Starting phenix.real_space_refine
on Wed Mar  4 09:17:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fd8_31536/03_2026/7fd8_31536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fd8_31536/03_2026/7fd8_31536.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fd8_31536/03_2026/7fd8_31536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fd8_31536/03_2026/7fd8_31536.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fd8_31536/03_2026/7fd8_31536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fd8_31536/03_2026/7fd8_31536.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     114      5.16       5
     C    7824      2.51       5
     N    2004      2.21       5
     O    2210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12152
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 764, 6014
          Classifications: {'peptide': 764}
          Link IDs: {'PTRANS': 32, 'TRANS': 731}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 62
          Unusual residues: {'NAG': 1, 'QUS': 1, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.57, per 1000 atoms: 0.38
  Number of scatterers: 12152
  At special positions: 0
  Unit cell: (77.43, 102.35, 173.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     114     16.00
     O    2210      8.00
     N    2004      7.00
     C    7824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  57 " - pdb=" SG  CYS A  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 530 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 276 " - pdb=" SG  CYS A 278 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 365 " - pdb=" SG  CYS A 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 419 " - pdb=" SG  CYS A 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 537 " - pdb=" SG  CYS A 549 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 552 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 644 " - pdb=" SG  CYS A 733 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  57 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 530 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 278 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 365 " - pdb=" SG  CYS B 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 419 " - pdb=" SG  CYS B 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 511 " - pdb=" SG  CYS B 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 515 " - pdb=" SG  CYS B 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 537 " - pdb=" SG  CYS B 549 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 552 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 644 " - pdb=" SG  CYS B 733 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG A 901 " - " ASN A 210 "
      " NAG B 901 " - " ASN B 210 "
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 587.3 milliseconds
  

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2852

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 12 sheets defined
      48.4% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 81
    Processing helix  chain 'A' and resid 101 through 113
    Processing helix  chain 'A' and resid 151 through 163
      removed outlier: 3.800A  pdb=" N   LEU A 161 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 181
      removed outlier: 3.776A  pdb=" N   ASP A 181 " --> pdb=" O   ASP A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 209
    Processing helix  chain 'A' and resid 221 through 238
    Processing helix  chain 'A' and resid 253 through 266
    Processing helix  chain 'A' and resid 279 through 293
    Processing helix  chain 'A' and resid 317 through 321
      removed outlier: 3.521A  pdb=" N   ALA A 321 " --> pdb=" O   GLN A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 342
    Processing helix  chain 'A' and resid 354 through 364
      removed outlier: 3.815A  pdb=" N   PHE A 363 " --> pdb=" O   TRP A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 419
    Processing helix  chain 'A' and resid 433 through 444
      removed outlier: 3.669A  pdb=" N   LYS A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 604
      removed outlier: 3.517A  pdb=" N   ALA A 583 " --> pdb=" O   GLU A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 612
    Processing helix  chain 'A' and resid 614 through 636
      removed outlier: 3.862A  pdb=" N   THR A 632 " --> pdb=" O   GLY A 628 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   PHE A 633 " --> pdb=" O   TYR A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 671
      removed outlier: 3.737A  pdb=" N   ARG A 648 " --> pdb=" O   CYS A 644 " (cutoff:3.500A)
      Proline residue:  A 655  - end of helix
    Processing helix  chain 'A' and resid 692 through 715
      removed outlier: 3.943A  pdb=" N   GLN A 704 " --> pdb=" O   LEU A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 760
      Proline residue:  A 743  - end of helix
    Processing helix  chain 'A' and resid 765 through 788
      removed outlier: 5.756A  pdb=" N   ALA A 771 " --> pdb=" O   ASN A 767 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LYS A 772 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 795
      removed outlier: 4.274A  pdb=" N   PHE A 793 " --> pdb=" O   VAL A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 816
    Processing helix  chain 'A' and resid 818 through 826
    Processing helix  chain 'B' and resid 65 through 81
    Processing helix  chain 'B' and resid 101 through 113
    Processing helix  chain 'B' and resid 151 through 163
      removed outlier: 3.798A  pdb=" N   LEU B 161 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 181
