Starting phenix.real_space_refine
on Fri May 16 20:02:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xsj_38620/05_2025/8xsj_38620.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xsj_38620/05_2025/8xsj_38620.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xsj_38620/05_2025/8xsj_38620.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xsj_38620/05_2025/8xsj_38620.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xsj_38620/05_2025/8xsj_38620.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xsj_38620/05_2025/8xsj_38620.cif"
  }
  resolution = 2.61
  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=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6345 atoms to isotropic.
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
     Zn      1      6.06       5
     S      49      5.16       5
     C    6192      2.51       5
     N    1616      2.21       5
     O    1882      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9740
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4869
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4990
    Chain: "B"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1554
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
    Chain: "H"
      Number of atoms: 1583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1583
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 10, 'TRANS': 200}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "L"
      Number of atoms: 1621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1621
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 8.50, per 1000 atoms: 0.87
  Number of scatterers: 9740
  At special positions: 0
  Unit cell: (76.5, 83.3, 180.2, 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)
     Zn      1     29.99
     S      49     16.00
     O    1882      8.00
     N    1616      7.00
     C    6192      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 149 " - pdb=" SG  CYS H 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03

  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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A 901 " - " ASN A  53 "
      " NAG A 902 " - " ASN A  90 "
      " NAG A 903 " - " ASN A 103 "
      " NAG A 904 " - " ASN A 322 "
      " NAG A 905 " - " ASN A 432 "
      " NAG B 601 " - " ASN B 343 "
      " NAG C   1 " - " ASN A 546 "
  Time building additional restraints: 2.31
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 906 "
        pdb="ZN    ZN A 906 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 906 " - pdb=" NE2 HIS A 374 "


  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 16 sheets defined
      37.0% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.550A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 4.026A  pdb=" N   GLN A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 102
      removed outlier: 3.755A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 107
      removed outlier: 3.653A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 103 through 107'
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 147 through 154
    Processing helix  chain 'A' and resid 157 through 172
      removed outlier: 3.666A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 175
      No H-bonds generated for 'chain 'A' and resid 173 through 175'
    Processing helix  chain 'A' and resid 176 through 194
      removed outlier: 3.635A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TYR A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL A 184 " --> pdb=" O   TYR A 180 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 232
      removed outlier: 3.910A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 249
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.741A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.704A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 3.798A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA A 412 " --> pdb=" O   MET A 408 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 420
    Processing helix  chain 'A' and resid 433 through 447
      removed outlier: 3.819A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 472 through 480
      removed outlier: 3.661A  pdb=" N   LYS A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.305A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 3.602A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   LEU A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A 559 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.804A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
      removed outlier: 3.783A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 366 through 370
    Processing helix  chain 'B' and resid 384 through 388
      removed outlier: 4.250A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.392A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.650A  pdb=" N   ASN H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.580A  pdb=" N   ASP H  90 " --> pdb=" O   ARG H  87 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'L' and resid 121 through 127
      removed outlier: 3.817A  pdb=" N   LEU L 125 " --> pdb=" O   SER L 121 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 150 through 153
    Processing helix  chain 'L' and resid 183 through 189
      removed outlier: 3.502A  pdb=" N   HIS L 189 " --> pdb=" O   ASP L 185 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.493A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.058A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.785A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 129 through 133
      removed outlier: 6.207A  pdb=" N   TYR H 185 " --> pdb=" O   ASP H 153 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 129 through 133
      removed outlier: 6.207A  pdb=" N   TYR H 185 " --> pdb=" O   ASP H 153 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 160 through 163
      removed outlier: 4.127A  pdb=" N   TYR H 203 " --> pdb=" O   VAL H 220 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 6 through 7
    Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.773A  pdb=" N   ILE L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 129 through 139
      removed outlier: 5.979A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 145 through 148

    412 hydrogen bonds defined for protein.
