Starting phenix.real_space_refine
on Mon Jan 20 05:52:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xsj_38620/01_2025/8xsj_38620.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xsj_38620/01_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_38620/01_2025/8xsj_38620.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xsj_38620/01_2025/8xsj_38620.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xsj_38620/01_2025/8xsj_38620.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xsj_38620/01_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-5571/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: 8.23, per 1000 atoms: 0.84
  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: 2.25
  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: 1.11
  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: 2.82

  Time building geometry restraints manager: 2.64 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:             1.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     28.460
  Find NCS groups from input model:        0.280
  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:12.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.720
-------------------------------------------------------------------------------
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      :  0.003   0.091   9997  Z= 0.216
  Angle     :  0.627   7.421  13593  Z= 0.341
  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 

*********************** 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  : 1.004 
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: 0.9843
  time to fit residues: 206.9576
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  : 0.969 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.4736

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.162075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.137364 restraints weight = 19371.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 2.61
r_work: 0.3730 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.0976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9997  Z= 0.208
  Angle     :  0.591   7.254  13593  Z= 0.306
  Chirality :  0.044   0.226   1474
  Planarity :  0.006   0.096   1751
  Dihedral  :  5.715  58.995   1488
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.90 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.51 %
    Favored  : 89.16 %
  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:  0.11 (0.24), residues: 1206
  helix:  1.05 (0.28), residues: 374
  sheet:  1.07 (0.33), residues: 260
  loop : -1.09 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 271 
 HIS   0.004   0.001   HIS A 239 
 PHE   0.019   0.001   PHE A 400 
 TYR   0.016   0.002   TYR A 385 
 ARG   0.009   0.001   ARG A 177 

*********************** 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
  197 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 183
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 THR cc_start: 0.7978 (m) cc_final: 0.7748 (p)
REVERT: A   82 MET cc_start: 0.7187 (ppp) cc_final: 0.6980 (pp-130)
REVERT: A   98 GLN cc_start: 0.8171 (tt0) cc_final: 0.7930 (tt0)
REVERT: A  186 LEU cc_start: 0.8135 (tp) cc_final: 0.7898 (tp)
REVERT: A  202 TYR cc_start: 0.7583 (t80) cc_final: 0.6756 (t80)
REVERT: A  408 MET cc_start: 0.8186 (mmt) cc_final: 0.7738 (mmt)
REVERT: H   60 TYR cc_start: 0.8175 (m-80) cc_final: 0.7811 (m-80)
REVERT: L  105 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6956 (mp0)
  outliers start: 14
  outliers final: 7
  residues processed: 187
  average time/residue: 0.9213
  time to fit residues: 188.8083
Evaluate side-chains
  180 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 172
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
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  597 ASP
Chi-restraints excluded: chain B residue  433 VAL
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:    0.6980
   chunk 19 optimal weight:    0.0170
   chunk 77 optimal weight:    2.9990
   chunk 88 optimal weight:    0.3980
   chunk 5 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 100 optimal weight:    0.6980
   chunk 117 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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
** 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 = 0.4146 r_free = 0.4146 target = 0.161318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.138154 restraints weight = 13990.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 2.14
r_work: 0.3760 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9997  Z= 0.211
  Angle     :  0.583   9.082  13593  Z= 0.300
  Chirality :  0.044   0.216   1474
  Planarity :  0.005   0.094   1751
  Dihedral  :  5.333  59.963   1484
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.32 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 10.17 %
    Favored  : 87.64 %
  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:  0.11 (0.25), residues: 1206
  helix:  1.04 (0.28), residues: 373
  sheet:  1.06 (0.34), residues: 261
  loop : -1.08 (0.25), residues: 572

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   0.019   0.001   PHE A 400 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.007   0.000   ARG A 177 

*********************** 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
  199 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 176
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7518 (ppp) cc_final: 0.7292 (pp-130)
REVERT: A   98 GLN cc_start: 0.8193 (tt0) cc_final: 0.7967 (tt0)
REVERT: A  117 ASN cc_start: 0.7389 (t0) cc_final: 0.7160 (t0)
REVERT: A  186 LEU cc_start: 0.8193 (tp) cc_final: 0.7983 (tp)
REVERT: A  202 TYR cc_start: 0.7737 (t80) cc_final: 0.6910 (t80)
REVERT: A  419 LYS cc_start: 0.6780 (mtpp) cc_final: 0.6549 (mttm)
REVERT: A  479 GLU cc_start: 0.7690 (tt0) cc_final: 0.7327 (mt-10)
REVERT: H   60 TYR cc_start: 0.8337 (m-80) cc_final: 0.7885 (m-80)
REVERT: L   17 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.5943 (m-30)
  outliers start: 23
  outliers final: 12
  residues processed: 186
  average time/residue: 0.9075
  time to fit residues: 186.5165
Evaluate side-chains
  184 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 171
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
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  394 ASN
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:    0.9980
   chunk 58 optimal weight:    0.0050
   chunk 81 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0370
   chunk 78 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 93 optimal weight:    0.2980
   chunk 101 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.4272

