Starting phenix.real_space_refine
on Sat Aug 23 05:01:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g14_29661/08_2025/8g14_29661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g14_29661/08_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_29661/08_2025/8g14_29661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g14_29661/08_2025/8g14_29661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g14_29661/08_2025/8g14_29661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g14_29661/08_2025/8g14_29661.cif"
  }
  resolution = 2.3
  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=   0.001
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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:
    B, C, D
  Time building chain proxies: 1.49, per 1000 atoms: 0.15
  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: 0.59
  Conformation dependent library (CDL) restraints added in 251.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.26
  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: 1.09

  Time building geometry restraints manager: 0.77 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.540
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.480
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.006   0.001   ARG C 234 
 TYR   0.017   0.002   TYR B 314 
 PHE   0.009   0.001   PHE D 295 
 TRP   0.007   0.001   TRP B  87 
 HIS   0.003   0.001   HIS A  53 

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

*********************** 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  : 0.226 
Fit side-chains
  outliers start: 12
  outliers final: 16
  residues processed: 88
  average time/residue: 0.6173
  time to fit residues: 57.8941
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  : 0.433 
-------------------------------------------------------------------------------
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 98 optimal weight:    3.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.2875 r_free = 0.2875 target = 0.061190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.047906 restraints weight = 19341.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2565 rms_B_bonded: 2.40
r_work: 0.2431 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2308 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9224
moved from start:          0.0889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  10220  Z= 0.207
  Angle     :  0.554   8.149  13860  Z= 0.311
  Chirality :  0.050   0.184   1580
  Planarity :  0.005   0.052   1800
  Dihedral  :  7.601 102.403   1436
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 1.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.91 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.24), residues: 1328
  helix:  0.87 (0.27), residues: 368
  sheet: -0.15 (0.35), residues: 276
  loop : -0.25 (0.25), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 197 
 TYR   0.013   0.001   TYR C 314 
 PHE   0.009   0.001   PHE C 286 
 TRP   0.006   0.001   TRP A 313 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 (10220)
  covalent geometry    : angle       0.55430 (13860)
  hydrogen bonds       : bond        0.05243 (  464)
  hydrogen bonds       : angle       5.98664 ( 1248)

*********************** 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  : 0.312 
Fit side-chains
  outliers start: 16
  outliers final: 4
  residues processed: 68
  average time/residue: 0.6338
  time to fit residues: 45.8901
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  : 0.238 
-------------------------------------------------------------------------------
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 104 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 113 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0970
   chunk 77 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   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 = 0.2926 r_free = 0.2926 target = 0.063879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.050618 restraints weight = 19374.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.2625 rms_B_bonded: 2.43
r_work: 0.2496 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2377 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9174
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      :  0.002   0.015  10220  Z= 0.096
  Angle     :  0.452   6.076  13860  Z= 0.252
  Chirality :  0.046   0.136   1580
  Planarity :  0.004   0.042   1800
  Dihedral  :  7.408 114.923   1416
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 15.47 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.24), residues: 1328
  helix:  1.37 (0.27), residues: 372
  sheet: -0.30 (0.33), residues: 288
  loop : -0.11 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 197 
 TYR   0.009   0.001   TYR B 314 
 PHE   0.005   0.001   PHE B 295 
 TRP   0.005   0.001   TRP D 313 
 HIS   0.002   0.000   HIS D  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (10220)
  covalent geometry    : angle       0.45217 (13860)
  hydrogen bonds       : bond        0.03547 (  464)
  hydrogen bonds       : angle       5.51238 ( 1248)

*********************** 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
  64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.421 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 64
  average time/residue: 0.6225
  time to fit residues: 42.8958
Evaluate side-chains
  60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 126 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 61 optimal weight:    0.0980
   chunk 81 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0030
   chunk 131 optimal weight:    2.9990
   overall best weight:    1.0192

-------------------------------------------------------------------------------
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 = 0.2929 r_free = 0.2929 target = 0.064071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.050855 restraints weight = 19382.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.2632 rms_B_bonded: 2.42
r_work: 0.2505 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2387 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9167
moved from start:          0.1142

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= 0.089
  Angle     :  0.443   5.855  13860  Z= 0.246
  Chirality :  0.046   0.138   1580
  Planarity :  0.004   0.044   1800
  Dihedral  :  4.059  18.009   1408
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 15.47 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.25), residues: 1328
  helix:  1.58 (0.28), residues: 372
  sheet: -0.27 (0.32), residues: 288
  loop : -0.02 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 234 
 TYR   0.008   0.001   TYR D 314 
 PHE   0.005   0.001   PHE C 295 
 TRP   0.005   0.001   TRP C 313 
 HIS   0.001   0.000   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 (10220)
  covalent geometry    : angle       0.44291 (13860)
  hydrogen bonds       : bond        0.03299 (  464)
  hydrogen bonds       : angle       5.19799 ( 1248)

