Starting phenix.real_space_refine
on Thu Jul  2 16:00:53 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7rph_24614/07_2026/7rph_24614.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rph_24614/07_2026/7rph_24614.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2026/7rph_24614.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2026/7rph_24614.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2026/7rph_24614.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2026/7rph_24614.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2026/7rph_24614.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2026/7rph_24614.cif"
  }
  resolution = 2.5
  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=   0.006 sd=   0.579
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: 5
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     Na      3      4.78       5
     C    5742      2.51       5
     N    1185      2.21       5
     O    1578      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8573
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7366
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 926, 7358
          Classifications: {'peptide': 926}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 926, 7358
          Classifications: {'peptide': 926}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 7547
    Chain: "A"
      Number of atoms: 1207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 1207
          Unusual residues: {' NA': 3, 'AV0': 2, 'NAG': 5, 'Y01': 26}
          Classifications: {'undetermined': 36, 'water': 86}
          Link IDs: {None: 121}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen chiralities: 5
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AMET A 557 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET A 557 " occ=0.50
  Time building chain proxies: 3.32, per 1000 atoms: 0.39
  Number of scatterers: 8573
  At special positions: 0
  Unit cell: (88.51, 88.51, 127.755, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      65     16.00
     Na      3     11.00
     O    1578      8.00
     N    1185      7.00
     C    5742      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 292 " - pdb=" SG  CYS A 348 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 366 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 347 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 384 " - pdb=" SG  CYS A 417 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 397 " - pdb=" SG  CYS A 410 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 829 " - pdb=" SG  CYS A 849 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 863 " - pdb=" SG  CYS A 872 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 871 " - pdb=" SG  CYS A 887 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1632 " - " ASN A 915 "
      " NAG A1633 " - " ASN A 475 "
      " NAG A1634 " - " ASN A 834 "
      " NAG A1635 " - " ASN A 362 "
      " NAG A1636 " - " ASN A 390 "
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 547.2 milliseconds
  

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1766

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 3 sheets defined
      67.8% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 187
    Processing helix  chain 'A' and resid 187 through 209
      removed outlier: 3.550A  pdb=" N   VAL A 191 " --> pdb=" O   TRP A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 242
    Processing helix  chain 'A' and resid 253 through 262
      removed outlier: 3.606A  pdb=" N   ARG A 262 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 329
      removed outlier: 3.547A  pdb=" N   CYS A 322 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 339
    Processing helix  chain 'A' and resid 352 through 361
    Processing helix  chain 'A' and resid 365 through 369
    Processing helix  chain 'A' and resid 370 through 390
      removed outlier: 3.518A  pdb=" N   VAL A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   LYS A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   HIS A 387 " --> pdb=" O   THR A 383 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   TYR A 388 " --> pdb=" O   CYS A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 419
      removed outlier: 3.973A  pdb=" N   THR A 418 " --> pdb=" O   PRO A 414 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LYS A 419 " --> pdb=" O   ARG A 415 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 414 through 419'
    Processing helix  chain 'A' and resid 421 through 430
    Processing helix  chain 'A' and resid 437 through 442
      removed outlier: 4.001A  pdb=" N   ASP A 442 " --> pdb=" O   PRO A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 463 through 471
    Processing helix  chain 'A' and resid 491 through 493
      No H-bonds generated for 'chain 'A' and resid 491 through 493'
    Processing helix  chain 'A' and resid 494 through 502
      removed outlier: 3.567A  pdb=" N   TYR A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 522
    Processing helix  chain 'A' and resid 523 through 548
      removed outlier: 3.813A  pdb=" N   LEU A 538 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 559
    Processing helix  chain 'A' and resid 560 through 569
    Processing helix  chain 'A' and resid 570 through 587
    Processing helix  chain 'A' and resid 591 through 621
      removed outlier: 5.641A  pdb=" N   LEU A 605 " --> pdb=" O   GLN A 601 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   SER A 606 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   THR A 614 " --> pdb=" O   THR A 610 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASN A 621 " --> pdb=" O   ALA A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 624
      No H-bonds generated for 'chain 'A' and resid 622 through 624'