    1130 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: 2.85

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3109
        1.34 -     1.46: 2109
        1.46 -     1.58: 4704
        1.58 -     1.69: 1
        1.69 -     1.81: 74
  Bond restraints: 9997
  Sorted by residual:
  bond pdb=" N   LYS B 356 "
       pdb=" CA  LYS B 356 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.24e-02 6.50e+03 5.92e+00
  bond pdb=" CB  PRO B 479 "
       pdb=" CG  PRO B 479 "
    ideal  model  delta    sigma   weight residual
    1.492  1.583 -0.091 5.00e-02 4.00e+02 3.32e+00
  bond pdb=" N   ASN B 360 "
       pdb=" CA  ASN B 360 "
    ideal  model  delta    sigma   weight residual
    1.462  1.488 -0.027 1.46e-02 4.69e+03 3.30e+00
  bond pdb=" C   ARG B 355 "
       pdb=" N   LYS B 356 "
    ideal  model  delta    sigma   weight residual
    1.331  1.353 -0.022 1.38e-02 5.25e+03 2.48e+00
  bond pdb=" C1  NAG A 904 "
       pdb=" O5  NAG A 904 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  ... (remaining 9992 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 13109
        1.48 -     2.97: 386
        2.97 -     4.45: 77
        4.45 -     5.94: 13
        5.94 -     7.42: 8
  Bond angle restraints: 13593
  Sorted by residual:
  angle pdb=" C   ASP H  54 "
        pdb=" N   ALA H  55 "
        pdb=" CA  ALA H  55 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.27e+01
  angle pdb=" C   LYS B 462 "
        pdb=" CA  LYS B 462 "
        pdb=" CB  LYS B 462 "
      ideal   model   delta    sigma   weight residual
     110.47  116.73   -6.26 1.77e+00 3.19e-01 1.25e+01
  angle pdb=" CA  GLU H 157 "
        pdb=" C   GLU H 157 "
        pdb=" N   PRO H 158 "
      ideal   model   delta    sigma   weight residual
     117.68  120.14   -2.46 7.10e-01 1.98e+00 1.20e+01
  angle pdb=" N   LYS B 462 "
        pdb=" CA  LYS B 462 "
        pdb=" C   LYS B 462 "
      ideal   model   delta    sigma   weight residual
     110.13  106.21    3.92 1.15e+00 7.56e-01 1.16e+01
  angle pdb=" CA  PRO B 479 "
        pdb=" N   PRO B 479 "
        pdb=" CD  PRO B 479 "
      ideal   model   delta    sigma   weight residual
     112.00  107.30    4.70 1.40e+00 5.10e-01 1.13e+01
  ... (remaining 13588 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 5455
       17.64 -    35.28: 448
       35.28 -    52.92: 89
       52.92 -    70.56: 18
       70.56 -    88.20: 10
  Dihedral angle restraints: 6020
    sinusoidal: 2475
      harmonic: 3545
  Sorted by residual:
  dihedral pdb=" CA  LEU L  94 "
           pdb=" C   LEU L  94 "
           pdb=" N   PRO L  95 "
           pdb=" CA  PRO L  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -126.04  -53.96     0      5.00e+00 4.00e-02 1.16e+02
  dihedral pdb=" CA  PHE H 155 "
           pdb=" C   PHE H 155 "
           pdb=" N   PRO H 156 "
           pdb=" CA  PRO H 156 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.80  -31.20     0      5.00e+00 4.00e-02 3.89e+01
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.03   40.03     1      1.00e+01 1.00e-02 2.25e+01
  ... (remaining 6017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1081
       0.044 -    0.089: 282
       0.089 -    0.133: 104
       0.133 -    0.177: 5
       0.177 -    0.221: 2
  Chirality restraints: 1474
  Sorted by residual:
  chirality pdb=" C1  NAG A 901 "
            pdb=" ND2 ASN A  53 "
            pdb=" C2  NAG A 901 "
            pdb=" O5  NAG A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" C1  NAG A 902 "
            pdb=" ND2 ASN A  90 "
            pdb=" C2  NAG A 902 "
            pdb=" O5  NAG A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.47e-01
  chirality pdb=" CA  PRO H 156 "
            pdb=" N   PRO H 156 "
            pdb=" C   PRO H 156 "
            pdb=" CB  PRO H 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.46e-01
  ... (remaining 1471 not shown)

  Planarity restraints: 1758
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 478 "   -0.068 5.00e-02 4.00e+02   1.01e-01 1.62e+01
        pdb=" N   PRO B 479 "    0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO B 479 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO B 479 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU L  94 "   -0.065 5.00e-02 4.00e+02   9.83e-02 1.55e+01
        pdb=" N   PRO L  95 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO L  95 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO L  95 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 257 "   -0.057 5.00e-02 4.00e+02   8.68e-02 1.21e+01
        pdb=" N   PRO A 258 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A 258 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 258 "   -0.047 5.00e-02 4.00e+02
  ... (remaining 1755 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 63
        2.58 -     3.16: 7683
        3.16 -     3.74: 14387
        3.74 -     4.32: 20363
        4.32 -     4.90: 34694
  Nonbonded interactions: 77190
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 906 "
     model   vdw
     2.001 2.230