*********************** 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
  68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A   86 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8956 (mmmm)
REVERT: B   86 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8940 (mmmm)
REVERT: C   86 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8946 (mmmm)
REVERT: D   86 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8948 (mmmm)
  outliers start: 8
  outliers final: 0
  residues processed: 68
  average time/residue: 0.7391
  time to fit residues: 53.7007
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  : 0.506 
-------------------------------------------------------------------------------
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 120 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 126 optimal weight:    0.3980
   chunk 54 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    2.6788

-------------------------------------------------------------------------------
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 = 0.2878 r_free = 0.2878 target = 0.061823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.048203 restraints weight = 19484.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.2564 rms_B_bonded: 2.42
r_work: 0.2428 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2308 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9157
moved from start:          0.1043

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= 0.173
  Angle     :  0.511   7.326  13860  Z= 0.284
  Chirality :  0.049   0.157   1580
  Planarity :  0.004   0.046   1800
  Dihedral  :  4.332  16.483   1408
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 0.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.24), residues: 1328
  helix:  1.52 (0.28), residues: 368
  sheet: -0.05 (0.33), residues: 276
  loop : -0.10 (0.25), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  16 
 TYR   0.012   0.001   TYR A 314 
 PHE   0.008   0.001   PHE A 286 
 TRP   0.005   0.001   TRP A 313 
 HIS   0.002   0.001   HIS D  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (10220)
  covalent geometry    : angle       0.51079 (13860)
  hydrogen bonds       : bond        0.04536 (  464)
  hydrogen bonds       : angle       5.47770 ( 1248)

*********************** 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
  60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.440 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.7272
  time to fit residues: 46.7302
Evaluate side-chains
  60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 90 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 125 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 101 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.2869 r_free = 0.2869 target = 0.061416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.047707 restraints weight = 19593.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.2554 rms_B_bonded: 2.44
r_work: 0.2416 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2294 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9164
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      :  0.005   0.026  10220  Z= 0.190
  Angle     :  0.522   7.502  13860  Z= 0.290
  Chirality :  0.049   0.162   1580
  Planarity :  0.004   0.047   1800
  Dihedral  :  4.404  16.586   1408
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 0.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.24), residues: 1328
  helix:  1.55 (0.27), residues: 368
  sheet:  0.01 (0.33), residues: 276
  loop : -0.12 (0.26), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 200 
 TYR   0.013   0.001   TYR D 314 
 PHE   0.008   0.001   PHE B 286 
 TRP   0.005   0.001   TRP B 313 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (10220)
  covalent geometry    : angle       0.52232 (13860)
  hydrogen bonds       : bond        0.04715 (  464)
  hydrogen bonds       : angle       5.47683 ( 1248)

*********************** 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
  68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.427 
Fit side-chains
  outliers start: 8
  outliers final: 0
  residues processed: 68
  average time/residue: 0.6600
  time to fit residues: 48.2994
Evaluate side-chains
  60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 52 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 120 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.2894 r_free = 0.2894 target = 0.062666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.049079 restraints weight = 19396.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.2584 rms_B_bonded: 2.43
r_work: 0.2447 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2327 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9144
moved from start:          0.1086

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= 0.125
  Angle     :  0.475   6.651  13860  Z= 0.264
  Chirality :  0.047   0.145   1580
  Planarity :  0.004   0.045   1800
  Dihedral  :  4.260  17.522   1408
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 0.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 16.79 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.24), residues: 1328
  helix:  1.67 (0.27), residues: 372
  sheet:  0.08 (0.33), residues: 276
  loop : -0.11 (0.26), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 197 
 TYR   0.010   0.001   TYR D 314 
 PHE   0.007   0.001   PHE B 295 
 TRP   0.005   0.001   TRP D 313 
 HIS   0.002   0.000   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10220)
  covalent geometry    : angle       0.47508 (13860)
  hydrogen bonds       : bond        0.03955 (  464)
  hydrogen bonds       : angle       5.29897 ( 1248)

