Starting phenix.real_space_refine
on Thu Sep 18 05:22:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gtr_51565/09_2025/9gtr_51565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gtr_51565/09_2025/9gtr_51565.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gtr_51565/09_2025/9gtr_51565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gtr_51565/09_2025/9gtr_51565.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gtr_51565/09_2025/9gtr_51565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gtr_51565/09_2025/9gtr_51565.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    8979      2.51       5
     N    2583      2.21       5
     O    2754      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14343
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "q"
      Number of atoms: 4781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 641, 4781
          Classifications: {'peptide': 641}
          Link IDs: {'PTRANS': 34, 'TRANS': 606}
    Chain: "r"
      Number of atoms: 4781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 641, 4781
          Classifications: {'peptide': 641}
          Link IDs: {'PTRANS': 34, 'TRANS': 606}
    Chain: "s"
      Number of atoms: 4781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 641, 4781
          Classifications: {'peptide': 641}
          Link IDs: {'PTRANS': 34, 'TRANS': 606}
  Time building chain proxies: 3.91, per 1000 atoms: 0.27
  Number of scatterers: 14343
  At special positions: 0
  Unit cell: (95.85, 93.72, 192.765, 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      27     16.00
     O    2754      8.00
     N    2583      7.00
     C    8979      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 675.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3396