  nonbonded pdb=" NH1 ARG A 306 "
            pdb=" OE2 GLU A 310 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" OD1 ASP L  50 "
            pdb=" OH  TYR L  91 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" NZ  LYS A  31 "
            pdb=" OE2 GLU A  35 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" NH1 ARG B 457 "
            pdb=" OD2 ASP B 467 "
     model   vdw
     2.244 3.120
  ... (remaining 77185 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.45 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:             3.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     29.390
  Find NCS groups from input model:        0.120
  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:13.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
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      :  0.004   0.201  10018  Z= 0.184
  Angle     :  0.632   7.421  13639  Z= 0.342
  Chirality :  0.045   0.221   1474
  Planarity :  0.006   0.101   1751
  Dihedral  : 13.657  88.198   3719
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.40 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.10 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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: -0.03 (0.24), residues: 1206
  helix:  0.73 (0.28), residues: 384
  sheet:  1.09 (0.33), residues: 261
  loop : -1.10 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 271 
 HIS   0.008   0.001   HIS A 401 
 PHE   0.020   0.001   PHE A 400 
 TYR   0.014   0.001   TYR A 385 
 ARG   0.007   0.001   ARG A 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00294 (    7)
  link_NAG-ASN         : angle       2.06734 (   21)
  link_BETA1-4         : bond        0.00330 (    1)
  link_BETA1-4         : angle       0.95411 (    3)
  hydrogen bonds       : bond        0.13705 (  399)
  hydrogen bonds       : angle       6.46027 ( 1130)
  metal coordination   : bond        0.19939 (    2)
  SS BOND              : bond        0.00196 (   11)
  SS BOND              : angle       0.71108 (   22)
  covalent geometry    : bond        0.00338 ( 9997)
  covalent geometry    : angle       0.62723 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 LEU cc_start: 0.7861 (tp) cc_final: 0.7586 (tp)
REVERT: A  249 MET cc_start: 0.8232 (mtm) cc_final: 0.8010 (mtm)
REVERT: A  351 LEU cc_start: 0.8658 (mt) cc_final: 0.8356 (mp)
REVERT: A  586 ASN cc_start: 0.7030 (m-40) cc_final: 0.6810 (m-40)
REVERT: B  438 SER cc_start: 0.7960 (t) cc_final: 0.7720 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 193
  average time/residue: 0.9174
  time to fit residues: 193.3556
Evaluate side-chains
  183 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  356 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0870
   chunk 50 optimal weight:    0.3980
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0870
   chunk 48 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
A 374 HIS
A 401 HIS
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  53 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.161829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.137580 restraints weight = 19399.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 2.57
r_work: 0.3733 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3733 r_free = 0.3733    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.0948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.791  10018  Z= 0.299
  Angle     :  0.596   7.290  13639  Z= 0.306
  Chirality :  0.044   0.217   1474
  Planarity :  0.006   0.096   1751
  Dihedral  :  5.722  58.834   1488
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.73 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  9.41 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.12 (0.24), residues: 1206
  helix:  1.06 (0.28), residues: 374
  sheet:  1.07 (0.33), residues: 260
  loop : -1.08 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 271 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.018   0.001   PHE A 400 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.009   0.001   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00351 (    7)
  link_NAG-ASN         : angle       2.01885 (   21)
  link_BETA1-4         : bond        0.00217 (    1)
  link_BETA1-4         : angle       1.27864 (    3)
  hydrogen bonds       : bond        0.04499 (  399)
  hydrogen bonds       : angle       5.13811 ( 1130)
  metal coordination   : bond        0.55926 (    2)
  SS BOND              : bond        0.00273 (   11)
  SS BOND              : angle       0.74307 (   22)
  covalent geometry    : bond        0.00326 ( 9997)
  covalent geometry    : angle       0.59047 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 183
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7160 (ppp) cc_final: 0.6942 (pp-130)
REVERT: A   98 GLN cc_start: 0.8173 (tt0) cc_final: 0.7929 (tt0)
REVERT: A  186 LEU cc_start: 0.8105 (tp) cc_final: 0.7874 (tp)
REVERT: A  202 TYR cc_start: 0.7569 (t80) cc_final: 0.6747 (t80)
REVERT: A  408 MET cc_start: 0.8181 (mmt) cc_final: 0.7720 (mmt)