      removed outlier: 3.776A  pdb=" N   ASP B 181 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 209
    Processing helix  chain 'B' and resid 221 through 238
    Processing helix  chain 'B' and resid 253 through 266
    Processing helix  chain 'B' and resid 279 through 293
    Processing helix  chain 'B' and resid 317 through 321
      removed outlier: 3.522A  pdb=" N   ALA B 321 " --> pdb=" O   GLN B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 342
    Processing helix  chain 'B' and resid 354 through 364
      removed outlier: 3.814A  pdb=" N   PHE B 363 " --> pdb=" O   TRP B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 419
    Processing helix  chain 'B' and resid 433 through 444
      removed outlier: 3.669A  pdb=" N   LYS B 443 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 604
      removed outlier: 3.517A  pdb=" N   ALA B 583 " --> pdb=" O   GLU B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 612
    Processing helix  chain 'B' and resid 614 through 636
      removed outlier: 3.862A  pdb=" N   THR B 632 " --> pdb=" O   GLY B 628 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   PHE B 633 " --> pdb=" O   TYR B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 671
      removed outlier: 3.737A  pdb=" N   ARG B 648 " --> pdb=" O   CYS B 644 " (cutoff:3.500A)
      Proline residue:  B 655  - end of helix
    Processing helix  chain 'B' and resid 692 through 715
      removed outlier: 3.943A  pdb=" N   GLN B 704 " --> pdb=" O   LEU B 700 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 736 through 760
      Proline residue:  B 743  - end of helix
    Processing helix  chain 'B' and resid 765 through 788
      removed outlier: 5.757A  pdb=" N   ALA B 771 " --> pdb=" O   ASN B 767 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LYS B 772 " --> pdb=" O   PHE B 768 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 789 through 795
      removed outlier: 4.275A  pdb=" N   PHE B 793 " --> pdb=" O   VAL B 789 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 797 through 816
    Processing helix  chain 'B' and resid 818 through 826
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
      removed outlier: 5.827A  pdb=" N   ILE A  35 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   GLU A  94 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ILE A  37 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   ARG A  96 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ALA A  39 " --> pdb=" O   ARG A  96 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   ILE A  36 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   VAL A 146 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLY A  38 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 8.610A  pdb=" N   ILE A 170 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A 146 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 219
      removed outlier: 7.713A  pdb=" N   VAL A 214 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   SER A 245 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ALA A 216 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   LYS A 247 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 276
      removed outlier: 6.241A  pdb=" N   VAL A 274 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A 325 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A 327 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLY A 324 " --> pdb=" O   PHE A 471 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   TYR A 466 " --> pdb=" O   SER A 486 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   SER A 486 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ILE A 468 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 447
      removed outlier: 3.523A  pdb=" N   PHE A 446 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 523
      removed outlier: 3.571A  pdb=" N   THR A 535 " --> pdb=" O   LYS A 521 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 722
    Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31
      removed outlier: 5.827A  pdb=" N   ILE B  35 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   GLU B  94 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ILE B  37 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   ARG B  96 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ALA B  39 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   ILE B  36 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLY B  38 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 8.611A  pdb=" N   ILE B 170 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 213 through 219
      removed outlier: 7.712A  pdb=" N   VAL B 214 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   SER B 245 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ALA B 216 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   LYS B 247 " --> pdb=" O   ALA B 216 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   HIS B 218 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 274 through 276
      removed outlier: 6.240A  pdb=" N   VAL B 274 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE B 325 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE B 327 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLY B 324 " --> pdb=" O   PHE B 471 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   TYR B 466 " --> pdb=" O   SER B 486 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   SER B 486 " --> pdb=" O   TYR B 466 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ILE B 468 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 446 through 447
      removed outlier: 3.523A  pdb=" N   PHE B 446 " --> pdb=" O   ILE B 454 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 520 through 523
