Starting phenix.real_space_refine
on Sun Aug 24 11:00:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nlx_49525/08_2025/9nlx_49525.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nlx_49525/08_2025/9nlx_49525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nlx_49525/08_2025/9nlx_49525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nlx_49525/08_2025/9nlx_49525.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nlx_49525/08_2025/9nlx_49525.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nlx_49525/08_2025/9nlx_49525.cif"
  }
  resolution = 3.2
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     423      5.49       5
     S      21      5.16       5
     C   11079      2.51       5
     N    3438      2.21       5
     O    4809      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: 19770
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3589
          Classifications: {'peptide': 481}
          Incomplete info: {'truncation_to_alanine': 116}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 463}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 369
          Unresolved non-hydrogen angles: 439
          Unresolved non-hydrogen dihedrals: 300
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 4, 'ARG:plan': 9, 'ASP:plan': 14, 'ASN:plan1': 12}
          Unresolved non-hydrogen planarities: 211
    Chain: "G"
      Number of atoms: 3001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 3001
          Classifications: {'RNA': 141}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 18, 'rna3p_pur': 59, 'rna3p_pyr': 52}
          Link IDs: {'rna2p': 30, 'rna3p': 110}
  Restraints were copied for chains:
    B, C, H, I
  Time building chain proxies: 5.42, per 1000 atoms: 0.27
  Number of scatterers: 19770
  At special positions: 0
  Unit cell: (192.093, 179.408, 86.0795, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P     423     15.00
     O    4809      8.00
     N    3438      7.00
     C   11079      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.56
  Conformation dependent library (CDL) restraints added in 699.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2754

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 9 sheets defined
      61.7% alpha, 6.7% beta
      48 base pairs and 216 stacking pairs defined.
    Time for finding SS restraints: 3.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 40
      removed outlier: 3.666A  pdb=" N   ARG A   9 " --> pdb=" O   GLN A   5 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLU A  14 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ALA A  17 " --> pdb=" O   GLU A  13 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   LEU A  18 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE A  19 " --> pdb=" O   ALA A  15 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   HIS A  30 " --> pdb=" O   HIS A  26 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS A  37 " --> pdb=" O   SER A  33 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LYS A  38 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG A  39 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A  40 " --> pdb=" O   ASN A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 44
      removed outlier: 3.860A  pdb=" N   ALA A  44 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 41 through 44'
    Processing helix  chain 'A' and resid 52 through 57
      removed outlier: 3.766A  pdb=" N   SER A  56 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 61
    Processing helix  chain 'A' and resid 62 through 69
    Processing helix  chain 'A' and resid 71 through 84
    Processing helix  chain 'A' and resid 110 through 128
    Processing helix  chain 'A' and resid 144 through 159
      removed outlier: 3.993A  pdb=" N   ALA A 148 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASN A 159 " --> pdb=" O   ASP A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 186
      removed outlier: 3.516A  pdb=" N   PHE A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ASN A 186 " --> pdb=" O   ASN A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 204
    Processing helix  chain 'A' and resid 216 through 226
      removed outlier: 4.263A  pdb=" N   PHE A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   CYS A 226 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 237
    Processing helix  chain 'A' and resid 253 through 272
    Processing helix  chain 'A' and resid 316 through 336
    Processing helix  chain 'A' and resid 337 through 341
      removed outlier: 3.979A  pdb=" N   LYS A 341 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 370
      removed outlier: 3.964A  pdb=" N   LEU A 359 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 383
    Processing helix  chain 'A' and resid 393 through 398
    Processing helix  chain 'A' and resid 404 through 433
    Processing helix  chain 'A' and resid 445 through 447
      No H-bonds generated for 'chain 'A' and resid 445 through 447'
