Starting phenix.real_space_refine
on Sun Jul 27 08:31:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rph_24614/07_2025/7rph_24614.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rph_24614/07_2025/7rph_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2025/7rph_24614.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2025/7rph_24614.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2025/7rph_24614.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rph_24614/07_2025/7rph_24614.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 15
          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: 9.03, per 1000 atoms: 1.05
  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: 2.07
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 0.82
  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: 2.48

  Time building geometry restraints manager: 2.47 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: 6352
       27.95 -    55.91: 258
       55.91 -    83.86: 25
       83.86 -   111.82: 15
      111.82 -   139.77: 9
  Dihedral angle restraints: 6659
    sinusoidal: 3931
      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 6656 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:             1.510
  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:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     26.640
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.050
  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:11.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
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  : 15.182 139.770   4869
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.134   0.021   TRP A 313 
 HIS   0.019   0.004   HIS A 777 
 PHE   0.065   0.012   PHE A 929 
 TYR   0.110   0.020   TYR A 762 
 ARG   0.008   0.001   ARG A 833 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01152 (    5)
  link_NAG-ASN         : angle       4.24441 (   15)
  hydrogen bonds       : bond        0.19911 (  439)
  hydrogen bonds       : angle       7.08388 ( 1287)
  SS BOND              : bond        0.01313 (    8)
  SS BOND              : angle       2.68640 (   16)
  covalent geometry    : bond        0.01682 ( 8767)
  covalent geometry    : angle       1.88912 (12066)

*********************** 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  : 0.899 
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: 1.2020
  time to fit residues: 189.6551
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  : 0.847 
-------------------------------------------------------------------------------
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 77 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0370
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A 251 ASN
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.179743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.126839 restraints weight = 17040.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.58
r_work: 0.3228 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8780  Z= 0.134
  Angle     :  0.707   9.540  12097  Z= 0.329
  Chirality :  0.046   0.340   1441
  Planarity :  0.004   0.040   1340
  Dihedral  : 12.204 167.812   3202
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  7.62 %
    Favored  : 90.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.28), residues: 921
  helix:  1.40 (0.21), residues: 579
  sheet:  0.21 (0.94), residues: 29
  loop :  0.57 (0.39), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 313 
 HIS   0.005   0.001   HIS A 428 
 PHE   0.013   0.001   PHE A 454 
 TYR   0.017   0.002   TYR A 762 
 ARG   0.002   0.000   ARG A 754 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00574 (    5)
  link_NAG-ASN         : angle       3.90404 (   15)
  hydrogen bonds       : bond        0.05517 (  439)
  hydrogen bonds       : angle       4.53455 ( 1287)
  SS BOND              : bond        0.00369 (    8)
  SS BOND              : angle       0.81181 (   16)
  covalent geometry    : bond        0.00272 ( 8767)
  covalent geometry    : angle       0.69385 (12066)

