Starting phenix.real_space_refine
on Wed Mar  4 03:15:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ilr_35543/03_2026/8ilr_35543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ilr_35543/03_2026/8ilr_35543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ilr_35543/03_2026/8ilr_35543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ilr_35543/03_2026/8ilr_35543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ilr_35543/03_2026/8ilr_35543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ilr_35543/03_2026/8ilr_35543.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.105
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      73      5.16       5
     C    6603      2.51       5
     N    1792      2.21       5
     O    1906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 10374
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7981
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 977, 7981
          Classifications: {'peptide': 977}
          Link IDs: {'PTRANS': 47, 'TRANS': 929}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2346
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 4, 'TRANS': 271}
    Chain: "A"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 47
          Unusual residues: {'7TZ': 1}
          Classifications: {'undetermined': 1, 'water': 7}
          Link IDs: {None: 7}
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N  BGLU A 950 " occ=0.46
      ... (7 atoms not shown)
      pdb=" OE2BGLU A 950 " occ=0.46
    residue:
      pdb=" N  BARG A 951 " occ=0.46
      ... (9 atoms not shown)
      pdb=" NH2BARG A 951 " occ=0.46
    residue:
      pdb=" N  BPRO A 953 " occ=0.46
      ... (5 atoms not shown)
      pdb=" CD BPRO A 953 " occ=0.46
    residue:
      pdb=" N  BVAL A 955 " occ=0.46
      ... (5 atoms not shown)
      pdb=" CG2BVAL A 955 " occ=0.46
    residue:
      pdb=" N  BLEU A 956 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CD2BLEU A 956 " occ=0.50
  Time building chain proxies: 2.21, per 1000 atoms: 0.21
  Number of scatterers: 10374
  At special positions: 0
  Unit cell: (86.751, 112.455, 129.591, 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      73     16.00
     O    1906      8.00
     N    1792      7.00
     C    6603      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 520.3 milliseconds
  

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2398

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 11 sheets defined
      52.0% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 51
    Processing helix  chain 'A' and resid 88 through 93
      removed outlier: 4.205A  pdb=" N   ARG A  93 " --> pdb=" O   CYS A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 122
      removed outlier: 3.596A  pdb=" N   LEU A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.774A  pdb=" N   ASP A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 143
    Processing helix  chain 'A' and resid 143 through 155
    Processing helix  chain 'A' and resid 158 through 167
    Processing helix  chain 'A' and resid 178 through 184
    Processing helix  chain 'A' and resid 199 through 203
      removed outlier: 3.643A  pdb=" N   ASP A 203 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 227
      removed outlier: 3.811A  pdb=" N   LYS A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 289 through 297
      removed outlier: 3.529A  pdb=" N   LEU A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLN A 296 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 310
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 488 through 496
    Processing helix  chain 'A' and resid 528 through 537
      removed outlier: 3.590A  pdb=" N   ARG A 537 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
      removed outlier: 3.805A  pdb=" N   SER A 553 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 559
      removed outlier: 3.828A  pdb=" N   VAL A 559 " --> pdb=" O   HIS A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 563
      No H-bonds generated for 'chain 'A' and resid 561 through 563'
    Processing helix  chain 'A' and resid 564 through 569
    Processing helix  chain 'A' and resid 576 through 589
      removed outlier: 3.520A  pdb=" N   GLN A 582 " --> pdb=" O   ASP A 578 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 600 through 603
      removed outlier: 3.794A  pdb=" N   ASP A 603 " --> pdb=" O   GLU A 600 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 600 through 603'
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.595A  pdb=" N   LYS A 621 " --> pdb=" O   ARG A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 639
      removed outlier: 3.775A  pdb=" N   GLN A 630 " --> pdb=" O   ASP A 626 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   ILE A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   GLN A 634 " --> pdb=" O   GLN A 630 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A 637 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 658
    Processing helix  chain 'A' and resid 660 through 674
      removed outlier: 3.642A  pdb=" N   GLU A 674 " --> pdb=" O   HIS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
    Processing helix  chain 'A' and resid 697 through 720
      removed outlier: 4.182A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 718 " --> pdb=" O   ASN A 714 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU A 719 " --> pdb=" O   LEU A 715 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS A 720 " --> pdb=" O   THR A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 738
      removed outlier: 3.763A  pdb=" N   GLN A 731 " --> pdb=" O   THR A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 748