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.161702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.137002 restraints weight = 18777.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3840 rms_B_bonded: 2.57
r_work: 0.3732 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3732 r_free = 0.3732    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 = 0.3732 r_free = 0.3732    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9997  Z= 0.193
  Angle     :  0.573   8.122  13593  Z= 0.295
  Chirality :  0.044   0.212   1474
  Planarity :  0.005   0.093   1751
  Dihedral  :  5.210  59.482   1484
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.07 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.41 %
    Favored  : 86.50 %
  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:  0.16 (0.25), residues: 1206
  helix:  1.06 (0.28), residues: 374
  sheet:  1.18 (0.35), residues: 250
  loop : -1.04 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 478 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.018   0.001   PHE A 428 
 TYR   0.015   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 177 

*********************** 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
  198 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7039 (mp0)
REVERT: A  186 LEU cc_start: 0.8127 (tp) cc_final: 0.7923 (tp)
REVERT: A  202 TYR cc_start: 0.7614 (t80) cc_final: 0.6795 (t80)
REVERT: A  270 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6538 (tpt)
REVERT: A  401 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7620 (m-70)
REVERT: A  419 LYS cc_start: 0.6590 (mtpp) cc_final: 0.6338 (mttm)
REVERT: A  479 GLU cc_start: 0.7447 (tt0) cc_final: 0.7139 (mt-10)
REVERT: H   86 LEU cc_start: 0.8851 (mt) cc_final: 0.8644 (mp)
REVERT: L   17 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6024 (m-30)
REVERT: L   90 GLN cc_start: 0.8452 (pp30) cc_final: 0.8107 (pp30)
  outliers start: 22
  outliers final: 11
  residues processed: 183
  average time/residue: 0.9466
  time to fit residues: 190.5533
Evaluate side-chains
  183 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
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  401 HIS
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 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:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0980
   chunk 97 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
A 374 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 = 0.4133 r_free = 0.4133 target = 0.160479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.136152 restraints weight = 16037.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 2.38
r_work: 0.3724 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3572 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
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      :  0.004   0.038   9997  Z= 0.263
  Angle     :  0.606   8.073  13593  Z= 0.314
  Chirality :  0.045   0.217   1474
  Planarity :  0.005   0.096   1751
  Dihedral  :  5.275  57.636   1484
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.65 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 11.79 %
    Favored  : 85.55 %
  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:  0.06 (0.24), residues: 1206
  helix:  0.98 (0.28), residues: 374
  sheet:  1.16 (0.35), residues: 250
  loop : -1.12 (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 A 239 
 PHE   0.021   0.001   PHE A 400 
 TYR   0.020   0.002   TYR A 385 
 ARG   0.009   0.000   ARG A 177 

*********************** 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
  202 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 174
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 LEU cc_start: 0.8238 (tp) cc_final: 0.8027 (tp)
REVERT: A  202 TYR cc_start: 0.7828 (t80) cc_final: 0.7005 (t80)
REVERT: A  270 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6892 (tpt)
REVERT: H   86 LEU cc_start: 0.8895 (mt) cc_final: 0.8680 (mp)
REVERT: L   17 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6218 (m-30)
REVERT: L   90 GLN cc_start: 0.8482 (pp30) cc_final: 0.8273 (pp30)
  outliers start: 28
  outliers final: 18
  residues processed: 183
  average time/residue: 0.8953
  time to fit residues: 181.2436
Evaluate side-chains
  189 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
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  394 ASN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  463 VAL
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:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 108 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4126 r_free = 0.4126 target = 0.159957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.134023 restraints weight = 23176.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 2.95
r_work: 0.3677 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9997  Z= 0.281
  Angle     :  0.616   7.513  13593  Z= 0.319
  Chirality :  0.046   0.218   1474
  Planarity :  0.006   0.097   1751
  Dihedral  :  5.281  55.132   1484
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.65 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 12.36 %
    Favored  : 84.70 %
  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:  1.12 (0.35), residues: 250
  loop : -1.19 (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   0.021   0.001   PHE A 400 
 TYR   0.021   0.002   TYR A 385 
 ARG   0.010   0.001   ARG A 177 