REVERT: H   60 TYR cc_start: 0.8159 (m-80) cc_final: 0.7794 (m-80)
REVERT: L  105 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6938 (mp0)
  outliers start: 13
  outliers final: 7
  residues processed: 186
  average time/residue: 0.8725
  time to fit residues: 178.1865
Evaluate side-chains
  183 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 175
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain L residue  105 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 117 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
A 401 HIS
B 405 ASN
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.160954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.137821 restraints weight = 13978.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.13
r_work: 0.3752 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3616 r_free = 0.3616    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3616 r_free = 0.3616    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.749  10018  Z= 0.293
  Angle     :  0.597   8.911  13639  Z= 0.306
  Chirality :  0.044   0.218   1474
  Planarity :  0.006   0.096   1751
  Dihedral  :  5.364  59.887   1484
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.32 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  :  9.79 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.10 (0.25), residues: 1206
  helix:  1.03 (0.28), residues: 374
  sheet:  1.05 (0.34), residues: 261
  loop : -1.08 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 353 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.021   0.001   PHE A 400 
 TYR   0.019   0.002   TYR A 385 
 ARG   0.006   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00310 (    7)
  link_NAG-ASN         : angle       2.02477 (   21)
  link_BETA1-4         : bond        0.00296 (    1)
  link_BETA1-4         : angle       1.18959 (    3)
  hydrogen bonds       : bond        0.04544 (  399)
  hydrogen bonds       : angle       4.96798 ( 1130)
  metal coordination   : bond        0.52938 (    2)
  SS BOND              : bond        0.00363 (   11)
  SS BOND              : angle       0.72389 (   22)
  covalent geometry    : bond        0.00361 ( 9997)
  covalent geometry    : angle       0.59168 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 178
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 SER cc_start: 0.7341 (t) cc_final: 0.7136 (m)
REVERT: A   75 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7494 (mt-10)
REVERT: A   82 MET cc_start: 0.7478 (ppp) cc_final: 0.7250 (pp-130)
REVERT: A   98 GLN cc_start: 0.8213 (tt0) cc_final: 0.7982 (tt0)
REVERT: A  117 ASN cc_start: 0.7389 (t0) cc_final: 0.7157 (t0)
REVERT: A  186 LEU cc_start: 0.8196 (tp) cc_final: 0.7973 (tp)
REVERT: A  202 TYR cc_start: 0.7740 (t80) cc_final: 0.6914 (t80)
REVERT: A  419 LYS cc_start: 0.6777 (mtpp) cc_final: 0.6547 (mttm)
REVERT: A  479 GLU cc_start: 0.7718 (tt0) cc_final: 0.7357 (mt-10)
REVERT: H   60 TYR cc_start: 0.8345 (m-80) cc_final: 0.7892 (m-80)
REVERT: L   17 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.5997 (m-30)
  outliers start: 26
  outliers final: 15
  residues processed: 189
  average time/residue: 0.8771
  time to fit residues: 182.0771
Evaluate side-chains
  189 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 172
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  170 SER
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Chi-restraints excluded: chain L residue   92 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 84 optimal weight:    0.2980
   chunk 82 optimal weight:    0.0030
   chunk 3 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
B 405 ASN
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.161421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.136742 restraints weight = 18569.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 2.56
r_work: 0.3727 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3728 r_free = 0.3728    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3728 r_free = 0.3728    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3728
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.752  10018  Z= 0.286
  Angle     :  0.584   7.854  13639  Z= 0.299
  Chirality :  0.044   0.214   1474
  Planarity :  0.005   0.093   1751
  Dihedral  :  5.243  58.847   1484
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.15 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.31 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.13 (0.25), residues: 1206
  helix:  1.06 (0.28), residues: 374
  sheet:  1.16 (0.35), residues: 250
  loop : -1.06 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 353 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.022   0.001   PHE A 428 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00297 (    7)
  link_NAG-ASN         : angle       1.98511 (   21)
  link_BETA1-4         : bond        0.00228 (    1)
  link_BETA1-4         : angle       1.18126 (    3)
  hydrogen bonds       : bond        0.04326 (  399)
