Starting phenix.real_space_refine
on Wed Mar  4 12:08:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ld5_23282/03_2026/7ld5_23282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ld5_23282/03_2026/7ld5_23282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ld5_23282/03_2026/7ld5_23282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ld5_23282/03_2026/7ld5_23282.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ld5_23282/03_2026/7ld5_23282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ld5_23282/03_2026/7ld5_23282.map"
  }
  resolution = 3.07
  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=  -0.001 sd=   0.110
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: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      6      5.21       5
     S      54      5.16       5
     C    8451      2.51       5
     N    2358      2.21       5
     O    2664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 132 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13542
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4416
          Classifications: {'peptide': 587}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 555}
    Chain: "D"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 96
          Classifications: {'DNA': 1, 'RNA': 4}
          Modifications used: {'5*END': 2, 'rna3p_pur': 4}
          Link IDs: {'rna3p': 4}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, E, F
  Residues with excluded nonbonded symmetry interactions: 15
    residue:
      pdb=" O5'   A D   1 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C4    A D   1 " occ=0.30
    residue:
      pdb=" P     A D   2 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A D   2 " occ=0.30
    residue:
      pdb=" P     A D   3 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A D   3 " occ=0.30
    residue:
      pdb=" P     A D   4 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A D   4 " occ=0.30
    residue:
      pdb=" C1'   A D   9 " occ=0.30
      ... (9 atoms not shown)
      pdb=" C4    A D   9 " occ=0.30
    residue:
      pdb=" O5'   A E   1 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C4    A E   1 " occ=0.30
    residue:
      pdb=" P     A E   2 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A E   2 " occ=0.30
    residue:
      pdb=" P     A E   3 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A E   3 " occ=0.30
    residue:
      pdb=" P     A E   4 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A E   4 " occ=0.30
    residue:
      pdb=" C1'   A E   9 " occ=0.30
      ... (9 atoms not shown)
      pdb=" C4    A E   9 " occ=0.30
    residue:
      pdb=" O5'   A F   1 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C4    A F   1 " occ=0.30
    residue:
      pdb=" P     A F   2 " occ=0.30
      ... (20 atoms not shown)
      pdb=" C4    A F   2 " occ=0.30
    ... (remaining 3 not shown)
  Time building chain proxies: 3.67, per 1000 atoms: 0.27
  Number of scatterers: 13542
  At special positions: 0
  Unit cell: (114.912, 122.36, 89.376, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      54     16.00
     P       9     15.00
     Mg      6     11.99
     O    2664      8.00
     N    2358      7.00
     C    8451      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: 1.13
  Conformation dependent library (CDL) restraints added in 625.3 milliseconds
  

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3240

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 12 sheets defined
      37.8% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 97 through 112
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 138 through 153
      removed outlier: 4.043A  pdb=" N   ASN A 144 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA A 153 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 224
    Processing helix  chain 'A' and resid 229 through 240
    Processing helix  chain 'A' and resid 240 through 258
      removed outlier: 3.520A  pdb=" N   ILE A 244 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 292
      removed outlier: 3.657A  pdb=" N   TYR A 276 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLU A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ALA A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 314
    Processing helix  chain 'A' and resid 321 through 345
    Processing helix  chain 'A' and resid 390 through 394
    Processing helix  chain 'A' and resid 415 through 419
      removed outlier: 3.629A  pdb=" N   THR A 419 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 441
      removed outlier: 3.587A  pdb=" N   ILE A 433 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 447
    Processing helix  chain 'A' and resid 470 through 485
    Processing helix  chain 'A' and resid 523 through 527
      removed outlier: 3.594A  pdb=" N   ASP A 526 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 581
      removed outlier: 4.005A  pdb=" N   GLU A 579 " --> pdb=" O   ASP A 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA A 580 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE A 581 " --> pdb=" O   MET A 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 97 through 112
      Proline residue:  B 110  - end of helix
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 138 through 153
      removed outlier: 4.044A  pdb=" N   ASN B 144 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA B 153 " --> pdb=" O   SER B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 229 through 240
    Processing helix  chain 'B' and resid 240 through 258
      removed outlier: 3.520A  pdb=" N   ILE B 244 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 292
      removed outlier: 3.657A  pdb=" N   TYR B 276 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLU B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ALA B 286 " --> pdb=" O   VAL B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 314
    Processing helix  chain 'B' and resid 321 through 345
    Processing helix  chain 'B' and resid 390 through 394
    Processing helix  chain 'B' and resid 415 through 419
      removed outlier: 3.629A  pdb=" N   THR B 419 " --> pdb=" O   PRO B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 441
      removed outlier: 3.588A  pdb=" N   ILE B 433 " --> pdb=" O   LYS B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 447
    Processing helix  chain 'B' and resid 470 through 485
    Processing helix  chain 'B' and resid 523 through 527
      removed outlier: 3.595A  pdb=" N   ASP B 526 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 581
      removed outlier: 4.005A  pdb=" N   GLU B 579 " --> pdb=" O   ASP B 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA B 580 " --> pdb=" O   VAL B 576 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE B 581 " --> pdb=" O   MET B 577 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 83
