Starting phenix.real_space_refine (version: dev)
on Tue Apr  5 08:36:09 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/04_2022/7lid_23374_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/04_2022/7lid_23374.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/04_2022/7lid_23374.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/04_2022/7lid_23374.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/04_2022/7lid_23374_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lid_23374/04_2022/7lid_23374_updated.pdb"
  }
  resolution = 2.9
  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
-------------------------------------------------------------------------------
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=   0.002 sd=   0.105
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 12140
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3023
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 9, 'TRANS': 371}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3023
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 9, 'TRANS': 371}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3023
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 9, 'TRANS': 371}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 3023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3023
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 9, 'TRANS': 371}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'EOL': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'EOL': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'EOL': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'EOL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.32, per 1000 atoms: 0.60
  Number of scatterers: 12140
  At special positions: 0
  Unit cell: (112.27, 112.27, 92.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     120     16.00
     O    2092      8.00
     N    1936      7.00
     C    7992      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  - 3.50
        Amino acid           : False - 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: 5.31
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2928

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      77.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 30
      removed outlier: 3.601A  pdb=" N   ARG A  18 " --> pdb=" O   TYR A  14 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLY A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 47
      No H-bonds generated for 'chain 'A' and resid 45 through 47'
    Processing helix  chain 'A' and resid 49 through 74
      removed outlier: 3.718A  pdb=" N   CYS A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A  73 " --> pdb=" O   TYR A  69 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   CYS A  74 " --> pdb=" O   CYS A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 104
      removed outlier: 4.344A  pdb=" N   THR A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   VAL A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 115
    Processing helix  chain 'A' and resid 126 through 168
      removed outlier: 3.919A  pdb=" N   SER A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 147 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      Proline residue:  A 162  - end of helix
    Processing helix  chain 'A' and resid 195 through 246
      removed outlier: 4.410A  pdb=" N   ALA A 215 " --> pdb=" O   PHE A 211 " (cutoff:3.500A)
      Proline residue:  A 216  - end of helix
    Processing helix  chain 'A' and resid 319 through 365
      removed outlier: 4.166A  pdb=" N   SER A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   VAL A 341 " --> pdb=" O   ILE A 337 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   TYR A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 406
      removed outlier: 3.771A  pdb=" N   LEU A 379 " --> pdb=" O   PRO A 375 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   VAL A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA A 399 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 415
      No H-bonds generated for 'chain 'A' and resid 412 through 415'
    Processing helix  chain 'A' and resid 419 through 432
      removed outlier: 3.693A  pdb=" N   GLN A 426 " --> pdb=" O   ARG A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 468
      removed outlier: 3.677A  pdb=" N   ILE A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL A 464 " --> pdb=" O   THR A 460 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU A 465 " --> pdb=" O   TYR A 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 30
      removed outlier: 3.601A  pdb=" N   ARG B  18 " --> pdb=" O   TYR B  14 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLY B  25 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 47
      No H-bonds generated for 'chain 'B' and resid 45 through 47'
    Processing helix  chain 'B' and resid 49 through 74
      removed outlier: 3.716A  pdb=" N   CYS B  56 " --> pdb=" O   GLN B  52 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU B  73 " --> pdb=" O   TYR B  69 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   CYS B  74 " --> pdb=" O   CYS B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 104
      removed outlier: 4.344A  pdb=" N   THR B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   VAL B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 115
    Processing helix  chain 'B' and resid 126 through 168
      removed outlier: 3.919A  pdb=" N   SER B 131 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU B 147 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      Proline residue:  B 162  - end of helix
    Processing helix  chain 'B' and resid 195 through 246
      removed outlier: 4.411A  pdb=" N   ALA B 215 " --> pdb=" O   PHE B 211 " (cutoff:3.500A)
      Proline residue:  B 216  - end of helix
    Processing helix  chain 'B' and resid 319 through 365
      removed outlier: 4.166A  pdb=" N   SER B 340 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   VAL B 341 " --> pdb=" O   ILE B 337 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   TYR B 342 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 406