    Processing helix  chain 'A' and resid 448 through 455
      removed outlier: 3.734A  pdb=" N   LYS A 455 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 484
      removed outlier: 4.003A  pdb=" N   ILE A 472 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 489
    Processing helix  chain 'B' and resid 2 through 40
      removed outlier: 3.666A  pdb=" N   ARG B   9 " --> pdb=" O   GLN B   5 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLU B  14 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ALA B  17 " --> pdb=" O   GLU B  13 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   LEU B  18 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE B  19 " --> pdb=" O   ALA B  15 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   HIS B  30 " --> pdb=" O   HIS B  26 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS B  37 " --> pdb=" O   SER B  33 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   LYS B  38 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG B  39 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU B  40 " --> pdb=" O   ASN B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 44
      removed outlier: 3.861A  pdb=" N   ALA B  44 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 41 through 44'
    Processing helix  chain 'B' and resid 52 through 57
      removed outlier: 3.766A  pdb=" N   SER B  56 " --> pdb=" O   ASN B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 61
    Processing helix  chain 'B' and resid 62 through 69
    Processing helix  chain 'B' and resid 71 through 84
    Processing helix  chain 'B' and resid 110 through 128
    Processing helix  chain 'B' and resid 144 through 159
      removed outlier: 3.993A  pdb=" N   ALA B 148 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASN B 159 " --> pdb=" O   ASP B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 186
      removed outlier: 3.516A  pdb=" N   PHE B 185 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ASN B 186 " --> pdb=" O   ASN B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 204
    Processing helix  chain 'B' and resid 216 through 226
      removed outlier: 4.263A  pdb=" N   PHE B 220 " --> pdb=" O   SER B 216 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   CYS B 226 " --> pdb=" O   ALA B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 237
    Processing helix  chain 'B' and resid 253 through 272
    Processing helix  chain 'B' and resid 316 through 336
    Processing helix  chain 'B' and resid 337 through 341
      removed outlier: 3.978A  pdb=" N   LYS B 341 " --> pdb=" O   PRO B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 370
      removed outlier: 3.964A  pdb=" N   LEU B 359 " --> pdb=" O   ASP B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 383
    Processing helix  chain 'B' and resid 393 through 398
    Processing helix  chain 'B' and resid 404 through 433
    Processing helix  chain 'B' and resid 445 through 447
      No H-bonds generated for 'chain 'B' and resid 445 through 447'
    Processing helix  chain 'B' and resid 448 through 455
      removed outlier: 3.734A  pdb=" N   LYS B 455 " --> pdb=" O   ASP B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 484
      removed outlier: 4.002A  pdb=" N   ILE B 472 " --> pdb=" O   SER B 468 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS B 474 " --> pdb=" O   LEU B 470 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA B 475 " --> pdb=" O   LEU B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 489
    Processing helix  chain 'C' and resid 2 through 40
      removed outlier: 3.666A  pdb=" N   ARG C   9 " --> pdb=" O   GLN C   5 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU C  14 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ALA C  17 " --> pdb=" O   GLU C  13 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   LEU C  18 " --> pdb=" O   GLU C  14 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE C  19 " --> pdb=" O   ALA C  15 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   HIS C  30 " --> pdb=" O   HIS C  26 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ARG C  35 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LYS C  37 " --> pdb=" O   SER C  33 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LYS C  38 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG C  39 " --> pdb=" O   ARG C  35 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU C  40 " --> pdb=" O   ASN C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 44
      removed outlier: 3.861A  pdb=" N   ALA C  44 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 41 through 44'
    Processing helix  chain 'C' and resid 52 through 57
      removed outlier: 3.766A  pdb=" N   SER C  56 " --> pdb=" O   ASN C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 61
    Processing helix  chain 'C' and resid 62 through 69
    Processing helix  chain 'C' and resid 71 through 84