      removed outlier: 3.570A  pdb=" N   THR B 535 " --> pdb=" O   LYS B 521 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 719 through 722

    576 hydrogen bonds defined for protein.
    1692 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: 2.09

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1946
        1.30 -     1.43: 3302
        1.43 -     1.56: 7022
        1.56 -     1.69: 0
        1.69 -     1.82: 164
  Bond restraints: 12434
  Sorted by residual:
  bond pdb=" CAY Y01 B 903 "
       pdb=" OAG Y01 B 903 "
    ideal  model  delta    sigma   weight residual
    1.207  1.422 -0.215 2.00e-02 2.50e+03 1.15e+02
  bond pdb=" CAY Y01 A 903 "
       pdb=" OAG Y01 A 903 "
    ideal  model  delta    sigma   weight residual
    1.207  1.422 -0.215 2.00e-02 2.50e+03 1.15e+02
  bond pdb=" CAI Y01 B 903 "
       pdb=" CAZ Y01 B 903 "
    ideal  model  delta    sigma   weight residual
    1.332  1.498 -0.166 2.00e-02 2.50e+03 6.93e+01
  bond pdb=" CAI Y01 A 903 "
       pdb=" CAZ Y01 A 903 "
    ideal  model  delta    sigma   weight residual
    1.332  1.498 -0.166 2.00e-02 2.50e+03 6.93e+01
  bond pdb=" C01 QUS A 902 "
       pdb=" C02 QUS A 902 "
    ideal  model  delta    sigma   weight residual
    1.556  1.458  0.098 2.00e-02 2.50e+03 2.41e+01
  ... (remaining 12429 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 14746
        2.01 -     4.03: 1950
        4.03 -     6.04: 134
        6.04 -     8.05: 22
        8.05 -    10.06: 10
  Bond angle restraints: 16862
  Sorted by residual:
  angle pdb=" C   LYS B 379 "
        pdb=" N   THR B 380 "
        pdb=" CA  THR B 380 "
      ideal   model   delta    sigma   weight residual
     121.31  127.44   -6.13 1.49e+00 4.50e-01 1.69e+01
  angle pdb=" C   LYS A 379 "
        pdb=" N   THR A 380 "
        pdb=" CA  THR A 380 "
      ideal   model   delta    sigma   weight residual
     121.31  127.36   -6.05 1.49e+00 4.50e-01 1.65e+01
  angle pdb=" N   LYS B 517 "
        pdb=" CA  LYS B 517 "
        pdb=" C   LYS B 517 "
      ideal   model   delta    sigma   weight residual
     112.57  108.07    4.50 1.13e+00 7.83e-01 1.58e+01
  angle pdb=" N   LYS A 517 "
        pdb=" CA  LYS A 517 "
        pdb=" C   LYS A 517 "
      ideal   model   delta    sigma   weight residual
     112.57  108.09    4.48 1.13e+00 7.83e-01 1.57e+01
  angle pdb=" C   TYR A 317 "
        pdb=" N   GLN A 318 "
        pdb=" CA  GLN A 318 "
      ideal   model   delta    sigma   weight residual
     120.28  125.90   -5.62 1.44e+00 4.82e-01 1.52e+01
  ... (remaining 16857 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.63: 7278
       22.63 -    45.25: 247
       45.25 -    67.88: 45
       67.88 -    90.50: 18
       90.50 -   113.13: 14
  Dihedral angle restraints: 7602
    sinusoidal: 3154
      harmonic: 4448
  Sorted by residual:
  dihedral pdb=" CB  CYS B 537 "
           pdb=" SG  CYS B 537 "
           pdb=" SG  CYS B 549 "
           pdb=" CB  CYS B 549 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.64  -63.64     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS A 537 "
           pdb=" SG  CYS A 537 "
           pdb=" SG  CYS A 549 "
           pdb=" CB  CYS A 549 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.63  -63.63     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS A 552 "
           pdb=" SG  CYS A 552 "
           pdb=" SG  CYS A 565 "
           pdb=" CB  CYS A 565 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.41   43.41     1      1.00e+01 1.00e-02 2.63e+01
  ... (remaining 7599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.345: 1892
       0.345 -    0.689: 4
       0.689 -    1.033: 0
       1.033 -    1.378: 0
       1.378 -    1.722: 2
  Chirality restraints: 1898
  Sorted by residual:
  chirality pdb=" C02 QUS B 902 "
            pdb=" C01 QUS B 902 "
            pdb=" C03 QUS B 902 "
            pdb=" NP3 QUS B 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    0.78    1.72 2.00e-01 2.50e+01 7.41e+01
  chirality pdb=" C02 QUS A 902 "
            pdb=" C01 QUS A 902 "
            pdb=" C03 QUS A 902 "
            pdb=" NP3 QUS A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    0.78    1.72 2.00e-01 2.50e+01 7.38e+01
  chirality pdb=" C1  NAG B 901 "
            pdb=" ND2 ASN B 210 "
            pdb=" C2  NAG B 901 "
            pdb=" O5  NAG B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-01 2.50e+01 6.75e+00
  ... (remaining 1895 not shown)

  Planarity restraints: 2116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAM Y01 B 903 "   -0.025 2.00e-02 2.50e+03   4.43e-02 1.97e+01
        pdb=" CAY Y01 B 903 "    0.077 2.00e-02 2.50e+03
        pdb=" OAG Y01 B 903 "   -0.027 2.00e-02 2.50e+03
        pdb=" OAW Y01 B 903 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAM Y01 A 903 "    0.025 2.00e-02 2.50e+03   4.35e-02 1.89e+01
        pdb=" CAY Y01 A 903 "   -0.075 2.00e-02 2.50e+03
        pdb=" OAG Y01 A 903 "    0.027 2.00e-02 2.50e+03
        pdb=" OAW Y01 A 903 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C01 QUS B 902 "   -0.046 2.00e-02 2.50e+03   2.64e-02 6.99e+00
        pdb=" C02 QUS B 902 "    0.013 2.00e-02 2.50e+03
        pdb=" O16 QUS B 902 "    0.016 2.00e-02 2.50e+03
        pdb=" O17 QUS B 902 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2113 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 3556
        2.84 -     3.36: 11937
        3.36 -     3.87: 20567
        3.87 -     4.39: 23303
        4.39 -     4.90: 39011
  Nonbonded interactions: 98374
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 250 "