    Processing helix  chain 'A' and resid 626 through 648
    Processing helix  chain 'A' and resid 649 through 662
    Processing helix  chain 'A' and resid 682 through 706
    Processing helix  chain 'A' and resid 706 through 715
      removed outlier: 3.581A  pdb=" N   CYS A 710 " --> pdb=" O   LYS A 706 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE A 715 " --> pdb=" O   ILE A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 736
      removed outlier: 3.527A  pdb=" N   ILE A 721 " --> pdb=" O   TYR A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 750
    Processing helix  chain 'A' and resid 757 through 765
      removed outlier: 3.646A  pdb=" N   ASP A 763 " --> pdb=" O   PHE A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 769
    Processing helix  chain 'A' and resid 770 through 779
      removed outlier: 4.013A  pdb=" N   HIS A 776 " --> pdb=" O   PHE A 772 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   HIS A 777 " --> pdb=" O   GLU A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 834
      removed outlier: 3.547A  pdb=" N   ASN A 834 " --> pdb=" O   GLN A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 859
      removed outlier: 3.763A  pdb=" N   THR A 853 " --> pdb=" O   CYS A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 872
      Proline residue:  A 870  - end of helix
    Processing helix  chain 'A' and resid 880 through 899
      removed outlier: 4.099A  pdb=" N   LYS A 889 " --> pdb=" O   GLU A 885 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG A 897 " --> pdb=" O   MET A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 954
      removed outlier: 3.514A  pdb=" N   GLN A 940 " --> pdb=" O   GLU A 936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 1002
    Processing helix  chain 'A' and resid 1003 through 1028
    Processing helix  chain 'A' and resid 1033 through 1061
      removed outlier: 3.719A  pdb=" N   VAL A1038 " --> pdb=" O   VAL A1034 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A1040 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   SER A1041 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   VAL A1044 " --> pdb=" O   ILE A1040 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   ASP A1049 " --> pdb=" O   GLY A1045 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   PHE A1050 " --> pdb=" O   LEU A1046 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ALA A1051 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1094
      removed outlier: 5.233A  pdb=" N   SER A1079 " --> pdb=" O   SER A1075 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   ALA A1080 " --> pdb=" O   ARG A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1100 through 1123
    Processing helix  chain 'A' and resid 1123 through 1133
    Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458
      removed outlier: 3.952A  pdb=" N   SER A 300 " --> pdb=" O   SER A 455 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   ARG A 301 " --> pdb=" O   ILE A 486 " (cutoff:3.500A)
      removed outlier: 4.869A  pdb=" N   ILE A 486 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   VAL A 303 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 343
      removed outlier: 4.828A  pdb=" N   THR A 343 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER A 346 " --> pdb=" O   THR A 343 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 910 through 912
      removed outlier: 7.955A  pdb=" N   LEU A 923 " --> pdb=" O   TRP A 789 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   TRP A 789 " --> pdb=" O   LEU A 923 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   PHE A 925 " --> pdb=" O   VAL A 787 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   VAL A 787 " --> pdb=" O   PHE A 925 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   SER A 927 " --> pdb=" O   ILE A 785 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   ILE A 785 " --> pdb=" O   SER A 927 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   PHE A 929 " --> pdb=" O   MET A 783 " (cutoff:3.500A)

    439 hydrogen bonds defined for protein.
    1287 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: 1.34

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1239
        1.29 -     1.42: 2196
        1.42 -     1.56: 4867
        1.56 -     1.69: 367
        1.69 -     1.83: 98
  Bond restraints: 8767
  Sorted by residual:
  bond pdb=" C   LEU A1086 "
       pdb=" O   LEU A1086 "
    ideal  model  delta    sigma   weight residual
    1.237  1.156  0.081 1.17e-02 7.31e+03 4.75e+01
  bond pdb=" C   THR A 613 "
       pdb=" O   THR A 613 "
    ideal  model  delta    sigma   weight residual
    1.236  1.150  0.086 1.26e-02 6.30e+03 4.71e+01
  bond pdb=" C   ALA A 615 "
       pdb=" O   ALA A 615 "
    ideal  model  delta    sigma   weight residual
    1.237  1.159  0.078 1.16e-02 7.43e+03 4.53e+01
  bond pdb=" C   PHE A 608 "
       pdb=" O   PHE A 608 "
    ideal  model  delta    sigma   weight residual
    1.237  1.162  0.075 1.16e-02 7.43e+03 4.18e+01
  bond pdb=" C   ALA A 573 "
       pdb=" O   ALA A 573 "
    ideal  model  delta    sigma   weight residual
    1.237  1.161  0.076 1.19e-02 7.06e+03 4.08e+01
  ... (remaining 8762 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 8682
        1.94 -     3.87: 2828
        3.87 -     5.81: 493
        5.81 -     7.75: 53
        7.75 -     9.69: 10
  Bond angle restraints: 12066
  Sorted by residual:
  angle pdb=" N   PHE A 612 "
        pdb=" CA  PHE A 612 "
        pdb=" C   PHE A 612 "
      ideal   model   delta    sigma   weight residual
     111.71  121.40   -9.69 1.15e+00 7.56e-01 7.10e+01
  angle pdb=" N   LEU A1086 "
        pdb=" CA  LEU A1086 "
        pdb=" C   LEU A1086 "
      ideal   model   delta    sigma   weight residual