*********************** 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
  207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 176
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7169 (m-80)
REVERT: A  117 ASN cc_start: 0.7330 (t0) cc_final: 0.7103 (t0)
REVERT: A  186 LEU cc_start: 0.8196 (tp) cc_final: 0.7975 (tp)
REVERT: A  202 TYR cc_start: 0.7699 (t80) cc_final: 0.6890 (t80)
REVERT: A  408 MET cc_start: 0.8308 (mmt) cc_final: 0.7847 (mmt)
REVERT: A  479 GLU cc_start: 0.7654 (pt0) cc_final: 0.7390 (pt0)
REVERT: H   86 LEU cc_start: 0.8854 (mt) cc_final: 0.8631 (mp)
REVERT: L   17 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6234 (m-30)
REVERT: L   90 GLN cc_start: 0.8406 (pp30) cc_final: 0.8170 (pp30)
  outliers start: 31
  outliers final: 19
  residues processed: 184
  average time/residue: 0.9316
  time to fit residues: 188.0648
Evaluate side-chains
  191 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
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 A residue  463 VAL
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  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:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0770
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.160597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.134881 restraints weight = 22384.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 2.89
r_work: 0.3693 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9997  Z= 0.214
  Angle     :  0.590   7.189  13593  Z= 0.306
  Chirality :  0.044   0.210   1474
  Planarity :  0.005   0.095   1751
  Dihedral  :  5.125  54.359   1484
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.32 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 13.50 %
    Favored  : 84.22 %
  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:  0.05 (0.24), residues: 1206
  helix:  1.03 (0.28), residues: 374
  sheet:  1.08 (0.35), residues: 250
  loop : -1.13 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 353 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.015   0.001   PHE A 400 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.009   0.000   ARG A 177 

*********************** 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
  202 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7123 (m-80)
REVERT: A  202 TYR cc_start: 0.7691 (t80) cc_final: 0.6890 (t80)
REVERT: A  408 MET cc_start: 0.8295 (mmt) cc_final: 0.7860 (mmt)
REVERT: A  431 ASP cc_start: 0.7267 (p0) cc_final: 0.6970 (p0)
REVERT: A  479 GLU cc_start: 0.7651 (pt0) cc_final: 0.7369 (pt0)
REVERT: L   17 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6234 (m-30)
  outliers start: 24
  outliers final: 18
  residues processed: 183
  average time/residue: 0.8952
  time to fit residues: 180.6721
Evaluate side-chains
  198 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 119 optimal weight:    4.9990
   chunk 118 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 107 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4121 r_free = 0.4121 target = 0.159497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.135510 restraints weight = 15184.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 2.30
r_work: 0.3719 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3574
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3574
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9997  Z= 0.278
  Angle     :  0.616   8.416  13593  Z= 0.319
  Chirality :  0.046   0.217   1474
  Planarity :  0.005   0.097   1751
  Dihedral  :  5.110  55.490   1484
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.06 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.59 %
    Favored  : 83.65 %
  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: -0.07 (0.24), residues: 1206
  helix:  0.86 (0.28), residues: 380
  sheet:  1.08 (0.35), residues: 250
  loop : -1.20 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 353 
 HIS   0.007   0.001   HIS H  35 
 PHE   0.019   0.001   PHE A 400 
 TYR   0.021   0.002   TYR A 385 
 ARG   0.009   0.001   ARG A 177 

*********************** 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
  206 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 177
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7240 (m-80)
REVERT: A  117 ASN cc_start: 0.7410 (t0) cc_final: 0.7182 (t0)
REVERT: A  202 TYR cc_start: 0.7811 (t80) cc_final: 0.7009 (t80)
REVERT: A  270 MET cc_start: 0.7844 (tpp) cc_final: 0.7634 (tpt)
REVERT: A  408 MET cc_start: 0.8428 (mmt) cc_final: 0.8002 (mmt)
REVERT: A  431 ASP cc_start: 0.7434 (p0) cc_final: 0.7167 (p0)
REVERT: A  479 GLU cc_start: 0.7885 (pt0) cc_final: 0.7623 (pt0)
REVERT: L   17 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6364 (m-30)
  outliers start: 29
  outliers final: 19
  residues processed: 185
  average time/residue: 0.8847
  time to fit residues: 180.7642
Evaluate side-chains
  190 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   92 THR
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 A residue  597 ASP
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   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:    0.9990
   chunk 84 optimal weight:    0.0980
   chunk 79 optimal weight:    0.0050
   chunk 21 optimal weight:    0.6980
   chunk 104 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0030
   chunk 16 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.3004

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.161461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.136257 restraints weight = 21005.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 2.74
r_work: 0.3720 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3719 r_free = 0.3719    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3719 r_free = 0.3719    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9997  Z= 0.168
  Angle     :  0.575   7.573  13593  Z= 0.298
  Chirality :  0.043   0.204   1474
  Planarity :  0.005   0.093   1751
  Dihedral  :  4.846  53.527   1484
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.23 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.83 %
    Favored  : 83.56 %
  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 (0.25), residues: 1206
  helix:  1.07 (0.28), residues: 374
  sheet:  1.03 (0.35), residues: 252
  loop : -1.09 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 478 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.026   0.001   PHE A 504 
 TYR   0.011   0.001   TYR A 385 
 ARG   0.009   0.000   ARG A 177 