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 25 sheets defined
      10.3% alpha, 24.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'q' and resid 23 through 25
      No H-bonds generated for 'chain 'q' and resid 23 through 25'
    Processing helix  chain 'q' and resid 53 through 58
      removed outlier: 3.748A  pdb=" N   ASN q  58 " --> pdb=" O   LEU q  54 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 108 through 113
    Processing helix  chain 'q' and resid 123 through 135
    Processing helix  chain 'q' and resid 159 through 170
    Processing helix  chain 'q' and resid 259 through 267
      removed outlier: 3.720A  pdb=" N   ALA q 263 " --> pdb=" O   THR q 259 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE q 267 " --> pdb=" O   ALA q 263 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 281 through 298
    Processing helix  chain 'r' and resid 23 through 25
      No H-bonds generated for 'chain 'r' and resid 23 through 25'
    Processing helix  chain 'r' and resid 53 through 58
      removed outlier: 3.667A  pdb=" N   ASN r  58 " --> pdb=" O   LEU r  54 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 107 through 113
      removed outlier: 3.764A  pdb=" N   MET r 111 " --> pdb=" O   GLY r 107 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 124 through 135
    Processing helix  chain 'r' and resid 159 through 170
    Processing helix  chain 'r' and resid 259 through 266
      removed outlier: 3.590A  pdb=" N   ALA r 263 " --> pdb=" O   THR r 259 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 281 through 298
    Processing helix  chain 's' and resid 23 through 25
      No H-bonds generated for 'chain 's' and resid 23 through 25'
    Processing helix  chain 's' and resid 108 through 113
    Processing helix  chain 's' and resid 124 through 135
    Processing helix  chain 's' and resid 159 through 170
    Processing helix  chain 's' and resid 189 through 193
      removed outlier: 3.553A  pdb=" N   GLY s 192 " --> pdb=" O   PRO s 189 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 259 through 267
      removed outlier: 3.692A  pdb=" N   ALA s 263 " --> pdb=" O   THR s 259 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE s 267 " --> pdb=" O   ALA s 263 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 281 through 298
    Processing sheet with id=AA1, first strand: chain 'q' and resid 8 through 14
  WARNING: can't find start of bonding for strands!
    previous: chain 'q' and resid 17 through 18
    current: chain 'q' and resid 41 through 47
  WARNING: can't find start of bonding for strands!
    previous: chain 'q' and resid 41 through 47
    current: chain 'q' and resid 81 through 92
      removed outlier: 5.340A  pdb=" N   VAL q  85 " --> pdb=" O   TYR q 104 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   TYR q 104 " --> pdb=" O   VAL q  85 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'q' and resid 97 through 105
    current: chain 'q' and resid 301 through 307
  WARNING: can't find start of bonding for strands!
    previous: chain 'q' and resid 301 through 307
    current: chain 'q' and resid 345 through 353
  WARNING: can't find start of bonding for strands!
    previous: chain 'q' and resid 345 through 353
    current: chain 'r' and resid 17 through 18
  WARNING: can't find start of bonding for strands!
    previous: chain 'r' and resid 17 through 18
    current: chain 'r' and resid 41 through 47
  WARNING: can't find start of bonding for strands!
    previous: chain 'r' and resid 41 through 47
    current: chain 'r' and resid 81 through 92
      removed outlier: 5.309A  pdb=" N   VAL r  85 " --> pdb=" O   TYR r 104 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   TYR r 104 " --> pdb=" O   VAL r  85 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'r' and resid 97 through 105
    current: chain 'r' and resid 301 through 307
  WARNING: can't find start of bonding for strands!
    previous: chain 'r' and resid 301 through 307
    current: chain 'r' and resid 345 through 353
  WARNING: can't find start of bonding for strands!
    previous: chain 'r' and resid 345 through 353
    current: chain 's' and resid 17 through 18
  WARNING: can't find start of bonding for strands!
    previous: chain 's' and resid 17 through 18
    current: chain 's' and resid 41 through 47
  WARNING: can't find start of bonding for strands!
    previous: chain 's' and resid 41 through 47
    current: chain 's' and resid 81 through 92
      removed outlier: 5.312A  pdb=" N   VAL s  85 " --> pdb=" O   TYR s 104 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   TYR s 104 " --> pdb=" O   VAL s  85 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 's' and resid 97 through 105
    current: chain 's' and resid 301 through 307
  WARNING: can't find start of bonding for strands!
    previous: chain 's' and resid 301 through 307
    current: chain 's' and resid 345 through 353
    Processing sheet with id=AA2, first strand: chain 'q' and resid 114 through 120
      removed outlier: 5.808A  pdb=" N   ARG q 115 " --> pdb=" O   ASN q 156 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'q' and resid 139 through 142
      removed outlier: 7.263A  pdb=" N   PHE q 184 " --> pdb=" O   GLY q 140 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   ILE q 142 " --> pdb=" O   PHE q 184 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'q' and resid 206 through 208
    Processing sheet with id=AA5, first strand: chain 'q' and resid 240 through 247
      removed outlier: 3.757A  pdb=" N   LEU q 272 " --> pdb=" O   LYS q 228 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU q 274 " --> pdb=" O   GLU q 230 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   ARG q 232 " --> pdb=" O   GLU q 274 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'q' and resid 414 through 415
      removed outlier: 3.695A  pdb=" N   ASP q 389 " --> pdb=" O   LYS q 400 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   GLN q 402 " --> pdb=" O   VAL q 387 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   VAL q 387 " --> pdb=" O   GLN q 402 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   GLU q 436 " --> pdb=" O   GLY q 454 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   GLY q 454 " --> pdb=" O   GLU q 436 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   LEU q 438 " --> pdb=" O   ILE q 452 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   HIS q 448 " --> pdb=" O   ASP q 442 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'q' and resid 479 through 483
    Processing sheet with id=AA8, first strand: chain 'q' and resid 531 through 534
      removed outlier: 7.124A  pdb=" N   SER q 531 " --> pdb=" O   ILE r 524 " (cutoff:3.500A)
      removed outlier: 8.389A  pdb=" N   VAL r 526 " --> pdb=" O   SER q 531 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   SER q 533 " --> pdb=" O   VAL r 526 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   SER r 528 " --> pdb=" O   SER q 533 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'q' and resid 542 through 551
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 's' and resid 542 through 543
      removed outlier: 7.039A  pdb=" N   THR q 557 " --> pdb=" O   LEU r 550 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ASN r 573 " --> pdb=" O   ILE s 566 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   GLY s 568 " --> pdb=" O   ASN r 573 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   LEU q 579 " --> pdb=" O   ILE r 572 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   MET r 574 " --> pdb=" O   LEU q 579 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   GLY q 581 " --> pdb=" O   MET r 574 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   GLY q 578 " --> pdb=" O   ALA s 587 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   ASN s 589 " --> pdb=" O   GLY q 578 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL q 580 " --> pdb=" O   ASN s 589 " (cutoff:3.500A)
      removed outlier: 8.574A  pdb=" N   GLY s 591 " --> pdb=" O   VAL q 580 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   VAL q 582 " --> pdb=" O   GLY s 591 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   THR r 597 " --> pdb=" O   LEU s 590 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   THR q 604 " --> pdb=" O   ASN s 611 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   MET r 618 " --> pdb=" O   VAL s 612 " (cutoff:3.500A)
      removed outlier: 8.946A  pdb=" N   ILE s 614 " --> pdb=" O   MET r 618 " (cutoff:3.500A)
      removed outlier: 9.286A  pdb=" N   ARG r 620 " --> pdb=" O   ILE s 614 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   PHE q 626 " --> pdb=" O   PHE s 633 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'q' and resid 596 through 597
      removed outlier: 3.666A  pdb=" N   THR q 597 " --> pdb=" O   LEU r 588 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'q' and resid 611 through 614
      removed outlier: 6.137A  pdb=" N   VAL q 612 " --> pdb=" O   ARG s 620 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLU r 627 " --> pdb=" O   VAL s 621 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'r' and resid 114 through 123
      removed outlier: 5.707A  pdb=" N   ARG r 115 " --> pdb=" O   ASN r 156 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA r 117 " --> pdb=" O   GLN r 154 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ALA r 150 " --> pdb=" O   ASN r 121 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LYS r 123 " --> pdb=" O   THR r 148 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   THR r 148 " --> pdb=" O   LYS r 123 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'r' and resid 139 through 142
      removed outlier: 7.165A  pdb=" N   PHE r 184 " --> pdb=" O   GLY r 140 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   ILE r 142 " --> pdb=" O   PHE r 184 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'r' and resid 206 through 207
    Processing sheet with id=AB7, first strand: chain 'r' and resid 240 through 247
      removed outlier: 3.735A  pdb=" N   LEU r 272 " --> pdb=" O   LYS r 228 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU r 274 " --> pdb=" O   GLU r 230 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   ARG r 232 " --> pdb=" O   GLU r 274 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'r' and resid 414 through 415
      removed outlier: 3.575A  pdb=" N   VAL r 399 " --> pdb=" O   ALA r 415 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   LYS r 400 " --> pdb=" O   THR r 388 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLY r 453 " --> pdb=" O   LEU r 438 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ALA r 440 " --> pdb=" O   VAL r 451 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   VAL r 451 " --> pdb=" O   ALA r 440 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   ASP r 442 " --> pdb=" O   PRO r 449 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'r' and resid 531 through 534
      removed outlier: 7.014A  pdb=" N   SER r 531 " --> pdb=" O   ILE s 524 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   VAL s 526 " --> pdb=" O   SER r 531 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   SER r 533 " --> pdb=" O   VAL s 526 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   SER s 528 " --> pdb=" O   SER r 533 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'r' and resid 632 through 633
    Processing sheet with id=AC2, first strand: chain 's' and resid 114 through 123
      removed outlier: 5.812A  pdb=" N   ARG s 115 " --> pdb=" O   ASN s 156 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN s 156 " --> pdb=" O   ARG s 115 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA s 117 " --> pdb=" O   GLN s 154 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   ALA s 150 " --> pdb=" O   ASN s 121 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LYS s 123 " --> pdb=" O   THR s 148 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   THR s 148 " --> pdb=" O   LYS s 123 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 's' and resid 139 through 142
      removed outlier: 5.465A  pdb=" N   VAL s 139 " --> pdb=" O   PHE s 182 " (cutoff:3.500A)
      removed outlier: 9.038A  pdb=" N   PHE s 184 " --> pdb=" O   VAL s 139 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   ARG s 141 " --> pdb=" O   PHE s 184 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 's' and resid 206 through 207
    Processing sheet with id=AC5, first strand: chain 's' and resid 240 through 247
      removed outlier: 3.645A  pdb=" N   LEU s 272 " --> pdb=" O   LYS s 228 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLU s 274 " --> pdb=" O   GLU s 230 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   ARG s 232 " --> pdb=" O   GLU s 274 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 's' and resid 383 through 386
      removed outlier: 4.047A  pdb=" N   GLY s 453 " --> pdb=" O   LEU s 438 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ALA s 440 " --> pdb=" O   VAL s 451 " (cutoff:3.500A)
      removed outlier: 5.726A  pdb=" N   VAL s 451 " --> pdb=" O   ALA s 440 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ASP s 442 " --> pdb=" O   PRO s 449 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 's' and resid 470 through 471
      removed outlier: 3.966A  pdb=" N   ASP s 471 " --> pdb=" O   LYS s 476 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LYS s 476 " --> pdb=" O   ASP s 471 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC7