     111.28  119.12   -7.84 1.09e+00 8.42e-01 5.17e+01
  angle pdb=" CA  PHE A 759 "
        pdb=" CB  PHE A 759 "
        pdb=" CG  PHE A 759 "
      ideal   model   delta    sigma   weight residual
     113.80  120.09   -6.29 1.00e+00 1.00e+00 3.96e+01
  angle pdb=" N   ASP A1049 "
        pdb=" CA  ASP A1049 "
        pdb=" C   ASP A1049 "
      ideal   model   delta    sigma   weight residual
     111.07  117.58   -6.51 1.07e+00 8.73e-01 3.70e+01
  angle pdb=" N   ASP A 571 "
        pdb=" CA  ASP A 571 "
        pdb=" C   ASP A 571 "
      ideal   model   delta    sigma   weight residual
     111.33  118.66   -7.33 1.21e+00 6.83e-01 3.67e+01
  ... (remaining 12061 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.95: 4638
       27.95 -    55.91: 171
       55.91 -    83.86: 20
       83.86 -   111.82: 2
      111.82 -   139.77: 3
  Dihedral angle restraints: 4834
    sinusoidal: 2106
      harmonic: 2728
  Sorted by residual:
  dihedral pdb=" CB  CYS A 863 "
           pdb=" SG  CYS A 863 "
           pdb=" SG  CYS A 872 "
           pdb=" CB  CYS A 872 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.15   77.15     1      1.00e+01 1.00e-02 7.46e+01
  dihedral pdb=" CA  VAL A1048 "
           pdb=" C   VAL A1048 "
           pdb=" N   ASP A1049 "
           pdb=" CA  ASP A1049 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.08  -27.92     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CB  CYS A 384 "
           pdb=" SG  CYS A 384 "
           pdb=" SG  CYS A 417 "
           pdb=" CB  CYS A 417 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.34  -41.34     1      1.00e+01 1.00e-02 2.39e+01
  ... (remaining 4831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 971
       0.109 -    0.219: 384
       0.219 -    0.328: 70
       0.328 -    0.437: 14
       0.437 -    0.546: 2
  Chirality restraints: 1441
  Sorted by residual:
  chirality pdb=" CA  LEU A1086 "
            pdb=" N   LEU A1086 "
            pdb=" C   LEU A1086 "
            pdb=" CB  LEU A1086 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.46e+00
  chirality pdb=" CA  PHE A 612 "
            pdb=" N   PHE A 612 "
            pdb=" C   PHE A 612 "
            pdb=" CB  PHE A 612 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.45 2.00e-01 2.50e+01 4.95e+00
  chirality pdb=" CA  GLN A 334 "
            pdb=" N   GLN A 334 "
            pdb=" C   GLN A 334 "
            pdb=" CB  GLN A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.71e+00
  ... (remaining 1438 not shown)

  Planarity restraints: 1345
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 475 "    0.125 2.00e-02 2.50e+03   1.32e-01 2.17e+02
        pdb=" CG  ASN A 475 "   -0.073 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 475 "   -0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 475 "   -0.202 2.00e-02 2.50e+03
        pdb=" C1  NAG A1633 "    0.158 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 313 "    0.134 2.00e-02 2.50e+03   6.63e-02 1.10e+02
        pdb=" CG  TRP A 313 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 313 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 313 "   -0.037 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 313 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 313 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 313 "   -0.079 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 313 "    0.078 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 313 "   -0.045 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 313 "    0.062 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 351 "   -0.106 2.00e-02 2.50e+03   5.66e-02 8.00e+01
        pdb=" CG  TRP A 351 "    0.001 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 351 "    0.084 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 351 "    0.026 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 351 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 351 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 351 "    0.082 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 351 "   -0.050 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 351 "    0.026 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 351 "   -0.052 2.00e-02 2.50e+03
  ... (remaining 1342 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 19
        2.54 -     3.13: 6250
        3.13 -     3.72: 12578
        3.72 -     4.31: 19701
        4.31 -     4.90: 31303
  Nonbonded interactions: 69851
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 571 "
            pdb="NA    NA A1602 "
     model   vdw
     1.952 2.470
  nonbonded pdb=" OD1 ASP A1049 "
            pdb="NA    NA A1601 "
     model   vdw
     2.174 2.470
  nonbonded pdb=" O   GLY A 567 "
            pdb="NA    NA A1602 "
     model   vdw
     2.186 2.470
  nonbonded pdb=" OG1 THR A 613 "
            pdb="NA    NA A1601 "
     model   vdw
     2.201 2.470
  nonbonded pdb=" OD2 ASP A 572 "
            pdb="NA    NA A1603 "
     model   vdw
     2.251 2.470
  ... (remaining 69846 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.380
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.440
  Find NCS groups from input model:        0.050
  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:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
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      :  0.017   0.128   8780  Z= 0.984
  Angle     :  1.895   9.687  12097  Z= 1.230
  Chirality :  0.115   0.546   1441
  Planarity :  0.014   0.105   1340
  Dihedral  : 14.717 139.770   3044
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.56 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.45 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.70 (0.25), residues: 921
  helix: -0.48 (0.19), residues: 563
  sheet: -0.16 (0.97), residues: 29
