Starting phenix.real_space_refine
on Thu Sep 18 06:52:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xsj_38620/09_2025/8xsj_38620.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xsj_38620/09_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_38620/09_2025/8xsj_38620.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xsj_38620/09_2025/8xsj_38620.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xsj_38620/09_2025/8xsj_38620.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xsj_38620/09_2025/8xsj_38620.cif"
  }
  resolution = 2.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.30, per 1000 atoms: 0.34
  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: 0.70
  Conformation dependent library (CDL) restraints added in 463.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  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: 0.37
  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: 1.50

  Time building geometry restraints manager: 0.94 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.45 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.230
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.201  10018  Z= 0.184
  Angle     :  0.632   7.421  13639  Z= 0.342
  Chirality :  0.045   0.221   1474
  Planarity :  0.006   0.101   1751
  Dihedral  : 13.657  88.198   3719
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.40 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.10 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.001   ARG A 306 
 TYR   0.014   0.001   TYR A 385 
 PHE   0.020   0.001   PHE A 400 
 TRP   0.024   0.001   TRP A 271 
 HIS   0.008   0.001   HIS A 401 

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

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

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.360 
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: 0.4653
  time to fit residues: 97.7045
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  : 0.357 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0170
   chunk 117 optimal weight:    5.9990
   overall best weight:    0.6618

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.160723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.137039 restraints weight = 14941.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 2.25
r_work: 0.3740 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3598 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3600
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10018  Z= 0.176
  Angle     :  0.628   7.197  13639  Z= 0.323
  Chirality :  0.046   0.239   1474
  Planarity :  0.006   0.100   1751
  Dihedral  :  5.806  59.440   1488
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.48 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  9.32 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.24), residues: 1206
  helix:  0.95 (0.28), residues: 375
  sheet:  1.04 (0.34), residues: 255
  loop : -1.14 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 177 
 TYR   0.020   0.002   TYR A 385 
 PHE   0.026   0.002   PHE A 400 
 TRP   0.013   0.001   TRP B 353 
 HIS   0.006   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 9997)
  covalent geometry    : angle       0.62239 (13593)
  SS BOND              : bond        0.00334 (   11)
  SS BOND              : angle       0.88790 (   22)
  hydrogen bonds       : bond        0.04878 (  399)
  hydrogen bonds       : angle       5.15148 ( 1130)
  metal coordination   : bond        0.00525 (    2)
  link_BETA1-4         : bond        0.00423 (    1)
  link_BETA1-4         : angle       1.29434 (    3)
  link_NAG-ASN         : bond        0.00373 (    7)
  link_NAG-ASN         : angle       2.07564 (   21)

*********************** 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
  199 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7450 (mp0)
REVERT: A   78 THR cc_start: 0.8099 (m) cc_final: 0.7892 (p)
REVERT: A   82 MET cc_start: 0.7479 (ppp) cc_final: 0.7276 (pp-130)
REVERT: A  117 ASN cc_start: 0.7424 (t0) cc_final: 0.7209 (t0)
REVERT: A  186 LEU cc_start: 0.8234 (tp) cc_final: 0.7996 (tp)
REVERT: A  202 TYR cc_start: 0.7726 (t80) cc_final: 0.6894 (t80)
REVERT: A  351 LEU cc_start: 0.8822 (mt) cc_final: 0.8605 (mp)
REVERT: A  408 MET cc_start: 0.8371 (mmt) cc_final: 0.7927 (mmt)
REVERT: A  479 GLU cc_start: 0.7863 (tt0) cc_final: 0.7454 (mt-10)
REVERT: H   60 TYR cc_start: 0.8358 (m-80) cc_final: 0.7992 (m-80)
REVERT: H   86 LEU cc_start: 0.8894 (mp) cc_final: 0.8690 (mp)
REVERT: L  105 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7191 (mp0)
  outliers start: 17
  outliers final: 8
  residues processed: 189
  average time/residue: 0.4408
  time to fit residues: 91.2816
Evaluate side-chains
  184 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 174
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
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  503 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  170 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 75 optimal weight:    0.0970
   chunk 44 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 108 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.4136 r_free = 0.4136 target = 0.160714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.136766 restraints weight = 16143.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 2.35
r_work: 0.3733 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3587 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10018  Z= 0.154
  Angle     :  0.592   6.890  13639  Z= 0.305
  Chirality :  0.044   0.220   1474
  Planarity :  0.006   0.096   1751
  Dihedral  :  5.424  59.909   1484
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.23 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.08 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.24), residues: 1206
  helix:  1.01 (0.28), residues: 374
  sheet:  1.11 (0.34), residues: 250
  loop : -1.15 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 177 
 TYR   0.019   0.001   TYR A 385 
 PHE   0.020   0.001   PHE A 400 
 TRP   0.011   0.001   TRP B 353 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9997)
  covalent geometry    : angle       0.58640 (13593)
  SS BOND              : bond        0.00291 (   11)
  SS BOND              : angle       0.74799 (   22)
  hydrogen bonds       : bond        0.04589 (  399)
  hydrogen bonds       : angle       5.00969 ( 1130)
  metal coordination   : bond        0.00383 (    2)
  link_BETA1-4         : bond        0.00235 (    1)
  link_BETA1-4         : angle       1.20286 (    3)
  link_NAG-ASN         : bond        0.00285 (    7)
  link_NAG-ASN         : angle       2.04368 (   21)