    Processing helix  chain 'C' and resid 110 through 128
    Processing helix  chain 'C' and resid 144 through 159
      removed outlier: 3.993A  pdb=" N   ALA C 148 " --> pdb=" O   ASN C 144 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASN C 159 " --> pdb=" O   ASP C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 186
      removed outlier: 3.516A  pdb=" N   PHE C 185 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ASN C 186 " --> pdb=" O   ASN C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 204
    Processing helix  chain 'C' and resid 216 through 226
      removed outlier: 4.262A  pdb=" N   PHE C 220 " --> pdb=" O   SER C 216 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU C 221 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   CYS C 226 " --> pdb=" O   ALA C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 226 through 237
    Processing helix  chain 'C' and resid 253 through 272
    Processing helix  chain 'C' and resid 316 through 336
    Processing helix  chain 'C' and resid 337 through 341
      removed outlier: 3.978A  pdb=" N   LYS C 341 " --> pdb=" O   PRO C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 355 through 370
      removed outlier: 3.964A  pdb=" N   LEU C 359 " --> pdb=" O   ASP C 355 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 374 through 383
    Processing helix  chain 'C' and resid 393 through 398
    Processing helix  chain 'C' and resid 404 through 433
    Processing helix  chain 'C' and resid 445 through 447
      No H-bonds generated for 'chain 'C' and resid 445 through 447'
    Processing helix  chain 'C' and resid 448 through 455
      removed outlier: 3.734A  pdb=" N   LYS C 455 " --> pdb=" O   ASP C 451 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 468 through 484
      removed outlier: 4.003A  pdb=" N   ILE C 472 " --> pdb=" O   SER C 468 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS C 474 " --> pdb=" O   LEU C 470 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA C 475 " --> pdb=" O   LEU C 471 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 484 through 489
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 95
    Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 243
      removed outlier: 3.667A  pdb=" N   LYS A 239 " --> pdb=" O   TRP A 250 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE A 167 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY A 282 " --> pdb=" O   GLU A 166 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   LYS A 298 " --> pdb=" O   ILE A 283 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   LEU A 285 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 303
    Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 95
    Processing sheet with id=AA5, first strand: chain 'B' and resid 239 through 243
      removed outlier: 3.667A  pdb=" N   LYS B 239 " --> pdb=" O   TRP B 250 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE B 167 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY B 282 " --> pdb=" O   GLU B 166 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   LYS B 298 " --> pdb=" O   ILE B 283 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   LEU B 285 " --> pdb=" O   LYS B 298 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 301 through 303
    Processing sheet with id=AA7, first strand: chain 'C' and resid 92 through 95
    Processing sheet with id=AA8, first strand: chain 'C' and resid 239 through 243
      removed outlier: 3.667A  pdb=" N   LYS C 239 " --> pdb=" O   TRP C 250 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE C 167 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLY C 282 " --> pdb=" O   GLU C 166 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   LYS C 298 " --> pdb=" O   ILE C 283 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   LEU C 285 " --> pdb=" O   LYS C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 303

    630 hydrogen bonds defined for protein.
    1782 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      108 hydrogen bonds
      108 hydrogen bond angles
      0 basepair planarities
      48 basepair parallelities
      216 stacking parallelities
  Total time for adding SS restraints: 4.19

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3580
        1.33 -     1.45: 7148
        1.45 -     1.57: 9477
        1.57 -     1.69: 843
        1.69 -     1.81: 27
  Bond restraints: 21075
  Sorted by residual:
  bond pdb=" C   ARG A  75 "
       pdb=" N   SER A  76 "
    ideal  model  delta    sigma   weight residual
    1.335  1.262  0.073 1.31e-02 5.83e+03 3.09e+01
  bond pdb=" C   ARG B  75 "
       pdb=" N   SER B  76 "
    ideal  model  delta    sigma   weight residual
    1.335  1.262  0.073 1.31e-02 5.83e+03 3.09e+01
  bond pdb=" C   ARG C  75 "
       pdb=" N   SER C  76 "
    ideal  model  delta    sigma   weight residual
    1.335  1.262  0.073 1.31e-02 5.83e+03 3.09e+01
  bond pdb=" C   ALA B  74 "