    298 hydrogen bonds defined for protein.
    840 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: 2.51

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2430
        1.32 -     1.44: 3698
        1.44 -     1.56: 8434
        1.56 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 14616
  Sorted by residual:
  bond pdb=" C   ARG q   3 "
       pdb=" O   ARG q   3 "
    ideal  model  delta    sigma   weight residual
    1.244  1.207  0.037 9.10e-03 1.21e+04 1.64e+01
  bond pdb=" N   THR r 630 "
       pdb=" CA  THR r 630 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.035 9.20e-03 1.18e+04 1.47e+01
  bond pdb=" C   ARG r 519 "
       pdb=" N   THR r 520 "
    ideal  model  delta    sigma   weight residual
    1.335  1.285  0.050 1.38e-02 5.25e+03 1.30e+01
  bond pdb=" CA  SER q 616 "
       pdb=" CB  SER q 616 "
    ideal  model  delta    sigma   weight residual
    1.531  1.471  0.060 1.67e-02 3.59e+03 1.29e+01
  bond pdb=" N   ILE r 632 "
       pdb=" CA  ILE r 632 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.12e-02 7.97e+03 1.16e+01
  ... (remaining 14611 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 18257
        1.28 -     2.56: 1212
        2.56 -     3.85: 298
        3.85 -     5.13: 69
        5.13 -     6.41: 12
  Bond angle restraints: 19848
  Sorted by residual:
  angle pdb=" CA  PRO q   4 "
        pdb=" C   PRO q   4 "
        pdb=" N   SER q   5 "
      ideal   model   delta    sigma   weight residual
     114.74  119.27   -4.53 1.03e+00 9.43e-01 1.93e+01
  angle pdb=" CA  ARG q   3 "
        pdb=" C   ARG q   3 "
        pdb=" N   PRO q   4 "
      ideal   model   delta    sigma   weight residual
     120.58  117.35    3.23 7.40e-01 1.83e+00 1.91e+01
  angle pdb=" N   ARG q 356 "
        pdb=" CA  ARG q 356 "
        pdb=" C   ARG q 356 "
      ideal   model   delta    sigma   weight residual
     111.28  115.87   -4.59 1.09e+00 8.42e-01 1.77e+01
  angle pdb=" C   VAL q   2 "
        pdb=" N   ARG q   3 "
        pdb=" CA  ARG q   3 "
      ideal   model   delta    sigma   weight residual
     119.83  124.20   -4.37 1.11e+00 8.12e-01 1.55e+01
  angle pdb=" N   ALA r 624 "
        pdb=" CA  ALA r 624 "
        pdb=" C   ALA r 624 "
      ideal   model   delta    sigma   weight residual
     113.38  108.65    4.73 1.23e+00 6.61e-01 1.48e+01
  ... (remaining 19843 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 7935
       17.99 -    35.98: 672
       35.98 -    53.97: 95
       53.97 -    71.97: 14
       71.97 -    89.96: 8
  Dihedral angle restraints: 8724
    sinusoidal: 3369
      harmonic: 5355
  Sorted by residual:
  dihedral pdb=" CG  ARG s 165 "
           pdb=" CD  ARG s 165 "
           pdb=" NE  ARG s 165 "
           pdb=" CZ  ARG s 165 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -20.87  -69.13     2      1.50e+01 4.44e-03 1.86e+01
  dihedral pdb=" CA  THR q 520 "
           pdb=" C   THR q 520 "
           pdb=" N   LYS q 521 "
           pdb=" CA  LYS q 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.19   19.81     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  GLN r 419 "
           pdb=" C   GLN r 419 "
           pdb=" N   MET r 420 "
           pdb=" CA  MET r 420 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.49  -18.51     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 8721 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1672
       0.051 -    0.103: 385
       0.103 -    0.154: 179
       0.154 -    0.205: 26
       0.205 -    0.257: 6
  Chirality restraints: 2268
  Sorted by residual:
  chirality pdb=" CA  PHE s 184 "
            pdb=" N   PHE s 184 "
            pdb=" C   PHE s 184 "
            pdb=" CB  PHE s 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  ILE q 614 "
            pdb=" N   ILE q 614 "
            pdb=" C   ILE q 614 "
            pdb=" CB  ILE q 614 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  VAL r 617 "
            pdb=" N   VAL r 617 "
            pdb=" C   VAL r 617 "
            pdb=" CB  VAL r 617 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 2265 not shown)