            pdb=" OE2 GLU B 279 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OG  SER A 250 "
            pdb=" OE2 GLU A 279 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   GLY B 253 "
            pdb=" OG  SER B 256 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" O   GLY A 253 "
            pdb=" OG  SER A 256 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OG  SER A 152 "
            pdb=" OG  SER A 176 "
     model   vdw
     2.339 3.040
  ... (remaining 98369 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.790
  Find NCS groups from input model:        0.090
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
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      :  0.008   0.215  12456  Z= 0.494
  Angle     :  1.403  10.063  16908  Z= 0.935
  Chirality :  0.108   1.722   1898
  Planarity :  0.004   0.044   2114
  Dihedral  : 13.892 113.126   4690
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.58 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  2.88 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.25 (0.19), residues: 1516
  helix: -0.64 (0.16), residues: 706
  sheet: -2.08 (0.37), residues: 160
  loop : -2.24 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 351 
 TYR   0.019   0.002   TYR B 223 
 PHE   0.020   0.002   PHE B 337 
 TRP   0.014   0.003   TRP A 575 
 HIS   0.010   0.002   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00800 (12434)
  covalent geometry    : angle       1.39914 (16862)
  SS BOND              : bond        0.00335 (   20)
  SS BOND              : angle       1.52857 (   40)
  hydrogen bonds       : bond        0.12851 (  576)
  hydrogen bonds       : angle       5.79304 ( 1692)
  link_NAG-ASN         : bond        0.00930 (    2)
  link_NAG-ASN         : angle       5.28140 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.8661 (ttt) cc_final: 0.8382 (tmm)
REVERT: A  429 MET cc_start: 0.7534 (mpp) cc_final: 0.7218 (mpp)
REVERT: A  592 LEU cc_start: 0.8961 (mt) cc_final: 0.8749 (tt)
REVERT: A  714 MET cc_start: 0.6865 (mmt) cc_final: 0.5929 (ttp)
REVERT: B  414 MET cc_start: 0.8632 (ttt) cc_final: 0.8427 (tmm)
REVERT: B  429 MET cc_start: 0.7558 (mpp) cc_final: 0.7267 (mpp)
REVERT: B  592 LEU cc_start: 0.8903 (mt) cc_final: 0.8700 (tt)
REVERT: B  714 MET cc_start: 0.7060 (mmt) cc_final: 0.6244 (ttp)
  outliers start: 8
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1097
  time to fit residues: 21.4895
Evaluate side-chains
  72 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
A 222 ASN
B 159 GLN
B 222 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.063952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.047766 restraints weight = 64251.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.047122 restraints weight = 37841.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.047582 restraints weight = 29448.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.047996 restraints weight = 24187.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.048038 restraints weight = 21857.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
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      :  0.006   0.043  12456  Z= 0.258
  Angle     :  0.708  11.185  16908  Z= 0.352
  Chirality :  0.044   0.197   1898
  Planarity :  0.004   0.040   2114
  Dihedral  :  9.649  75.296   1862
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.74 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  7.12 %
    Favored  : 92.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.21), residues: 1516
  helix:  0.44 (0.19), residues: 720
  sheet: -2.30 (0.32), residues: 178
  loop : -1.79 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 208 
 TYR   0.012   0.001   TYR B 317 
 PHE   0.017   0.002   PHE B 337 
 TRP   0.018   0.002   TRP A 532 
 HIS   0.006   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (12434)
  covalent geometry    : angle       0.70597 (16862)
  SS BOND              : bond        0.00372 (   20)
  SS BOND              : angle       0.91607 (   40)
  hydrogen bonds       : bond        0.04191 (  576)
  hydrogen bonds       : angle       4.76043 ( 1692)
  link_NAG-ASN         : bond        0.00077 (    2)
  link_NAG-ASN         : angle       2.66941 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9112 (ttt) cc_final: 0.8656 (tmm)
REVERT: A  714 MET cc_start: 0.7016 (mmt) cc_final: 0.6261 (ttp)
REVERT: B  414 MET cc_start: 0.9116 (ttt) cc_final: 0.8650 (tmm)
REVERT: B  714 MET cc_start: 0.7168 (mmt) cc_final: 0.6285 (ttp)
  outliers start: 10
  outliers final: 8
  residues processed: 88
  average time/residue: 0.0874
  time to fit residues: 12.0013
Evaluate side-chains
  75 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 146 optimal weight:    1.9990
   chunk 145 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 61 optimal weight:   20.0000
   chunk 69 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 140 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 132 optimal weight:    7.9990
   chunk 126 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.063260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.046461 restraints weight = 64346.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.046353 restraints weight = 37421.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.046933 restraints weight = 27576.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.047067 restraints weight = 22567.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.047236 restraints weight = 20631.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  12456  Z= 0.290
  Angle     :  0.702   9.074  16908  Z= 0.352