      removed outlier: 3.517A  pdb=" N   ALA A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 3.555A  pdb=" N   CYS A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 828
      removed outlier: 3.562A  pdb=" N   GLN A 815 " --> pdb=" O   MET A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 857 through 864
    Processing helix  chain 'A' and resid 875 through 885
      removed outlier: 3.537A  pdb=" N   ASN A 885 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 888 through 912
      removed outlier: 4.396A  pdb=" N   ALA A 892 " --> pdb=" O   GLU A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 957 through 965
      removed outlier: 3.674A  pdb=" N   LEU A 961 " --> pdb=" O   THR A 957 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ILE A 962 " --> pdb=" O   GLN A 958 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 993
    Processing helix  chain 'A' and resid 994 through 1004
      removed outlier: 3.592A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1009
      removed outlier: 4.116A  pdb=" N   GLY A1009 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1026
      removed outlier: 3.855A  pdb=" N   ILE A1019 " --> pdb=" O   SER A1015 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   TYR A1021 " --> pdb=" O   ASP A1017 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   ILE A1022 " --> pdb=" O   ASP A1018 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG A1023 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1048
      removed outlier: 3.703A  pdb=" N   GLU A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 331
    Processing helix  chain 'B' and resid 339 through 348
      removed outlier: 3.511A  pdb=" N   GLU B 345 " --> pdb=" O   GLU B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 410
      removed outlier: 3.624A  pdb=" N   ASN B 410 " --> pdb=" O   ASN B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 416
      removed outlier: 4.319A  pdb=" N   GLN B 415 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 435
    Processing helix  chain 'B' and resid 441 through 505
      removed outlier: 3.577A  pdb=" N   GLU B 489 " --> pdb=" O   GLU B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 515
      removed outlier: 4.205A  pdb=" N   LYS B 511 " --> pdb=" O   GLU B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 587
      removed outlier: 3.805A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 517 " (cutoff:3.500A)
      Proline residue:  B 568  - end of helix
    Processing helix  chain 'B' and resid 590 through 598
      removed outlier: 4.022A  pdb=" N   LEU B 594 " --> pdb=" O   ARG B 590 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37
      removed outlier: 3.855A  pdb=" N   VAL A  32 " --> pdb=" O   CYS A  24 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   CYS A  36 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ILE A  20 " --> pdb=" O   CYS A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 212
      removed outlier: 4.296A  pdb=" N   LEU A 252 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 326
      removed outlier: 6.212A  pdb=" N   LYS A 325 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 392
      removed outlier: 4.488A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.556A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372
      removed outlier: 3.720A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ASN A 426 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   LEU A 404 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TRP A 424 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ILE A 406 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752
    Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771
    Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AB1, first strand: chain 'B' and resid 355 through 358
    Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386

    481 hydrogen bonds defined for protein.
    1362 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: 1.82

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1825
        1.32 -     1.44: 2672
        1.44 -     1.57: 5975
        1.57 -     1.69: 2
        1.69 -     1.81: 114
  Bond restraints: 10588
  Sorted by residual:
  bond pdb=" CA  ARG A 777 "
       pdb=" C   ARG A 777 "
    ideal  model  delta    sigma   weight residual
    1.524  1.479  0.045 1.26e-02 6.30e+03 1.25e+01
  bond pdb=" C16 7TZ A1101 "
       pdb=" N18 7TZ A1101 "
    ideal  model  delta    sigma   weight residual
    1.301  1.359 -0.058 2.00e-02 2.50e+03 8.30e+00
  bond pdb=" C   ARG A 777 "
       pdb=" O   ARG A 777 "
    ideal  model  delta    sigma   weight residual
    1.238  1.201  0.037 1.28e-02 6.10e+03 8.21e+00
  bond pdb=" C14 7TZ A1101 "
       pdb=" N13 7TZ A1101 "
    ideal  model  delta    sigma   weight residual
    1.302  1.356 -0.054 2.00e-02 2.50e+03 7.24e+00
  bond pdb=" C39 7TZ A1101 "
       pdb=" N40 7TZ A1101 "
    ideal  model  delta    sigma   weight residual
    1.302  1.355 -0.053 2.00e-02 2.50e+03 7.12e+00
  ... (remaining 10583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 14203
        2.49 -     4.99: 66
        4.99 -     7.48: 6
        7.48 -     9.98: 5
        9.98 -    12.47: 2
  Bond angle restraints: 14282
  Sorted by residual:
  angle pdb=" C   ARG A 777 "
        pdb=" N   PRO A 778 "
        pdb=" CA  PRO A 778 "
      ideal   model   delta    sigma   weight residual
     119.85  111.66    8.19 1.01e+00 9.80e-01 6.57e+01
  angle pdb=" N   ASN B 325 "
        pdb=" CA  ASN B 325 "
        pdb=" C   ASN B 325 "
      ideal   model   delta    sigma   weight residual
     107.37  117.92  -10.55 2.07e+00 2.33e-01 2.60e+01