  Planarity restraints: 2604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN q 615 "    0.017 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   ASN q 615 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ASN q 615 "    0.023 2.00e-02 2.50e+03
        pdb=" N   SER q 616 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE q 614 "    0.017 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        pdb=" C   ILE q 614 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ILE q 614 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ASN q 615 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG q   3 "    0.049 5.00e-02 4.00e+02   7.45e-02 8.89e+00
        pdb=" N   PRO q   4 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO q   4 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO q   4 "    0.041 5.00e-02 4.00e+02
  ... (remaining 2601 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1418
        2.75 -     3.29: 14051
        3.29 -     3.82: 22440
        3.82 -     4.36: 26278
        4.36 -     4.90: 46487
  Nonbonded interactions: 110674
  Sorted by model distance:
  nonbonded pdb=" O   THR q 625 "
            pdb=" OG1 THR r 619 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PHE r 441 "
            pdb=" OG  SER s 381 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OG  SER q 381 "
            pdb=" O   PHE s 441 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD2 ASP q 471 "
            pdb=" OG1 THR q 497 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OD1 ASP r 105 "
            pdb=" N   TYR r 106 "
     model   vdw
     2.267 3.120
  ... (remaining 110669 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'q'
  selection = chain 'r'
  selection = chain 's'
}

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 group one per residue
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:             5.060
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.110
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6750
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14616  Z= 0.338
  Angle     :  0.765   6.411  19848  Z= 0.494
  Chirality :  0.056   0.257   2268
  Planarity :  0.006   0.090   2604
  Dihedral  : 13.186  89.957   5328
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.71 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.19), residues: 1917
  helix:  1.01 (0.39), residues: 198
  sheet: -1.17 (0.22), residues: 555
  loop : -1.66 (0.18), residues: 1164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG r 232 
 TYR   0.017   0.001   TYR q 347 
 PHE   0.017   0.002   PHE r 151 
 TRP   0.014   0.001   TRP s  31 
 HIS   0.002   0.001   HIS q 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (14616)
  covalent geometry    : angle       0.76532 (19848)
  hydrogen bonds       : bond        0.16793 (  298)
  hydrogen bonds       : angle       8.81643 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: q  111 MET cc_start: 0.5309 (ttt) cc_final: 0.4975 (ttt)
REVERT: s  542 VAL cc_start: 0.8345 (t) cc_final: 0.8123 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2305
  time to fit residues: 23.8487
Evaluate side-chains
  41 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0040
   chunk 149 optimal weight:    9.9990
   overall best weight:    4.3998

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

Flipped N/Q/H residues before XYZ refinement:
q 448 HIS
q 589 ASN
r 470 HIS
s 339 HIS
** s 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
s 611 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.039178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.033535 restraints weight = 157925.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.033952 restraints weight = 91918.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.034370 restraints weight = 61409.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.034638 restraints weight = 43682.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.034892 restraints weight = 33161.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14616  Z= 0.134
  Angle     :  0.564   5.958  19848  Z= 0.297
  Chirality :  0.046   0.149   2268
  Planarity :  0.004   0.045   2604
  Dihedral  :  4.700  19.609   2073
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.91 %
    Favored  : 93.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.19), residues: 1917
  helix:  1.57 (0.39), residues: 198
  sheet: -0.80 (0.23), residues: 519
  loop : -1.52 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG s 575 
 TYR   0.010   0.001   TYR r 332 
 PHE   0.018   0.001   PHE r 151 
 TRP   0.008   0.001   TRP s 160 
 HIS   0.004   0.001   HIS r  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (14616)
  covalent geometry    : angle       0.56425 (19848)
  hydrogen bonds       : bond        0.03027 (  298)
  hydrogen bonds       : angle       6.39144 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
REVERT: q  111 MET cc_start: 0.5600 (ttt) cc_final: 0.5336 (ttt)
REVERT: s  172 MET cc_start: 0.9016 (mmm) cc_final: 0.8749 (mmm)
REVERT: s  574 MET cc_start: 0.7451 (tpp) cc_final: 0.7192 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1487
  time to fit residues: 11.1152
Evaluate side-chains
  39 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 156 optimal weight:    0.0050
   chunk 132 optimal weight:   20.0000
   chunk 79 optimal weight:   20.0000
   chunk 16 optimal weight:    4.9990
   chunk 62 optimal weight:   50.0000
   chunk 152 optimal weight:    6.9990
   chunk 81 optimal weight:   20.0000
   chunk 47 optimal weight:    3.9990
   chunk 103 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    4.4002