  Chirality :  0.045   0.205   1898
  Planarity :  0.004   0.040   2114
  Dihedral  :  8.346  71.611   1862
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.12 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  8.71 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.22), residues: 1516
  helix:  0.80 (0.19), residues: 708
  sheet: -2.11 (0.35), residues: 166
  loop : -1.67 (0.26), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 208 
 TYR   0.011   0.001   TYR A 317 
 PHE   0.021   0.002   PHE A 596 
 TRP   0.015   0.002   TRP A 532 
 HIS   0.006   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 (12434)
  covalent geometry    : angle       0.70003 (16862)
  SS BOND              : bond        0.00399 (   20)
  SS BOND              : angle       0.93692 (   40)
  hydrogen bonds       : bond        0.04151 (  576)
  hydrogen bonds       : angle       4.77725 ( 1692)
  link_NAG-ASN         : bond        0.00134 (    2)
  link_NAG-ASN         : angle       2.67344 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 66
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9129 (ttt) cc_final: 0.8746 (tmm)
REVERT: A  429 MET cc_start: 0.7913 (mpp) cc_final: 0.7640 (mpp)
REVERT: A  714 MET cc_start: 0.7021 (mmt) cc_final: 0.6241 (ttp)
REVERT: A  817 MET cc_start: 0.7424 (tpt) cc_final: 0.7216 (tpt)
REVERT: B  414 MET cc_start: 0.9105 (ttt) cc_final: 0.8723 (tmm)
REVERT: B  429 MET cc_start: 0.8016 (mpp) cc_final: 0.7676 (mpp)
REVERT: B  657 MET cc_start: 0.9480 (ptm) cc_final: 0.8996 (ppp)
REVERT: B  714 MET cc_start: 0.7211 (mmt) cc_final: 0.6295 (ttp)
  outliers start: 30
  outliers final: 19
  residues processed: 93
  average time/residue: 0.1011
  time to fit residues: 14.4404
Evaluate side-chains
  81 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  575 TRP
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  575 TRP
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 121 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3534 r_free = 0.3534 target = 0.064894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.048159 restraints weight = 64104.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.048258 restraints weight = 40048.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.048803 restraints weight = 27616.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.049040 restraints weight = 22634.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.049232 restraints weight = 19924.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12456  Z= 0.129
  Angle     :  0.578   9.573  16908  Z= 0.286
  Chirality :  0.042   0.189   1898
  Planarity :  0.003   0.043   2114
  Dihedral  :  7.389  60.790   1862
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.88 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  8.71 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.22), residues: 1516
  helix:  1.24 (0.19), residues: 720
  sheet: -1.91 (0.36), residues: 170
  loop : -1.64 (0.26), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 574 
 TYR   0.007   0.001   TYR A 340 
 PHE   0.011   0.001   PHE B 337 
 TRP   0.010   0.001   TRP B 532 
 HIS   0.003   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (12434)
  covalent geometry    : angle       0.57619 (16862)
  SS BOND              : bond        0.00181 (   20)
  SS BOND              : angle       0.83250 (   40)
  hydrogen bonds       : bond        0.03541 (  576)
  hydrogen bonds       : angle       4.39378 ( 1692)
  link_NAG-ASN         : bond        0.00422 (    2)
  link_NAG-ASN         : angle       2.06607 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.9268 (tpp) cc_final: 0.9008 (tpp)
REVERT: A  414 MET cc_start: 0.9148 (ttt) cc_final: 0.8770 (tmm)
REVERT: A  429 MET cc_start: 0.7910 (mpp) cc_final: 0.7671 (mpp)
REVERT: A  714 MET cc_start: 0.7179 (mmt) cc_final: 0.6240 (ttp)
REVERT: B  407 MET cc_start: 0.9279 (tpp) cc_final: 0.9019 (tpp)
REVERT: B  414 MET cc_start: 0.9149 (ttt) cc_final: 0.8759 (tmm)
REVERT: B  429 MET cc_start: 0.7968 (mpp) cc_final: 0.7659 (mpp)
REVERT: B  657 MET cc_start: 0.9411 (ptm) cc_final: 0.9032 (ppp)
REVERT: B  714 MET cc_start: 0.7274 (mmt) cc_final: 0.6349 (ttp)
  outliers start: 22
  outliers final: 12
  residues processed: 90
  average time/residue: 0.0934
  time to fit residues: 13.1285
Evaluate side-chains
  81 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  575 TRP
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  575 TRP
Chi-restraints excluded: chain B residue  630 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 149 optimal weight:    0.0670
   chunk 38 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 126 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    2.7724

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

Flipped N/Q/H residues before XYZ refinement:
A 704 GLN
** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.063871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.047192 restraints weight = 64284.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.047056 restraints weight = 37692.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.047349 restraints weight = 27241.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.047803 restraints weight = 23391.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.047888 restraints weight = 20637.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12456  Z= 0.222
  Angle     :  0.620   9.243  16908  Z= 0.312
  Chirality :  0.043   0.166   1898
  Planarity :  0.003   0.041   2114
  Dihedral  :  7.146  68.551   1862
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.94 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  9.92 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.22), residues: 1516