  angle pdb=" CA  PRO A  97 "
        pdb=" N   PRO A  97 "
        pdb=" CD  PRO A  97 "
      ideal   model   delta    sigma   weight residual
     112.00  106.97    5.03 1.40e+00 5.10e-01 1.29e+01
  angle pdb=" N   ALA A 775 "
        pdb=" CA  ALA A 775 "
        pdb=" C   ALA A 775 "
      ideal   model   delta    sigma   weight residual
     110.80  118.00   -7.20 2.13e+00 2.20e-01 1.14e+01
  angle pdb=" C   ASN B 325 "
        pdb=" CA  ASN B 325 "
        pdb=" CB  ASN B 325 "
      ideal   model   delta    sigma   weight residual
     111.82  107.55    4.27 1.38e+00 5.25e-01 9.56e+00
  ... (remaining 14277 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 5560
       17.73 -    35.47: 724
       35.47 -    53.20: 152
       53.20 -    70.94: 23
       70.94 -    88.67: 10
  Dihedral angle restraints: 6469
    sinusoidal: 2774
      harmonic: 3695
  Sorted by residual:
  dihedral pdb=" C   ARG A 777 "
           pdb=" N   ARG A 777 "
           pdb=" CA  ARG A 777 "
           pdb=" CB  ARG A 777 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.69   12.09     0      2.50e+00 1.60e-01 2.34e+01
  dihedral pdb=" N   ARG A 777 "
           pdb=" C   ARG A 777 "
           pdb=" CA  ARG A 777 "
           pdb=" CB  ARG A 777 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.42  -11.62     0      2.50e+00 1.60e-01 2.16e+01
  dihedral pdb=" CB  GLU A 768 "
           pdb=" CG  GLU A 768 "
           pdb=" CD  GLU A 768 "
           pdb=" OE1 GLU A 768 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.67  -88.67     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 6466 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1532
       0.118 -    0.237: 5
       0.237 -    0.355: 0
       0.355 -    0.474: 0
       0.474 -    0.592: 1
  Chirality restraints: 1538
  Sorted by residual:
  chirality pdb=" CA  ARG A 777 "
            pdb=" N   ARG A 777 "
            pdb=" C   ARG A 777 "
            pdb=" CB  ARG A 777 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.59 2.00e-01 2.50e+01 8.76e+00
  chirality pdb=" CA  ALA A 775 "
            pdb=" N   ALA A 775 "
            pdb=" C   ALA A 775 "
            pdb=" CB  ALA A 775 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.28    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  ASN B 325 "
            pdb=" N   ASN B 325 "
            pdb=" C   ASN B 325 "
            pdb=" CB  ASN B 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1535 not shown)

  Planarity restraints: 1835
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C22 7TZ A1101 "    0.153 2.00e-02 2.50e+03   8.10e-02 1.48e+02
        pdb=" C23 7TZ A1101 "    0.008 2.00e-02 2.50e+03
        pdb=" C24 7TZ A1101 "   -0.055 2.00e-02 2.50e+03
        pdb=" C25 7TZ A1101 "   -0.056 2.00e-02 2.50e+03
        pdb=" C26 7TZ A1101 "   -0.051 2.00e-02 2.50e+03
        pdb=" C27 7TZ A1101 "   -0.095 2.00e-02 2.50e+03
        pdb=" C28 7TZ A1101 "   -0.053 2.00e-02 2.50e+03
        pdb=" C29 7TZ A1101 "    0.030 2.00e-02 2.50e+03
        pdb=" C30 7TZ A1101 "    0.119 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C29 7TZ A1101 "   -0.149 2.00e-02 2.50e+03   6.54e-02 1.28e+02
        pdb=" C30 7TZ A1101 "    0.001 2.00e-02 2.50e+03
        pdb=" C31 7TZ A1101 "    0.066 2.00e-02 2.50e+03
        pdb=" C32 7TZ A1101 "    0.044 2.00e-02 2.50e+03
        pdb=" C33 7TZ A1101 "    0.022 2.00e-02 2.50e+03
        pdb=" C34 7TZ A1101 "    0.093 2.00e-02 2.50e+03
        pdb=" C35 7TZ A1101 "    0.051 2.00e-02 2.50e+03
        pdb=" C36 7TZ A1101 "    0.012 2.00e-02 2.50e+03
        pdb=" C38 7TZ A1101 "   -0.077 2.00e-02 2.50e+03
        pdb=" C39 7TZ A1101 "   -0.044 2.00e-02 2.50e+03
        pdb=" N37 7TZ A1101 "   -0.047 2.00e-02 2.50e+03
        pdb=" N40 7TZ A1101 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C08 7TZ A1101 "    0.000 2.00e-02 2.50e+03   4.09e-02 5.43e+01
        pdb=" C09 7TZ A1101 "    0.036 2.00e-02 2.50e+03
        pdb=" C10 7TZ A1101 "    0.055 2.00e-02 2.50e+03
        pdb=" C11 7TZ A1101 "   -0.007 2.00e-02 2.50e+03
        pdb=" C12 7TZ A1101 "   -0.047 2.00e-02 2.50e+03
        pdb=" C14 7TZ A1101 "   -0.020 2.00e-02 2.50e+03
        pdb=" C15 7TZ A1101 "    0.084 2.00e-02 2.50e+03
        pdb=" C16 7TZ A1101 "   -0.015 2.00e-02 2.50e+03
        pdb=" C17 7TZ A1101 "    0.033 2.00e-02 2.50e+03
        pdb=" C19 7TZ A1101 "   -0.027 2.00e-02 2.50e+03
        pdb=" C20 7TZ A1101 "    0.007 2.00e-02 2.50e+03
        pdb=" N13 7TZ A1101 "   -0.069 2.00e-02 2.50e+03
        pdb=" N18 7TZ A1101 "   -0.031 2.00e-02 2.50e+03
  ... (remaining 1832 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.55: 89
        2.55 -     3.14: 8480
        3.14 -     3.73: 15653
        3.73 -     4.31: 22460
        4.31 -     4.90: 37705
  Nonbonded interactions: 84387
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 431 "
            pdb=" OG1 THR A 433 "
     model   vdw
     1.967 3.040
  nonbonded pdb=" O   GLU A 970 "
            pdb=" OG1 THR A 974 "
     model   vdw
     1.984 3.040
  nonbonded pdb=" OG  SER B 399 "
            pdb=" OE1 GLU B 403 "
     model   vdw
     2.116 3.040
  nonbonded pdb=" OD1 ASN A 428 "
            pdb=" NE2 GLN A 643 "
     model   vdw
     2.130 3.120
  nonbonded pdb=" OE1 GLU A 642 "
            pdb=" O   HOH A1201 "
     model   vdw
     2.134 3.040
  ... (remaining 84382 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.46 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.400
  Find NCS groups from input model:        0.030
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
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      :  0.003   0.076  10588  Z= 0.128