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

Flipped N/Q/H residues before XYZ refinement:
q 573 ASN
r 108 HIS
** s 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.038777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.033231 restraints weight = 161183.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.033548 restraints weight = 97921.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.033986 restraints weight = 65346.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.034202 restraints weight = 45558.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.034547 restraints weight = 33869.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14616  Z= 0.129
  Angle     :  0.540   6.495  19848  Z= 0.283
  Chirality :  0.046   0.155   2268
  Planarity :  0.004   0.086   2604
  Dihedral  :  4.610  18.382   2073
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.05 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  8.01 %
    Favored  : 91.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.19), residues: 1917
  helix:  1.91 (0.40), residues: 198
  sheet: -0.87 (0.22), residues: 525
  loop : -1.46 (0.18), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG r 479 
 TYR   0.010   0.001   TYR s 175 
 PHE   0.018   0.001   PHE r 151 
 TRP   0.006   0.001   TRP s 160 
 HIS   0.004   0.001   HIS q 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (14616)
  covalent geometry    : angle       0.54014 (19848)
  hydrogen bonds       : bond        0.02555 (  298)
  hydrogen bonds       : angle       5.53751 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: q  111 MET cc_start: 0.5511 (ttt) cc_final: 0.5247 (ttt)
REVERT: q  493 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8466 (pp)
REVERT: q  574 MET cc_start: 0.7748 (tpp) cc_final: 0.7523 (tpp)
REVERT: r  493 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8444 (pp)
REVERT: r  618 MET cc_start: 0.6092 (tmm) cc_final: 0.5861 (tmm)
REVERT: s  172 MET cc_start: 0.9091 (mmm) cc_final: 0.8806 (mmm)
  outliers start: 12
  outliers final: 4
  residues processed: 52
  average time/residue: 0.1410
  time to fit residues: 11.2514
Evaluate side-chains
  46 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  134 MET
Chi-restraints excluded: chain q residue  431 MET
Chi-restraints excluded: chain q residue  493 LEU
Chi-restraints excluded: chain q residue  520 THR
Chi-restraints excluded: chain r residue  493 LEU
Chi-restraints excluded: chain s residue   59 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 153 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 127 optimal weight:    2.9990
   chunk 57 optimal weight:   50.0000
   chunk 173 optimal weight:   20.0000
   chunk 133 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 43 optimal weight:   30.0000
   chunk 97 optimal weight:   30.0000
   chunk 154 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** s 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** s 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.038668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.033030 restraints weight = 160483.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.033670 restraints weight = 96552.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.033876 restraints weight = 58570.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.034192 restraints weight = 43880.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.034395 restraints weight = 34508.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14616  Z= 0.144
  Angle     :  0.550   6.467  19848  Z= 0.286
  Chirality :  0.046   0.151   2268
  Planarity :  0.004   0.032   2604
  Dihedral  :  4.612  18.161   2073
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.00 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  9.97 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.19), residues: 1917
  helix:  1.98 (0.39), residues: 195
  sheet: -0.64 (0.23), residues: 489
  loop : -1.50 (0.17), residues: 1233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG s 575 
 TYR   0.012   0.001   TYR s 175 
 PHE   0.015   0.001   PHE r 151 
 TRP   0.006   0.001   TRP s 160 
 HIS   0.005   0.001   HIS q 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (14616)
  covalent geometry    : angle       0.55022 (19848)
  hydrogen bonds       : bond        0.02639 (  298)
  hydrogen bonds       : angle       5.28514 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: q  493 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8412 (pp)
REVERT: q  574 MET cc_start: 0.7803 (tpp) cc_final: 0.7571 (tpp)
REVERT: r  493 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8461 (pp)
REVERT: r  575 ARG cc_start: 0.8404 (mtm110) cc_final: 0.8160 (mtm110)
  outliers start: 16
  outliers final: 8
  residues processed: 56
  average time/residue: 0.1391
  time to fit residues: 11.9347
Evaluate side-chains
  50 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue   59 VAL
Chi-restraints excluded: chain q residue  116 VAL
Chi-restraints excluded: chain q residue  134 MET
Chi-restraints excluded: chain q residue  431 MET
Chi-restraints excluded: chain q residue  493 LEU
Chi-restraints excluded: chain q residue  520 THR
Chi-restraints excluded: chain r residue  493 LEU
Chi-restraints excluded: chain s residue   59 VAL
Chi-restraints excluded: chain s residue  238 THR
Chi-restraints excluded: chain s residue  493 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 119 optimal weight:   20.0000
   chunk 121 optimal weight:   50.0000
   chunk 17 optimal weight:   10.0000
   chunk 56 optimal weight:   40.0000
   chunk 151 optimal weight:   20.0000
   chunk 98 optimal weight:   30.0000
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 52 optimal weight:   40.0000
   chunk 191 optimal weight:    8.9990
   overall best weight:    8.3992