  loop : -0.11 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 833 
 TYR   0.110   0.020   TYR A 762 
 PHE   0.065   0.012   PHE A 929 
 TRP   0.134   0.021   TRP A 313 
 HIS   0.019   0.004   HIS A 777 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01682 /  0.98 ( 8767)
  covalent geometry    : angle       1.88912 /  1.23 (12066)
  SS BOND              : bond        0.01313 /  0.68 (    8)
  SS BOND              : angle       2.68640 /  1.56 (   16)
  hydrogen bonds       : bond        0.19911 / 13.62 (  439)
  hydrogen bonds       : angle       7.08388 /  4.89 ( 1287)
  link_NAG-ASN         : bond        0.01152 /  0.66 (    5)
  link_NAG-ASN         : angle       4.24441 /  2.57 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 146
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.6381 (mtm) cc_final: 0.5288 (mmp)
REVERT: A  198 LEU cc_start: 0.7679 (mt) cc_final: 0.7339 (mt)
REVERT: A  256 TYR cc_start: 0.6588 (t80) cc_final: 0.6197 (t80)
REVERT: A  364 SER cc_start: 0.7742 (m) cc_final: 0.7072 (t)
REVERT: A  449 LYS cc_start: 0.7677 (tttt) cc_final: 0.7436 (tttm)
REVERT: A  478 ASP cc_start: 0.7320 (t0) cc_final: 0.7104 (t70)
REVERT: A  524 MET cc_start: 0.6868 (tpt) cc_final: 0.6467 (tpt)
REVERT: A  754 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6093 (ptt90)
REVERT: A  774 ARG cc_start: 0.6698 (mtp85) cc_final: 0.6093 (mtt-85)
REVERT: A  840 GLN cc_start: 0.7642 (mt0) cc_final: 0.6944 (mp10)
REVERT: A  846 PHE cc_start: 0.7302 (m-80) cc_final: 0.6841 (m-10)
REVERT: A  852 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6715 (mt-10)
REVERT: A  858 MET cc_start: 0.8132 (mmm) cc_final: 0.7691 (mmt)
REVERT: A  936 GLU cc_start: 0.7275 (tp30) cc_final: 0.6898 (mp0)
REVERT: A  968 ASN cc_start: 0.7907 (m-40) cc_final: 0.7029 (t0)
REVERT: A 1095 MET cc_start: 0.8652 (mmm) cc_final: 0.8357 (mmp)
  outliers start: 4
  outliers final: 0
  residues processed: 148
  average time/residue: 0.5864
  time to fit residues: 92.6744
Evaluate side-chains
  111 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  754 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0370
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.3636

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 367 GLN
A 376 HIS
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 389 GLN
A 856 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.181716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.129704 restraints weight = 18302.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.36
r_work: 0.3274 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8780  Z= 0.124
  Angle     :  0.664   8.889  12097  Z= 0.313
  Chirality :  0.043   0.280   1441
  Planarity :  0.004   0.040   1340
  Dihedral  : 12.205 148.922   1377
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  7.99 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.28), residues: 921
  helix:  1.48 (0.21), residues: 579
  sheet:  0.21 (0.92), residues: 29
  loop :  0.63 (0.39), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 241 
 TYR   0.014   0.001   TYR A 762 
 PHE   0.012   0.001   PHE A 454 
 TRP   0.015   0.002   TRP A 313 
 HIS   0.004   0.001   HIS A 387 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.12 ( 8767)
  covalent geometry    : angle       0.65150 /  0.31 (12066)
  SS BOND              : bond        0.00329 /  0.15 (    8)
  SS BOND              : angle       0.75509 /  0.54 (   16)
  hydrogen bonds       : bond        0.05059 /  3.31 (  439)
  hydrogen bonds       : angle       4.47386 /  3.15 ( 1287)
  link_NAG-ASN         : bond        0.00392 /  0.21 (    5)
  link_NAG-ASN         : angle       3.62389 /  2.35 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7612 (mtm) cc_final: 0.6416 (mmp)
REVERT: A  259 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6072 (tm-30)
REVERT: A  321 MET cc_start: 0.8042 (mtm) cc_final: 0.7833 (mtm)
REVERT: A  478 ASP cc_start: 0.7410 (t0) cc_final: 0.7151 (t0)
REVERT: A  515 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7827 (tp)
REVERT: A  768 LYS cc_start: 0.7371 (mtmt) cc_final: 0.6768 (mttt)
REVERT: A  774 ARG cc_start: 0.7129 (mtp85) cc_final: 0.6572 (mtt-85)
REVERT: A  840 GLN cc_start: 0.7658 (mt0) cc_final: 0.6965 (mp10)
REVERT: A  848 SER cc_start: 0.8553 (p) cc_final: 0.8348 (t)
REVERT: A  882 GLU cc_start: 0.6093 (pm20) cc_final: 0.5588 (mp0)
REVERT: A  924 GLU cc_start: 0.8370 (tt0) cc_final: 0.8123 (tt0)
REVERT: A  936 GLU cc_start: 0.7811 (tp30) cc_final: 0.7576 (mp0)
REVERT: A  937 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7794 (tptp)
REVERT: A  968 ASN cc_start: 0.8358 (m-40) cc_final: 0.7805 (t0)
REVERT: A 1011 ILE cc_start: 0.7793 (tp) cc_final: 0.7423 (pt)
REVERT: A 1095 MET cc_start: 0.9029 (mmm) cc_final: 0.8811 (mmp)
  outliers start: 11
  outliers final: 5
  residues processed: 137
  average time/residue: 0.5200
  time to fit residues: 76.4207
Evaluate side-chains
  103 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  382 ARG
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain A residue  983 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0980
   chunk 63 optimal weight:    1.9990
   chunk 75 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0570
   chunk 69 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 22 optimal weight:    0.3980
   overall best weight:    0.3098

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.182809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.129177 restraints weight = 20809.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.64
r_work: 0.3279 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8780  Z= 0.109
  Angle     :  0.588   7.798  12097  Z= 0.276
  Chirality :  0.040   0.234   1441
  Planarity :  0.004   0.037   1340