    Processing helix  chain 'C' and resid 97 through 112
      Proline residue:  C 110  - end of helix
    Processing helix  chain 'C' and resid 113 through 115
      No H-bonds generated for 'chain 'C' and resid 113 through 115'
    Processing helix  chain 'C' and resid 138 through 153
      removed outlier: 4.043A  pdb=" N   ASN C 144 " --> pdb=" O   VAL C 140 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA C 153 " --> pdb=" O   SER C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 224
    Processing helix  chain 'C' and resid 229 through 240
    Processing helix  chain 'C' and resid 240 through 258
      removed outlier: 3.520A  pdb=" N   ILE C 244 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 292
      removed outlier: 3.657A  pdb=" N   TYR C 276 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLU C 285 " --> pdb=" O   SER C 281 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ALA C 286 " --> pdb=" O   VAL C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 314
    Processing helix  chain 'C' and resid 321 through 345
    Processing helix  chain 'C' and resid 390 through 394
    Processing helix  chain 'C' and resid 415 through 419
      removed outlier: 3.629A  pdb=" N   THR C 419 " --> pdb=" O   PRO C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 441
      removed outlier: 3.588A  pdb=" N   ILE C 433 " --> pdb=" O   LYS C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 447
    Processing helix  chain 'C' and resid 470 through 485
    Processing helix  chain 'C' and resid 523 through 527
      removed outlier: 3.594A  pdb=" N   ASP C 526 " --> pdb=" O   GLY C 523 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 581
      removed outlier: 4.004A  pdb=" N   GLU C 579 " --> pdb=" O   ASP C 575 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA C 580 " --> pdb=" O   VAL C 576 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE C 581 " --> pdb=" O   MET C 577 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 18
      removed outlier: 6.206A  pdb=" N   MET A  51 " --> pdb=" O   MET A 130 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175
      removed outlier: 4.424A  pdb=" N   PHE A 187 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   VAL A 186 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   ALA A 213 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP A 188 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA A 211 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A 190 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL A 209 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA A 192 " --> pdb=" O   MET A 207 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   MET A 207 " --> pdb=" O   THR A 549 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR A 543 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363
      removed outlier: 6.303A  pdb=" N   GLN A 381 " --> pdb=" O   LEU A 464 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET A 409 " --> pdb=" O   GLN A 459 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   SER A 461 " --> pdb=" O   MET A 409 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS A 411 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ALA A 463 " --> pdb=" O   HIS A 411 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ASN A 413 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   GLY A 465 " --> pdb=" O   ASN A 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 18
      removed outlier: 6.206A  pdb=" N   MET B  51 " --> pdb=" O   MET B 130 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175
      removed outlier: 4.425A  pdb=" N   PHE B 187 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   VAL B 186 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ALA B 213 " --> pdb=" O   VAL B 186 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP B 188 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA B 211 " --> pdb=" O   ASP B 188 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL B 190 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL B 209 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA B 192 " --> pdb=" O   MET B 207 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   MET B 207 " --> pdb=" O   THR B 549 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR B 543 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 363
      removed outlier: 6.303A  pdb=" N   GLN B 381 " --> pdb=" O   LEU B 464 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET B 409 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   SER B 461 " --> pdb=" O   MET B 409 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS B 411 " --> pdb=" O   SER B 461 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   ALA B 463 " --> pdb=" O   HIS B 411 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   ASN B 413 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   GLY B 465 " --> pdb=" O   ASN B 413 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 396
    Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 18
      removed outlier: 6.206A  pdb=" N   MET C  51 " --> pdb=" O   MET C 130 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 172 through 175
      removed outlier: 4.425A  pdb=" N   PHE C 187 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   VAL C 186 " --> pdb=" O   ALA C 213 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ALA C 213 " --> pdb=" O   VAL C 186 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASP C 188 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA C 211 " --> pdb=" O   ASP C 188 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL C 190 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL C 209 " --> pdb=" O   VAL C 190 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ALA C 192 " --> pdb=" O   MET C 207 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   MET C 207 " --> pdb=" O   THR C 549 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR C 543 " --> pdb=" O   ALA C 213 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 359 through 363
      removed outlier: 6.304A  pdb=" N   GLN C 381 " --> pdb=" O   LEU C 464 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET C 409 " --> pdb=" O   GLN C 459 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   SER C 461 " --> pdb=" O   MET C 409 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS C 411 " --> pdb=" O   SER C 461 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ALA C 463 " --> pdb=" O   HIS C 411 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ASN C 413 " --> pdb=" O   ALA C 463 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLY C 465 " --> pdb=" O   ASN C 413 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 395 through 396

    720 hydrogen bonds defined for protein.