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

Flipped N/Q/H residues before XYZ refinement:
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
r 391 GLN
** s 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** s 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.038251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.032697 restraints weight = 159922.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.033203 restraints weight = 95505.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.033571 restraints weight = 59156.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.033789 restraints weight = 43686.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.034092 restraints weight = 30880.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  14616  Z= 0.207
  Angle     :  0.610   7.755  19848  Z= 0.316
  Chirality :  0.046   0.151   2268
  Planarity :  0.005   0.041   2604
  Dihedral  :  4.970  18.410   2073
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.99 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.68 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.19), residues: 1917
  helix:  1.72 (0.38), residues: 195
  sheet: -0.69 (0.23), residues: 489
  loop : -1.65 (0.17), residues: 1233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG q 359 
 TYR   0.020   0.002   TYR s 175 
 PHE   0.019   0.002   PHE r 184 
 TRP   0.008   0.001   TRP q 414 
 HIS   0.007   0.002   HIS s 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (14616)
  covalent geometry    : angle       0.61002 (19848)
  hydrogen bonds       : bond        0.02941 (  298)
  hydrogen bonds       : angle       5.38315 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
REVERT: q  172 MET cc_start: 0.8759 (mmm) cc_final: 0.8430 (mmm)
REVERT: q  493 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8398 (pp)
REVERT: r  493 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8443 (pp)
  outliers start: 17
  outliers final: 9
  residues processed: 55
  average time/residue: 0.1180
  time to fit residues: 10.4892
Evaluate side-chains
  47 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue   59 VAL
Chi-restraints excluded: chain q residue  116 VAL
Chi-restraints excluded: chain q residue  134 MET
Chi-restraints excluded: chain q residue  431 MET
Chi-restraints excluded: chain q residue  493 LEU
Chi-restraints excluded: chain q residue  520 THR
Chi-restraints excluded: chain r residue  493 LEU
Chi-restraints excluded: chain r residue  611 ASN
Chi-restraints excluded: chain s residue   59 VAL
Chi-restraints excluded: chain s residue  493 LEU
Chi-restraints excluded: chain s residue  630 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 157 optimal weight:    5.9990
   chunk 161 optimal weight:    8.9990
   chunk 73 optimal weight:    5.9990
   chunk 187 optimal weight:   50.0000
   chunk 39 optimal weight:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 48 optimal weight:   20.0000
   chunk 159 optimal weight:    2.9990
   chunk 178 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 45 optimal weight:   20.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** s 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
s 611 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.038405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.032878 restraints weight = 159961.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.033365 restraints weight = 96657.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.033702 restraints weight = 57490.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.033886 restraints weight = 42145.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.034040 restraints weight = 34320.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14616  Z= 0.151
  Angle     :  0.568  11.198  19848  Z= 0.292
  Chirality :  0.046   0.153   2268
  Planarity :  0.004   0.050   2604
  Dihedral  :  4.782  18.822   2073
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.42 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.73 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.19), residues: 1917
  helix:  1.81 (0.38), residues: 195
  sheet: -0.64 (0.24), residues: 489
  loop : -1.62 (0.17), residues: 1233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG r 575 
 TYR   0.014   0.001   TYR s 175 
 PHE   0.015   0.001   PHE r 151 
 TRP   0.007   0.001   TRP r  31 
 HIS   0.005   0.001   HIS q 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (14616)
  covalent geometry    : angle       0.56814 (19848)
  hydrogen bonds       : bond        0.02526 (  298)
  hydrogen bonds       : angle       5.28338 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: q  172 MET cc_start: 0.8785 (mmm) cc_final: 0.8117 (mmm)
REVERT: q  420 MET cc_start: 0.8050 (ttm) cc_final: 0.7770 (ttt)
REVERT: q  493 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8365 (pp)
REVERT: r  493 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8461 (pp)
REVERT: r  575 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7416 (ptt90)
  outliers start: 18
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1228
  time to fit residues: 10.7039
Evaluate side-chains
  45 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  116 VAL
Chi-restraints excluded: chain q residue  493 LEU
Chi-restraints excluded: chain r residue   65 VAL
Chi-restraints excluded: chain r residue  104 TYR
Chi-restraints excluded: chain r residue  493 LEU
Chi-restraints excluded: chain s residue   59 VAL
Chi-restraints excluded: chain s residue  493 LEU
Chi-restraints excluded: chain s residue  630 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 170 optimal weight:   30.0000
   chunk 157 optimal weight:    8.9990
   chunk 159 optimal weight:    6.9990
   chunk 99 optimal weight:    9.9990
   chunk 167 optimal weight:   20.0000
   chunk 85 optimal weight:   30.0000
   chunk 40 optimal weight:    9.9990
   chunk 34 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 127 optimal weight:   20.0000
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
r 211 HIS
s 396 GLN
** s 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
s 611 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.038164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.032711 restraints weight = 161502.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.033210 restraints weight = 98150.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.033615 restraints weight = 57921.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.033716 restraints weight = 42682.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.033881 restraints weight = 35010.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  14616  Z= 0.199
  Angle     :  0.610   9.366  19848  Z= 0.315
  Chirality :  0.047   0.214   2268
  Planarity :  0.004   0.039   2604
  Dihedral  :  4.975  18.605   2073
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.77 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.12 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.19), residues: 1917
  helix:  1.65 (0.38), residues: 198
  sheet: -0.63 (0.24), residues: 471
  loop : -1.74 (0.17), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG r 575 
 TYR   0.018   0.001   TYR s 175 
 PHE   0.022   0.002   PHE r 184 
 TRP   0.008   0.001   TRP r 160 
 HIS   0.006   0.002   HIS s 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (14616)
  covalent geometry    : angle       0.60973 (19848)
  hydrogen bonds       : bond        0.02868 (  298)
  hydrogen bonds       : angle       5.36110 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: q   50 TYR cc_start: 0.4495 (OUTLIER) cc_final: 0.2104 (m-80)
REVERT: q  172 MET cc_start: 0.8764 (mmm) cc_final: 0.8458 (mmm)
REVERT: q  420 MET cc_start: 0.8068 (ttm) cc_final: 0.7755 (ttt)
REVERT: q  493 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8213 (pp)
REVERT: r  493 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8484 (pp)
REVERT: r  575 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7404 (ptt90)
REVERT: s  172 MET cc_start: 0.8689 (mmm) cc_final: 0.8169 (mmm)
  outliers start: 21
  outliers final: 9
  residues processed: 57
  average time/residue: 0.1235
  time to fit residues: 11.1354
Evaluate side-chains
  49 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue   50 TYR
Chi-restraints excluded: chain q residue  116 VAL
Chi-restraints excluded: chain q residue  134 MET
Chi-restraints excluded: chain q residue  364 LEU
Chi-restraints excluded: chain q residue  431 MET
Chi-restraints excluded: chain q residue  493 LEU
Chi-restraints excluded: chain r residue   65 VAL
Chi-restraints excluded: chain r residue  104 TYR
Chi-restraints excluded: chain r residue  493 LEU
Chi-restraints excluded: chain s residue   59 VAL
Chi-restraints excluded: chain s residue  493 LEU
Chi-restraints excluded: chain s residue  632 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 190 optimal weight:    6.9990
   chunk 100 optimal weight:   30.0000
   chunk 104 optimal weight:    0.7980
   chunk 113 optimal weight:    3.9990
   chunk 101 optimal weight:   20.0000
   chunk 68 optimal weight:    6.9990
   chunk 130 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 127 optimal weight:    8.9990
   chunk 43 optimal weight:   30.0000
   chunk 188 optimal weight:   20.0000
   overall best weight:    5.1588