*********************** 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
  197 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 180
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7123 (m-80)
REVERT: A  117 ASN cc_start: 0.7303 (t0) cc_final: 0.7092 (t0)
REVERT: A  202 TYR cc_start: 0.7667 (t80) cc_final: 0.6830 (t80)
REVERT: A  270 MET cc_start: 0.7612 (tpp) cc_final: 0.7356 (tpt)
REVERT: A  383 MET cc_start: 0.7767 (mtp) cc_final: 0.7471 (mtp)
REVERT: A  431 ASP cc_start: 0.7227 (p0) cc_final: 0.6965 (p0)
REVERT: A  479 GLU cc_start: 0.7533 (pt0) cc_final: 0.7205 (pp20)
REVERT: L   17 ASP cc_start: 0.6770 (OUTLIER) cc_final: 0.5989 (m-30)
  outliers start: 17
  outliers final: 15
  residues processed: 181
  average time/residue: 0.9256
  time to fit residues: 183.5825
Evaluate side-chains
  197 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 180
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  186 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  461 LEU
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   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:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 114 optimal weight:    4.9990
   chunk 59 optimal weight:    0.3980
   chunk 97 optimal weight:    0.6980
   chunk 99 optimal weight:    0.0980
   chunk 30 optimal weight:    0.0060
   chunk 38 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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 = 0.4143 r_free = 0.4143 target = 0.161465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.135726 restraints weight = 22461.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 2.94
r_work: 0.3703 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    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 = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9997  Z= 0.197
  Angle     :  0.590  10.357  13593  Z= 0.305
  Chirality :  0.044   0.203   1474
  Planarity :  0.005   0.094   1751
  Dihedral  :  4.778  54.011   1484
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.48 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.49 %
    Favored  : 82.70 %
  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:  0.05 (0.24), residues: 1206
  helix:  1.00 (0.28), residues: 380
  sheet:  1.08 (0.35), residues: 250
  loop : -1.13 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 353 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.025   0.001   PHE A 504 
 TYR   0.016   0.001   TYR L  49 
 ARG   0.008   0.000   ARG A 177 

********************** 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
  197 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 178
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.7450 (mp0) cc_final: 0.7088 (mp0)
REVERT: A  202 TYR cc_start: 0.7661 (t80) cc_final: 0.6844 (t80)
REVERT: A  270 MET cc_start: 0.7738 (tpp) cc_final: 0.7491 (tpt)
REVERT: A  369 PHE cc_start: 0.8214 (t80) cc_final: 0.7996 (t80)
REVERT: A  383 MET cc_start: 0.7803 (mtp) cc_final: 0.7476 (mtp)
REVERT: A  408 MET cc_start: 0.8261 (mmt) cc_final: 0.7838 (mmt)
REVERT: A  431 ASP cc_start: 0.7172 (p0) cc_final: 0.6912 (p0)
REVERT: A  479 GLU cc_start: 0.7565 (pt0) cc_final: 0.7148 (pp20)
REVERT: L   17 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.5913 (m-30)
  outliers start: 19
  outliers final: 15
  residues processed: 182
  average time/residue: 0.9043
  time to fit residues: 181.0540
Evaluate side-chains
  191 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 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 A residue  463 VAL
Chi-restraints excluded: chain B residue  461 LEU
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   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:    0.0770
   chunk 74 optimal weight:    0.1980
   chunk 111 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0470
   chunk 45 optimal weight:    0.6980
   chunk 99 optimal weight:    0.4980
   chunk 1 optimal weight:    0.0970
   chunk 113 optimal weight:    0.9990
   overall best weight:    0.1834

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.163175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.139243 restraints weight = 16763.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 2.42
r_work: 0.3769 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3627 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9997  Z= 0.151
  Angle     :  0.563  10.307  13593  Z= 0.290
  Chirality :  0.043   0.191   1474
  Planarity :  0.005   0.092   1751
  Dihedral  :  4.585  52.846   1484
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.49 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.35 %
    Favored  : 82.51 %
  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:  0.19 (0.25), residues: 1206
  helix:  1.15 (0.28), residues: 381
  sheet:  1.11 (0.34), residues: 250
  loop : -1.05 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 478 
 HIS   0.007   0.001   HIS H  35 
 PHE   0.025   0.001   PHE A 504 
 TYR   0.013   0.001   TYR L  49 
 ARG   0.008   0.000   ARG A 177 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8382.51 seconds
wall clock time: 149 minutes 50.37 seconds (8990.37 seconds total)