    1980 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: 2.38

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4601
        1.34 -     1.45: 1539
        1.45 -     1.57: 7531
        1.57 -     1.69: 18
        1.69 -     1.80: 99
  Bond restraints: 13788
  Sorted by residual:
  bond pdb=" CB  GLU A 298 "
       pdb=" CG  GLU A 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.19e+00
  bond pdb=" CB  GLU C 298 "
       pdb=" CG  GLU C 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.16e+00
  bond pdb=" CB  GLU B 298 "
       pdb=" CG  GLU B 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.10e+00
  bond pdb=" CA  ILE C 366 "
       pdb=" CB  ILE C 366 "
    ideal  model  delta    sigma   weight residual
    1.537  1.523  0.014 1.29e-02 6.01e+03 1.25e+00
  bond pdb=" CA  ILE B 366 "
       pdb=" CB  ILE B 366 "
    ideal  model  delta    sigma   weight residual
    1.537  1.523  0.014 1.29e-02 6.01e+03 1.20e+00
  ... (remaining 13783 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 18417
        1.88 -     3.77: 315
        3.77 -     5.65: 30
        5.65 -     7.53: 6
        7.53 -     9.42: 6
  Bond angle restraints: 18774
  Sorted by residual:
  angle pdb=" CA  GLU A 298 "
        pdb=" CB  GLU A 298 "
        pdb=" CG  GLU A 298 "
      ideal   model   delta    sigma   weight residual
     114.10  123.52   -9.42 2.00e+00 2.50e-01 2.22e+01
  angle pdb=" CA  GLU B 298 "
        pdb=" CB  GLU B 298 "
        pdb=" CG  GLU B 298 "
      ideal   model   delta    sigma   weight residual
     114.10  123.49   -9.39 2.00e+00 2.50e-01 2.21e+01
  angle pdb=" CA  GLU C 298 "
        pdb=" CB  GLU C 298 "
        pdb=" CG  GLU C 298 "
      ideal   model   delta    sigma   weight residual
     114.10  123.48   -9.38 2.00e+00 2.50e-01 2.20e+01
  angle pdb=" CG1 ILE B 293 "
        pdb=" CB  ILE B 293 "
        pdb=" CG2 ILE B 293 "
      ideal   model   delta    sigma   weight residual
     110.70  101.52    9.18 3.00e+00 1.11e-01 9.36e+00
  angle pdb=" CG1 ILE C 293 "
        pdb=" CB  ILE C 293 "
        pdb=" CG2 ILE C 293 "
      ideal   model   delta    sigma   weight residual
     110.70  101.54    9.16 3.00e+00 1.11e-01 9.31e+00
  ... (remaining 18769 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.59: 7259
       16.59 -    33.19: 768
       33.19 -    49.78: 256
       49.78 -    66.38: 54
       66.38 -    82.97: 15
  Dihedral angle restraints: 8352
    sinusoidal: 3312
      harmonic: 5040
  Sorted by residual:
  dihedral pdb=" CA  VAL C 507 "
           pdb=" C   VAL C 507 "
           pdb=" N   ASP C 508 "
           pdb=" CA  ASP C 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.33  -17.67     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  VAL B 507 "
           pdb=" C   VAL B 507 "
           pdb=" N   ASP B 508 "
           pdb=" CA  ASP B 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  VAL A 507 "
           pdb=" C   VAL A 507 "
           pdb=" N   ASP A 508 "
           pdb=" CA  ASP A 508 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 8349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1553
       0.046 -    0.091: 483
       0.091 -    0.137: 136
       0.137 -    0.183: 9
       0.183 -    0.229: 3
  Chirality restraints: 2184
  Sorted by residual:
  chirality pdb=" CB  ILE B 293 "
            pdb=" CA  ILE B 293 "
            pdb=" CG1 ILE B 293 "
            pdb=" CG2 ILE B 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CB  ILE C 293 "
            pdb=" CA  ILE C 293 "
            pdb=" CG1 ILE C 293 "
            pdb=" CG2 ILE C 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CB  ILE A 293 "
            pdb=" CA  ILE A 293 "
            pdb=" CG1 ILE A 293 "
            pdb=" CG2 ILE A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 2181 not shown)

  Planarity restraints: 2439
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 444 "   -0.033 5.00e-02 4.00e+02   4.90e-02 3.84e+00
        pdb=" N   PRO C 445 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO C 445 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 445 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 444 "   -0.033 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO B 445 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 445 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 445 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 444 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.80e+00
        pdb=" N   PRO A 445 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 445 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 445 "    0.027 5.00e-02 4.00e+02
  ... (remaining 2436 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 273
        2.66 -     3.22: 12389
        3.22 -     3.78: 19572
        3.78 -     4.34: 28398
        4.34 -     4.90: 48333
  Nonbonded interactions: 108965
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 418 "
            pdb=" O   ALA B 463 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OG  SER A 418 "
            pdb=" O   ALA A 463 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OG  SER C 418 "
            pdb=" O   ALA C 463 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" OE2 GLU C  77 "
            pdb=" OH  TYR C 138 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" OE2 GLU B  77 "
            pdb=" OH  TYR B 138 "
     model   vdw
     2.153 3.040