  Angle     :  0.447  12.469  14282  Z= 0.231
  Chirality :  0.039   0.592   1538
  Planarity :  0.005   0.133   1835
  Dihedral  : 15.946  88.671   4071
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 27.67
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.46 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 15.20 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.08 %
  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 (0.25), residues: 1239
  helix:  1.22 (0.24), residues: 547
  sheet: -1.07 (0.42), residues: 159
  loop : -0.73 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 503 
 TYR   0.006   0.001   TYR A  68 
 PHE   0.006   0.001   PHE A1039 
 TRP   0.009   0.001   TRP A 780 
 HIS   0.002   0.000   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10588)
  covalent geometry    : angle       0.44693 (14282)
  hydrogen bonds       : bond        0.26077 (  481)
  hydrogen bonds       : angle       7.68832 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 143
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7797 (mtm-85)
REVERT: B  503 ARG cc_start: 0.6996 (tmm160) cc_final: 0.6700 (tmm160)
  outliers start: 4
  outliers final: 1
  residues processed: 146
  average time/residue: 0.0895
  time to fit residues: 18.7857
Evaluate side-chains
  142 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 630 GLN
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.194776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.136352 restraints weight = 11578.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 2.36
r_work: 0.3351 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10588  Z= 0.227
  Angle     :  0.636   7.109  14282  Z= 0.329
  Chirality :  0.045   0.184   1538
  Planarity :  0.005   0.079   1835
  Dihedral  :  4.222  31.668   1390
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.28 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.68 %
    Favored  : 82.97 %
  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: -0.10 (0.24), residues: 1239
  helix:  1.16 (0.22), residues: 571
  sheet: -1.22 (0.40), residues: 143
  loop : -1.08 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 916 
 TYR   0.011   0.002   TYR B 334 
 PHE   0.014   0.002   PHE A 667 
 TRP   0.010   0.002   TRP A 552 
 HIS   0.008   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 (10588)
  covalent geometry    : angle       0.63634 (14282)
  hydrogen bonds       : bond        0.06916 (  481)
  hydrogen bonds       : angle       4.96575 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   93 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7374 (mtm-85)
REVERT: A  148 LYS cc_start: 0.7947 (tppt) cc_final: 0.7348 (ttpp)
REVERT: A  179 LYS cc_start: 0.7933 (tppt) cc_final: 0.7641 (mtmm)
REVERT: A  734 PHE cc_start: 0.8200 (t80) cc_final: 0.7948 (t80)
REVERT: A  796 ASN cc_start: 0.8147 (m-40) cc_final: 0.7876 (m-40)
REVERT: A  798 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7329 (mt-10)
REVERT: A 1033 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7087 (tt0)
REVERT: A 1034 GLU cc_start: 0.7942 (tp30) cc_final: 0.7718 (tp30)
REVERT: A 1037 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7402 (mp0)
REVERT: B  345 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7890 (pt0)
REVERT: B  417 ASN cc_start: 0.6603 (t0) cc_final: 0.6272 (t0)
REVERT: B  461 ARG cc_start: 0.7318 (tpt90) cc_final: 0.6838 (tpt90)
REVERT: B  479 MET cc_start: 0.7348 (mtt) cc_final: 0.7121 (mtt)
  outliers start: 27
  outliers final: 13
  residues processed: 170
  average time/residue: 0.0909
  time to fit residues: 21.7973
Evaluate side-chains
  153 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  922 MET
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  345 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 101 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.194757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.142416 restraints weight = 11577.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.58
r_work: 0.3366 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10588  Z= 0.183
  Angle     :  0.580   7.951  14282  Z= 0.297
  Chirality :  0.043   0.159   1538
  Planarity :  0.004   0.057   1835
  Dihedral  :  4.109  30.105   1388
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.38 %
    Favored  : 81.67 %
  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: -0.03 (0.23), residues: 1239
  helix:  1.30 (0.21), residues: 574
  sheet: -1.30 (0.39), residues: 138
  loop : -1.12 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 740 
 TYR   0.013   0.001   TYR A 904 
 PHE   0.015   0.002   PHE A 667 
 TRP   0.011   0.002   TRP B 583 
 HIS   0.006   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (10588)
  covalent geometry    : angle       0.57989 (14282)
  hydrogen bonds       : bond        0.05822 (  481)
  hydrogen bonds       : angle       4.49898 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 155
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7447 (mmp) cc_final: 0.7157 (mmp)
REVERT: A   93 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7651 (mtm-85)
REVERT: A  146 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8416 (p)
REVERT: A  148 LYS cc_start: 0.7990 (tppt) cc_final: 0.7368 (ttpp)
REVERT: A  282 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7373 (ptt)
REVERT: A  732 MET cc_start: 0.7150 (tpt) cc_final: 0.6744 (mmm)
REVERT: A  765 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7528 (ttm170)
REVERT: A  796 ASN cc_start: 0.8068 (m-40) cc_final: 0.7794 (m-40)
REVERT: A  825 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7394 (tp-100)