  helix:  1.27 (0.19), residues: 718
  sheet: -1.74 (0.36), residues: 166
  loop : -1.54 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 351 
 TYR   0.009   0.001   TYR B 340 
 PHE   0.014   0.002   PHE A 337 
 TRP   0.012   0.001   TRP A 532 
 HIS   0.005   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (12434)
  covalent geometry    : angle       0.61887 (16862)
  SS BOND              : bond        0.00298 (   20)
  SS BOND              : angle       0.79715 (   40)
  hydrogen bonds       : bond        0.03656 (  576)
  hydrogen bonds       : angle       4.53075 ( 1692)
  link_NAG-ASN         : bond        0.00172 (    2)
  link_NAG-ASN         : angle       1.96546 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.9297 (tpp) cc_final: 0.9009 (tpp)
REVERT: A  414 MET cc_start: 0.9153 (ttt) cc_final: 0.8785 (tmm)
REVERT: A  429 MET cc_start: 0.7879 (mpp) cc_final: 0.7605 (mpp)
REVERT: A  657 MET cc_start: 0.9404 (ptt) cc_final: 0.8968 (ppp)
REVERT: A  714 MET cc_start: 0.7048 (mmt) cc_final: 0.6164 (ttp)
REVERT: A  778 MET cc_start: 0.9036 (mmm) cc_final: 0.8339 (tpt)
REVERT: B  407 MET cc_start: 0.9295 (tpp) cc_final: 0.9007 (tpp)
REVERT: B  414 MET cc_start: 0.9135 (ttt) cc_final: 0.8760 (tmm)
REVERT: B  429 MET cc_start: 0.7912 (mpp) cc_final: 0.7686 (mpp)
REVERT: B  657 MET cc_start: 0.9444 (ptm) cc_final: 0.9066 (ppp)
REVERT: B  714 MET cc_start: 0.7169 (mmt) cc_final: 0.6301 (ttp)
  outliers start: 26
  outliers final: 21
  residues processed: 98
  average time/residue: 0.0925
  time to fit residues: 13.9503
Evaluate side-chains
  89 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  575 TRP
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  575 TRP
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 130 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 113 optimal weight:    0.5980
   chunk 80 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   chunk 90 optimal weight:    0.7980
   chunk 119 optimal weight:    0.9990
   chunk 136 optimal weight:    8.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.065260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.049008 restraints weight = 64040.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.048846 restraints weight = 37027.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.049281 restraints weight = 29021.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.049516 restraints weight = 23651.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.049843 restraints weight = 20574.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  12456  Z= 0.109
  Angle     :  0.568  10.013  16908  Z= 0.280
  Chirality :  0.042   0.182   1898
  Planarity :  0.003   0.041   2114
  Dihedral  :  6.576  61.201   1862
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.82 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.83 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.22), residues: 1516
  helix:  1.46 (0.19), residues: 722
  sheet: -1.48 (0.37), residues: 166
  loop : -1.49 (0.26), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 574 
 TYR   0.006   0.001   TYR B 340 
 PHE   0.010   0.001   PHE B 337 
 TRP   0.008   0.001   TRP B 532 
 HIS   0.002   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (12434)
  covalent geometry    : angle       0.56654 (16862)
  SS BOND              : bond        0.00164 (   20)
  SS BOND              : angle       0.79080 (   40)
  hydrogen bonds       : bond        0.03388 (  576)
  hydrogen bonds       : angle       4.32606 ( 1692)
  link_NAG-ASN         : bond        0.00471 (    2)
  link_NAG-ASN         : angle       1.76861 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9149 (ttt) cc_final: 0.8755 (tmm)
REVERT: A  657 MET cc_start: 0.9348 (ptt) cc_final: 0.8909 (ppp)
REVERT: A  714 MET cc_start: 0.7210 (mmt) cc_final: 0.6329 (ttp)
REVERT: B  414 MET cc_start: 0.9135 (ttt) cc_final: 0.8746 (tmm)
REVERT: B  657 MET cc_start: 0.9392 (ptm) cc_final: 0.9069 (ppp)
REVERT: B  714 MET cc_start: 0.7189 (mmt) cc_final: 0.6601 (mtp)
  outliers start: 15
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0931
  time to fit residues: 12.1386
Evaluate side-chains
  80 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 75 optimal weight:    9.9990
   chunk 84 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 151 optimal weight:    8.9990
   chunk 146 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 138 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 721 HIS
B 704 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.063294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.046591 restraints weight = 63500.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.046475 restraints weight = 36543.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.046771 restraints weight = 26661.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.047173 restraints weight = 23098.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.047252 restraints weight = 20682.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066  12456  Z= 0.314
  Angle     :  0.686   8.904  16908  Z= 0.347
  Chirality :  0.044   0.139   1898
  Planarity :  0.004   0.041   2114
  Dihedral  :  6.903  70.748   1862
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.07 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 10.15 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.23), residues: 1516
  helix:  1.31 (0.19), residues: 714
  sheet: -1.72 (0.36), residues: 176
  loop : -1.26 (0.27), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 310 