  Dihedral  : 11.372 150.384   1373
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.07 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.28), residues: 921
  helix:  1.92 (0.21), residues: 579
  sheet:  0.44 (0.95), residues: 31
  loop :  0.71 (0.39), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 241 
 TYR   0.012   0.001   TYR A 467 
 PHE   0.011   0.001   PHE A 846 
 TRP   0.015   0.001   TRP A 650 
 HIS   0.002   0.000   HIS A 428 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.11 ( 8767)
  covalent geometry    : angle       0.58020 /  0.27 (12066)
  SS BOND              : bond        0.00366 /  0.18 (    8)
  SS BOND              : angle       0.48719 /  0.33 (   16)
  hydrogen bonds       : bond        0.04369 /  2.86 (  439)
  hydrogen bonds       : angle       4.20380 /  2.95 ( 1287)
  link_NAG-ASN         : bond        0.00288 /  0.14 (    5)
  link_NAG-ASN         : angle       2.83983 /  1.78 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7580 (mtm) cc_final: 0.6328 (mmp)
REVERT: A  256 TYR cc_start: 0.6571 (t80) cc_final: 0.6295 (t80)
REVERT: A  478 ASP cc_start: 0.7355 (t0) cc_final: 0.7014 (t0)
REVERT: A  515 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7814 (tp)
REVERT: A  768 LYS cc_start: 0.7347 (mtmt) cc_final: 0.6888 (mttt)
REVERT: A  774 ARG cc_start: 0.7180 (mtp85) cc_final: 0.6587 (mtt-85)
REVERT: A  840 GLN cc_start: 0.7571 (mt0) cc_final: 0.6830 (mp10)
REVERT: A  848 SER cc_start: 0.8465 (p) cc_final: 0.8204 (t)
REVERT: A  882 GLU cc_start: 0.6012 (pm20) cc_final: 0.5437 (mp0)
REVERT: A  924 GLU cc_start: 0.8447 (tt0) cc_final: 0.8209 (tt0)
REVERT: A  936 GLU cc_start: 0.7780 (tp30) cc_final: 0.7493 (mp0)
REVERT: A  937 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7823 (mtmt)
REVERT: A 1011 ILE cc_start: 0.7810 (tp) cc_final: 0.7394 (pt)
  outliers start: 15
  outliers final: 8
  residues processed: 110
  average time/residue: 0.5523
  time to fit residues: 64.9296
Evaluate side-chains
  98 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  382 ARG
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Chi-restraints excluded: chain A residue 1106 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0980
   chunk 18 optimal weight:    0.9980
   chunk 60 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 ASN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.176582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.123347 restraints weight = 17276.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.39
r_work: 0.3171 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8780  Z= 0.148
  Angle     :  0.642   7.243  12097  Z= 0.304
  Chirality :  0.042   0.230   1441
  Planarity :  0.004   0.039   1340
  Dihedral  : 11.735 142.319   1373
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  9.46 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.28), residues: 921
  helix:  1.81 (0.21), residues: 579
  sheet:  0.20 (0.89), residues: 31
  loop :  0.56 (0.38), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 962 
 TYR   0.018   0.002   TYR A 762 
 PHE   0.016   0.002   PHE A 608 
 TRP   0.012   0.001   TRP A1002 
 HIS   0.003   0.001   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 ( 8767)
  covalent geometry    : angle       0.63554 /  0.30 (12066)
  SS BOND              : bond        0.00361 /  0.17 (    8)
  SS BOND              : angle       0.78610 /  0.49 (   16)
  hydrogen bonds       : bond        0.05977 /  3.91 (  439)
  hydrogen bonds       : angle       4.35147 /  3.06 ( 1287)
  link_NAG-ASN         : bond        0.00385 /  0.20 (    5)
  link_NAG-ASN         : angle       2.63068 /  1.87 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7681 (mtm) cc_final: 0.6471 (mmp)
REVERT: A  256 TYR cc_start: 0.6582 (t80) cc_final: 0.6344 (t80)
REVERT: A  478 ASP cc_start: 0.7485 (t0) cc_final: 0.7184 (t0)
REVERT: A  515 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7981 (tp)
REVERT: A  552 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7878 (mp0)
REVERT: A  593 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7833 (t)
REVERT: A  754 ARG cc_start: 0.8416 (ptp-110) cc_final: 0.7326 (ptt90)
REVERT: A  768 LYS cc_start: 0.7332 (mtmt) cc_final: 0.6920 (mttp)
REVERT: A  774 ARG cc_start: 0.7054 (mtp85) cc_final: 0.6794 (mtp85)
REVERT: A  840 GLN cc_start: 0.7653 (mt0) cc_final: 0.6911 (mp10)
REVERT: A  882 GLU cc_start: 0.6384 (pm20) cc_final: 0.5916 (mp0)
REVERT: A  936 GLU cc_start: 0.7926 (tp30) cc_final: 0.7621 (mp0)
REVERT: A  937 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7834 (tptp)
  outliers start: 19
  outliers final: 6
  residues processed: 113
  average time/residue: 0.5805
  time to fit residues: 70.2505
Evaluate side-chains
  102 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  382 ARG
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  552 GLU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 86 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    0.1980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 856 GLN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.178720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.126729 restraints weight = 19732.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.64
r_work: 0.3194 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8780  Z= 0.118
  Angle     :  0.585   6.987  12097  Z= 0.274
  Chirality :  0.040   0.205   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 11.380 139.630   1373
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  :  9.83 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.28), residues: 921
  helix:  1.99 (0.22), residues: 575
  sheet:  0.29 (0.91), residues: 31
  loop :  0.46 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 962 
 TYR   0.016   0.001   TYR A 467 