      removed outlier: 3.771A  pdb=" N   LEU B 379 " --> pdb=" O   PRO B 375 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   MET B 382 " --> pdb=" O   VAL B 378 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   VAL B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA B 399 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 415
      No H-bonds generated for 'chain 'B' and resid 412 through 415'
    Processing helix  chain 'B' and resid 419 through 432
      removed outlier: 3.693A  pdb=" N   GLN B 426 " --> pdb=" O   ARG B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 468
      removed outlier: 3.676A  pdb=" N   ILE B 463 " --> pdb=" O   LEU B 459 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL B 464 " --> pdb=" O   THR B 460 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU B 465 " --> pdb=" O   TYR B 461 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 30
      removed outlier: 3.600A  pdb=" N   ARG C  18 " --> pdb=" O   TYR C  14 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLY C  25 " --> pdb=" O   ILE C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 47
      No H-bonds generated for 'chain 'C' and resid 45 through 47'
    Processing helix  chain 'C' and resid 49 through 74
      removed outlier: 3.716A  pdb=" N   CYS C  56 " --> pdb=" O   GLN C  52 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU C  73 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   CYS C  74 " --> pdb=" O   CYS C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 104
      removed outlier: 4.345A  pdb=" N   THR C  87 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   VAL C  88 " --> pdb=" O   ASN C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 115
    Processing helix  chain 'C' and resid 126 through 168
      removed outlier: 3.918A  pdb=" N   SER C 131 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU C 147 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      Proline residue:  C 162  - end of helix
    Processing helix  chain 'C' and resid 195 through 246
      removed outlier: 4.411A  pdb=" N   ALA C 215 " --> pdb=" O   PHE C 211 " (cutoff:3.500A)
      Proline residue:  C 216  - end of helix
    Processing helix  chain 'C' and resid 319 through 365
      removed outlier: 4.165A  pdb=" N   SER C 340 " --> pdb=" O   GLU C 336 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   VAL C 341 " --> pdb=" O   ILE C 337 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TYR C 342 " --> pdb=" O   VAL C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 374 through 406
      removed outlier: 3.771A  pdb=" N   LEU C 379 " --> pdb=" O   PRO C 375 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET C 382 " --> pdb=" O   VAL C 378 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   VAL C 398 " --> pdb=" O   LEU C 394 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA C 399 " --> pdb=" O   ALA C 395 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 412 through 415
      No H-bonds generated for 'chain 'C' and resid 412 through 415'
    Processing helix  chain 'C' and resid 419 through 432
      removed outlier: 3.692A  pdb=" N   GLN C 426 " --> pdb=" O   ARG C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 468
      removed outlier: 3.677A  pdb=" N   ILE C 463 " --> pdb=" O   LEU C 459 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL C 464 " --> pdb=" O   THR C 460 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU C 465 " --> pdb=" O   TYR C 461 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 30
      removed outlier: 3.601A  pdb=" N   ARG D  18 " --> pdb=" O   TYR D  14 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLY D  25 " --> pdb=" O   ILE D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 47
      No H-bonds generated for 'chain 'D' and resid 45 through 47'
    Processing helix  chain 'D' and resid 49 through 74
      removed outlier: 3.716A  pdb=" N   CYS D  56 " --> pdb=" O   GLN D  52 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU D  73 " --> pdb=" O   TYR D  69 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   CYS D  74 " --> pdb=" O   CYS D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 104
      removed outlier: 4.344A  pdb=" N   THR D  87 " --> pdb=" O   LEU D  83 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   VAL D  88 " --> pdb=" O   ASN D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 115
    Processing helix  chain 'D' and resid 126 through 168
      removed outlier: 3.918A  pdb=" N   SER D 131 " --> pdb=" O   GLY D 127 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU D 147 " --> pdb=" O   VAL D 143 " (cutoff:3.500A)
      Proline residue:  D 162  - end of helix
    Processing helix  chain 'D' and resid 195 through 246
      removed outlier: 4.411A  pdb=" N   ALA D 215 " --> pdb=" O   PHE D 211 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 319 through 365
      removed outlier: 4.166A  pdb=" N   SER D 340 " --> pdb=" O   GLU D 336 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   VAL D 341 " --> pdb=" O   ILE D 337 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   TYR D 342 " --> pdb=" O   VAL D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 374 through 406
      removed outlier: 3.772A  pdb=" N   LEU D 379 " --> pdb=" O   PRO D 375 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET D 382 " --> pdb=" O   VAL D 378 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   VAL D 398 " --> pdb=" O   LEU D 394 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA D 399 " --> pdb=" O   ALA D 395 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 412 through 415
      No H-bonds generated for 'chain 'D' and resid 412 through 415'
    Processing helix  chain 'D' and resid 419 through 432
      removed outlier: 3.693A  pdb=" N   GLN D 426 " --> pdb=" O   ARG D 422 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 468
      removed outlier: 3.676A  pdb=" N   ILE D 463 " --> pdb=" O   LEU D 459 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL D 464 " --> pdb=" O   THR D 460 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU D 465 " --> pdb=" O   TYR D 461 " (cutoff:3.500A)