  ... (remaining 108960 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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=0.30 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.140
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  13788  Z= 0.262
  Angle     :  0.671   9.415  18774  Z= 0.375
  Chirality :  0.048   0.229   2184
  Planarity :  0.004   0.049   2439
  Dihedral  : 16.010  82.970   5112
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 15.84 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole: -2.06 (0.18), residues: 1755
  helix: -0.76 (0.20), residues: 549
  sheet: -0.72 (0.23), residues: 444
  loop : -2.17 (0.21), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 313 
 TYR   0.011   0.002   TYR A  45 
 PHE   0.016   0.001   PHE A 157 
 TRP   0.003   0.001   TRP B 173 
 HIS   0.001   0.000   HIS B 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 (13788)
  covalent geometry    : angle       0.67138 (18774)
  hydrogen bonds       : bond        0.14108 (  720)
  hydrogen bonds       : angle       6.74148 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 193
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.7657 (ptpp) cc_final: 0.7378 (ptpt)
REVERT: A   79 MET cc_start: 0.8695 (tpp) cc_final: 0.8370 (tpp)
REVERT: A  130 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7981 (mtt)
REVERT: A  356 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7221 (mt)
REVERT: B   74 ASP cc_start: 0.7829 (m-30) cc_final: 0.7628 (m-30)
REVERT: B  329 PHE cc_start: 0.8412 (t80) cc_final: 0.8060 (t80)
REVERT: B  348 ILE cc_start: 0.8425 (pt) cc_final: 0.8210 (pt)
REVERT: B  356 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7441 (mt)
REVERT: B  397 ILE cc_start: 0.8574 (mm) cc_final: 0.8334 (mm)
REVERT: C   63 LYS cc_start: 0.7607 (ptpp) cc_final: 0.7272 (ptpp)
REVERT: C   95 ARG cc_start: 0.7801 (ptt180) cc_final: 0.7391 (ptm-80)
REVERT: C  122 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7202 (tm-30)
REVERT: C  130 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8291 (mtt)
REVERT: C  383 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8176 (tp)
  outliers start: 90
  outliers final: 49
  residues processed: 272
  average time/residue: 0.1134
  time to fit residues: 45.9204
Evaluate side-chains
  223 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 168
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  549 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   59 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  130 MET
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  383 LEU
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  422 THR
Chi-restraints excluded: chain C residue  449 SER
Chi-restraints excluded: chain C residue  471 SER
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    0.3980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A  61 ASN
A 339 GLN
A 381 GLN
A 546 GLN
B  61 ASN
B 339 GLN
B 381 GLN
B 546 GLN
C  36 GLN
C  61 ASN
C 381 GLN
C 396 GLN
C 546 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.165984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.125632 restraints weight = 14388.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.94
r_work: 0.3349 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13788  Z= 0.129
  Angle     :  0.532   5.324  18774  Z= 0.280
  Chirality :  0.044   0.133   2184
  Planarity :  0.004   0.034   2439
  Dihedral  :  6.634  48.845   2123
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.93 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole: -0.54 (0.20), residues: 1755
  helix:  1.02 (0.21), residues: 558
  sheet: -0.23 (0.23), residues: 444
  loop : -1.48 (0.22), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 330 
 TYR   0.012   0.001   TYR C  80 
 PHE   0.014   0.001   PHE A 157 
 TRP   0.010   0.002   TRP B 173 
 HIS   0.001   0.000   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (13788)
  covalent geometry    : angle       0.53224 (18774)
  hydrogen bonds       : bond        0.03735 (  720)
  hydrogen bonds       : angle       5.07298 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 182
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.7566 (ptpp) cc_final: 0.7009 (ptpt)
REVERT: A  122 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7579 (tm-30)
REVERT: A  330 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7417 (mtm-85)
REVERT: B   74 ASP cc_start: 0.8626 (m-30) cc_final: 0.8377 (m-30)
REVERT: B  330 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7291 (mtm-85)
REVERT: B  397 ILE cc_start: 0.8567 (mm) cc_final: 0.8278 (mm)
REVERT: C   63 LYS cc_start: 0.7730 (ptpp) cc_final: 0.7476 (ptpt)
REVERT: C  332 LEU cc_start: 0.8398 (tp) cc_final: 0.8190 (mp)
REVERT: C  470 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7931 (p)
  outliers start: 36
  outliers final: 26
  residues processed: 211
  average time/residue: 0.1112
  time to fit residues: 35.0993
Evaluate side-chains
  201 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  538 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 152 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 89 optimal weight:   20.0000
   chunk 59 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0370
   chunk 86 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   chunk 149 optimal weight:    5.9990
   chunk 164 optimal weight:    0.8980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
C 339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.166112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.125686 restraints weight = 14464.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.97