REVERT: A 1033 GLN cc_start: 0.7792 (tp-100) cc_final: 0.7543 (tt0)
REVERT: B  345 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7913 (pt0)
REVERT: B  417 ASN cc_start: 0.6738 (t0) cc_final: 0.6384 (t0)
REVERT: B  461 ARG cc_start: 0.7377 (tpt90) cc_final: 0.6855 (tpt90)
REVERT: B  475 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7292 (tm-30)
REVERT: B  479 MET cc_start: 0.7407 (mtt) cc_final: 0.7151 (mtt)
REVERT: B  582 MET cc_start: 0.7398 (ptt) cc_final: 0.7187 (mtm)
  outliers start: 34
  outliers final: 16
  residues processed: 178
  average time/residue: 0.0976
  time to fit residues: 24.5676
Evaluate side-chains
  164 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  922 MET
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  929 LEU
Chi-restraints excluded: chain A residue  955 VAL
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  356 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 102 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 35 optimal weight:    0.4980
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4216 r_free = 0.4216 target = 0.195606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.137282 restraints weight = 11616.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.83
r_work: 0.3322 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3322
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3322
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10588  Z= 0.156
  Angle     :  0.554   7.943  14282  Z= 0.283
  Chirality :  0.041   0.146   1538
  Planarity :  0.004   0.059   1835
  Dihedral  :  4.047  30.301   1388
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.25 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.24), residues: 1239
  helix:  1.51 (0.22), residues: 574
  sheet: -1.21 (0.38), residues: 136
  loop : -1.11 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 740 
 TYR   0.011   0.001   TYR A 904 
 PHE   0.021   0.002   PHE A1039 
 TRP   0.009   0.001   TRP A 669 
 HIS   0.006   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10588)
  covalent geometry    : angle       0.55376 (14282)
  hydrogen bonds       : bond        0.05195 (  481)
  hydrogen bonds       : angle       4.24726 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LYS cc_start: 0.7993 (tppt) cc_final: 0.7380 (ttpp)
REVERT: A  179 LYS cc_start: 0.7893 (tppt) cc_final: 0.7625 (mtmt)
REVERT: A  282 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7416 (mtm)
REVERT: A  431 ASP cc_start: 0.8517 (p0) cc_final: 0.8054 (p0)
REVERT: A  732 MET cc_start: 0.7140 (tpt) cc_final: 0.6656 (mmm)
REVERT: A  765 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7362 (mtt180)
REVERT: A  796 ASN cc_start: 0.8198 (m-40) cc_final: 0.7880 (m-40)
REVERT: A  954 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.5078 (m-80)
REVERT: A 1033 GLN cc_start: 0.7717 (tp-100) cc_final: 0.6869 (tt0)
REVERT: A 1034 GLU cc_start: 0.7810 (tp30) cc_final: 0.7603 (tp30)
REVERT: A 1037 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7316 (mp0)
REVERT: B  345 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7946 (pt0)
REVERT: B  417 ASN cc_start: 0.6802 (t0) cc_final: 0.6385 (t0)
REVERT: B  461 ARG cc_start: 0.7343 (tpt90) cc_final: 0.6777 (tpt90)
REVERT: B  475 GLN cc_start: 0.7431 (tm-30) cc_final: 0.6830 (tm-30)
REVERT: B  476 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7143 (mp0)
REVERT: B  582 MET cc_start: 0.7531 (ptt) cc_final: 0.6772 (mmt)
  outliers start: 36
  outliers final: 23
  residues processed: 182
  average time/residue: 0.1069
  time to fit residues: 27.7950
Evaluate side-chains
  173 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  922 MET
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  929 LEU
Chi-restraints excluded: chain A residue  954 PHE
Chi-restraints excluded: chain A residue  955 VAL
Chi-restraints excluded: chain A residue  973 LYS
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  436 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 115 optimal weight:   20.0000
   chunk 101 optimal weight:    0.3980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.196506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.140313 restraints weight = 11556.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.65
r_work: 0.3356 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10588  Z= 0.137
  Angle     :  0.530   8.523  14282  Z= 0.272
  Chirality :  0.041   0.144   1538
  Planarity :  0.004   0.059   1835
  Dihedral  :  3.963  30.701   1388
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.55 %
    Favored  : 79.84 %
  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:  0.31 (0.24), residues: 1239
  helix:  1.61 (0.22), residues: 576
  sheet: -1.15 (0.39), residues: 129
  loop : -1.00 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 503 
 TYR   0.011   0.001   TYR A 904 
 PHE   0.015   0.001   PHE A 667 
 TRP   0.009   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10588)
  covalent geometry    : angle       0.53041 (14282)
  hydrogen bonds       : bond        0.04803 (  481)
  hydrogen bonds       : angle       4.06010 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LYS cc_start: 0.8016 (tppt) cc_final: 0.7378 (ttpp)
REVERT: A  179 LYS cc_start: 0.7940 (tppt) cc_final: 0.7714 (mttt)
REVERT: A  282 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7396 (mtm)
REVERT: A  431 ASP cc_start: 0.8442 (p0) cc_final: 0.7979 (p0)
REVERT: A  732 MET cc_start: 0.7171 (tpt) cc_final: 0.6653 (mmm)
REVERT: A  765 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7286 (mtt180)
REVERT: A  796 ASN cc_start: 0.8104 (m-40) cc_final: 0.7844 (m-40)
REVERT: A  954 PHE cc_start: 0.5477 (OUTLIER) cc_final: 0.5110 (m-80)