    880 hydrogen bonds defined for protein.
    2640 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.43

  Time building geometry restraints manager: 5.73 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3354
        1.34 -     1.46: 2242
        1.46 -     1.57: 6648
        1.57 -     1.69: 0
        1.69 -     1.81: 172
  Bond restraints: 12416
  Sorted by residual:
  bond pdb=" C8  EOL B 900 "
       pdb=" C9  EOL B 900 "
    ideal  model  delta    sigma   weight residual
    1.328  1.525 -0.197 2.00e-02 2.50e+03 9.72e+01
  bond pdb=" C8  EOL A 900 "
       pdb=" C9  EOL A 900 "
    ideal  model  delta    sigma   weight residual
    1.328  1.525 -0.197 2.00e-02 2.50e+03 9.72e+01
  bond pdb=" C8  EOL D 900 "
       pdb=" C9  EOL D 900 "
    ideal  model  delta    sigma   weight residual
    1.328  1.525 -0.197 2.00e-02 2.50e+03 9.71e+01
  bond pdb=" C8  EOL C 900 "
       pdb=" C9  EOL C 900 "
    ideal  model  delta    sigma   weight residual
    1.328  1.525 -0.197 2.00e-02 2.50e+03 9.65e+01
  bond pdb=" C   SER D 195 "
       pdb=" N   PRO D 196 "
    ideal  model  delta    sigma   weight residual
    1.336  1.377 -0.041 1.23e-02 6.61e+03 1.13e+01
  ... (remaining 12411 not shown)