       pdb=" N   ARG B  75 "
    ideal  model  delta    sigma   weight residual
    1.334  1.400 -0.066 1.27e-02 6.20e+03 2.68e+01
  bond pdb=" C   ALA A  74 "
       pdb=" N   ARG A  75 "
    ideal  model  delta    sigma   weight residual
    1.334  1.400 -0.066 1.27e-02 6.20e+03 2.67e+01
  ... (remaining 21070 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 29138
        1.40 -     2.79: 1226
        2.79 -     4.19: 203
        4.19 -     5.58: 48
        5.58 -     6.98: 12
  Bond angle restraints: 30627
  Sorted by residual:
  angle pdb=" O   ALA B  74 "
        pdb=" C   ALA B  74 "
        pdb=" N   ARG B  75 "
      ideal   model   delta    sigma   weight residual
     122.07  126.61   -4.54 1.03e+00 9.43e-01 1.95e+01
  angle pdb=" O   ALA C  74 "
        pdb=" C   ALA C  74 "
        pdb=" N   ARG C  75 "
      ideal   model   delta    sigma   weight residual
     122.07  126.59   -4.52 1.03e+00 9.43e-01 1.92e+01
  angle pdb=" O   ALA A  74 "
        pdb=" C   ALA A  74 "
        pdb=" N   ARG A  75 "
      ideal   model   delta    sigma   weight residual
     122.12  126.62   -4.50 1.06e+00 8.90e-01 1.80e+01
  angle pdb=" C3'   A I  46 "
        pdb=" O3'   A I  46 "
        pdb=" P     A I  47 "
      ideal   model   delta    sigma   weight residual
     120.20  126.35   -6.15 1.50e+00 4.44e-01 1.68e+01
  angle pdb=" C3'   A H  46 "
        pdb=" O3'   A H  46 "
        pdb=" P     A H  47 "
      ideal   model   delta    sigma   weight residual
     120.20  126.33   -6.13 1.50e+00 4.44e-01 1.67e+01
  ... (remaining 30622 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.39: 11622
       35.39 -    70.78: 1287
       70.78 -   106.16: 183
      106.16 -   141.55: 15
      141.55 -   176.94: 24
  Dihedral angle restraints: 13131
    sinusoidal: 8880
      harmonic: 4251
  Sorted by residual:
  dihedral pdb=" O4'   U H 138 "
           pdb=" C1'   U H 138 "
           pdb=" N1    U H 138 "
           pdb=" C2    U H 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -0.39 -159.61     1      1.50e+01 4.44e-03 8.27e+01
  dihedral pdb=" O4'   U I 138 "
           pdb=" C1'   U I 138 "
           pdb=" N1    U I 138 "
           pdb=" C2    U I 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -0.44 -159.56     1      1.50e+01 4.44e-03 8.26e+01
  dihedral pdb=" O4'   U G 138 "
           pdb=" C1'   U G 138 "
           pdb=" N1    U G 138 "
           pdb=" C2    U G 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -0.45 -159.55     1      1.50e+01 4.44e-03 8.26e+01
  ... (remaining 13128 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 3128
       0.054 -    0.109: 569
       0.109 -    0.163: 101
       0.163 -    0.217: 27
       0.217 -    0.272: 3
  Chirality restraints: 3828
  Sorted by residual:
  chirality pdb=" C3'   U I  59 "
            pdb=" C4'   U I  59 "
            pdb=" O3'   U I  59 "
            pdb=" C2'   U I  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.47   -0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" C3'   U H  59 "
            pdb=" C4'   U H  59 "
            pdb=" O3'   U H  59 "
            pdb=" C2'   U H  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.48   -0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" C3'   U G  59 "
            pdb=" C4'   U G  59 "
            pdb=" O3'   U G  59 "
            pdb=" C2'   U G  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.48   -0.27 2.00e-01 2.50e+01 1.81e+00
  ... (remaining 3825 not shown)

  Planarity restraints: 2313
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 448 "    0.013 2.00e-02 2.50e+03   2.63e-02 6.91e+00
        pdb=" C   ASP B 448 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ASP B 448 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ILE B 449 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 448 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.84e+00
        pdb=" C   ASP A 448 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 448 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ILE A 449 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 448 "    0.013 2.00e-02 2.50e+03   2.61e-02 6.80e+00
        pdb=" C   ASP C 448 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ASP C 448 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ILE C 449 "    0.015 2.00e-02 2.50e+03
  ... (remaining 2310 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 5656
        2.81 -     3.33: 16937
        3.33 -     3.86: 36330
        3.86 -     4.38: 40211
        4.38 -     4.90: 59377
  Nonbonded interactions: 158511
  Sorted by model distance:
  nonbonded pdb=" O4'   U H 138 "
            pdb=" O2    U H 138 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O4'   U G 138 "
            pdb=" O2    U G 138 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O4'   U I 138 "
            pdb=" O2    U I 138 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG  SER C 383 "