REVERT: A 1033 GLN cc_start: 0.7790 (tp-100) cc_final: 0.6944 (tt0)
REVERT: A 1034 GLU cc_start: 0.7785 (tp30) cc_final: 0.7580 (tp30)
REVERT: A 1037 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7323 (mp0)
REVERT: B  345 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7872 (pt0)
REVERT: B  417 ASN cc_start: 0.6740 (t0) cc_final: 0.6349 (t0)
REVERT: B  461 ARG cc_start: 0.7407 (tpt90) cc_final: 0.6877 (tpt90)
REVERT: B  475 GLN cc_start: 0.7431 (tm-30) cc_final: 0.6946 (tm-30)
REVERT: B  476 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6885 (mp0)
REVERT: B  582 MET cc_start: 0.7537 (ptt) cc_final: 0.6827 (mmt)
  outliers start: 30
  outliers final: 18
  residues processed: 178
  average time/residue: 0.0967
  time to fit residues: 24.9252
Evaluate side-chains
  169 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  929 LEU
Chi-restraints excluded: chain A residue  954 PHE
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  345 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 115 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 110 optimal weight:    6.9990
   chunk 89 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0970
   chunk 80 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A1047 HIS
B 406 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.197186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.140623 restraints weight = 11594.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.70
r_work: 0.3358 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3363
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10588  Z= 0.126
  Angle     :  0.522   8.794  14282  Z= 0.268
  Chirality :  0.040   0.146   1538
  Planarity :  0.004   0.060   1835
  Dihedral  :  3.898  31.098   1388
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.72 %
    Favored  : 80.02 %
  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:  0.43 (0.24), residues: 1239
  helix:  1.70 (0.22), residues: 577
  sheet: -1.22 (0.38), residues: 146
  loop : -0.86 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 662 
 TYR   0.010   0.001   TYR A 904 
 PHE   0.016   0.001   PHE A 667 
 TRP   0.009   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10588)
  covalent geometry    : angle       0.52182 (14282)
  hydrogen bonds       : bond        0.04556 (  481)
  hydrogen bonds       : angle       3.96180 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 157
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LYS cc_start: 0.7888 (tppt) cc_final: 0.7200 (ttpp)
REVERT: A  179 LYS cc_start: 0.7958 (tppt) cc_final: 0.7691 (mttt)
REVERT: A  282 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7325 (mtm)
REVERT: A  431 ASP cc_start: 0.8392 (p0) cc_final: 0.7951 (p0)
REVERT: A  732 MET cc_start: 0.7175 (tpt) cc_final: 0.6646 (mmm)
REVERT: A  765 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7331 (ttm170)
REVERT: A  796 ASN cc_start: 0.8122 (m-40) cc_final: 0.7810 (m-40)
REVERT: A 1033 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7501 (tt0)
REVERT: B  417 ASN cc_start: 0.6822 (t0) cc_final: 0.6335 (t0)
REVERT: B  461 ARG cc_start: 0.7364 (tpt90) cc_final: 0.7032 (tpt90)
REVERT: B  475 GLN cc_start: 0.7329 (tm-30) cc_final: 0.6763 (tm-30)
REVERT: B  476 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6990 (mp0)
  outliers start: 26
  outliers final: 19
  residues processed: 173
  average time/residue: 0.1024
  time to fit residues: 25.4911
Evaluate side-chains
  169 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   70 PHE
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  929 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain B residue  341 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0060
   chunk 79 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0020
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.7608

-------------------------------------------------------------------------------
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 = 0.4229 r_free = 0.4229 target = 0.197081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.145289 restraints weight = 11453.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.29
r_work: 0.3367 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3374
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3374
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10588  Z= 0.131
  Angle     :  0.536   9.182  14282  Z= 0.274
  Chirality :  0.041   0.146   1538
  Planarity :  0.004   0.059   1835
  Dihedral  :  3.874  30.451   1388
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.85 %
    Favored  : 78.80 %
  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 (0.24), residues: 1239
  helix:  1.69 (0.22), residues: 579
  sheet: -1.22 (0.38), residues: 146
  loop : -0.87 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 503 
 TYR   0.011   0.001   TYR B 470 
 PHE   0.015   0.001   PHE A 734 
 TRP   0.008   0.001   TRP A 386 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10588)
  covalent geometry    : angle       0.53607 (14282)
  hydrogen bonds       : bond        0.04507 (  481)
  hydrogen bonds       : angle       3.90351 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 153
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 GLU cc_start: 0.7448 (tp30) cc_final: 0.6999 (tt0)
REVERT: A  148 LYS cc_start: 0.7963 (tppt) cc_final: 0.7321 (ttpp)
REVERT: A  179 LYS cc_start: 0.8019 (tppt) cc_final: 0.7750 (mttt)
REVERT: A  282 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7272 (mtm)
REVERT: A  410 LYS cc_start: 0.6947 (tppp) cc_final: 0.6600 (mttp)
REVERT: A  431 ASP cc_start: 0.8378 (p0) cc_final: 0.7964 (p0)