  Histogram of bond angle deviations from ideal:
       99.77 -   106.62: 264
      106.62 -   113.48: 6990
      113.48 -   120.33: 4844
      120.33 -   127.19: 4628
      127.19 -   134.04: 114
  Bond angle restraints: 16840
  Sorted by residual:
  angle pdb=" C7  EOL D 900 "
        pdb=" C8  EOL D 900 "
        pdb=" C9  EOL D 900 "
      ideal   model   delta    sigma   weight residual
     124.74  111.99   12.75 3.00e+00 1.11e-01 1.81e+01
  angle pdb=" C7  EOL A 900 "
        pdb=" C8  EOL A 900 "
        pdb=" C9  EOL A 900 "
      ideal   model   delta    sigma   weight residual
     124.74  112.02   12.72 3.00e+00 1.11e-01 1.80e+01
  angle pdb=" C7  EOL C 900 "
        pdb=" C8  EOL C 900 "
        pdb=" C9  EOL C 900 "
      ideal   model   delta    sigma   weight residual
     124.74  112.05   12.69 3.00e+00 1.11e-01 1.79e+01
  angle pdb=" C7  EOL B 900 "
        pdb=" C8  EOL B 900 "
        pdb=" C9  EOL B 900 "
      ideal   model   delta    sigma   weight residual
     124.74  112.05   12.69 3.00e+00 1.11e-01 1.79e+01
  angle pdb=" C   THR D 194 "
        pdb=" N   SER D 195 "
        pdb=" CA  SER D 195 "
      ideal   model   delta    sigma   weight residual
     120.26  125.27   -5.01 1.34e+00 5.57e-01 1.40e+01
  ... (remaining 16835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6487
       17.99 -    35.98: 610
       35.98 -    53.97: 155
       53.97 -    71.96: 20
       71.96 -    89.96: 4
  Dihedral angle restraints: 7276
    sinusoidal: 2768
      harmonic: 4508
  Sorted by residual:
  dihedral pdb=" CA  ILE C  21 "
           pdb=" C   ILE C  21 "
           pdb=" N   LYS C  22 "
           pdb=" CA  LYS C  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.99   20.01     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  ILE D  21 "
           pdb=" C   ILE D  21 "
           pdb=" N   LYS D  22 "
           pdb=" CA  LYS D  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.01   19.99     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  ILE B  21 "
           pdb=" C   ILE B  21 "
           pdb=" N   LYS B  22 "
           pdb=" CA  LYS B  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.02   19.98     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 7273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1151
       0.032 -    0.064: 593
       0.064 -    0.095: 180
       0.095 -    0.127: 60
       0.127 -    0.159: 32
  Chirality restraints: 2016
  Sorted by residual:
  chirality pdb=" CB  VAL B 184 "
            pdb=" CA  VAL B 184 "
            pdb=" CG1 VAL B 184 "
            pdb=" CG2 VAL B 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CB  VAL C 184 "
            pdb=" CA  VAL C 184 "
            pdb=" CG1 VAL C 184 "
            pdb=" CG2 VAL C 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.18e-01
  chirality pdb=" CB  VAL D 184 "
            pdb=" CA  VAL D 184 "
            pdb=" CG1 VAL D 184 "
            pdb=" CG2 VAL D 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.12e-01
  ... (remaining 2013 not shown)

  Planarity restraints: 2016
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  38 "    0.041 5.00e-02 4.00e+02   6.22e-02 6.18e+00
        pdb=" N   PRO B  39 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  38 "   -0.041 5.00e-02 4.00e+02   6.21e-02 6.18e+00
        pdb=" N   PRO A  39 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A  39 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  39 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C  38 "    0.041 5.00e-02 4.00e+02   6.21e-02 6.17e+00
        pdb=" N   PRO C  39 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO C  39 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  39 "    0.035 5.00e-02 4.00e+02
  ... (remaining 2013 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 4077
        2.84 -     3.36: 11778
        3.36 -     3.87: 20108
        3.87 -     4.39: 21484
        4.39 -     4.90: 37801
  Nonbonded interactions: 95248
  Sorted by model distance:
  nonbonded pdb=" O   THR A 348 "
            pdb=" OG1 THR A 352 "
     model   vdw
     2.330 2.440
  nonbonded pdb=" O   THR C 348 "
            pdb=" OG1 THR C 352 "
     model   vdw
     2.330 2.440
  nonbonded pdb=" O   THR D 348 "
            pdb=" OG1 THR D 352 "
     model   vdw
     2.330 2.440
  nonbonded pdb=" O   THR B 348 "
            pdb=" OG1 THR B 352 "
     model   vdw
     2.331 2.440
  nonbonded pdb=" OG  SER D  78 "
            pdb=" OE1 GLN D  81 "
     model   vdw
     2.388 2.440
  ... (remaining 95243 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     120      5.16       5
     C    7992      2.51       5
     N    1936      2.21       5
     O    2092      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
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:             2.300
  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:          6.830
  Check model and map are aligned:         0.190
  Convert atoms to be neutral:             0.110
  Process input model:                     35.760
  Find NCS groups from input model:        0.800
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:12.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
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      :  0.006   0.197  12416  Z= 0.405
  Angle     :  0.877  12.753  16840  Z= 0.494
  Chirality :  0.044   0.159   2016
  Planarity :  0.007   0.062   2016
  Dihedral  : 15.132  89.956   4348
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer Outliers :  1.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.19), residues: 1500
  helix: -0.77 (0.13), residues: 1188
  sheet:  None (None), residues: 0
  loop : -3.07 (0.31), residues: 312