r_work: 0.3352 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3222 r_free = 0.3222    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3222
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13788  Z= 0.118
  Angle     :  0.507   4.903  18774  Z= 0.265
  Chirality :  0.043   0.141   2184
  Planarity :  0.004   0.035   2439
  Dihedral  :  5.629  48.398   2072
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.15 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.11 (0.20), residues: 1755
  helix:  1.63 (0.22), residues: 558
  sheet:  0.10 (0.23), residues: 444
  loop : -1.13 (0.22), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 330 
 TYR   0.013   0.001   TYR B 318 
 PHE   0.014   0.001   PHE A 157 
 TRP   0.007   0.002   TRP B 173 
 HIS   0.001   0.000   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (13788)
  covalent geometry    : angle       0.50659 (18774)
  hydrogen bonds       : bond        0.03454 (  720)
  hydrogen bonds       : angle       4.74329 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 176
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7652 (tm-30)
REVERT: B   66 PHE cc_start: 0.7977 (m-80) cc_final: 0.7681 (m-80)
REVERT: B  314 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7739 (tp)
REVERT: B  330 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7311 (mtm-85)
REVERT: B  397 ILE cc_start: 0.8553 (mm) cc_final: 0.8287 (mm)
REVERT: C   63 LYS cc_start: 0.7678 (ptpp) cc_final: 0.7439 (ptpt)
REVERT: C  330 ARG cc_start: 0.7688 (mtm110) cc_final: 0.7403 (mtm110)
REVERT: C  397 ILE cc_start: 0.8453 (mm) cc_final: 0.8205 (mm)
REVERT: C  470 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7919 (p)
REVERT: C  502 SER cc_start: 0.9220 (t) cc_final: 0.9005 (t)
  outliers start: 37
  outliers final: 28
  residues processed: 203
  average time/residue: 0.1105
  time to fit residues: 33.4339
Evaluate side-chains
  202 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 135 optimal weight:    6.9990
   chunk 99 optimal weight:    0.0470
   chunk 100 optimal weight:    0.8980
   chunk 173 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 144 optimal weight:    0.0970
   chunk 23 optimal weight:    0.0980
   chunk 83 optimal weight:    0.3980
   overall best weight:    0.2476

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.169871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.129542 restraints weight = 14382.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 1.98
r_work: 0.3399 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3254
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3254
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13788  Z= 0.087
  Angle     :  0.468  11.177  18774  Z= 0.242
  Chirality :  0.042   0.133   2184
  Planarity :  0.004   0.035   2439
  Dihedral  :  5.103  47.392   2063
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.15 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.58 (0.20), residues: 1755
  helix:  2.00 (0.22), residues: 558
  sheet:  0.39 (0.24), residues: 444
  loop : -0.84 (0.22), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 313 
 TYR   0.010   0.001   TYR C  80 
 PHE   0.011   0.001   PHE B 157 
 TRP   0.006   0.001   TRP B 173 
 HIS   0.001   0.000   HIS B 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 (13788)
  covalent geometry    : angle       0.46774 (18774)
  hydrogen bonds       : bond        0.02887 (  720)
  hydrogen bonds       : angle       4.41620 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 191
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7696 (tm-30)
REVERT: A  238 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7456 (tp30)
REVERT: B   66 PHE cc_start: 0.7979 (m-80) cc_final: 0.7737 (m-80)
REVERT: B  122 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6646 (tm-30)
REVERT: B  148 MET cc_start: 0.8130 (tpt) cc_final: 0.7760 (tpt)
REVERT: B  397 ILE cc_start: 0.8480 (mm) cc_final: 0.8243 (mm)
REVERT: C   63 LYS cc_start: 0.7605 (ptpp) cc_final: 0.7404 (ptpt)
REVERT: C  330 ARG cc_start: 0.7734 (mtm110) cc_final: 0.7469 (mtm180)
REVERT: C  332 LEU cc_start: 0.8396 (tp) cc_final: 0.8187 (mp)
REVERT: C  429 LYS cc_start: 0.8181 (mptt) cc_final: 0.7907 (mmtt)
  outliers start: 36
  outliers final: 24
  residues processed: 217
  average time/residue: 0.1172
  time to fit residues: 37.2219
Evaluate side-chains
  202 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  538 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0870
   chunk 130 optimal weight:    0.4980
   chunk 173 optimal weight:    0.0070
   chunk 78 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0070
   chunk 151 optimal weight:    0.0030
   chunk 23 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 152 optimal weight:    1.9990
   overall best weight:    0.1204

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
C  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.174286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135176 restraints weight = 14309.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 1.91
r_work: 0.3443 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13788  Z= 0.080
  Angle     :  0.452   9.233  18774  Z= 0.234
  Chirality :  0.041   0.133   2184
  Planarity :  0.003   0.033   2439
  Dihedral  :  4.626  38.356   2058