REVERT: A  732 MET cc_start: 0.7223 (tpt) cc_final: 0.6648 (mmm)
REVERT: A  739 MET cc_start: 0.8087 (mtt) cc_final: 0.7845 (mtp)
REVERT: A  765 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7479 (ttm170)
REVERT: A  796 ASN cc_start: 0.8112 (m-40) cc_final: 0.7805 (m-40)
REVERT: A 1033 GLN cc_start: 0.7611 (tp-100) cc_final: 0.7355 (tt0)
REVERT: B  417 ASN cc_start: 0.6788 (t0) cc_final: 0.6339 (t0)
REVERT: B  461 ARG cc_start: 0.7405 (tpt90) cc_final: 0.7089 (tpt90)
REVERT: B  503 ARG cc_start: 0.7182 (tmm160) cc_final: 0.6932 (tmm160)
REVERT: B  525 MET cc_start: 0.7320 (mmm) cc_final: 0.7074 (mmm)
REVERT: B  560 ASP cc_start: 0.7675 (t0) cc_final: 0.7191 (t0)
REVERT: B  582 MET cc_start: 0.7331 (ptt) cc_final: 0.6677 (mmp)
  outliers start: 27
  outliers final: 21
  residues processed: 169
  average time/residue: 0.0994
  time to fit residues: 24.5743
Evaluate side-chains
  173 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 PHE
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  929 LEU
Chi-restraints excluded: chain A residue  973 LYS
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain B residue  343 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4208 r_free = 0.4208 target = 0.194829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.146468 restraints weight = 11397.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.05
r_work: 0.3417 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10588  Z= 0.143
  Angle     :  0.542   9.478  14282  Z= 0.276
  Chirality :  0.041   0.146   1538
  Planarity :  0.004   0.060   1835
  Dihedral  :  3.875  29.706   1388
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.94 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.24), residues: 1239
  helix:  1.65 (0.22), residues: 582
  sheet: -1.13 (0.39), residues: 129
  loop : -0.96 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 662 
 TYR   0.011   0.001   TYR B 470 
 PHE   0.015   0.002   PHE A 667 
 TRP   0.008   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10588)
  covalent geometry    : angle       0.54190 (14282)
  hydrogen bonds       : bond        0.04525 (  481)
  hydrogen bonds       : angle       3.89480 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7696 (mmp) cc_final: 0.7280 (mmp)
REVERT: A  108 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7901 (tpt90)
REVERT: A  148 LYS cc_start: 0.7892 (tppt) cc_final: 0.7179 (ttpp)
REVERT: A  179 LYS cc_start: 0.8043 (tppt) cc_final: 0.7624 (pttm)
REVERT: A  205 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.6003 (tm-30)
REVERT: A  282 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7285 (mtm)
REVERT: A  431 ASP cc_start: 0.8509 (p0) cc_final: 0.8130 (p0)
REVERT: A  732 MET cc_start: 0.7209 (tpt) cc_final: 0.6596 (mmm)
REVERT: A  765 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7365 (mtt180)
REVERT: A  796 ASN cc_start: 0.8235 (m-40) cc_final: 0.7917 (m-40)
REVERT: A 1033 GLN cc_start: 0.7670 (tp-100) cc_final: 0.7411 (tt0)
REVERT: B  417 ASN cc_start: 0.6759 (t0) cc_final: 0.6275 (t0)
REVERT: B  461 ARG cc_start: 0.7367 (tpt90) cc_final: 0.7063 (tpt90)
REVERT: B  475 GLN cc_start: 0.7289 (tm-30) cc_final: 0.6445 (mt0)
REVERT: B  476 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7202 (mp0)
REVERT: B  503 ARG cc_start: 0.7136 (tmm160) cc_final: 0.6870 (tmm160)
REVERT: B  560 ASP cc_start: 0.7739 (t0) cc_final: 0.7283 (t0)
REVERT: B  582 MET cc_start: 0.7416 (ptt) cc_final: 0.6767 (mmp)
  outliers start: 28
  outliers final: 23
  residues processed: 170
  average time/residue: 0.0955
  time to fit residues: 23.4417
Evaluate side-chains
  175 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 PHE
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  205 GLN
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  929 LEU
Chi-restraints excluded: chain A residue  973 LYS
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  343 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 112 optimal weight:    3.9990
   chunk 119 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A1047 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.196528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.138408 restraints weight = 11518.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.84
r_work: 0.3360 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3307
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3307 r_free = 0.3307    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3307
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10588  Z= 0.155
  Angle     :  0.554   7.855  14282  Z= 0.283
  Chirality :  0.041   0.146   1538
  Planarity :  0.004   0.059   1835
  Dihedral  :  3.908  28.400   1388
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.85 %
    Favored  : 78.71 %
  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:  0.31 (0.24), residues: 1239
  helix:  1.58 (0.22), residues: 582
  sheet: -1.13 (0.40), residues: 129
  loop : -0.99 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 662 
 TYR   0.011   0.001   TYR B 470 
 PHE   0.016   0.002   PHE A 734 
 TRP   0.008   0.001   TRP A 669 
 HIS   0.006   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (10588)
  covalent geometry    : angle       0.55370 (14282)
  hydrogen bonds       : bond        0.04619 (  481)
  hydrogen bonds       : angle       3.90630 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7511 (mmp) cc_final: 0.7150 (mmp)
REVERT: A  108 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7892 (tpt90)
REVERT: A  148 LYS cc_start: 0.7888 (tppt) cc_final: 0.7212 (ttpp)
REVERT: A  205 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.5977 (tm-30)
REVERT: A  282 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7230 (mtm)