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

Flipped N/Q/H residues before XYZ refinement:
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s 611 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.038370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.032882 restraints weight = 158997.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.033253 restraints weight = 96680.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.033650 restraints weight = 62786.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.033959 restraints weight = 44942.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.034084 restraints weight = 34131.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14616  Z= 0.137
  Angle     :  0.563  10.883  19848  Z= 0.291
  Chirality :  0.046   0.205   2268
  Planarity :  0.004   0.032   2604
  Dihedral  :  4.743  19.419   2073
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.00 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 13.32 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.19), residues: 1917
  helix:  1.86 (0.38), residues: 198
  sheet: -0.59 (0.24), residues: 477
  loop : -1.64 (0.17), residues: 1242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG r 575 
 TYR   0.011   0.001   TYR s 175 
 PHE   0.015   0.001   PHE r 151 
 TRP   0.006   0.001   TRP r 160 
 HIS   0.004   0.001   HIS s 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (14616)
  covalent geometry    : angle       0.56293 (19848)
  hydrogen bonds       : bond        0.02459 (  298)
  hydrogen bonds       : angle       5.22441 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: q   50 TYR cc_start: 0.4458 (OUTLIER) cc_final: 0.2146 (m-80)
REVERT: q  420 MET cc_start: 0.7955 (ttm) cc_final: 0.7627 (ttt)
REVERT: q  493 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8206 (pp)
REVERT: r  493 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8469 (pp)
REVERT: r  575 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7412 (ptt90)
REVERT: s  172 MET cc_start: 0.8721 (mmm) cc_final: 0.8198 (mmm)
  outliers start: 14
  outliers final: 8
  residues processed: 52
  average time/residue: 0.1415
  time to fit residues: 11.2508
Evaluate side-chains
  50 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue   50 TYR
Chi-restraints excluded: chain q residue   68 THR
Chi-restraints excluded: chain q residue  116 VAL
Chi-restraints excluded: chain q residue  364 LEU
Chi-restraints excluded: chain q residue  437 VAL
Chi-restraints excluded: chain q residue  493 LEU
Chi-restraints excluded: chain r residue  104 TYR
Chi-restraints excluded: chain r residue  493 LEU
Chi-restraints excluded: chain s residue   59 VAL
Chi-restraints excluded: chain s residue  493 LEU
Chi-restraints excluded: chain s residue  632 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 119 optimal weight:   20.0000
   chunk 169 optimal weight:    9.9990
   chunk 184 optimal weight:   50.0000
   chunk 9 optimal weight:   20.0000
   chunk 92 optimal weight:    7.9990
   chunk 112 optimal weight:   10.0000
   chunk 12 optimal weight:   30.0000
   chunk 51 optimal weight:   30.0000
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0970
   overall best weight:    5.2186