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.15 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.99 (0.20), residues: 1755
  helix:  2.34 (0.22), residues: 555
  sheet:  0.67 (0.24), residues: 444
  loop : -0.64 (0.23), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 330 
 TYR   0.010   0.001   TYR C  80 
 PHE   0.010   0.001   PHE A 157 
 TRP   0.005   0.001   TRP B 173 
 HIS   0.002   0.000   HIS B 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00169 (13788)
  covalent geometry    : angle       0.45180 (18774)
  hydrogen bonds       : bond        0.02667 (  720)
  hydrogen bonds       : angle       4.19702 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 186
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   47 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6253 (m-30)
REVERT: A   66 PHE cc_start: 0.7936 (m-80) cc_final: 0.7275 (t80)
REVERT: A  122 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7607 (tm-30)
REVERT: A  238 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7467 (tp30)
REVERT: A  330 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7451 (mtm-85)
REVERT: A  339 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8118 (mm-40)
REVERT: B   63 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6238 (ptpt)
REVERT: B  122 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7354 (mt-10)
REVERT: B  148 MET cc_start: 0.8156 (tpt) cc_final: 0.7783 (tpt)
REVERT: B  314 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7800 (tp)
REVERT: B  397 ILE cc_start: 0.8502 (mm) cc_final: 0.8258 (mm)
REVERT: C   47 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6360 (m-30)
REVERT: C  330 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7399 (mtm110)
REVERT: C  332 LEU cc_start: 0.8409 (tp) cc_final: 0.8197 (mp)
REVERT: C  528 PHE cc_start: 0.7470 (m-10) cc_final: 0.7153 (m-10)
  outliers start: 42
  outliers final: 21
  residues processed: 218
  average time/residue: 0.1157
  time to fit residues: 37.2494
Evaluate side-chains
  199 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 171
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   63 LYS
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  122 GLU
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain C residue   47 ASP
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 144 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 124 optimal weight:    4.9990
   chunk 140 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0030
   chunk 162 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 155 optimal weight:    4.9990
   chunk 136 optimal weight:    4.9990
   chunk 167 optimal weight:    0.0040
   chunk 127 optimal weight:    0.7980
   overall best weight:    0.7404

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
C 396 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.169730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.129478 restraints weight = 14352.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.97
r_work: 0.3368 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13788  Z= 0.123
  Angle     :  0.499  11.396  18774  Z= 0.255
  Chirality :  0.043   0.137   2184
  Planarity :  0.004   0.033   2439
  Dihedral  :  4.510  38.066   2055
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.09 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  1.06 (0.20), residues: 1755
  helix:  2.24 (0.22), residues: 561
  sheet:  0.75 (0.24), residues: 444
  loop : -0.51 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 330 
 TYR   0.013   0.001   TYR A  80 
 PHE   0.013   0.001   PHE A 157 
 TRP   0.005   0.001   TRP B 173 
 HIS   0.003   0.000   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (13788)
  covalent geometry    : angle       0.49917 (18774)
  hydrogen bonds       : bond        0.03285 (  720)
  hydrogen bonds       : angle       4.35956 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 175
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7746 (tm-30)
REVERT: A  339 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8255 (mm-40)
REVERT: A  528 PHE cc_start: 0.7468 (m-10) cc_final: 0.7188 (m-10)
REVERT: B  314 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7834 (tp)
REVERT: B  397 ILE cc_start: 0.8498 (mm) cc_final: 0.8222 (mm)
REVERT: C  111 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7637 (mp)
REVERT: C  330 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7306 (mtm110)
REVERT: C  332 LEU cc_start: 0.8405 (tp) cc_final: 0.8157 (mp)
REVERT: C  528 PHE cc_start: 0.7492 (m-10) cc_final: 0.7164 (m-10)
  outliers start: 43
  outliers final: 38
  residues processed: 204
  average time/residue: 0.1094
  time to fit residues: 33.2210
Evaluate side-chains
  210 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 169
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 80 optimal weight:    0.5980
   chunk 126 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0030
   chunk 145 optimal weight:   20.0000
   chunk 74 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
C  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.169752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.129440 restraints weight = 14364.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 1.99
r_work: 0.3368 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13788  Z= 0.116
  Angle     :  0.486   9.803  18774  Z= 0.249
  Chirality :  0.042   0.136   2184
  Planarity :  0.004   0.032   2439
  Dihedral  :  4.331  37.066   2052