*********************** 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
  143 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7650 (mtm) cc_final: 0.6453 (mmp)
REVERT: A  259 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6066 (tm-30)
REVERT: A  321 MET cc_start: 0.8100 (mtm) cc_final: 0.7872 (mtm)
REVERT: A  478 ASP cc_start: 0.7457 (t0) cc_final: 0.7179 (t70)
REVERT: A  515 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7864 (tp)
REVERT: A  754 ARG cc_start: 0.8281 (ptp-110) cc_final: 0.7123 (ptt90)
REVERT: A  768 LYS cc_start: 0.7390 (mtmt) cc_final: 0.6773 (mttt)
REVERT: A  774 ARG cc_start: 0.7150 (mtp85) cc_final: 0.6568 (mtt-85)
REVERT: A  840 GLN cc_start: 0.7686 (mt0) cc_final: 0.7002 (mp10)
REVERT: A  882 GLU cc_start: 0.6059 (pm20) cc_final: 0.5543 (mp0)
REVERT: A  936 GLU cc_start: 0.7884 (tp30) cc_final: 0.7612 (mp0)
REVERT: A  937 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7790 (tptp)
REVERT: A  968 ASN cc_start: 0.8405 (m-40) cc_final: 0.7855 (t0)
REVERT: A 1011 ILE cc_start: 0.7807 (tp) cc_final: 0.7422 (pt)
REVERT: A 1095 MET cc_start: 0.9041 (mmm) cc_final: 0.8838 (mmp)
  outliers start: 12
  outliers final: 5
  residues processed: 137
  average time/residue: 1.1202
  time to fit residues: 164.7505
Evaluate side-chains
  107 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
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 47 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.177881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126313 restraints weight = 12486.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.25
r_work: 0.3236 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8780  Z= 0.134
  Angle     :  0.649   7.902  12097  Z= 0.305
  Chirality :  0.043   0.249   1441
  Planarity :  0.004   0.037   1340
  Dihedral  : 11.314 175.315   3198
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  9.21 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.28), residues: 921
  helix:  1.71 (0.21), residues: 579
  sheet:  0.19 (0.89), residues: 31
  loop :  0.52 (0.38), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 650 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.013   0.001   PHE A 608 
 TYR   0.017   0.002   TYR A 762 
 ARG   0.002   0.000   ARG A 415 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00294 (    5)
  link_NAG-ASN         : angle       3.25898 (   15)
  hydrogen bonds       : bond        0.05517 (  439)
  hydrogen bonds       : angle       4.34786 ( 1287)
  SS BOND              : bond        0.00427 (    8)
  SS BOND              : angle       0.65170 (   16)
  covalent geometry    : bond        0.00285 ( 8767)
  covalent geometry    : angle       0.63939 (12066)

*********************** 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
  122 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7597 (mtm) cc_final: 0.6382 (mmp)
REVERT: A  256 TYR cc_start: 0.6582 (t80) cc_final: 0.6306 (t80)
REVERT: A  478 ASP cc_start: 0.7498 (t0) cc_final: 0.7091 (t0)
REVERT: A  515 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7919 (tp)
REVERT: A  552 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7776 (mp0)
REVERT: A  754 ARG cc_start: 0.8326 (ptp-110) cc_final: 0.7210 (ptt90)
REVERT: A  768 LYS cc_start: 0.7379 (mtmt) cc_final: 0.6849 (mttt)
REVERT: A  774 ARG cc_start: 0.7138 (mtp85) cc_final: 0.6511 (mtt-85)
REVERT: A  840 GLN cc_start: 0.7628 (mt0) cc_final: 0.6890 (mp10)
REVERT: A  848 SER cc_start: 0.8538 (p) cc_final: 0.8268 (t)
REVERT: A  882 GLU cc_start: 0.6228 (pm20) cc_final: 0.5885 (mp0)
REVERT: A  924 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7971 (tt0)
REVERT: A  936 GLU cc_start: 0.7835 (tp30) cc_final: 0.7623 (mp0)
REVERT: A  937 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7763 (tptp)
  outliers start: 18
  outliers final: 8
  residues processed: 115
  average time/residue: 1.2904
  time to fit residues: 158.2454
Evaluate side-chains
  105 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 ASP
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  552 GLU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  924 GLU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0070
   chunk 39 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 66 optimal weight:    0.2980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.7802

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4030 r_free = 0.4030 target = 0.178586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.124829 restraints weight = 20232.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.45
r_work: 0.3216 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8780  Z= 0.121
  Angle     :  0.597   7.143  12097  Z= 0.281
  Chirality :  0.041   0.216   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 11.043 175.550   3198
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  9.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.28), residues: 921
  helix:  1.92 (0.21), residues: 574
  sheet:  0.24 (0.90), residues: 31
  loop :  0.41 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 650 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.013   0.001   PHE A 608 
 TYR   0.016   0.001   TYR A 467 
 ARG   0.002   0.000   ARG A 962 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00207 (    5)
  link_NAG-ASN         : angle       2.67521 (   15)
  hydrogen bonds       : bond        0.05068 (  439)
  hydrogen bonds       : angle       4.23198 ( 1287)
  SS BOND              : bond        0.00331 (    8)
  SS BOND              : angle       0.58090 (   16)
  covalent geometry    : bond        0.00258 ( 8767)
  covalent geometry    : angle       0.58952 (12066)