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

Flipped N/Q/H residues before XYZ refinement:
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
s 611 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.038413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.032911 restraints weight = 160655.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.033400 restraints weight = 97334.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.033813 restraints weight = 56867.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.034063 restraints weight = 41159.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.034150 restraints weight = 31057.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14616  Z= 0.139
  Angle     :  0.570  12.682  19848  Z= 0.291
  Chirality :  0.046   0.200   2268
  Planarity :  0.004   0.032   2604
  Dihedral  :  4.692  19.001   2073
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.20 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 13.32 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.19), residues: 1917
  helix:  1.97 (0.38), residues: 198
  sheet: -0.59 (0.24), residues: 468
  loop : -1.63 (0.17), residues: 1251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG r 575 
 TYR   0.011   0.001   TYR s 175 
 PHE   0.015   0.001   PHE r 151 
 TRP   0.007   0.001   TRP r 160 
 HIS   0.004   0.001   HIS s 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (14616)
  covalent geometry    : angle       0.57048 (19848)
  hydrogen bonds       : bond        0.02459 (  298)
  hydrogen bonds       : angle       5.15524 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: q   50 TYR cc_start: 0.4545 (OUTLIER) cc_final: 0.2260 (m-80)
REVERT: q  493 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8227 (pp)
REVERT: r  493 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8453 (pp)
REVERT: r  575 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7765 (mtm110)
  outliers start: 16
  outliers final: 10
  residues processed: 53
  average time/residue: 0.1488
  time to fit residues: 11.9255
Evaluate side-chains
  52 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue   50 TYR
Chi-restraints excluded: chain q residue   68 THR
Chi-restraints excluded: chain q residue  116 VAL
Chi-restraints excluded: chain q residue  134 MET
Chi-restraints excluded: chain q residue  364 LEU
Chi-restraints excluded: chain q residue  437 VAL
Chi-restraints excluded: chain q residue  493 LEU
Chi-restraints excluded: chain r residue  104 TYR
Chi-restraints excluded: chain r residue  174 MET
Chi-restraints excluded: chain r residue  493 LEU
Chi-restraints excluded: chain s residue   59 VAL
Chi-restraints excluded: chain s residue  493 LEU
Chi-restraints excluded: chain s residue  632 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 123 optimal weight:   50.0000
   chunk 150 optimal weight:    0.0000
   chunk 82 optimal weight:    0.0970
   chunk 78 optimal weight:   20.0000
   chunk 115 optimal weight:    5.9990
   chunk 55 optimal weight:   40.0000
   chunk 156 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0870
   chunk 84 optimal weight:   30.0000
   chunk 10 optimal weight:    9.9990
   overall best weight:    2.6364

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

Flipped N/Q/H residues before XYZ refinement:
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
s 396 GLN
s 611 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.038769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.033223 restraints weight = 158287.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.033738 restraints weight = 94409.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.034023 restraints weight = 57840.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.034200 restraints weight = 44160.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.034574 restraints weight = 34177.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  14616  Z= 0.097
  Angle     :  0.545  10.308  19848  Z= 0.278
  Chirality :  0.046   0.187   2268
  Planarity :  0.004   0.031   2604
  Dihedral  :  4.470  19.708   2073
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 13.91 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.19), residues: 1917
  helix:  2.18 (0.38), residues: 198
  sheet: -0.52 (0.24), residues: 486
  loop : -1.48 (0.17), residues: 1233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG r 575 
 TYR   0.009   0.001   TYR q 332 
 PHE   0.012   0.001   PHE r 151 
 TRP   0.008   0.001   TRP r 160 
 HIS   0.003   0.001   HIS q 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (14616)
  covalent geometry    : angle       0.54498 (19848)
  hydrogen bonds       : bond        0.02142 (  298)
  hydrogen bonds       : angle       5.03559 (  840)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: q  493 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8197 (pp)
REVERT: r  493 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8439 (pp)
REVERT: r  575 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7727 (mtm110)
  outliers start: 11
  outliers final: 7
  residues processed: 46
  average time/residue: 0.1518
  time to fit residues: 10.6087
Evaluate side-chains
  44 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue   68 THR
Chi-restraints excluded: chain q residue  116 VAL
Chi-restraints excluded: chain q residue  134 MET
Chi-restraints excluded: chain q residue  493 LEU
Chi-restraints excluded: chain r residue  174 MET
Chi-restraints excluded: chain r residue  493 LEU
Chi-restraints excluded: chain s residue   59 VAL
Chi-restraints excluded: chain s residue  493 LEU
Chi-restraints excluded: chain s residue  632 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 125 optimal weight:    8.9990
   chunk 65 optimal weight:    8.9990
   chunk 166 optimal weight:   30.0000
   chunk 81 optimal weight:   20.0000
   chunk 74 optimal weight:   20.0000
   chunk 83 optimal weight:    4.9990
   chunk 190 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0030
   chunk 29 optimal weight:    0.0370
   chunk 71 optimal weight:   30.0000
   chunk 155 optimal weight:    5.9990
   overall best weight:    3.8074

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

Flipped N/Q/H residues before XYZ refinement:
** q 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** r 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
s 611 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.038707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.033165 restraints weight = 158592.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.033542 restraints weight = 95427.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.033775 restraints weight = 64982.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.034055 restraints weight = 48934.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.034386 restraints weight = 38107.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14616  Z= 0.114
  Angle     :  0.553  10.168  19848  Z= 0.283
  Chirality :  0.046   0.185   2268
  Planarity :  0.004   0.031   2604
  Dihedral  :  4.474  19.339   2073
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 13.85 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.19), residues: 1917
  helix:  2.11 (0.38), residues: 201
  sheet: -0.51 (0.24), residues: 486
  loop : -1.44 (0.17), residues: 1230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG r 575 
 TYR   0.008   0.001   TYR s 175 
 PHE   0.013   0.001   PHE r 151 
 TRP   0.007   0.001   TRP r 160 
 HIS   0.003   0.001   HIS s 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (14616)
  covalent geometry    : angle       0.55345 (19848)
  hydrogen bonds       : bond        0.02204 (  298)
  hydrogen bonds       : angle       4.99589 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2109.52 seconds
wall clock time: 37 minutes 31.60 seconds (2251.60 seconds total)