  hydrogen bonds       : angle       4.85417 ( 1130)
  metal coordination   : bond        0.53177 (    2)
  SS BOND              : bond        0.00259 (   11)
  SS BOND              : angle       0.59338 (   22)
  covalent geometry    : bond        0.00325 ( 9997)
  covalent geometry    : angle       0.57940 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 LEU cc_start: 0.8137 (tp) cc_final: 0.7925 (tp)
REVERT: A  202 TYR cc_start: 0.7621 (t80) cc_final: 0.6797 (t80)
REVERT: A  270 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6585 (tpt)
REVERT: A  479 GLU cc_start: 0.7470 (tt0) cc_final: 0.7148 (mt-10)
REVERT: H   86 LEU cc_start: 0.8869 (mt) cc_final: 0.8666 (mp)
REVERT: H  108 MET cc_start: 0.7152 (ttp) cc_final: 0.6850 (ttm)
REVERT: L   17 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6060 (m-30)
REVERT: L   90 GLN cc_start: 0.8467 (pp30) cc_final: 0.8133 (pp30)
  outliers start: 24
  outliers final: 13
  residues processed: 183
  average time/residue: 0.8352
  time to fit residues: 168.4423
Evaluate side-chains
  185 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 170
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  170 SER
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 103 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
A  98 GLN
A 374 HIS
B 405 ASN
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.160152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.135715 restraints weight = 16028.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 2.39
r_work: 0.3715 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3566 r_free = 0.3566    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3566 r_free = 0.3566    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.758  10018  Z= 0.320
  Angle     :  0.628   8.154  13639  Z= 0.323
  Chirality :  0.046   0.221   1474
  Planarity :  0.006   0.097   1751
  Dihedral  :  5.316  56.137   1484
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.81 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 11.60 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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: -0.01 (0.24), residues: 1206
  helix:  0.92 (0.28), residues: 374
  sheet:  1.13 (0.35), residues: 250
  loop : -1.17 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 353 
 HIS   0.005   0.001   HIS A 239 
 PHE   0.023   0.002   PHE A 400 
 TYR   0.022   0.002   TYR A 385 
 ARG   0.009   0.001   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00270 (    7)
  link_NAG-ASN         : angle       2.07609 (   21)
  link_BETA1-4         : bond        0.00153 (    1)
  link_BETA1-4         : angle       1.33082 (    3)
  hydrogen bonds       : bond        0.04867 (  399)
  hydrogen bonds       : angle       4.94038 ( 1130)
  metal coordination   : bond        0.53570 (    2)
  SS BOND              : bond        0.00339 (   11)
  SS BOND              : angle       0.83490 (   22)
  covalent geometry    : bond        0.00473 ( 9997)
  covalent geometry    : angle       0.62283 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 177
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7153 (mp0)
REVERT: A  117 ASN cc_start: 0.7440 (t0) cc_final: 0.7221 (t0)
REVERT: A  186 LEU cc_start: 0.8246 (tp) cc_final: 0.8028 (tp)
REVERT: A  202 TYR cc_start: 0.7829 (t80) cc_final: 0.7002 (t80)
REVERT: A  270 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6868 (tpt)
REVERT: A  408 MET cc_start: 0.8452 (mmt) cc_final: 0.8038 (mmt)
REVERT: A  479 GLU cc_start: 0.7824 (tt0) cc_final: 0.7459 (mt-10)
REVERT: H   86 LEU cc_start: 0.8898 (mt) cc_final: 0.8679 (mp)
REVERT: L   17 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6260 (m-30)
REVERT: L   90 GLN cc_start: 0.8489 (pp30) cc_final: 0.8217 (pp30)
  outliers start: 31
  outliers final: 18
  residues processed: 187
  average time/residue: 0.8160
  time to fit residues: 168.9023
Evaluate side-chains
  194 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 173
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  170 SER
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 68 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0570
   chunk 100 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 108 optimal weight:    0.5980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
B 405 ASN
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.160574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.134425 restraints weight = 23331.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 3.00
r_work: 0.3682 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.777  10018  Z= 0.304
  Angle     :  0.601   7.652  13639  Z= 0.310
  Chirality :  0.045   0.214   1474
  Planarity :  0.005   0.095   1751
  Dihedral  :  5.200  54.649   1484
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.48 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.60 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.01 (0.24), residues: 1206
  helix:  0.94 (0.28), residues: 374
  sheet:  1.13 (0.35), residues: 250