*********************** 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
  124 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7629 (mtm) cc_final: 0.6415 (mmp)
REVERT: A  478 ASP cc_start: 0.7391 (t0) cc_final: 0.7135 (t0)
REVERT: A  515 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7924 (tp)
REVERT: A  552 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7917 (mp0)
REVERT: A  593 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7805 (t)
REVERT: A  754 ARG cc_start: 0.8394 (ptp-110) cc_final: 0.7302 (ptt90)
REVERT: A  768 LYS cc_start: 0.7331 (mtmt) cc_final: 0.6994 (mttp)
REVERT: A  774 ARG cc_start: 0.7095 (mtp85) cc_final: 0.6826 (mtp85)
REVERT: A  840 GLN cc_start: 0.7587 (mt0) cc_final: 0.6823 (mp10)
REVERT: A  882 GLU cc_start: 0.6308 (pm20) cc_final: 0.5811 (mp0)
REVERT: A  936 GLU cc_start: 0.7933 (tp30) cc_final: 0.7691 (mp0)
REVERT: A  937 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7830 (tptp)
  outliers start: 21
  outliers final: 5
  residues processed: 114
  average time/residue: 1.1969
  time to fit residues: 145.8208
Evaluate side-chains
  103 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  378 LEU
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  983 LEU
Chi-restraints excluded: chain A residue 1106 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4038 r_free = 0.4038 target = 0.179247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.124791 restraints weight = 20471.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.66
r_work: 0.3207 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3209
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2920

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= 0.113
  Angle     :  0.572   6.941  12097  Z= 0.269
  Chirality :  0.040   0.211   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 10.804 175.994   3198
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 10.07 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.28), residues: 921
  helix:  2.01 (0.22), residues: 575
  sheet:  0.20 (0.89), residues: 31
  loop :  0.44 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.011   0.001   PHE A 608 
 TYR   0.015   0.001   TYR A 256 
 ARG   0.002   0.000   ARG A 962 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00268 (    5)
  link_NAG-ASN         : angle       2.35969 (   15)
  hydrogen bonds       : bond        0.04815 (  439)
  hydrogen bonds       : angle       4.19718 ( 1287)
  SS BOND              : bond        0.00318 (    8)
  SS BOND              : angle       0.60020 (   16)
  covalent geometry    : bond        0.00235 ( 8767)
  covalent geometry    : angle       0.56632 (12066)

*********************** 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
  120 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7548 (mtm) cc_final: 0.6363 (mmp)
REVERT: A  478 ASP cc_start: 0.7227 (t0) cc_final: 0.7026 (t0)
REVERT: A  515 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7893 (tp)
REVERT: A  552 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7922 (mp0)
REVERT: A  593 SER cc_start: 0.8024 (OUTLIER) cc_final: 0.7768 (t)
REVERT: A  754 ARG cc_start: 0.8408 (ptp-110) cc_final: 0.7284 (ptt90)
REVERT: A  768 LYS cc_start: 0.7354 (mtmt) cc_final: 0.7153 (mttp)
REVERT: A  774 ARG cc_start: 0.7064 (mtp85) cc_final: 0.6615 (mtp-110)
REVERT: A  840 GLN cc_start: 0.7559 (mt0) cc_final: 0.6778 (mp10)
REVERT: A  848 SER cc_start: 0.8516 (p) cc_final: 0.8267 (t)
REVERT: A  882 GLU cc_start: 0.6307 (pm20) cc_final: 0.5735 (mp0)
REVERT: A  936 GLU cc_start: 0.7913 (tp30) cc_final: 0.7650 (mp0)
REVERT: A  937 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7869 (mtmt)
REVERT: A 1011 ILE cc_start: 0.7870 (tp) cc_final: 0.7385 (pp)
  outliers start: 20
  outliers final: 5
  residues processed: 113
  average time/residue: 1.8560
  time to fit residues: 224.6317
Evaluate side-chains
  102 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  378 LEU
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  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Chi-restraints excluded: chain A residue 1106 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4010 r_free = 0.4010 target = 0.176351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.123876 restraints weight = 15913.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.28
r_work: 0.3193 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2870