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 251
  time to evaluate  : 1.479 
Fit side-chains
  outliers start: 20
  outliers final: 9
  residues processed: 268
  average time/residue: 0.7330
  time to fit residues: 224.1329
Evaluate side-chains
  165 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 156
  time to evaluate  : 1.461 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 9
  residues processed: 0
  time to fit residues: 2.0916
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.7980
   chunk 115 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 138 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 105 ASN
A 178 GLN
B  52 GLN
B 105 ASN
B 467 GLN
C  52 GLN
C 198 ASN
C 467 GLN
D  52 GLN
D 105 ASN
D 178 GLN
D 467 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12416  Z= 0.212
  Angle     :  0.553   6.814  16840  Z= 0.279
  Chirality :  0.037   0.135   2016
  Planarity :  0.004   0.040   2016
  Dihedral  :  4.347  29.867   1652
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer Outliers :  4.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.22), residues: 1500
  helix:  0.95 (0.15), residues: 1212
  sheet:  None (None), residues: 0
  loop : -2.73 (0.35), residues: 288

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 193
  time to evaluate  : 1.462 
Fit side-chains
  outliers start: 65
  outliers final: 28
  residues processed: 234
  average time/residue: 0.6664
  time to fit residues: 180.7054
Evaluate side-chains
  200 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 172
  time to evaluate  : 1.464 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 20
  residues processed: 11
  average time/residue: 0.1354
  time to fit residues: 4.5477
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 114 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 138 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 137 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 110 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  46 HIS
A 178 GLN
B  46 HIS
B 467 GLN
C  46 HIS
C  52 GLN
D  46 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.028  12416  Z= 0.257
  Angle     :  0.569   9.023  16840  Z= 0.284
  Chirality :  0.038   0.138   2016
  Planarity :  0.003   0.034   2016
  Dihedral  :  3.965  19.856   1652
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer Outliers :  4.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.22), residues: 1500
  helix:  1.51 (0.15), residues: 1216
  sheet:  None (None), residues: 0
  loop : -2.40 (0.37), residues: 284

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 177
  time to evaluate  : 1.381 
Fit side-chains
  outliers start: 57
  outliers final: 39
  residues processed: 211
  average time/residue: 0.6026
  time to fit residues: 148.9821
Evaluate side-chains
  197 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 158
  time to evaluate  : 1.385 
Switching outliers to nearest non-outliers
  outliers start: 39
  outliers final: 26
  residues processed: 16
  average time/residue: 0.2060
  time to fit residues: 6.7976
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 138 optimal weight:    0.6980
   chunk 146 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 131 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0170
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
C  52 GLN
C 178 GLN
D 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.021  12416  Z= 0.182
  Angle     :  0.531   8.790  16840  Z= 0.261
  Chirality :  0.037   0.134   2016
  Planarity :  0.003   0.030   2016
  Dihedral  :  3.817  19.545   1652
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer Outliers :  4.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.22), residues: 1500
  helix:  1.93 (0.15), residues: 1208
  sheet:  None (None), residues: 0
  loop : -2.02 (0.36), residues: 292

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 175
  time to evaluate  : 1.483 
Fit side-chains
  outliers start: 57
  outliers final: 29
  residues processed: 210
  average time/residue: 0.6555
  time to fit residues: 159.9114
Evaluate side-chains
  191 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 1.451 
Switching outliers to nearest non-outliers
  outliers start: 29
  outliers final: 25
  residues processed: 9
  average time/residue: 0.2674
  time to fit residues: 5.2423
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 125 optimal weight:    0.0770
   chunk 101 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 75 optimal weight:    0.7980
   chunk 131 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
C  52 GLN
C 178 GLN
D 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.022  12416  Z= 0.171
  Angle     :  0.531   8.769  16840  Z= 0.262
  Chirality :  0.036   0.140   2016
  Planarity :  0.003   0.028   2016
  Dihedral  :  3.682  19.187   1652
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer Outliers :  3.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.23), residues: 1500
  helix:  2.06 (0.15), residues: 1216
  sheet:  None (None), residues: 0
  loop : -2.10 (0.37), residues: 284