            pdb=" O2'   G I  58 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OG  SER A 383 "
            pdb=" O2'   G G  58 "
     model   vdw
     2.314 3.040
  ... (remaining 158506 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}

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:             12.010
  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:             0.020
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     22.130
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
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      :  0.004   0.073  21075  Z= 0.244
  Angle     :  0.658   6.979  30627  Z= 0.405
  Chirality :  0.046   0.272   3828
  Planarity :  0.004   0.026   2313
  Dihedral  : 26.029 176.940  10377
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.07 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.22), residues: 1431
  helix:  1.67 (0.20), residues: 771
  sheet: -0.33 (0.47), residues: 120
  loop : -0.58 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 385 
 TYR   0.012   0.001   TYR B 306 
 PHE   0.009   0.001   PHE C 440 
 TRP   0.008   0.001   TRP C 250 
 HIS   0.008   0.001   HIS C  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (21075)
  covalent geometry    : angle       0.65837 (30627)
  hydrogen bonds       : bond        0.17833 (  738)
  hydrogen bonds       : angle       5.31728 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.571 
Fit side-chains
  outliers start: 16
  outliers final: 3
  residues processed: 71
  average time/residue: 0.1594
  time to fit residues: 17.5464
Evaluate side-chains
  44 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue  301 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0040
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    0.7980
   overall best weight:    1.0794

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.096375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.063275 restraints weight = 55067.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 1.77
r_work: 0.2735 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  21075  Z= 0.160
  Angle     :  0.593  10.471  30627  Z= 0.306
  Chirality :  0.038   0.287   3828
  Planarity :  0.004   0.031   2313
  Dihedral  : 26.224 177.710   8172
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.76 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.47 (0.23), residues: 1431
  helix:  2.09 (0.19), residues: 786
  sheet: -0.07 (0.44), residues: 117
  loop : -0.47 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 161 
 TYR   0.017   0.001   TYR B  70 
 PHE   0.010   0.001   PHE B 120 
 TRP   0.011   0.001   TRP C 250 
 HIS   0.007   0.001   HIS B  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (21075)
  covalent geometry    : angle       0.59345 (30627)
  hydrogen bonds       : bond        0.07532 (  738)
  hydrogen bonds       : angle       3.85305 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.568 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8216 (mt-10)
  outliers start: 14
  outliers final: 7
  residues processed: 60
  average time/residue: 0.1294
  time to fit residues: 13.6358
Evaluate side-chains
  56 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  264 ILE
Chi-restraints excluded: chain C residue  265 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 142 optimal weight:    0.6980
   chunk 54 optimal weight:   10.0000
   chunk 140 optimal weight:    2.9990
   chunk 135 optimal weight:    0.9990
   chunk 183 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 122 optimal weight:    7.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.095417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.060347 restraints weight = 55156.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 1.81
r_work: 0.2730 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  21075  Z= 0.154
  Angle     :  0.566   9.436  30627  Z= 0.295
  Chirality :  0.037   0.248   3828
  Planarity :  0.003   0.026   2313
  Dihedral  : 25.568 176.148   8168
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.45 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.77 (0.23), residues: 1431
  helix:  2.42 (0.19), residues: 786
  sheet:  0.17 (0.46), residues: 117
  loop : -0.52 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  84 
 TYR   0.014   0.001   TYR B  70 
 PHE   0.014   0.001   PHE B 120 
 TRP   0.011   0.001   TRP C 250 
 HIS   0.006   0.001   HIS B  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (21075)
  covalent geometry    : angle       0.56621 (30627)
  hydrogen bonds       : bond        0.08027 (  738)
  hydrogen bonds       : angle       3.68247 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.533 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8300 (mt-10)
  outliers start: 10
  outliers final: 6
  residues processed: 59
  average time/residue: 0.1076
  time to fit residues: 11.4977
Evaluate side-chains
  50 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  264 ILE