 PHE   0.012   0.001   PHE A 608 
 TRP   0.015   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 428 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.12 ( 8767)
  covalent geometry    : angle       0.58017 /  0.27 (12066)
  SS BOND              : bond        0.00321 /  0.15 (    8)
  SS BOND              : angle       0.65112 /  0.40 (   16)
  hydrogen bonds       : bond        0.04922 /  3.21 (  439)
  hydrogen bonds       : angle       4.19838 /  2.94 ( 1287)
  link_NAG-ASN         : bond        0.00471 /  0.24 (    5)
  link_NAG-ASN         : angle       2.20630 /  1.52 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7607 (mtm) cc_final: 0.6434 (mmp)
REVERT: A  478 ASP cc_start: 0.7215 (t0) cc_final: 0.6996 (t0)
REVERT: A  515 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7937 (tp)
REVERT: A  552 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7945 (mp0)
REVERT: A  586 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7473 (t70)
REVERT: A  754 ARG cc_start: 0.8461 (ptp-110) cc_final: 0.7349 (ptt90)
REVERT: A  768 LYS cc_start: 0.7318 (mtmt) cc_final: 0.6932 (mttp)
REVERT: A  774 ARG cc_start: 0.7033 (mtp85) cc_final: 0.6736 (mtp85)
REVERT: A  840 GLN cc_start: 0.7590 (mt0) cc_final: 0.6807 (mp10)
REVERT: A  882 GLU cc_start: 0.6220 (pm20) cc_final: 0.5677 (mp0)
REVERT: A  936 GLU cc_start: 0.7848 (tp30) cc_final: 0.7553 (mp0)
REVERT: A  937 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7858 (mtmt)
REVERT: A 1011 ILE cc_start: 0.7855 (tp) cc_final: 0.7365 (pp)
  outliers start: 23
  outliers final: 8
  residues processed: 114
  average time/residue: 0.6000
  time to fit residues: 72.9518
Evaluate side-chains
  107 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  552 GLU
Chi-restraints excluded: chain A residue  586 ASP
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  895 LEU
Chi-restraints excluded: chain A residue  915 ASN
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 73 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 856 GLN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.175876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.122212 restraints weight = 17579.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.60
r_work: 0.3156 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8780  Z= 0.152
  Angle     :  0.651  10.049  12097  Z= 0.305
  Chirality :  0.042   0.220   1441
  Planarity :  0.004   0.039   1340
  Dihedral  : 11.458 138.052   1373
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 10.20 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.28), residues: 921
  helix:  1.85 (0.21), residues: 573
  sheet:  0.16 (0.88), residues: 31
  loop :  0.35 (0.38), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 962 
 TYR   0.018   0.002   TYR A 762 
 PHE   0.016   0.002   PHE A 608 
 TRP   0.012   0.002   TRP A 650 
 HIS   0.004   0.001   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 ( 8767)
  covalent geometry    : angle       0.64410 /  0.30 (12066)
  SS BOND              : bond        0.00403 /  0.19 (    8)
  SS BOND              : angle       0.75621 /  0.48 (   16)
  hydrogen bonds       : bond        0.05938 /  3.88 (  439)
  hydrogen bonds       : angle       4.35442 /  3.06 ( 1287)
  link_NAG-ASN         : bond        0.00404 /  0.21 (    5)
  link_NAG-ASN         : angle       2.67007 /  1.85 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7623 (mtm) cc_final: 0.6502 (mmp)
REVERT: A  472 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7374 (tm-30)
REVERT: A  478 ASP cc_start: 0.7251 (t0) cc_final: 0.7011 (t0)
REVERT: A  515 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7987 (tp)
REVERT: A  552 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7860 (mp0)
REVERT: A  593 SER cc_start: 0.8030 (OUTLIER) cc_final: 0.7806 (t)
REVERT: A  754 ARG cc_start: 0.8489 (ptp-110) cc_final: 0.7403 (ptt90)
REVERT: A  774 ARG cc_start: 0.7025 (mtp85) cc_final: 0.6648 (mtp85)
REVERT: A  840 GLN cc_start: 0.7669 (mt0) cc_final: 0.6924 (mp10)
REVERT: A  882 GLU cc_start: 0.6428 (pm20) cc_final: 0.5913 (mp0)
REVERT: A  936 GLU cc_start: 0.7905 (tp30) cc_final: 0.7586 (mp0)
REVERT: A  937 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7837 (tptp)
  outliers start: 21
  outliers final: 9
  residues processed: 109
  average time/residue: 0.5871
  time to fit residues: 68.3972
Evaluate side-chains
  104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  472 GLU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  552 GLU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  895 LEU
Chi-restraints excluded: chain A residue  915 ASN
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 58 optimal weight:    0.2980
   chunk 8 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 83 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 856 GLN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.178434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.127466 restraints weight = 13468.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.98
r_work: 0.3254 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3256
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3256
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8780  Z= 0.114
  Angle     :  0.582   7.997  12097  Z= 0.271
  Chirality :  0.040   0.198   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 11.107 138.259   1373
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 10.44 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.28), residues: 921
  helix:  2.00 (0.22), residues: 575
  sheet:  0.23 (0.89), residues: 31
  loop :  0.37 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 701 
 TYR   0.017   0.001   TYR A 256 
 PHE   0.012   0.001   PHE A 608 
 TRP   0.015   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 8767)