  loop : -1.16 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 353 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.017   0.001   PHE A 400 
 TYR   0.018   0.002   TYR A 385 
 ARG   0.010   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00249 (    7)
  link_NAG-ASN         : angle       2.04052 (   21)
  link_BETA1-4         : bond        0.00168 (    1)
  link_BETA1-4         : angle       1.26972 (    3)
  hydrogen bonds       : bond        0.04526 (  399)
  hydrogen bonds       : angle       4.85880 ( 1130)
  metal coordination   : bond        0.54934 (    2)
  SS BOND              : bond        0.00323 (   11)
  SS BOND              : angle       0.67542 (   22)
  covalent geometry    : bond        0.00377 ( 9997)
  covalent geometry    : angle       0.59592 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6947 (mp0)
REVERT: A   83 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7103 (m-80)
REVERT: A  186 LEU cc_start: 0.8166 (tp) cc_final: 0.7950 (tp)
REVERT: A  202 TYR cc_start: 0.7685 (t80) cc_final: 0.6875 (t80)
REVERT: A  408 MET cc_start: 0.8285 (mmt) cc_final: 0.7833 (mmt)
REVERT: A  479 GLU cc_start: 0.7511 (tt0) cc_final: 0.7223 (mt-10)
REVERT: H   86 LEU cc_start: 0.8845 (mt) cc_final: 0.8632 (mp)
REVERT: L   17 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6241 (m-30)
REVERT: L   90 GLN cc_start: 0.8403 (pp30) cc_final: 0.8156 (pp30)
  outliers start: 32
  outliers final: 19
  residues processed: 186
  average time/residue: 0.8610
  time to fit residues: 176.2010
Evaluate side-chains
  196 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0270
   overall best weight:    0.7438

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
B 405 ASN
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.159633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.133758 restraints weight = 22251.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 2.89
r_work: 0.3673 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.793  10018  Z= 0.325
  Angle     :  0.627   7.191  13639  Z= 0.324
  Chirality :  0.046   0.219   1474
  Planarity :  0.006   0.098   1751
  Dihedral  :  5.178  55.653   1484
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.65 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 12.83 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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: -0.09 (0.24), residues: 1206
  helix:  0.78 (0.27), residues: 381
  sheet:  1.08 (0.35), residues: 250
  loop : -1.19 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 353 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.020   0.001   PHE A 400 
 TYR   0.020   0.002   TYR A 385 
 ARG   0.010   0.001   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00229 (    7)
  link_NAG-ASN         : angle       2.11833 (   21)
  link_BETA1-4         : bond        0.00143 (    1)
  link_BETA1-4         : angle       1.34146 (    3)
  hydrogen bonds       : bond        0.04846 (  399)
  hydrogen bonds       : angle       4.92487 ( 1130)
  metal coordination   : bond        0.56062 (    2)
  SS BOND              : bond        0.00319 (   11)
  SS BOND              : angle       0.69767 (   22)
  covalent geometry    : bond        0.00453 ( 9997)
  covalent geometry    : angle       0.62185 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 177
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6979 (mp0)
REVERT: A   83 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7132 (m-80)
REVERT: A  117 ASN cc_start: 0.7363 (t0) cc_final: 0.7161 (t0)
REVERT: A  186 LEU cc_start: 0.8191 (tp) cc_final: 0.7975 (tp)
REVERT: A  202 TYR cc_start: 0.7705 (t80) cc_final: 0.6891 (t80)
REVERT: A  270 MET cc_start: 0.7394 (tpp) cc_final: 0.7166 (tpt)
REVERT: A  408 MET cc_start: 0.8324 (mmt) cc_final: 0.7865 (mmt)
REVERT: A  431 ASP cc_start: 0.7290 (p0) cc_final: 0.7003 (p0)
REVERT: H   80 TYR cc_start: 0.7022 (m-80) cc_final: 0.6821 (m-80)
REVERT: H   86 LEU cc_start: 0.8827 (mt) cc_final: 0.8625 (mp)
REVERT: L   17 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6336 (m-30)
  outliers start: 30
  outliers final: 22
  residues processed: 184
  average time/residue: 0.8650
  time to fit residues: 175.2797
Evaluate side-chains
  196 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 113 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9990
   chunk 118 optimal weight:    0.5980
   chunk 100 optimal weight:    0.3980
   chunk 107 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   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 374 HIS
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.159966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.135932 restraints weight = 15316.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 2.32
r_work: 0.3718 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3576 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3575
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3575 r_free = 0.3575    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3575 r_free = 0.3575    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3575