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.09 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  1.14 (0.20), residues: 1755
  helix:  2.31 (0.22), residues: 555
  sheet:  0.77 (0.24), residues: 444
  loop : -0.42 (0.23), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 330 
 TYR   0.012   0.001   TYR A  80 
 PHE   0.013   0.001   PHE A 157 
 TRP   0.006   0.001   TRP B 173 
 HIS   0.001   0.000   HIS C 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (13788)
  covalent geometry    : angle       0.48643 (18774)
  hydrogen bonds       : bond        0.03180 (  720)
  hydrogen bonds       : angle       4.34801 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 176
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A   66 PHE cc_start: 0.8032 (m-80) cc_final: 0.7280 (t80)
REVERT: A  330 ARG cc_start: 0.7667 (mtm110) cc_final: 0.7203 (mtm-85)
REVERT: A  528 PHE cc_start: 0.7554 (m-10) cc_final: 0.7264 (m-10)
REVERT: B  314 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8056 (tp)
REVERT: B  397 ILE cc_start: 0.8503 (mm) cc_final: 0.8228 (mm)
REVERT: C  111 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7665 (mp)
REVERT: C  330 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7294 (mtm110)
REVERT: C  332 LEU cc_start: 0.8409 (tp) cc_final: 0.8183 (mp)
REVERT: C  528 PHE cc_start: 0.7458 (m-10) cc_final: 0.7165 (m-10)
  outliers start: 45
  outliers final: 40
  residues processed: 205
  average time/residue: 0.1087
  time to fit residues: 33.2330
Evaluate side-chains
  215 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 173
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 46 optimal weight:    0.0670
   chunk 118 optimal weight:    2.9990
   chunk 8 optimal weight:    0.1980
   chunk 155 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 168 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 140 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7720

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.167056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.126963 restraints weight = 14324.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.95
r_work: 0.3373 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13788  Z= 0.123
  Angle     :  0.496   9.077  18774  Z= 0.255
  Chirality :  0.043   0.136   2184
  Planarity :  0.004   0.049   2439
  Dihedral  :  4.222  38.204   2049
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.74 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  1.15 (0.20), residues: 1755
  helix:  2.27 (0.22), residues: 555
  sheet:  0.78 (0.24), residues: 444
  loop : -0.38 (0.23), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 330 
 TYR   0.012   0.001   TYR A  80 
 PHE   0.014   0.001   PHE A 157 
 TRP   0.006   0.001   TRP B 173 
 HIS   0.001   0.000   HIS C 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (13788)
  covalent geometry    : angle       0.49625 (18774)
  hydrogen bonds       : bond        0.03280 (  720)
  hydrogen bonds       : angle       4.36936 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 173
  time to evaluate  : 0.507 
Fit side-chains
REVERT: A   66 PHE cc_start: 0.8081 (m-80) cc_final: 0.7227 (t80)
REVERT: A  330 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7243 (mtm-85)
REVERT: A  344 ASP cc_start: 0.8124 (m-30) cc_final: 0.7230 (t0)
REVERT: B  314 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8067 (tp)
REVERT: B  397 ILE cc_start: 0.8531 (mm) cc_final: 0.8250 (mm)
REVERT: C  111 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7704 (mp)
REVERT: C  330 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7292 (mtm110)
REVERT: C  332 LEU cc_start: 0.8430 (tp) cc_final: 0.8197 (mp)
REVERT: C  528 PHE cc_start: 0.7487 (m-10) cc_final: 0.7210 (m-10)
  outliers start: 44
  outliers final: 41
  residues processed: 200
  average time/residue: 0.1070
  time to fit residues: 32.3479
Evaluate side-chains
  215 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 172
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 129 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 51 optimal weight:    0.2980
   chunk 151 optimal weight:    0.0670
   overall best weight:    0.8520

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A 339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.166689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.126311 restraints weight = 14453.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.97
r_work: 0.3352 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13788  Z= 0.131
  Angle     :  0.500   8.706  18774  Z= 0.257
  Chirality :  0.043   0.139   2184
  Planarity :  0.004   0.046   2439
  Dihedral  :  4.239  39.307   2049
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.52 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  1.16 (0.20), residues: 1755
  helix:  2.24 (0.22), residues: 555
  sheet:  0.79 (0.24), residues: 444
  loop : -0.33 (0.23), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 330 
 TYR   0.011   0.001   TYR A  80 
 PHE   0.013   0.001   PHE A 157 
 TRP   0.005   0.001   TRP C 173 
 HIS   0.001   0.000   HIS C 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (13788)
  covalent geometry    : angle       0.50042 (18774)
  hydrogen bonds       : bond        0.03343 (  720)
  hydrogen bonds       : angle       4.39042 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 173
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   66 PHE cc_start: 0.8039 (m-80) cc_final: 0.7190 (t80)