 TYR   0.010   0.002   TYR B 341 
 PHE   0.018   0.002   PHE A 596 
 TRP   0.014   0.002   TRP A 532 
 HIS   0.006   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 (12434)
  covalent geometry    : angle       0.68427 (16862)
  SS BOND              : bond        0.00435 (   20)
  SS BOND              : angle       0.84859 (   40)
  hydrogen bonds       : bond        0.03863 (  576)
  hydrogen bonds       : angle       4.75771 ( 1692)
  link_NAG-ASN         : bond        0.00126 (    2)
  link_NAG-ASN         : angle       2.02843 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 69
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.9338 (tpp) cc_final: 0.9051 (tpp)
REVERT: A  414 MET cc_start: 0.9150 (ttt) cc_final: 0.8777 (tmm)
REVERT: A  657 MET cc_start: 0.9372 (ptt) cc_final: 0.8901 (ppp)
REVERT: A  714 MET cc_start: 0.7159 (mmt) cc_final: 0.6381 (ttp)
REVERT: B  407 MET cc_start: 0.9328 (tpp) cc_final: 0.9044 (tpp)
REVERT: B  414 MET cc_start: 0.9140 (ttt) cc_final: 0.8771 (tmm)
REVERT: B  714 MET cc_start: 0.7219 (mmt) cc_final: 0.6402 (ttp)
  outliers start: 31
  outliers final: 25
  residues processed: 99
  average time/residue: 0.0883
  time to fit residues: 13.9867
Evaluate side-chains
  92 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  151 SER
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  548 THR
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  695 VAL
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 91 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 63 optimal weight:   20.0000
   chunk 84 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 125 optimal weight:    9.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.065139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.048618 restraints weight = 63385.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.048728 restraints weight = 35807.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.049179 restraints weight = 27351.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.049416 restraints weight = 22686.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.049520 restraints weight = 19904.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12456  Z= 0.127
  Angle     :  0.595   9.907  16908  Z= 0.292
  Chirality :  0.042   0.171   1898
  Planarity :  0.003   0.041   2114
  Dihedral  :  6.383  62.253   1862
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.75 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.59 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.22), residues: 1516
  helix:  1.48 (0.19), residues: 720
  sheet: -1.41 (0.38), residues: 166
  loop : -1.38 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 574 
 TYR   0.007   0.001   TYR A 340 
 PHE   0.012   0.001   PHE A 337 
 TRP   0.008   0.001   TRP A 532 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (12434)
  covalent geometry    : angle       0.59407 (16862)
  SS BOND              : bond        0.00170 (   20)
  SS BOND              : angle       0.81501 (   40)
  hydrogen bonds       : bond        0.03430 (  576)
  hydrogen bonds       : angle       4.37103 ( 1692)
  link_NAG-ASN         : bond        0.00392 (    2)
  link_NAG-ASN         : angle       1.64118 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9143 (ttt) cc_final: 0.8739 (tmm)
REVERT: A  657 MET cc_start: 0.9304 (ptt) cc_final: 0.8830 (ppp)
REVERT: A  714 MET cc_start: 0.7154 (mmt) cc_final: 0.6315 (ttp)
REVERT: A  778 MET cc_start: 0.9072 (mmm) cc_final: 0.8346 (tpt)
REVERT: B  414 MET cc_start: 0.9125 (ttt) cc_final: 0.8724 (tmm)
REVERT: B  657 MET cc_start: 0.9301 (ptm) cc_final: 0.9024 (ppp)
REVERT: B  714 MET cc_start: 0.7235 (mmt) cc_final: 0.6650 (mtp)
  outliers start: 19
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0871
  time to fit residues: 12.4272
Evaluate side-chains
  88 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  151 SER
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 136 optimal weight:    0.0870
   chunk 44 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 96 optimal weight:    0.5980
   chunk 125 optimal weight:    8.9990
   chunk 141 optimal weight:   20.0000
   chunk 83 optimal weight:    5.9990
   chunk 137 optimal weight:    7.9990
   chunk 123 optimal weight:    0.9990
   overall best weight:    0.8962

-------------------------------------------------------------------------------
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 = 0.3542 r_free = 0.3542 target = 0.065479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.048365 restraints weight = 62827.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.049165 restraints weight = 34599.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.049443 restraints weight = 23911.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.049617 restraints weight = 21667.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.049797 restraints weight = 19572.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12456  Z= 0.115
  Angle     :  0.577   9.402  16908  Z= 0.281
  Chirality :  0.041   0.166   1898
  Planarity :  0.003   0.041   2114
  Dihedral  :  6.129  62.080   1862
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.62 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.36 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.22), residues: 1516
  helix:  1.57 (0.19), residues: 720
  sheet: -1.25 (0.39), residues: 166
  loop : -1.29 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.008   0.001   TYR B 340 
 PHE   0.011   0.001   PHE A 337 
 TRP   0.007   0.001   TRP B 532 
 HIS   0.002   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (12434)
