Starting phenix.real_space_refine
on Tue Jun 17 01:15:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nlx_49525/06_2025/9nlx_49525.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nlx_49525/06_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_49525/06_2025/9nlx_49525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nlx_49525/06_2025/9nlx_49525.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nlx_49525/06_2025/9nlx_49525.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nlx_49525/06_2025/9nlx_49525.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'GLU:plan': 18, 'ARG:plan': 9, 'ASN:plan1': 12, 'ASP:plan': 14}
          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:
    I, H, C, B
  Time building chain proxies: 13.49, per 1000 atoms: 0.68
  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: 4.99
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 7.57
  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: 6.70

  Time building geometry restraints manager: 5.93 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'G'
  selection = chain 'I'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             6.530
  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:          0.810
  Check model and map are aligned:         0.150
  Set scattering table:                    0.180
  Process input model:                     49.910
  Find NCS groups from input model:        0.330
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.870
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (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
 TRP   0.008   0.001   TRP C 250 
 HIS   0.008   0.001   HIS C  26 
 PHE   0.009   0.001   PHE C 440 
 TYR   0.012   0.001   TYR B 306 
 ARG   0.002   0.000   ARG B 385 

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

*********************** 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  : 1.490 
Fit side-chains
  outliers start: 16
  outliers final: 3
  residues processed: 71
  average time/residue: 0.3182
  time to fit residues: 35.2596
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  : 1.499 
-------------------------------------------------------------------------------
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 157 optimal weight:    0.9980
   chunk 140 optimal weight:    0.2980
   chunk 78 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 95 optimal weight:    0.5980
   chunk 75 optimal weight:    0.1980
   chunk 145 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 168 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.097292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.064682 restraints weight = 55221.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 1.76
r_work: 0.2769 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  21075  Z= 0.143
  Angle     :  0.580  10.411  30627  Z= 0.298
  Chirality :  0.037   0.283   3828
  Planarity :  0.004   0.033   2313
  Dihedral  : 26.206 177.119   8172
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 14.96 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.23), residues: 1431
  helix:  2.14 (0.19), residues: 786
  sheet: -0.04 (0.43), residues: 117
  loop : -0.42 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 250 
 HIS   0.007   0.001   HIS B  26 
 PHE   0.010   0.001   PHE A 180 
 TYR   0.016   0.001   TYR B  70 
 ARG   0.002   0.000   ARG A 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06909 (  738)
  hydrogen bonds       : angle       3.78130 ( 1890)
  covalent geometry    : bond        0.00291 (21075)
  covalent geometry    : angle       0.58010 (30627)

*********************** 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
  55 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 1.695 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 55
  average time/residue: 0.2461
  time to fit residues: 24.5361
Evaluate side-chains
  49 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 1.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A 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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 114 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 162 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3676 r_free = 0.3676 target = 0.095763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.060850 restraints weight = 54303.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 1.76
r_work: 0.2745 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  21075  Z= 0.150
  Angle     :  0.558   9.974  30627  Z= 0.289
  Chirality :  0.036   0.250   3828
  Planarity :  0.003   0.027   2313
  Dihedral  : 25.595 176.968   8168
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.96 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.23), residues: 1431
  helix:  2.51 (0.19), residues: 786
  sheet:  0.19 (0.46), residues: 117
  loop : -0.46 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 250 
 HIS   0.005   0.001   HIS C  26 
 PHE   0.012   0.001   PHE B 120 
 TYR   0.015   0.001   TYR B  70 
 ARG   0.003   0.000   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07771 (  738)
  hydrogen bonds       : angle       3.65436 ( 1890)
  covalent geometry    : bond        0.00318 (21075)
  covalent geometry    : angle       0.55810 (30627)

*********************** 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
  65 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 1.619 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8223 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 63
  average time/residue: 0.2360
  time to fit residues: 27.0045
Evaluate side-chains
  55 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 1.618 
-------------------------------------------------------------------------------
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  257 ILE
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
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 38 optimal weight:    0.7980
   chunk 160 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 128 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9990
   chunk 96 optimal weight:    0.7980
   chunk 155 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 143 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.096804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.062056 restraints weight = 55738.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 1.80
r_work: 0.2772 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.2453

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= 0.129
  Angle     :  0.530   8.229  30627  Z= 0.272
  Chirality :  0.035   0.225   3828
  Planarity :  0.003   0.029   2313
  Dihedral  : 25.279 176.933   8168
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 15.48 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.23), residues: 1431
  helix:  2.60 (0.19), residues: 786
  sheet:  0.31 (0.46), residues: 117
  loop : -0.47 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 250 
 HIS   0.006   0.001   HIS C  26 
 PHE   0.012   0.001   PHE B 120 
 TYR   0.013   0.001   TYR A 329 
 ARG   0.002   0.000   ARG B 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06634 (  738)
  hydrogen bonds       : angle       3.42277 ( 1890)
  covalent geometry    : bond        0.00271 (21075)
  covalent geometry    : angle       0.53012 (30627)