  covalent geometry    : angle       0.57582 /  0.27 (12066)
  SS BOND              : bond        0.00321 /  0.15 (    8)
  SS BOND              : angle       0.59298 /  0.37 (   16)
  hydrogen bonds       : bond        0.04879 /  3.18 (  439)
  hydrogen bonds       : angle       4.19750 /  2.94 ( 1287)
  link_NAG-ASN         : bond        0.00252 /  0.13 (    5)
  link_NAG-ASN         : angle       2.37876 /  1.68 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7541 (mtm) cc_final: 0.6430 (mmp)
REVERT: A  472 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7305 (tm-30)
REVERT: A  515 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7921 (tp)
REVERT: A  552 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7858 (mp0)
REVERT: A  593 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7790 (t)
REVERT: A  701 ARG cc_start: 0.7724 (ttt-90) cc_final: 0.6707 (tpm-80)
REVERT: A  754 ARG cc_start: 0.8386 (ptp-110) cc_final: 0.7332 (ptt90)
REVERT: A  774 ARG cc_start: 0.7004 (mtp85) cc_final: 0.6721 (mtp-110)
REVERT: A  840 GLN cc_start: 0.7606 (mt0) cc_final: 0.6858 (mp10)
REVERT: A  937 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7858 (mtmt)
REVERT: A 1011 ILE cc_start: 0.7847 (tp) cc_final: 0.7391 (pp)
  outliers start: 18
  outliers final: 7
  residues processed: 103
  average time/residue: 0.5956
  time to fit residues: 65.3907
Evaluate side-chains
  101 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  472 GLU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  552 GLU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  895 LEU
Chi-restraints excluded: chain A residue  915 ASN
Chi-restraints excluded: chain A residue  954 SER
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 4 optimal weight:    0.4980
   chunk 90 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 69 optimal weight:    0.3980
   chunk 49 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 856 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.178953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.126288 restraints weight = 16113.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.49
r_work: 0.3222 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3223
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8780  Z= 0.110
  Angle     :  0.568   9.470  12097  Z= 0.266
  Chirality :  0.039   0.195   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 10.915 138.643   1373
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.06 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.28), residues: 921
  helix:  2.07 (0.22), residues: 574
  sheet:  0.28 (0.90), residues: 31
  loop :  0.32 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 382 
 TYR   0.017   0.001   TYR A 256 
 PHE   0.010   0.001   PHE A 608 
 TRP   0.015   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 428 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.11 ( 8767)
  covalent geometry    : angle       0.56332 /  0.27 (12066)
  SS BOND              : bond        0.00303 /  0.14 (    8)
  SS BOND              : angle       0.54464 /  0.34 (   16)
  hydrogen bonds       : bond        0.04663 /  3.03 (  439)
  hydrogen bonds       : angle       4.16960 /  2.92 ( 1287)
  link_NAG-ASN         : bond        0.00217 /  0.11 (    5)
  link_NAG-ASN         : angle       2.23063 /  1.50 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7558 (mtm) cc_final: 0.6432 (mmp)
REVERT: A  472 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7267 (tm-30)
REVERT: A  515 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7929 (tp)
REVERT: A  552 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7897 (mp0)
REVERT: A  593 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7764 (t)
REVERT: A  754 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.7366 (ptt90)
REVERT: A  774 ARG cc_start: 0.7040 (mtp85) cc_final: 0.6778 (mtp-110)
REVERT: A  840 GLN cc_start: 0.7604 (mt0) cc_final: 0.6824 (mp10)
REVERT: A  937 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7956 (mtmt)
REVERT: A 1011 ILE cc_start: 0.7853 (tp) cc_final: 0.7366 (pp)
  outliers start: 17
  outliers final: 8
  residues processed: 104
  average time/residue: 0.6023
  time to fit residues: 66.6821
Evaluate side-chains
  105 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  472 GLU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  552 GLU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  895 LEU
Chi-restraints excluded: chain A residue  915 ASN
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0270
   chunk 47 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.7038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 856 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.183365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.136708 restraints weight = 18070.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.09
r_work: 0.3377 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8780  Z= 0.116
  Angle     :  0.592  11.872  12097  Z= 0.275
  Chirality :  0.039   0.194   1441
  Planarity :  0.004   0.037   1340
  Dihedral  : 10.921 138.347   1373
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.30 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.28), residues: 921
  helix:  2.04 (0.22), residues: 575
  sheet:  0.20 (0.89), residues: 31
  loop :  0.29 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 382 
 TYR   0.016   0.001   TYR A 256 
 PHE   0.012   0.001   PHE A 608 
 TRP   0.014   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.12 ( 8767)
  covalent geometry    : angle       0.58764 /  0.27 (12066)
  SS BOND              : bond        0.00324 /  0.15 (    8)
  SS BOND              : angle       0.53450 /  0.35 (   16)
  hydrogen bonds       : bond        0.04904 /  3.19 (  439)