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= 0.141
  Angle     :  0.625  10.365  12097  Z= 0.294
  Chirality :  0.042   0.210   1441
  Planarity :  0.004   0.039   1340
  Dihedral  : 10.937 174.560   3198
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  :  9.71 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.28), residues: 921
  helix:  1.91 (0.22), residues: 574
  sheet:  0.10 (0.87), residues: 31
  loop :  0.30 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 650 
 HIS   0.003   0.001   HIS A 332 
 PHE   0.015   0.001   PHE A 608 
 TYR   0.016   0.002   TYR A 762 
 ARG   0.003   0.000   ARG A 962 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00440 (    5)
  link_NAG-ASN         : angle       2.44896 (   15)
  hydrogen bonds       : bond        0.05712 (  439)
  hydrogen bonds       : angle       4.30976 ( 1287)
  SS BOND              : bond        0.00394 (    8)
  SS BOND              : angle       0.76704 (   16)
  covalent geometry    : bond        0.00313 ( 8767)
  covalent geometry    : angle       0.61898 (12066)

*********************** 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
  118 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7569 (mtm) cc_final: 0.6441 (mmp)
REVERT: A  472 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7272 (tm-30)
REVERT: A  478 ASP cc_start: 0.7186 (t0) cc_final: 0.6967 (t0)
REVERT: A  515 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7939 (tp)
REVERT: A  552 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7828 (mp0)
REVERT: A  593 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.7815 (t)
REVERT: A  754 ARG cc_start: 0.8400 (ptp-110) cc_final: 0.7343 (ptt90)
REVERT: A  774 ARG cc_start: 0.7023 (mtp85) cc_final: 0.6707 (mtp-110)
REVERT: A  840 GLN cc_start: 0.7631 (mt0) cc_final: 0.6877 (mp10)
REVERT: A  882 GLU cc_start: 0.6473 (pm20) cc_final: 0.5964 (mp0)
REVERT: A  936 GLU cc_start: 0.7908 (tp30) cc_final: 0.7649 (mp0)
REVERT: A  937 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7849 (tptp)
  outliers start: 25
  outliers final: 7
  residues processed: 110
  average time/residue: 1.2492
  time to fit residues: 147.1040
Evaluate side-chains
  103 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  421 ASN
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  915 ASN
Chi-restraints excluded: chain A residue  983 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 64 optimal weight:    0.2980
   chunk 50 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 856 GLN
A 860 ASN
A 968 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.178248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.124892 restraints weight = 17651.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.60
r_work: 0.3211 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3055

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= 0.115
  Angle     :  0.572   8.180  12097  Z= 0.269
  Chirality :  0.040   0.209   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 10.602 174.211   3198
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 10.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.28), residues: 921
  helix:  2.00 (0.22), residues: 575
  sheet:  0.15 (0.88), residues: 31
  loop :  0.29 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.011   0.001   PHE A 608 
 TYR   0.017   0.001   TYR A 256 
 ARG   0.003   0.000   ARG A 701 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00139 (    5)
  link_NAG-ASN         : angle       2.37189 (   15)
  hydrogen bonds       : bond        0.04894 (  439)
  hydrogen bonds       : angle       4.20470 ( 1287)
  SS BOND              : bond        0.00318 (    8)
  SS BOND              : angle       0.66300 (   16)
  covalent geometry    : bond        0.00246 ( 8767)
  covalent geometry    : angle       0.56659 (12066)

*********************** 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
  113 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7555 (mtm) cc_final: 0.6400 (mmp)
REVERT: A  515 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7894 (tp)
REVERT: A  552 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7882 (mp0)
REVERT: A  593 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7783 (t)
REVERT: A  774 ARG cc_start: 0.7038 (mtp85) cc_final: 0.6739 (mtp-110)
REVERT: A  840 GLN cc_start: 0.7602 (mt0) cc_final: 0.6815 (mp10)
REVERT: A  936 GLU cc_start: 0.7834 (tp30) cc_final: 0.7575 (mp0)
REVERT: A  937 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7855 (mtmt)
  outliers start: 20
  outliers final: 9
  residues processed: 105
  average time/residue: 1.2268
  time to fit residues: 137.4028
Evaluate side-chains
  102 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  378 LEU
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  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
Chi-restraints excluded: chain A residue 1114 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0030
   chunk 77 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 16 optimal weight:    0.2980
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.5592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.179341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.124806 restraints weight = 20648.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.64
r_work: 0.3213 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3169