  covalent geometry    : angle       0.57621 (16862)
  SS BOND              : bond        0.00156 (   20)
  SS BOND              : angle       0.81621 (   40)
  hydrogen bonds       : bond        0.03292 (  576)
  hydrogen bonds       : angle       4.28176 ( 1692)
  link_NAG-ASN         : bond        0.00395 (    2)
  link_NAG-ASN         : angle       1.46755 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9164 (ttt) cc_final: 0.8726 (tmm)
REVERT: A  657 MET cc_start: 0.9281 (ptt) cc_final: 0.8863 (ppp)
REVERT: A  714 MET cc_start: 0.7113 (mmt) cc_final: 0.6483 (ttp)
REVERT: A  778 MET cc_start: 0.9110 (mmm) cc_final: 0.8381 (tpt)
REVERT: B  414 MET cc_start: 0.9155 (ttt) cc_final: 0.8722 (tmm)
REVERT: B  657 MET cc_start: 0.9296 (ptm) cc_final: 0.9029 (ppp)
REVERT: B  714 MET cc_start: 0.7162 (mmt) cc_final: 0.6475 (ttp)
  outliers start: 22
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0895
  time to fit residues: 12.7727
Evaluate side-chains
  87 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  151 SER
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 125 optimal weight:   10.0000
   chunk 114 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 130 optimal weight:   20.0000
   chunk 45 optimal weight:    7.9990
   chunk 73 optimal weight:    0.6980
   chunk 96 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 115 optimal weight:    0.8980
   chunk 118 optimal weight:    7.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.064911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.048107 restraints weight = 63795.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.048444 restraints weight = 36034.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.048482 restraints weight = 28678.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.048955 restraints weight = 23753.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.049050 restraints weight = 20753.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.3497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12456  Z= 0.151
  Angle     :  0.584   9.171  16908  Z= 0.287
  Chirality :  0.041   0.162   1898
  Planarity :  0.003   0.041   2114
  Dihedral  :  6.151  65.502   1862
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.88 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.52 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.23), residues: 1516
  helix:  1.63 (0.19), residues: 722
  sheet: -1.34 (0.39), residues: 172
  loop : -1.17 (0.27), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 574 
 TYR   0.008   0.001   TYR B 340 
 PHE   0.011   0.001   PHE A 337 
 TRP   0.010   0.001   TRP B 532 
 HIS   0.003   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (12434)
  covalent geometry    : angle       0.58300 (16862)
  SS BOND              : bond        0.00168 (   20)
  SS BOND              : angle       0.75747 (   40)
  hydrogen bonds       : bond        0.03324 (  576)
  hydrogen bonds       : angle       4.26366 ( 1692)
  link_NAG-ASN         : bond        0.00256 (    2)
  link_NAG-ASN         : angle       1.48865 (    6)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9159 (ttt) cc_final: 0.8715 (tmm)
REVERT: A  657 MET cc_start: 0.9279 (ptt) cc_final: 0.8867 (ppp)
REVERT: A  714 MET cc_start: 0.7043 (mmt) cc_final: 0.6392 (ttp)
REVERT: B  414 MET cc_start: 0.9166 (ttt) cc_final: 0.8707 (tmm)
REVERT: B  657 MET cc_start: 0.9302 (ptm) cc_final: 0.9047 (ppp)
REVERT: B  714 MET cc_start: 0.7163 (mmt) cc_final: 0.6464 (ttp)
  outliers start: 20
  outliers final: 20
  residues processed: 88
  average time/residue: 0.0895
  time to fit residues: 12.4161
Evaluate side-chains
  89 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  151 SER
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0670
   chunk 132 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 101 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    2.2126

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.064542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.047347 restraints weight = 64184.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.047932 restraints weight = 35855.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.048062 restraints weight = 25442.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.048432 restraints weight = 22502.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.048554 restraints weight = 20856.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12456  Z= 0.185
  Angle     :  0.607   9.163  16908  Z= 0.300
  Chirality :  0.042   0.166   1898
  Planarity :  0.003   0.040   2114
  Dihedral  :  6.214  66.291   1862
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.08 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.14 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.23), residues: 1516
  helix:  1.62 (0.19), residues: 716
  sheet: -1.36 (0.38), residues: 172
  loop : -1.10 (0.27), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  96 
 TYR   0.008   0.001   TYR B 340 
 PHE   0.013   0.001   PHE A 337 
 TRP   0.011   0.001   TRP B 532 
 HIS   0.004   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (12434)
  covalent geometry    : angle       0.60605 (16862)
  SS BOND              : bond        0.00242 (   20)
  SS BOND              : angle       0.78773 (   40)
  hydrogen bonds       : bond        0.03462 (  576)
  hydrogen bonds       : angle       4.33983 ( 1692)
  link_NAG-ASN         : bond        0.00170 (    2)
  link_NAG-ASN         : angle       1.52519 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1621.42 seconds
wall clock time: 29 minutes 5.34 seconds (1745.34 seconds total)