  hydrogen bonds       : angle       4.19177 /  2.93 ( 1287)
  link_NAG-ASN         : bond        0.00247 /  0.13 (    5)
  link_NAG-ASN         : angle       2.12233 /  1.43 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7674 (mtm) cc_final: 0.6638 (mmp)
REVERT: A  472 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7350 (tm-30)
REVERT: A  515 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8092 (tp)
REVERT: A  552 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7845 (mp0)
REVERT: A  593 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7918 (t)
REVERT: A  698 GLU cc_start: 0.7426 (tp30) cc_final: 0.7015 (pp20)
REVERT: A  754 ARG cc_start: 0.8465 (ptp-110) cc_final: 0.7480 (ptt90)
REVERT: A  774 ARG cc_start: 0.7064 (mtp85) cc_final: 0.6861 (mtp-110)
REVERT: A  840 GLN cc_start: 0.7678 (mt0) cc_final: 0.7008 (mp10)
REVERT: A  937 LYS cc_start: 0.8266 (ttpt) cc_final: 0.8048 (mtmt)
REVERT: A 1011 ILE cc_start: 0.7904 (tp) cc_final: 0.7492 (pp)
REVERT: A 1111 MET cc_start: 0.9110 (mtm) cc_final: 0.8812 (mtm)
  outliers start: 18
  outliers final: 10
  residues processed: 102
  average time/residue: 0.6238
  time to fit residues: 67.6567
Evaluate side-chains
  101 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  472 GLU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  552 GLU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  895 LEU
Chi-restraints excluded: chain A residue  915 ASN
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  954 SER
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 40 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 856 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.181589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.133664 restraints weight = 20873.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 2.30
r_work: 0.3356 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3336
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3336
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8780  Z= 0.126
  Angle     :  0.619  12.261  12097  Z= 0.287
  Chirality :  0.040   0.197   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 11.015 137.878   1373
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.92 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.28), residues: 921
  helix:  1.99 (0.22), residues: 575
  sheet:  0.14 (0.89), residues: 31
  loop :  0.23 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 382 
 TYR   0.016   0.002   TYR A 256 
 PHE   0.014   0.001   PHE A 608 
 TRP   0.013   0.001   TRP A 650 
 HIS   0.003   0.001   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 ( 8767)
  covalent geometry    : angle       0.61203 /  0.29 (12066)
  SS BOND              : bond        0.00352 /  0.17 (    8)
  SS BOND              : angle       0.59466 /  0.38 (   16)
  hydrogen bonds       : bond        0.05235 /  3.41 (  439)
  hydrogen bonds       : angle       4.23952 /  2.96 ( 1287)
  link_NAG-ASN         : bond        0.00305 /  0.16 (    5)
  link_NAG-ASN         : angle       2.64739 /  1.69 (   15)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  472 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7365 (tm-30)
REVERT: A  515 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8137 (tp)
REVERT: A  552 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7819 (mp0)
REVERT: A  593 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7937 (t)
REVERT: A  698 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7013 (pp20)
REVERT: A  754 ARG cc_start: 0.8496 (ptp-110) cc_final: 0.7516 (ptt90)
REVERT: A  840 GLN cc_start: 0.7690 (mt0) cc_final: 0.7026 (mp10)
REVERT: A  937 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7992 (mtmt)
  outliers start: 15
  outliers final: 10
  residues processed: 101
  average time/residue: 0.6017
  time to fit residues: 64.7120
Evaluate side-chains
  106 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  472 GLU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  552 GLU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  895 LEU
Chi-restraints excluded: chain A residue  915 ASN
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  954 SER
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 856 GLN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.181731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.135614 restraints weight = 18377.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.08
r_work: 0.3372 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3335
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3335
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8780  Z= 0.123
  Angle     :  0.616  12.227  12097  Z= 0.284
  Chirality :  0.040   0.194   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 11.014 137.905   1373
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.16 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.28), residues: 921
  helix:  1.96 (0.22), residues: 575
  sheet:  0.12 (0.89), residues: 31
  loop :  0.21 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 382 
 TYR   0.016   0.001   TYR A 256 
 PHE   0.013   0.001   PHE A 608 
 TRP   0.013   0.001   TRP A 650 
 HIS   0.003   0.001   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 8767)
  covalent geometry    : angle       0.61023 /  0.28 (12066)
  SS BOND              : bond        0.00343 /  0.16 (    8)
  SS BOND              : angle       0.57886 /  0.37 (   16)
  hydrogen bonds       : bond        0.05131 /  3.34 (  439)
  hydrogen bonds       : angle       4.22801 /  2.95 ( 1287)
  link_NAG-ASN         : bond        0.00318 /  0.16 (    5)
  link_NAG-ASN         : angle       2.52733 /  1.69 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3617.01 seconds
wall clock time: 62 minutes 27.29 seconds (3747.29 seconds total)