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= 0.109
  Angle     :  0.565   9.521  12097  Z= 0.266
  Chirality :  0.040   0.208   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 10.451 173.853   3198
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.18 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.28), residues: 921
  helix:  2.02 (0.22), residues: 575
  sheet:  0.21 (0.90), residues: 31
  loop :  0.29 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.009   0.001   PHE A 608 
 TYR   0.017   0.001   TYR A 256 
 ARG   0.008   0.000   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00144 (    5)
  link_NAG-ASN         : angle       2.18884 (   15)
  hydrogen bonds       : bond        0.04671 (  439)
  hydrogen bonds       : angle       4.17124 ( 1287)
  SS BOND              : bond        0.00308 (    8)
  SS BOND              : angle       0.60486 (   16)
  covalent geometry    : bond        0.00226 ( 8767)
  covalent geometry    : angle       0.55994 (12066)

*********************** 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: 18
    poor density    : 92
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7538 (mtm) cc_final: 0.6389 (mmp)
REVERT: A  256 TYR cc_start: 0.6696 (t80) cc_final: 0.6433 (t80)
REVERT: A  472 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7256 (tm-30)
REVERT: A  515 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7893 (tp)
REVERT: A  552 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7908 (mp0)
REVERT: A  593 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7765 (t)
REVERT: A  774 ARG cc_start: 0.7040 (mtp85) cc_final: 0.6777 (mtp-110)
REVERT: A  840 GLN cc_start: 0.7606 (mt0) cc_final: 0.6807 (mp10)
REVERT: A  882 GLU cc_start: 0.6251 (pm20) cc_final: 0.5739 (mp0)
REVERT: A  936 GLU cc_start: 0.7824 (tp30) cc_final: 0.7548 (mp0)
REVERT: A  937 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7911 (mtmt)
REVERT: A 1011 ILE cc_start: 0.7848 (tp) cc_final: 0.7359 (pp)
  outliers start: 18
  outliers final: 9
  residues processed: 102
  average time/residue: 1.4585
  time to fit residues: 159.8861
Evaluate side-chains
  105 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  214 ASP
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  983 LEU
Chi-restraints excluded: chain A residue  996 VAL
Chi-restraints excluded: chain A residue 1114 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   overall best weight:    1.4184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.174979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.122267 restraints weight = 17885.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.44
r_work: 0.3171 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.3025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8780  Z= 0.159
  Angle     :  0.656  11.528  12097  Z= 0.308
  Chirality :  0.043   0.231   1441
  Planarity :  0.004   0.039   1340
  Dihedral  : 10.905 172.080   3198
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.67 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.28), residues: 921
  helix:  1.85 (0.22), residues: 573
  sheet:  0.13 (0.89), residues: 31
  loop :  0.12 (0.37), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 857 
 HIS   0.004   0.001   HIS A 332 
 PHE   0.015   0.002   PHE A 608 
 TYR   0.017   0.002   TYR A 762 
 ARG   0.010   0.001   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00590 (    5)
  link_NAG-ASN         : angle       3.05486 (   15)
  hydrogen bonds       : bond        0.06051 (  439)
  hydrogen bonds       : angle       4.36335 ( 1287)
  SS BOND              : bond        0.00412 (    8)
  SS BOND              : angle       0.83682 (   16)
  covalent geometry    : bond        0.00367 ( 8767)
  covalent geometry    : angle       0.64750 (12066)