Chi-restraints excluded: chain C residue  275 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 156 optimal weight:    3.9990
   chunk 163 optimal weight:    0.0870
   chunk 30 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 135 optimal weight:    1.9990
   chunk 179 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 119 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.7160

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.097076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.062567 restraints weight = 55490.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.78
r_work: 0.2788 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  21075  Z= 0.120
  Angle     :  0.524   8.450  30627  Z= 0.268
  Chirality :  0.035   0.222   3828
  Planarity :  0.003   0.025   2313
  Dihedral  : 25.298 177.321   8168
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 15.38 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.23), residues: 1431
  helix:  2.65 (0.19), residues: 786
  sheet:  0.26 (0.46), residues: 117
  loop : -0.46 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.012   0.001   TYR B  70 
 PHE   0.012   0.001   PHE B 120 
 TRP   0.008   0.001   TRP B 250 
 HIS   0.006   0.001   HIS B  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (21075)
  covalent geometry    : angle       0.52366 (30627)
  hydrogen bonds       : bond        0.06344 (  738)
  hydrogen bonds       : angle       3.36291 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.542 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8182 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 53
  average time/residue: 0.1104
  time to fit residues: 10.6172
Evaluate side-chains
  52 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  264 ILE
Chi-restraints excluded: chain C residue  265 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 166 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 144 optimal weight:    0.6980
   chunk 140 optimal weight:    0.9980
   chunk 143 optimal weight:    0.6980
   chunk 72 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3702 r_free = 0.3702 target = 0.097073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.062344 restraints weight = 55478.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 1.80
r_work: 0.2783 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  21075  Z= 0.114
  Angle     :  0.508   7.817  30627  Z= 0.261
  Chirality :  0.034   0.224   3828
  Planarity :  0.003   0.023   2313
  Dihedral  : 25.120 176.072   8166
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 15.17 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.23), residues: 1431
  helix:  2.80 (0.19), residues: 786
  sheet:  0.51 (0.46), residues: 117
  loop : -0.41 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 385 
 TYR   0.013   0.001   TYR B 329 
 PHE   0.012   0.001   PHE C 120 
 TRP   0.010   0.001   TRP C 250 
 HIS   0.006   0.001   HIS B  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (21075)
  covalent geometry    : angle       0.50754 (30627)
  hydrogen bonds       : bond        0.06427 (  738)
  hydrogen bonds       : angle       3.30139 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.551 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8253 (mt-10)
  outliers start: 10
  outliers final: 9
  residues processed: 52
  average time/residue: 0.1103
  time to fit residues: 10.3834
Evaluate side-chains
  53 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  458 ILE
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  264 ILE
Chi-restraints excluded: chain C residue  265 THR
Chi-restraints excluded: chain C residue  458 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 125 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 177 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 143 optimal weight:    0.9980
   chunk 132 optimal weight:    1.9990
   chunk 142 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0170
   overall best weight:    0.9422

-------------------------------------------------------------------------------
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 = 0.3675 r_free = 0.3675 target = 0.095614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.060507 restraints weight = 55123.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 1.78
r_work: 0.2735 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  21075  Z= 0.135
  Angle     :  0.529   8.416  30627  Z= 0.273
  Chirality :  0.035   0.233   3828
  Planarity :  0.003   0.025   2313
  Dihedral  : 24.955 176.202   8166
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.69 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.23), residues: 1431
  helix:  2.75 (0.19), residues: 786
  sheet:  0.69 (0.47), residues: 117
  loop : -0.46 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 385 
 TYR   0.015   0.001   TYR C 329 
 PHE   0.013   0.001   PHE B 120 
 TRP   0.011   0.001   TRP C 250 