*********************** 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: 9
    poor density    : 44
  time to evaluate  : 1.702 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8187 (mt-10)
  outliers start: 9
  outliers final: 7
  residues processed: 52
  average time/residue: 0.2621
  time to fit residues: 24.7498
Evaluate side-chains
  48 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 1.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  265 THR
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 58 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 127 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 122 optimal weight:    7.9990
   chunk 149 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.096190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.061298 restraints weight = 55244.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 1.78
r_work: 0.2758 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  21075  Z= 0.129
  Angle     :  0.521   8.171  30627  Z= 0.269
  Chirality :  0.035   0.229   3828
  Planarity :  0.003   0.026   2313
  Dihedral  : 25.045 175.699   8166
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.79 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.23), residues: 1431
  helix:  2.78 (0.19), residues: 786
  sheet:  0.57 (0.46), residues: 117
  loop : -0.44 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 250 
 HIS   0.006   0.001   HIS A  26 
 PHE   0.014   0.001   PHE C 120 
 TYR   0.014   0.001   TYR C 329 
 ARG   0.002   0.000   ARG B 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07147 (  738)
  hydrogen bonds       : angle       3.41308 ( 1890)
  covalent geometry    : bond        0.00270 (21075)
  covalent geometry    : angle       0.52143 (30627)

*********************** 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
  56 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 1.630 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8200 (mt-10)
  outliers start: 11
  outliers final: 10
  residues processed: 55
  average time/residue: 0.2392
  time to fit residues: 23.9912
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  : 1.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 61 optimal weight:    5.9990
   chunk 167 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0970
   chunk 130 optimal weight:    1.9990
   chunk 171 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 177 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.094504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.059259 restraints weight = 54777.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 1.77
r_work: 0.2704 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  21075  Z= 0.169
  Angle     :  0.556   8.536  30627  Z= 0.289
  Chirality :  0.037   0.238   3828
  Planarity :  0.003   0.026   2313
  Dihedral  : 24.980 176.109   8166
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.48 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.23), residues: 1431
  helix:  2.59 (0.19), residues: 786
  sheet:  0.63 (0.46), residues: 117
  loop : -0.56 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 250 
 HIS   0.006   0.001   HIS B  26 
 PHE   0.014   0.001   PHE B 120 
 TYR   0.016   0.001   TYR B 329 
 ARG   0.002   0.000   ARG A 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08318 (  738)
  hydrogen bonds       : angle       3.66022 ( 1890)
  covalent geometry    : bond        0.00366 (21075)
  covalent geometry    : angle       0.55605 (30627)

*********************** 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: 12
    poor density    : 45
  time to evaluate  : 1.475 
Fit side-chains
  outliers start: 12
  outliers final: 9
  residues processed: 57
  average time/residue: 0.2301
  time to fit residues: 23.7353
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  : 1.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  458 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 141 optimal weight:    1.9990
   chunk 185 optimal weight:    5.9990
   chunk 84 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 138 optimal weight:    1.9990
   chunk 170 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 114 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0170
   chunk 177 optimal weight:    7.9990
   chunk 115 optimal weight:    7.9990
   overall best weight:    0.8420

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.096037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.060980 restraints weight = 55321.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 1.80
r_work: 0.2751 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  21075  Z= 0.125
  Angle     :  0.516   8.760  30627  Z= 0.266
  Chirality :  0.034   0.223   3828
  Planarity :  0.003   0.024   2313
  Dihedral  : 24.880 175.700   8166
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.58 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.23), residues: 1431
  helix:  2.77 (0.19), residues: 786
  sheet:  0.73 (0.47), residues: 117
  loop : -0.53 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 250 
 HIS   0.006   0.001   HIS B  26 
 PHE   0.013   0.001   PHE B 120 
 TYR   0.013   0.001   TYR A 329 
 ARG   0.001   0.000   ARG B 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06889 (  738)
  hydrogen bonds       : angle       3.39530 ( 1890)
  covalent geometry    : bond        0.00263 (21075)
  covalent geometry    : angle       0.51625 (30627)

*********************** 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
  60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 1.675 
Fit side-chains
  outliers start: 16
  outliers final: 16
  residues processed: 60
  average time/residue: 0.5371
  time to fit residues: 57.5284
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  : 3.582 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 161 optimal weight:    0.8980
   chunk 16 optimal weight:    0.4980
   chunk 127 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 115 optimal weight:    7.9990
   chunk 100 optimal weight:    0.0370
   chunk 119 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.6860

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.096231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.061215 restraints weight = 56050.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 1.81
r_work: 0.2757 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.3161