*********************** 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
  66 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.448 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 62
  average time/residue: 0.7290
  time to fit residues: 48.4591
Evaluate side-chains
  62 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 51 optimal weight:    0.0060
   chunk 4 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0170
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   chunk 22 optimal weight:    0.2980
   chunk 33 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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 = 0.2948 r_free = 0.2948 target = 0.065296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.051803 restraints weight = 19274.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.2647 rms_B_bonded: 2.46
r_work: 0.2516 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2397 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9113
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014  10220  Z= 0.074
  Angle     :  0.422   5.292  13860  Z= 0.233
  Chirality :  0.045   0.140   1580
  Planarity :  0.003   0.041   1800
  Dihedral  :  3.962  17.872   1408
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 17.17 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.25), residues: 1328
  helix:  1.92 (0.27), residues: 372
  sheet: -0.04 (0.32), residues: 288
  loop :  0.03 (0.27), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 234 
 TYR   0.006   0.001   TYR C 314 
 PHE   0.004   0.001   PHE C 295 
 TRP   0.005   0.001   TRP B 313 
 HIS   0.001   0.000   HIS C 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00155 (10220)
  covalent geometry    : angle       0.42245 (13860)
  hydrogen bonds       : bond        0.02863 (  464)
  hydrogen bonds       : angle       4.98555 ( 1248)

*********************** 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
  66 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.433 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 66
  average time/residue: 0.6778
  time to fit residues: 48.0756
Evaluate side-chains
  66 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue  243 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 22 optimal weight:    0.0570
   chunk 6 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.9100

-------------------------------------------------------------------------------
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 = 0.2939 r_free = 0.2939 target = 0.064772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.051250 restraints weight = 19267.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.2638 rms_B_bonded: 2.46
r_work: 0.2505 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2385 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9105
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014  10220  Z= 0.083
  Angle     :  0.429   5.592  13860  Z= 0.237
  Chirality :  0.046   0.139   1580
  Planarity :  0.003   0.041   1800
  Dihedral  :  3.951  16.848   1408
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 1.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 17.17 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.25), residues: 1328
  helix:  1.97 (0.27), residues: 372
  sheet:  0.06 (0.33), residues: 288
  loop :  0.06 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 197 
 TYR   0.008   0.001   TYR B 314 
 PHE   0.005   0.001   PHE A 295 
 TRP   0.004   0.001   TRP B 313 
 HIS   0.001   0.000   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00181 (10220)
  covalent geometry    : angle       0.42925 (13860)
  hydrogen bonds       : bond        0.03049 (  464)
  hydrogen bonds       : angle       4.95872 ( 1248)

*********************** 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
  70 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.427 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 70
  average time/residue: 0.6954
  time to fit residues: 52.1312
Evaluate side-chains
  66 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue  243 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 67 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 131 optimal weight:    1.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.2882 r_free = 0.2882 target = 0.062042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.048411 restraints weight = 19311.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.2568 rms_B_bonded: 2.43
r_work: 0.2431 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2310 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9156
moved from start:          0.1100

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= 0.167
  Angle     :  0.503   7.181  13860  Z= 0.278
  Chirality :  0.049   0.151   1580
  Planarity :  0.004   0.047   1800
  Dihedral  :  4.289  16.344   1408
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 0.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 17.17 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.24), residues: 1328
  helix:  1.84 (0.27), residues: 368
  sheet:  0.22 (0.33), residues: 276
  loop : -0.03 (0.26), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  16 
 TYR   0.012   0.001   TYR D 314 
 PHE   0.008   0.001   PHE B  23 
 TRP   0.005   0.001   TRP D 313 
 HIS   0.002   0.001   HIS D  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (10220)
  covalent geometry    : angle       0.50265 (13860)
  hydrogen bonds       : bond        0.04386 (  464)
  hydrogen bonds       : angle       5.32072 ( 1248)

********************** 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
  62 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.416 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 62
  average time/residue: 0.6997
  time to fit residues: 46.5680
Evaluate side-chains
  62 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue  243 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   chunk 101 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.2906 r_free = 0.2906 target = 0.063219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.049643 restraints weight = 19359.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.2597 rms_B_bonded: 2.45
r_work: 0.2462 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2343 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9133
moved from start:          0.1138

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= 0.113
  Angle     :  0.460   6.258  13860  Z= 0.255
  Chirality :  0.047   0.143   1580
  Planarity :  0.003   0.044   1800
  Dihedral  :  4.157  17.477   1408
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 17.17 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.25), residues: 1328
  helix:  1.90 (0.27), residues: 372
  sheet:  0.27 (0.34), residues: 276
  loop : -0.06 (0.26), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 200 
 TYR   0.010   0.001   TYR D 314 
 PHE   0.006   0.001   PHE A 295 
 TRP   0.005   0.001   TRP B 313 
 HIS   0.002   0.000   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10220)
  covalent geometry    : angle       0.46024 (13860)
  hydrogen bonds       : bond        0.03672 (  464)
  hydrogen bonds       : angle       5.17619 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3321.21 seconds
wall clock time: 57 minutes 40.97 seconds (3460.97 seconds total)