 HIS   0.006   0.001   HIS B  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (21075)
  covalent geometry    : angle       0.52940 (30627)
  hydrogen bonds       : bond        0.07584 (  738)
  hydrogen bonds       : angle       3.50341 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.484 
Fit side-chains
  outliers start: 11
  outliers final: 9
  residues processed: 56
  average time/residue: 0.1080
  time to fit residues: 10.9160
Evaluate side-chains
  53 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  458 ILE
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  264 ILE
Chi-restraints excluded: chain C residue  265 THR
Chi-restraints excluded: chain C residue  458 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 177 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 176 optimal weight:    9.9990
   chunk 40 optimal weight:    0.5980
   chunk 162 optimal weight:    0.0980
   chunk 136 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 182 optimal weight:    3.9990
   chunk 170 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.096180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.065864 restraints weight = 55736.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.22
r_work: 0.2690 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  21075  Z= 0.128
  Angle     :  0.515   8.628  30627  Z= 0.266
  Chirality :  0.035   0.223   3828
  Planarity :  0.003   0.023   2313
  Dihedral  : 24.884 176.065   8166
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.79 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.23), residues: 1431
  helix:  2.80 (0.19), residues: 786
  sheet:  0.79 (0.48), residues: 117
  loop : -0.49 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 385 
 TYR   0.014   0.001   TYR B 329 
 PHE   0.013   0.001   PHE A 120 
 TRP   0.009   0.001   TRP A 250 
 HIS   0.006   0.001   HIS B  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (21075)
  covalent geometry    : angle       0.51546 (30627)
  hydrogen bonds       : bond        0.06967 (  738)
  hydrogen bonds       : angle       3.38949 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.544 
Fit side-chains
  outliers start: 12
  outliers final: 10
  residues processed: 55
  average time/residue: 0.1092
  time to fit residues: 10.9574
Evaluate side-chains
  54 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  458 ILE
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  264 ILE
Chi-restraints excluded: chain C residue  265 THR
Chi-restraints excluded: chain C residue  458 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 99 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 94 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 162 optimal weight:    0.0570
   chunk 13 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 144 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.096542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.066355 restraints weight = 55572.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 2.25
r_work: 0.2699 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  21075  Z= 0.110
  Angle     :  0.509   8.646  30627  Z= 0.261
  Chirality :  0.034   0.225   3828
  Planarity :  0.003   0.024   2313
  Dihedral  : 24.878 176.079   8166
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.86 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.23), residues: 1431
  helix:  2.88 (0.19), residues: 786
  sheet:  0.73 (0.47), residues: 117
  loop : -0.47 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 385 
 TYR   0.014   0.001   TYR A 329 
 PHE   0.012   0.001   PHE B 120 
 TRP   0.010   0.001   TRP C 250 
 HIS   0.006   0.001   HIS C  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (21075)
  covalent geometry    : angle       0.50925 (30627)
  hydrogen bonds       : bond        0.06708 (  738)
  hydrogen bonds       : angle       3.34203 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 44
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8199 (mtmt)
  outliers start: 18
  outliers final: 15
  residues processed: 61
  average time/residue: 0.1098
  time to fit residues: 11.9110
Evaluate side-chains
  59 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  458 ILE
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  264 ILE
Chi-restraints excluded: chain C residue  265 THR
Chi-restraints excluded: chain C residue  458 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 157 optimal weight:    1.9990
   chunk 160 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 154 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 181 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 101 optimal weight:    0.5980
   chunk 88 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.095782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.064476 restraints weight = 54655.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.19
r_work: 0.2684 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  21075  Z= 0.134