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     :  0.511   8.767  30627  Z= 0.262
  Chirality :  0.034   0.222   3828
  Planarity :  0.003   0.024   2313
  Dihedral  : 24.880 175.787   8166
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.48 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.23), residues: 1431
  helix:  2.84 (0.19), residues: 786
  sheet:  0.73 (0.47), residues: 117
  loop : -0.51 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 250 
 HIS   0.006   0.001   HIS B  26 
 PHE   0.012   0.001   PHE B 120 
 TYR   0.014   0.001   TYR B 329 
 ARG   0.002   0.000   ARG B 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06737 (  738)
  hydrogen bonds       : angle       3.35274 ( 1890)
  covalent geometry    : bond        0.00231 (21075)
  covalent geometry    : angle       0.51117 (30627)

*********************** 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
  60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 2.619 
Fit side-chains
  outliers start: 17
  outliers final: 16
  residues processed: 60
  average time/residue: 0.3426
  time to fit residues: 36.6207
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  : 3.371 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 137 optimal weight:    0.0000
   chunk 165 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 140 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 149 optimal weight:    0.8980
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.096355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.061417 restraints weight = 55622.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 1.80
r_work: 0.2759 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.3188

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= 0.115
  Angle     :  0.514   9.786  30627  Z= 0.262
  Chirality :  0.034   0.221   3828
  Planarity :  0.003   0.024   2313
  Dihedral  : 24.870 175.836   8166
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.48 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.23), residues: 1431
  helix:  2.86 (0.19), residues: 786
  sheet:  0.66 (0.47), residues: 117
  loop : -0.52 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 250 
 HIS   0.006   0.001   HIS B  26 
 PHE   0.012   0.001   PHE A 120 
 TYR   0.013   0.001   TYR A 329 
 ARG   0.001   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06690 (  738)
  hydrogen bonds       : angle       3.33006 ( 1890)
  covalent geometry    : bond        0.00236 (21075)
  covalent geometry    : angle       0.51405 (30627)

*********************** 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
  63 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 1.679 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8129 (mtmt)
  outliers start: 19
  outliers final: 17
  residues processed: 63
  average time/residue: 0.2597
  time to fit residues: 29.3448
Evaluate side-chains
  60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
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  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  265 THR
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 150 optimal weight:    7.9990
   chunk 113 optimal weight:   10.0000
   chunk 156 optimal weight:    0.6980
   chunk 178 optimal weight:   10.0000
   chunk 154 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 169 optimal weight:    0.0040
   chunk 22 optimal weight:    1.9990
   chunk 167 optimal weight:    0.5980
   chunk 177 optimal weight:    7.9990
   overall best weight:    0.8394

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.096029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.061058 restraints weight = 55125.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 1.77
r_work: 0.2749 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.3283

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= 0.124
  Angle     :  0.518   9.287  30627  Z= 0.265
  Chirality :  0.034   0.222   3828
  Planarity :  0.003   0.023   2313
  Dihedral  : 24.824 176.541   8166
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.48 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.23), residues: 1431
  helix:  2.89 (0.19), residues: 786
  sheet:  0.65 (0.47), residues: 117
  loop : -0.52 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 250 
 HIS   0.007   0.001   HIS B  26 
 PHE   0.012   0.001   PHE B 120 
 TYR   0.015   0.001   TYR B 329 
 ARG   0.004   0.000   ARG C 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06947 (  738)
  hydrogen bonds       : angle       3.34395 ( 1890)
  covalent geometry    : bond        0.00258 (21075)
  covalent geometry    : angle       0.51825 (30627)

********************** 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
  66 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 2.335 
Fit side-chains
  outliers start: 18
  outliers final: 17
  residues processed: 65
  average time/residue: 0.2447
  time to fit residues: 29.3004
Evaluate side-chains
  61 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 1.590 
-------------------------------------------------------------------------------
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  265 THR
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 148 optimal weight:    0.9990
   chunk 92 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0000
   chunk 84 optimal weight:    0.9980
   chunk 121 optimal weight:    3.9990
   chunk 150 optimal weight:    0.1980
   chunk 46 optimal weight:    0.0570
   chunk 74 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 127 optimal weight:    0.9980
   chunk 122 optimal weight:    7.9990
   overall best weight:    0.3302

-------------------------------------------------------------------------------
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 = 0.3709 r_free = 0.3709 target = 0.097242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.062465 restraints weight = 56082.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.81
r_work: 0.2786 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  21075  Z= 0.099
  Angle     :  0.506   8.851  30627  Z= 0.258
  Chirality :  0.033   0.219   3828
  Planarity :  0.003   0.025   2313
  Dihedral  : 24.823 176.888   8166
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.10 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.23), residues: 1431
  helix:  3.03 (0.19), residues: 786
  sheet:  0.77 (0.48), residues: 117
  loop : -0.43 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 250 
 HIS   0.006   0.001   HIS C  26 
 PHE   0.012   0.001   PHE C 120 
 TYR   0.013   0.001   TYR B 329 
 ARG   0.001   0.000   ARG C 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06199 (  738)
  hydrogen bonds       : angle       3.23230 ( 1890)
  covalent geometry    : bond        0.00186 (21075)
  covalent geometry    : angle       0.50565 (30627)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10267.27 seconds
wall clock time: 182 minutes 37.99 seconds (10957.99 seconds total)