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 169
  time to evaluate  : 1.374 
Fit side-chains
  outliers start: 52
  outliers final: 38
  residues processed: 194
  average time/residue: 0.7075
  time to fit residues: 159.3336
Evaluate side-chains
  197 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 159
  time to evaluate  : 1.471 
Switching outliers to nearest non-outliers
  outliers start: 38
  outliers final: 24
  residues processed: 19
  average time/residue: 0.1687
  time to fit residues: 6.9884
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 132 optimal weight:    4.9990
   chunk 29 optimal weight:    0.2980
   chunk 86 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 147 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0170
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
C  52 GLN
C 178 GLN
D 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.023  12416  Z= 0.165
  Angle     :  0.544   8.782  16840  Z= 0.263
  Chirality :  0.036   0.157   2016
  Planarity :  0.003   0.026   2016
  Dihedral  :  3.617  18.970   1652
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer Outliers :  3.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.23), residues: 1500
  helix:  2.24 (0.15), residues: 1212
  sheet:  None (None), residues: 0
  loop : -1.99 (0.36), residues: 288

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 165
  time to evaluate  : 1.433 
Fit side-chains
  outliers start: 46
  outliers final: 35
  residues processed: 189
  average time/residue: 0.7268
  time to fit residues: 158.8215
Evaluate side-chains
  189 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 154
  time to evaluate  : 1.473 
Switching outliers to nearest non-outliers
  outliers start: 35
  outliers final: 25
  residues processed: 17
  average time/residue: 0.1684
  time to fit residues: 6.4665
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 141 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 107 optimal weight:    0.3980
   chunk 123 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 146 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
C  52 GLN
C 178 GLN
D 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12416  Z= 0.188
  Angle     :  0.574   9.343  16840  Z= 0.272
  Chirality :  0.037   0.155   2016
  Planarity :  0.003   0.025   2016
  Dihedral  :  3.572  18.597   1652
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer Outliers :  3.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.22), residues: 1500
  helix:  2.29 (0.15), residues: 1208
  sheet:  None (None), residues: 0
  loop : -1.96 (0.36), residues: 292

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 154
  time to evaluate  : 1.506 
Fit side-chains
  outliers start: 52
  outliers final: 37
  residues processed: 181
  average time/residue: 0.6914
  time to fit residues: 144.5186
Evaluate side-chains
  184 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 147
  time to evaluate  : 1.408 
Switching outliers to nearest non-outliers
  outliers start: 37
  outliers final: 25
  residues processed: 19
  average time/residue: 0.1555
  time to fit residues: 6.7452
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 87 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 93 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 115 optimal weight:    0.7980
   chunk 133 optimal weight:    0.9990
   chunk 140 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
C  52 GLN
C 178 GLN
D 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12416  Z= 0.191
  Angle     :  0.578   9.419  16840  Z= 0.272
  Chirality :  0.037   0.156   2016
  Planarity :  0.003   0.025   2016
  Dihedral  :  3.569  18.722   1652
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer Outliers :  3.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.23), residues: 1500
  helix:  2.29 (0.15), residues: 1212
  sheet:  None (None), residues: 0
  loop : -1.82 (0.36), residues: 288

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 154
  time to evaluate  : 1.449 
Fit side-chains
  outliers start: 44
  outliers final: 36
  residues processed: 177
  average time/residue: 0.7181
  time to fit residues: 146.1439
Evaluate side-chains
  185 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 149
  time to evaluate  : 1.528 
Switching outliers to nearest non-outliers
  outliers start: 36
  outliers final: 26
  residues processed: 17
  average time/residue: 0.1803
  time to fit residues: 6.8420
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.9990
   chunk 136 optimal weight:    3.9990
   chunk 140 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0570
   chunk 59 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 123 optimal weight:    0.6980
   chunk 129 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 144 optimal weight:    0.7980
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
A 467 GLN
C  52 GLN
C 178 GLN
D 178 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12416  Z= 0.196
  Angle     :  0.585   9.630  16840  Z= 0.276
  Chirality :  0.037   0.156   2016
  Planarity :  0.003   0.024   2016
  Dihedral  :  3.558  18.725   1652
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer Outliers :  2.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.22), residues: 1500
  helix:  2.29 (0.15), residues: 1216
  sheet:  None (None), residues: 0
  loop : -1.67 (0.37), residues: 284