*********************** 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
  106 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7529 (mtm) cc_final: 0.6453 (mmp)
REVERT: A  472 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7309 (tm-30)
REVERT: A  515 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7956 (tp)
REVERT: A  552 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7837 (mp0)
REVERT: A  593 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7817 (t)
REVERT: A  774 ARG cc_start: 0.7013 (mtp85) cc_final: 0.6798 (mtp-110)
REVERT: A  840 GLN cc_start: 0.7701 (mt0) cc_final: 0.6957 (mp10)
REVERT: A  882 GLU cc_start: 0.6349 (pm20) cc_final: 0.5806 (mp0)
REVERT: A  936 GLU cc_start: 0.7869 (tp30) cc_final: 0.7565 (mp0)
REVERT: A  937 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7831 (tptp)
  outliers start: 16
  outliers final: 9
  residues processed: 99
  average time/residue: 1.2154
  time to fit residues: 129.6814
Evaluate side-chains
  102 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  214 ASP
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 73 optimal weight:    0.4980
   chunk 65 optimal weight:    0.0370
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

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 = 0.178937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.124845 restraints weight = 21040.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.63
r_work: 0.3218 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8780  Z= 0.110
  Angle     :  0.584  11.793  12097  Z= 0.271
  Chirality :  0.040   0.206   1441
  Planarity :  0.004   0.039   1340
  Dihedral  : 10.545 171.546   3198
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.79 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.28), residues: 921
  helix:  2.00 (0.22), residues: 575
  sheet:  0.22 (0.91), residues: 31
  loop :  0.17 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.008   0.001   PHE A 454 
 TYR   0.017   0.001   TYR A 256 
 ARG   0.011   0.001   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00294 (    5)
  link_NAG-ASN         : angle       2.64967 (   15)
  hydrogen bonds       : bond        0.04665 (  439)
  hydrogen bonds       : angle       4.17805 ( 1287)
  SS BOND              : bond        0.00298 (    8)
  SS BOND              : angle       0.57270 (   16)
  covalent geometry    : bond        0.00229 ( 8767)
  covalent geometry    : angle       0.57737 (12066)

********************** 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
  104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7515 (mtm) cc_final: 0.6409 (mmp)
REVERT: A  472 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7232 (tm-30)
REVERT: A  515 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7884 (tp)
REVERT: A  552 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7887 (mp0)
REVERT: A  593 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.7793 (t)
REVERT: A  840 GLN cc_start: 0.7605 (mt0) cc_final: 0.6821 (mp10)
REVERT: A  882 GLU cc_start: 0.6255 (pm20) cc_final: 0.5778 (mp0)
REVERT: A  936 GLU cc_start: 0.7794 (tp30) cc_final: 0.7514 (mp0)
REVERT: A  937 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7912 (mtmt)
REVERT: A 1111 MET cc_start: 0.9119 (mtm) cc_final: 0.8821 (mtm)
  outliers start: 14
  outliers final: 9
  residues processed: 100
  average time/residue: 1.3164
  time to fit residues: 140.8340
Evaluate side-chains
  101 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  214 ASP
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0020
   chunk 27 optimal weight:    5.9990
   chunk 86 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0030
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.4198

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.185990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.137309 restraints weight = 19532.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.30
r_work: 0.3392 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3383
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3383
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8780  Z= 0.107
  Angle     :  0.592  12.483  12097  Z= 0.270
  Chirality :  0.040   0.385   1441
  Planarity :  0.004   0.038   1340
  Dihedral  : 10.412 171.642   3198
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 12.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.29), residues: 921
  helix:  2.10 (0.22), residues: 575
  sheet:  0.26 (0.91), residues: 31
  loop :  0.23 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 650 
 HIS   0.002   0.000   HIS A 428 
 PHE   0.008   0.001   PHE A 454 
 TYR   0.017   0.001   TYR A 256 
 ARG   0.010   0.000   ARG A 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01138 (    5)
  link_NAG-ASN         : angle       4.15206 (   15)
  hydrogen bonds       : bond        0.04416 (  439)
  hydrogen bonds       : angle       4.12389 ( 1287)
  SS BOND              : bond        0.00289 (    8)
  SS BOND              : angle       0.50641 (   16)
  covalent geometry    : bond        0.00217 ( 8767)
  covalent geometry    : angle       0.57371 (12066)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7863.82 seconds
wall clock time: 138 minutes 11.75 seconds (8291.75 seconds total)