  Angle     :  0.524   9.108  30627  Z= 0.269
  Chirality :  0.034   0.225   3828
  Planarity :  0.003   0.024   2313
  Dihedral  : 24.859 176.332   8166
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.58 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.23), residues: 1431
  helix:  2.85 (0.19), residues: 786
  sheet:  0.70 (0.47), residues: 117
  loop : -0.48 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 385 
 TYR   0.016   0.001   TYR B 329 
 PHE   0.013   0.001   PHE B 120 
 TRP   0.009   0.001   TRP C 250 
 HIS   0.007   0.001   HIS A  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (21075)
  covalent geometry    : angle       0.52391 (30627)
  hydrogen bonds       : bond        0.07267 (  738)
  hydrogen bonds       : angle       3.40385 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.586 
Fit side-chains
  outliers start: 15
  outliers final: 14
  residues processed: 61
  average time/residue: 0.0999
  time to fit residues: 10.8742
Evaluate side-chains
  58 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  458 ILE
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  264 ILE
Chi-restraints excluded: chain C residue  265 THR
Chi-restraints excluded: chain C residue  458 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 139 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    7.9990
   chunk 110 optimal weight:    3.9990
   chunk 159 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0070
   chunk 163 optimal weight:    0.6980
   chunk 108 optimal weight:    1.9990
   overall best weight:    0.8800

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.095979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.065333 restraints weight = 55479.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 2.20
r_work: 0.2688 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  21075  Z= 0.128
  Angle     :  0.515   8.721  30627  Z= 0.265
  Chirality :  0.034   0.225   3828
  Planarity :  0.003   0.023   2313
  Dihedral  : 24.856 176.323   8166
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.07 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.23), residues: 1431
  helix:  2.88 (0.19), residues: 786
  sheet:  0.72 (0.47), residues: 117
  loop : -0.48 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.016   0.001   TYR C 243 
 PHE   0.013   0.001   PHE A 120 
 TRP   0.011   0.001   TRP A 250 
 HIS   0.006   0.001   HIS B  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (21075)
  covalent geometry    : angle       0.51473 (30627)
  hydrogen bonds       : bond        0.07078 (  738)
  hydrogen bonds       : angle       3.38175 ( 1890)

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

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

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2862 Ramachandran restraints generated.
    1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.584 
Fit side-chains
  outliers start: 16
  outliers final: 16
  residues processed: 60
  average time/residue: 0.1159
  time to fit residues: 12.1982
Evaluate side-chains
  60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  458 ILE
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain C residue  264 ILE
Chi-restraints excluded: chain C residue  265 THR
Chi-restraints excluded: chain C residue  458 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 149 optimal weight:    1.9990
   chunk 173 optimal weight:    6.9990
   chunk 163 optimal weight:    0.6980
   chunk 158 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 179 optimal weight:    4.9990
   chunk 155 optimal weight:    0.7980
   chunk 166 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0980
   chunk 14 optimal weight:    0.0970
   chunk 122 optimal weight:    7.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.096817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.061886 restraints weight = 55671.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 1.80
r_work: 0.2771 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  21075  Z= 0.106
  Angle     :  0.507  10.359  30627  Z= 0.258
  Chirality :  0.034   0.220   3828
  Planarity :  0.003   0.024   2313
  Dihedral  : 24.843 176.601   8166
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.38 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.23), residues: 1431
  helix:  3.00 (0.19), residues: 783
  sheet:  0.80 (0.48), residues: 117
  loop : -0.42 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 385 
 TYR   0.013   0.001   TYR B 329 
 PHE   0.012   0.001   PHE C 120 
 TRP   0.010   0.001   TRP A 250 
 HIS   0.006   0.001   HIS C  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (21075)
  covalent geometry    : angle       0.50657 (30627)
  hydrogen bonds       : bond        0.06514 (  738)
  hydrogen bonds       : angle       3.28528 ( 1890)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4792.27 seconds
wall clock time: 82 minutes 57.59 seconds (4977.59 seconds total)