REVERT: B   66 PHE cc_start: 0.7875 (m-80) cc_final: 0.7383 (t80)
REVERT: B  314 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8081 (tp)
REVERT: B  397 ILE cc_start: 0.8551 (mm) cc_final: 0.8263 (mm)
REVERT: C   36 GLN cc_start: 0.8592 (mt0) cc_final: 0.8372 (mt0)
REVERT: C  111 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7709 (mp)
REVERT: C  330 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7293 (mtm110)
REVERT: C  332 LEU cc_start: 0.8412 (tp) cc_final: 0.8181 (mp)
REVERT: C  346 PHE cc_start: 0.7432 (m-80) cc_final: 0.7094 (m-80)
REVERT: C  528 PHE cc_start: 0.7457 (m-10) cc_final: 0.7178 (m-10)
  outliers start: 46
  outliers final: 42
  residues processed: 202
  average time/residue: 0.1111
  time to fit residues: 33.6615
Evaluate side-chains
  213 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 169
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 133 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 153 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.165185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.125082 restraints weight = 14447.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.94
r_work: 0.3336 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13788  Z= 0.163
  Angle     :  0.534   8.529  18774  Z= 0.274
  Chirality :  0.044   0.138   2184
  Planarity :  0.004   0.051   2439
  Dihedral  :  4.336  41.275   2049
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.74 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  1.05 (0.20), residues: 1755
  helix:  2.03 (0.22), residues: 561
  sheet:  0.75 (0.24), residues: 444
  loop : -0.32 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 330 
 TYR   0.012   0.001   TYR C  45 
 PHE   0.016   0.001   PHE A 533 
 TRP   0.006   0.002   TRP B 173 
 HIS   0.002   0.000   HIS C 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (13788)
  covalent geometry    : angle       0.53375 (18774)
  hydrogen bonds       : bond        0.03668 (  720)
  hydrogen bonds       : angle       4.52829 ( 1980)

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

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

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3510 Ramachandran restraints generated.
    1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 168
  time to evaluate  : 0.513 
Fit side-chains
REVERT: A   66 PHE cc_start: 0.8031 (m-80) cc_final: 0.7157 (t80)
REVERT: A  330 ARG cc_start: 0.7662 (mtm180) cc_final: 0.7083 (mtm-85)
REVERT: B   66 PHE cc_start: 0.7824 (m-80) cc_final: 0.7310 (t80)
REVERT: B  314 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8156 (tp)
REVERT: B  397 ILE cc_start: 0.8564 (mm) cc_final: 0.8270 (mm)
REVERT: C  111 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7800 (mp)
REVERT: C  330 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7302 (mtm110)
REVERT: C  332 LEU cc_start: 0.8430 (tp) cc_final: 0.8198 (mp)
REVERT: C  346 PHE cc_start: 0.7427 (m-80) cc_final: 0.7072 (m-80)
REVERT: C  528 PHE cc_start: 0.7473 (m-10) cc_final: 0.7237 (m-10)
  outliers start: 44
  outliers final: 40
  residues processed: 197
  average time/residue: 0.1018
  time to fit residues: 30.0461
Evaluate side-chains
  208 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 166
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   88 SER
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  522 LEU
Chi-restraints excluded: chain B residue  538 THR
Chi-restraints excluded: chain B residue  576 VAL
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  188 ASP
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  293 ILE
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  385 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  474 SER
Chi-restraints excluded: chain C residue  522 LEU
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  576 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 115 optimal weight:    0.0040
   chunk 113 optimal weight:    4.9990
   chunk 167 optimal weight:    0.3980
   chunk 109 optimal weight:    2.9990
   chunk 120 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 162 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.4798

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.163611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.123264 restraints weight = 14682.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.94
r_work: 0.3313 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13788  Z= 0.199
  Angle     :  0.568   8.305  18774  Z= 0.292
  Chirality :  0.045   0.141   2184
  Planarity :  0.004   0.033   2439
  Dihedral  :  4.500  45.257   2049
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.96 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.18 %
    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 are not related in a simple way.
  whole:  0.86 (0.20), residues: 1755
  helix:  1.82 (0.22), residues: 561
  sheet:  0.65 (0.24), residues: 450
  loop : -0.41 (0.23), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 330 
 TYR   0.013   0.002   TYR C  45 
 PHE   0.019   0.002   PHE A 533 
 TRP   0.006   0.002   TRP B 173 
 HIS   0.002   0.001   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (13788)
  covalent geometry    : angle       0.56781 (18774)
  hydrogen bonds       : bond        0.04011 (  720)
  hydrogen bonds       : angle       4.67398 ( 1980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3708.55 seconds
wall clock time: 63 minutes 59.37 seconds (3839.37 seconds total)