588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.062104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.048387 restraints weight = 19408.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.2572 rms_B_bonded: 2.44
r_work: 0.2435 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2314 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9153
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023  10220  Z= 0.155
  Angle     :  0.492   6.912  13860  Z= 0.274
  Chirality :  0.048   0.146   1580
  Planarity :  0.004   0.046   1800
  Dihedral  :  4.296  16.757   1408
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 0.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 16.23 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.24), residues: 1328
  helix:  1.60 (0.27), residues: 368
  sheet: -0.05 (0.33), residues: 276
  loop : -0.09 (0.26), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 313 
 HIS   0.002   0.001   HIS D  53 
 PHE   0.007   0.001   PHE A 286 
 TYR   0.012   0.001   TYR C 314 
 ARG   0.002   0.000   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04284 (  464)
  hydrogen bonds       : angle       5.37357 ( 1248)
  covalent geometry    : bond        0.00367 (10220)
  covalent geometry    : angle       0.49194 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 1.065 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8944 (mmmm)
REVERT: B   86 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8948 (mmmm)
REVERT: C   86 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8950 (mmmm)
REVERT: D   86 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8948 (mmmm)
  outliers start: 12
  outliers final: 0
  residues processed: 72
  average time/residue: 1.5759
  time to fit residues: 122.1332
Evaluate side-chains
  64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain D residue   86 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 51 optimal weight:    0.5980
   chunk 105 optimal weight:    8.9990
   chunk 126 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   overall best weight:    2.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.062342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.048646 restraints weight = 19622.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.2578 rms_B_bonded: 2.46
r_work: 0.2441 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2320 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9147
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10220  Z= 0.141
  Angle     :  0.482   6.788  13860  Z= 0.268
  Chirality :  0.048   0.144   1580
  Planarity :  0.004   0.045   1800
  Dihedral  :  4.271  17.400   1408
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 0.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 16.60 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.24), residues: 1328
  helix:  1.66 (0.27), residues: 372
  sheet:  0.00 (0.33), residues: 276
  loop : -0.10 (0.26), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 313 
 HIS   0.002   0.000   HIS A  53 
 PHE   0.007   0.001   PHE C 295 
 TYR   0.011   0.001   TYR A 314 
 ARG   0.001   0.000   ARG C 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04109 (  464)
  hydrogen bonds       : angle       5.32430 ( 1248)
  covalent geometry    : bond        0.00334 (10220)
  covalent geometry    : angle       0.48221 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 1.051 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8944 (mmmm)
REVERT: B   86 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8946 (mmmm)
REVERT: C   86 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8948 (mmmm)
REVERT: D   86 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8946 (mmmm)
  outliers start: 8
  outliers final: 0
  residues processed: 68
  average time/residue: 1.4987
  time to fit residues: 109.3581
Evaluate side-chains
  64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain D residue   86 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 81 optimal weight:    0.4980
   chunk 110 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.8386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.062782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.049149 restraints weight = 19440.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.2586 rms_B_bonded: 2.44
r_work: 0.2450 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2329 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9143
moved from start:          0.1111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  10220  Z= 0.127
  Angle     :  0.471   6.480  13860  Z= 0.262
  Chirality :  0.047   0.143   1580
  Planarity :  0.004   0.045   1800
  Dihedral  :  4.226  17.146   1408
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 0.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 16.70 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.24), residues: 1328
  helix:  1.74 (0.27), residues: 372
  sheet:  0.07 (0.33), residues: 276
  loop : -0.10 (0.26), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 313 
 HIS   0.002   0.000   HIS B  53 
 PHE   0.006   0.001   PHE C 295 
 TYR   0.011   0.001   TYR A 314 
 ARG   0.001   0.000   ARG C 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  464)
  hydrogen bonds       : angle       5.26112 ( 1248)
  covalent geometry    : bond        0.00296 (10220)
  covalent geometry    : angle       0.47149 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 1.156 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8951 (mmmm)
REVERT: B   86 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8954 (mmmm)
REVERT: C   86 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8955 (mmmm)
REVERT: D   86 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8953 (mmmm)
  outliers start: 8
  outliers final: 4
  residues processed: 68
  average time/residue: 1.4327
  time to fit residues: 104.5849
Evaluate side-chains