REVERT: A  431 ASP cc_start: 0.8431 (p0) cc_final: 0.7993 (p0)
REVERT: A  732 MET cc_start: 0.7147 (tpt) cc_final: 0.6537 (mmm)
REVERT: A  765 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7321 (mtt180)
REVERT: A  796 ASN cc_start: 0.8161 (m-40) cc_final: 0.7856 (m-40)
REVERT: B  461 ARG cc_start: 0.7300 (tpt90) cc_final: 0.7019 (tpt90)
REVERT: B  475 GLN cc_start: 0.7055 (tm-30) cc_final: 0.6527 (tm-30)
REVERT: B  476 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7152 (mp0)
REVERT: B  479 MET cc_start: 0.7439 (mtt) cc_final: 0.7104 (mtt)
REVERT: B  503 ARG cc_start: 0.7033 (tmm160) cc_final: 0.6634 (tmm160)
REVERT: B  560 ASP cc_start: 0.7648 (t0) cc_final: 0.7275 (t0)
REVERT: B  582 MET cc_start: 0.7243 (ptt) cc_final: 0.6702 (mmp)
  outliers start: 28
  outliers final: 24
  residues processed: 165
  average time/residue: 0.1001
  time to fit residues: 23.7808
Evaluate side-chains
  173 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   70 PHE
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  205 GLN
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  929 LEU
Chi-restraints excluded: chain A residue  973 LYS
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  343 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 86 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.192806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.136849 restraints weight = 11368.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.18
r_work: 0.3367 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10588  Z= 0.211
  Angle     :  0.612   8.065  14282  Z= 0.309
  Chirality :  0.043   0.147   1538
  Planarity :  0.004   0.059   1835
  Dihedral  :  4.065  25.812   1388
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.85 %
    Favored  : 78.80 %
  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:  0.05 (0.23), residues: 1239
  helix:  1.40 (0.21), residues: 584
  sheet: -1.22 (0.39), residues: 129
  loop : -1.20 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 770 
 TYR   0.018   0.001   TYR A 985 
 PHE   0.015   0.002   PHE A 930 
 TRP   0.009   0.002   TRP A  11 
 HIS   0.007   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 (10588)
  covalent geometry    : angle       0.61246 (14282)
  hydrogen bonds       : bond        0.05080 (  481)
  hydrogen bonds       : angle       4.02425 ( 1362)

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

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

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2478 Ramachandran restraints generated.
    1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7526 (mmp) cc_final: 0.7149 (mmp)
REVERT: A   81 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7731 (mm-30)
REVERT: A  108 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7998 (tpt90)
REVERT: A  148 LYS cc_start: 0.7991 (tppt) cc_final: 0.7376 (ttpp)
REVERT: A  179 LYS cc_start: 0.8009 (tppt) cc_final: 0.7529 (pttp)
REVERT: A  205 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.5947 (tm-30)
REVERT: A  282 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7246 (mtm)
REVERT: A  431 ASP cc_start: 0.8467 (p0) cc_final: 0.8036 (p0)
REVERT: A  732 MET cc_start: 0.7197 (tpt) cc_final: 0.6607 (mmm)
REVERT: A  765 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7476 (mtt180)
REVERT: A  796 ASN cc_start: 0.8096 (m-40) cc_final: 0.7786 (m-40)
REVERT: B  461 ARG cc_start: 0.7419 (tpt90) cc_final: 0.7098 (tpt90)
REVERT: B  476 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6846 (mp0)
REVERT: B  479 MET cc_start: 0.7527 (mtt) cc_final: 0.7216 (mtt)
REVERT: B  582 MET cc_start: 0.7214 (ptt) cc_final: 0.6696 (mmp)
  outliers start: 27
  outliers final: 23
  residues processed: 162
  average time/residue: 0.1061
  time to fit residues: 24.7463
Evaluate side-chains
  170 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  205 GLN
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  219 GLN
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  929 LEU
Chi-restraints excluded: chain A residue  973 LYS
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  343 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0170
   chunk 115 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 112 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.9822

-------------------------------------------------------------------------------
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 = 0.4221 r_free = 0.4221 target = 0.196216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.137500 restraints weight = 11549.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.73
r_work: 0.3355 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10588  Z= 0.151
  Angle     :  0.572   7.693  14282  Z= 0.291
  Chirality :  0.042   0.217   1538
  Planarity :  0.004   0.059   1835
  Dihedral  :  3.989  25.926   1388
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.68 %
    Favored  : 79.06 %
  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 (0.24), residues: 1239
  helix:  1.50 (0.22), residues: 585
  sheet: -1.24 (0.39), residues: 131
  loop : -1.18 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 662 
 TYR   0.018   0.001   TYR A 985 
 PHE   0.015   0.001   PHE A 667 
 TRP   0.008   0.001   TRP A  11 
 HIS   0.006   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (10588)
  covalent geometry    : angle       0.57187 (14282)
  hydrogen bonds       : bond        0.04603 (  481)
  hydrogen bonds       : angle       3.94381 ( 1362)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2864.14 seconds
wall clock time: 49 minutes 43.98 seconds (2983.98 seconds total)