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.831  10018  Z= 0.325
  Angle     :  0.619   7.321  13639  Z= 0.319
  Chirality :  0.045   0.215   1474
  Planarity :  0.005   0.096   1751
  Dihedral  :  5.026  55.295   1484
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.56 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.21 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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: -0.08 (0.24), residues: 1206
  helix:  0.84 (0.28), residues: 380
  sheet:  1.04 (0.35), residues: 250
  loop : -1.19 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 353 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.018   0.001   PHE A 400 
 TYR   0.018   0.002   TYR A 385 
 ARG   0.010   0.001   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    7)
  link_NAG-ASN         : angle       2.11773 (   21)
  link_BETA1-4         : bond        0.00234 (    1)
  link_BETA1-4         : angle       1.34668 (    3)
  hydrogen bonds       : bond        0.04635 (  399)
  hydrogen bonds       : angle       4.89129 ( 1130)
  metal coordination   : bond        0.58746 (    2)
  SS BOND              : bond        0.00283 (   11)
  SS BOND              : angle       0.71837 (   22)
  covalent geometry    : bond        0.00404 ( 9997)
  covalent geometry    : angle       0.61337 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7111 (mp0)
REVERT: A   83 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7209 (m-80)
REVERT: A  117 ASN cc_start: 0.7431 (t0) cc_final: 0.7226 (t0)
REVERT: A  186 LEU cc_start: 0.8239 (tp) cc_final: 0.8035 (tp)
REVERT: A  202 TYR cc_start: 0.7813 (t80) cc_final: 0.6968 (t80)
REVERT: A  270 MET cc_start: 0.7832 (tpp) cc_final: 0.7624 (tpt)
REVERT: A  408 MET cc_start: 0.8422 (mmt) cc_final: 0.7989 (mmt)
REVERT: A  431 ASP cc_start: 0.7433 (p0) cc_final: 0.7180 (p0)
REVERT: A  479 GLU cc_start: 0.7909 (pt0) cc_final: 0.7656 (pt0)
REVERT: H   68 PHE cc_start: 0.8276 (m-10) cc_final: 0.8011 (m-10)
REVERT: H   80 TYR cc_start: 0.7258 (m-80) cc_final: 0.7004 (m-80)
REVERT: L   17 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6350 (m-30)
  outliers start: 26
  outliers final: 20
  residues processed: 179
  average time/residue: 0.9588
  time to fit residues: 188.2849
Evaluate side-chains
  198 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 175
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 31 optimal weight:    0.3980
   chunk 84 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 405 ASN
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.160594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.135270 restraints weight = 20946.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.80
r_work: 0.3702 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3697 r_free = 0.3697    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3697 r_free = 0.3697    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10018  Z= 0.143
  Angle     :  0.603   9.048  13639  Z= 0.310
  Chirality :  0.044   0.209   1474
  Planarity :  0.005   0.095   1751
  Dihedral  :  4.876  54.771   1484
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.73 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.59 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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: -0.02 (0.24), residues: 1206
  helix:  0.93 (0.28), residues: 380
  sheet:  1.02 (0.35), residues: 252
  loop : -1.16 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 478 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.014   0.001   PHE A 400 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.009   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00224 (    7)
  link_NAG-ASN         : angle       2.10423 (   21)
  link_BETA1-4         : bond        0.00278 (    1)
  link_BETA1-4         : angle       1.28205 (    3)
  hydrogen bonds       : bond        0.04336 (  399)
  hydrogen bonds       : angle       4.83677 ( 1130)
  metal coordination   : bond        0.00770 (    2)
  SS BOND              : bond        0.00255 (   11)
  SS BOND              : angle       0.66195 (   22)
  covalent geometry    : bond        0.00336 ( 9997)
  covalent geometry    : angle       0.59786 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 179
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6941 (mp0)
REVERT: A   83 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7133 (m-80)
REVERT: A  202 TYR cc_start: 0.7703 (t80) cc_final: 0.6865 (t80)
REVERT: A  270 MET cc_start: 0.7655 (tpp) cc_final: 0.7419 (tpt)
REVERT: A  383 MET cc_start: 0.7857 (mtp) cc_final: 0.7512 (mtp)
REVERT: A  408 MET cc_start: 0.8280 (mmt) cc_final: 0.7845 (mmt)
REVERT: A  431 ASP cc_start: 0.7251 (p0) cc_final: 0.7000 (p0)
REVERT: A  479 GLU cc_start: 0.7648 (pt0) cc_final: 0.7391 (pt0)
REVERT: H   68 PHE cc_start: 0.8247 (m-10) cc_final: 0.8021 (m-10)
REVERT: L   17 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6186 (m-30)
  outliers start: 26
  outliers final: 20