  68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue   86 LYS
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 118 optimal weight:    0.4980
   chunk 38 optimal weight:    9.9990
   chunk 13 optimal weight:    0.5980
   chunk 87 optimal weight:    4.9990
   chunk 119 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   overall best weight:    1.1582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.063973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.050386 restraints weight = 19312.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.2616 rms_B_bonded: 2.46
r_work: 0.2482 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2363 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9119
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  10220  Z= 0.093
  Angle     :  0.442   5.831  13860  Z= 0.245
  Chirality :  0.046   0.141   1580
  Planarity :  0.003   0.043   1800
  Dihedral  :  4.075  17.562   1408
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 17.36 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.24), residues: 1328
  helix:  1.89 (0.27), residues: 372
  sheet: -0.07 (0.32), residues: 288
  loop : -0.02 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 313 
 HIS   0.001   0.000   HIS B  53 
 PHE   0.006   0.001   PHE C 295 
 TYR   0.009   0.001   TYR B 314 
 ARG   0.001   0.000   ARG D 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03330 (  464)
  hydrogen bonds       : angle       5.10088 ( 1248)
  covalent geometry    : bond        0.00208 (10220)
  covalent geometry    : angle       0.44173 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 1.130 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8941 (mmmm)
REVERT: B   86 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8946 (mmmm)
REVERT: C   86 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8945 (mmmm)
REVERT: D   86 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8944 (mmmm)
  outliers start: 4
  outliers final: 0
  residues processed: 64
  average time/residue: 1.4670
  time to fit residues: 100.6384
Evaluate side-chains
  64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain D residue   86 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 127 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 120 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 123 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.063351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.049760 restraints weight = 19352.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.2601 rms_B_bonded: 2.45
r_work: 0.2466 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2346 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9131
moved from start:          0.1163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018  10220  Z= 0.111
  Angle     :  0.456   6.134  13860  Z= 0.253
  Chirality :  0.047   0.142   1580
  Planarity :  0.003   0.044   1800
  Dihedral  :  4.119  16.854   1408
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 16.98 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.24), residues: 1328
  helix:  1.88 (0.27), residues: 372
  sheet:  0.20 (0.33), residues: 276
  loop : -0.06 (0.26), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 313 
 HIS   0.002   0.000   HIS D  53 
 PHE   0.006   0.001   PHE D 295 
 TYR   0.010   0.001   TYR A 314 
 ARG   0.001   0.000   ARG C 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03602 (  464)
  hydrogen bonds       : angle       5.14193 ( 1248)
  covalent geometry    : bond        0.00256 (10220)
  covalent geometry    : angle       0.45612 (13860)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 1.073 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8949 (mmmm)
REVERT: B   86 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8952 (mmmm)
REVERT: C   86 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8949 (mmmm)
REVERT: D   86 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8950 (mmmm)
  outliers start: 8
  outliers final: 4
  residues processed: 68
  average time/residue: 1.4748
  time to fit residues: 107.6698
Evaluate side-chains
  68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LYS
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue   86 LYS
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0570
   chunk 67 optimal weight:    7.9990
   chunk 127 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 125 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 129 optimal weight:    4.9990
   chunk 88 optimal weight:    7.9990
   overall best weight:    2.1904

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.062427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.048807 restraints weight = 19411.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.2579 rms_B_bonded: 2.44
r_work: 0.2442 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2321 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9148
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10220  Z= 0.145
  Angle     :  0.485   6.773  13860  Z= 0.269
  Chirality :  0.048   0.143   1580
  Planarity :  0.004   0.046   1800
  Dihedral  :  4.242  16.757   1408
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 0.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 16.98 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.24), residues: 1328
  helix:  1.80 (0.27), residues: 372
  sheet:  0.21 (0.33), residues: 276
  loop : -0.08 (0.26), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 313 
 HIS   0.002   0.000   HIS A  53 
 PHE   0.007   0.001   PHE A 295 
 TYR   0.011   0.001   TYR A 314 
 ARG   0.001   0.000   ARG C 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04115 (  464)
  hydrogen bonds       : angle       5.27203 ( 1248)
  covalent geometry    : bond        0.00344 (10220)
  covalent geometry    : angle       0.48462 (13860)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6545.57 seconds
wall clock time: 114 minutes 24.05 seconds (6864.05 seconds total)