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 154
  time to evaluate  : 1.479 
Fit side-chains
  outliers start: 37
  outliers final: 35
  residues processed: 175
  average time/residue: 0.7331
  time to fit residues: 148.3125
Evaluate side-chains
  186 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 151
  time to evaluate  : 1.544 
Switching outliers to nearest non-outliers
  outliers start: 35
  outliers final: 28
  residues processed: 17
  average time/residue: 0.1948
  time to fit residues: 7.1778
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 151 optimal weight:    0.8980
   chunk 139 optimal weight:    0.9990
   chunk 120 optimal weight:    0.0770
   chunk 12 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0270
   chunk 95 optimal weight:    0.9980
   chunk 128 optimal weight:    0.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
C  52 GLN
C 178 GLN
D 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12416  Z= 0.173
  Angle     :  0.588   9.933  16840  Z= 0.273
  Chirality :  0.037   0.163   2016
  Planarity :  0.003   0.024   2016
  Dihedral  :  3.523  19.134   1652
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer Outliers :  2.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.50 (0.23), residues: 1500
  helix:  2.37 (0.15), residues: 1212
  sheet:  None (None), residues: 0
  loop : -1.64 (0.37), residues: 288

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

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

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3000 Ramachandran restraints generated.
    1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 158
  time to evaluate  : 1.446 
Fit side-chains
  outliers start: 35
  outliers final: 32
  residues processed: 179
  average time/residue: 0.7190
  time to fit residues: 148.4756
Evaluate side-chains
  186 residues out of total 1356 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 1.469 
Switching outliers to nearest non-outliers
  outliers start: 32
  outliers final: 28
  residues processed: 14
  average time/residue: 0.1765
  time to fit residues: 5.8178
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 111 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 120 optimal weight:    0.0570
   chunk 50 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 106 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
C  52 GLN
C 178 GLN
D 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.150091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.118776 restraints weight = 17628.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 3.34
r_work: 0.3535 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3526 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work: 0.3517 rms_B_bonded: 3.10 restraints_weight: 0.1250
r_work: 0.3508 rms_B_bonded: 3.12 restraints_weight: 0.0625
r_work: 0.3500 rms_B_bonded: 3.17 restraints_weight: 0.0312
r_work: 0.3490 rms_B_bonded: 3.23 restraints_weight: 0.0156
r_work: 0.3481 rms_B_bonded: 3.30 restraints_weight: 0.0078
r_work: 0.3472 rms_B_bonded: 3.39 restraints_weight: 0.0039
r_work: 0.3463 rms_B_bonded: 3.49 restraints_weight: 0.0020
r_work: 0.3453 rms_B_bonded: 3.60 restraints_weight: 0.0010
r_work: 0.3444 rms_B_bonded: 3.72 restraints_weight: 0.0005
r_work: 0.3434 rms_B_bonded: 3.85 restraints_weight: 0.0002
r_work: 0.3424 rms_B_bonded: 4.00 restraints_weight: 0.0001
r_work: 0.3414 rms_B_bonded: 4.15 restraints_weight: 0.0001
r_work: 0.3404 rms_B_bonded: 4.32 restraints_weight: 0.0000
r_work: 0.3394 rms_B_bonded: 4.50 restraints_weight: 0.0000
r_work: 0.3383 rms_B_bonded: 4.70 restraints_weight: 0.0000
r_work: 0.3373 rms_B_bonded: 4.91 restraints_weight: 0.0000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6891
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12416  Z= 0.180
  Angle     :  0.592   9.988  16840  Z= 0.276
  Chirality :  0.037   0.158   2016
  Planarity :  0.003   0.024   2016
  Dihedral  :  3.510  18.757   1652
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer Outliers :  2.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.22), residues: 1500
  helix:  2.37 (0.15), residues: 1216
  sheet:  None (None), residues: 0
  loop : -1.54 (0.38), residues: 284

===============================================================================
Job complete
usr+sys time: 3328.80 seconds
wall clock time: 60 minutes 47.30 seconds (3647.30 seconds total)