  residues processed: 185
  average time/residue: 0.8608
  time to fit residues: 175.4212
Evaluate side-chains
  198 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 175
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 94 optimal weight:    0.5980
   chunk 26 optimal weight:    0.1980
   chunk 114 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 97 optimal weight:    4.9990
   chunk 99 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.160464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.134813 restraints weight = 22344.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 2.94
r_work: 0.3688 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10018  Z= 0.149
  Angle     :  0.611   9.595  13639  Z= 0.314
  Chirality :  0.045   0.209   1474
  Planarity :  0.005   0.096   1751
  Dihedral  :  4.833  54.872   1484
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.48 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.78 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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: -0.04 (0.24), residues: 1206
  helix:  0.91 (0.28), residues: 380
  sheet:  1.02 (0.35), residues: 250
  loop : -1.17 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 478 
 HIS   0.007   0.001   HIS H  35 
 PHE   0.015   0.001   PHE A 400 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.009   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    7)
  link_NAG-ASN         : angle       2.14209 (   21)
  link_BETA1-4         : bond        0.00245 (    1)
  link_BETA1-4         : angle       1.26351 (    3)
  hydrogen bonds       : bond        0.04358 (  399)
  hydrogen bonds       : angle       4.83230 ( 1130)
  metal coordination   : bond        0.00797 (    2)
  SS BOND              : bond        0.00259 (   11)
  SS BOND              : angle       0.65223 (   22)
  covalent geometry    : bond        0.00353 ( 9997)
  covalent geometry    : angle       0.60565 (13593)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 177
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.7472 (mp0) cc_final: 0.7162 (mp0)
REVERT: A   75 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6934 (mp0)
REVERT: A  202 TYR cc_start: 0.7684 (t80) cc_final: 0.6866 (t80)
REVERT: A  383 MET cc_start: 0.7882 (mtp) cc_final: 0.7526 (mtp)
REVERT: A  408 MET cc_start: 0.8287 (mmt) cc_final: 0.7846 (mmt)
REVERT: A  431 ASP cc_start: 0.7186 (p0) cc_final: 0.6918 (p0)
REVERT: A  479 GLU cc_start: 0.7675 (pt0) cc_final: 0.7351 (pp20)
REVERT: H   68 PHE cc_start: 0.8230 (m-10) cc_final: 0.8007 (m-10)
REVERT: L   17 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6142 (m-30)
  outliers start: 23
  outliers final: 19
  residues processed: 182
  average time/residue: 0.8225
  time to fit residues: 165.6572
Evaluate side-chains
  198 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9990
   chunk 111 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0670
   chunk 18 optimal weight:    0.0870
   chunk 35 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0970
   chunk 99 optimal weight:    0.4980
   chunk 1 optimal weight:    0.0370
   chunk 113 optimal weight:    0.9980
   overall best weight:    0.1572

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

Flipped N/Q/H residues before XYZ refinement:
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.163317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139350 restraints weight = 16765.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.42
r_work: 0.3778 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3631 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10018  Z= 0.105
  Angle     :  0.567   9.673  13639  Z= 0.291
  Chirality :  0.043   0.191   1474
  Planarity :  0.005   0.092   1751
  Dihedral  :  4.595  52.625   1484
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.73 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.59 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    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:  0.13 (0.25), residues: 1206
  helix:  1.14 (0.28), residues: 380
  sheet:  1.02 (0.34), residues: 253
  loop : -1.09 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 478 
 HIS   0.007   0.001   HIS H  35 
 PHE   0.010   0.001   PHE H 155 
 TYR   0.011   0.001   TYR A 516 
 ARG   0.009   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00294 (    7)
  link_NAG-ASN         : angle       2.12326 (   21)
  link_BETA1-4         : bond        0.00380 (    1)
  link_BETA1-4         : angle       1.10201 (    3)
  hydrogen bonds       : bond        0.03564 (  399)
  hydrogen bonds       : angle       4.67468 ( 1130)
  metal coordination   : bond        0.00103 (    2)
  SS BOND              : bond        0.00155 (   11)
  SS BOND              : angle       0.44560 (   22)
  covalent geometry    : bond        0.00230 ( 9997)
  covalent geometry    : angle       0.56120 (13593)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8567.05 seconds
wall clock time: 147 minutes 51.82 seconds (8871.82 seconds total)