*********************** 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
  197 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 177
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 SER cc_start: 0.7440 (t) cc_final: 0.7215 (m)
REVERT: A   82 MET cc_start: 0.7549 (ppp) cc_final: 0.7332 (pp-130)
REVERT: A  117 ASN cc_start: 0.7442 (t0) cc_final: 0.7207 (t0)
REVERT: A  186 LEU cc_start: 0.8222 (tp) cc_final: 0.8003 (tp)
REVERT: A  202 TYR cc_start: 0.7788 (t80) cc_final: 0.6911 (t80)
REVERT: A  270 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.6875 (tpt)
REVERT: A  351 LEU cc_start: 0.8833 (mt) cc_final: 0.8624 (mp)
REVERT: A  419 LYS cc_start: 0.6771 (mtpp) cc_final: 0.6548 (mttm)
REVERT: A  479 GLU cc_start: 0.7813 (tt0) cc_final: 0.7442 (mt-10)
REVERT: H   60 TYR cc_start: 0.8376 (m-80) cc_final: 0.7931 (m-80)
REVERT: H   86 LEU cc_start: 0.8913 (mp) cc_final: 0.8713 (mp)
REVERT: L   90 GLN cc_start: 0.8515 (pp30) cc_final: 0.8183 (pp30)
  outliers start: 20
  outliers final: 12
  residues processed: 185
  average time/residue: 0.4280
  time to fit residues: 86.4696
Evaluate side-chains
  188 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 175
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
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  503 VAL
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   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 75 optimal weight:    0.3980
   chunk 41 optimal weight:    0.0970
   chunk 1 optimal weight:    0.8980
   chunk 105 optimal weight:    5.9990
   chunk 89 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 113 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.4140 r_free = 0.4140 target = 0.161211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.137730 restraints weight = 13849.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 2.15
r_work: 0.3757 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3613 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10018  Z= 0.142
  Angle     :  0.573   6.805  13639  Z= 0.298
  Chirality :  0.044   0.215   1474
  Planarity :  0.005   0.095   1751
  Dihedral  :  5.259  59.149   1484
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.15 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 11.12 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.24), residues: 1206
  helix:  1.03 (0.28), residues: 374
  sheet:  1.13 (0.35), residues: 250
  loop : -1.11 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 177 
 TYR   0.017   0.001   TYR H 102 
 PHE   0.017   0.001   PHE A 400 
 TRP   0.011   0.001   TRP B 353 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 9997)
  covalent geometry    : angle       0.56806 (13593)
  SS BOND              : bond        0.00253 (   11)
  SS BOND              : angle       0.52765 (   22)
  hydrogen bonds       : bond        0.04361 (  399)
  hydrogen bonds       : angle       4.86372 ( 1130)
  metal coordination   : bond        0.00277 (    2)
  link_BETA1-4         : bond        0.00242 (    1)
  link_BETA1-4         : angle       1.21053 (    3)
  link_NAG-ASN         : bond        0.00305 (    7)
  link_NAG-ASN         : angle       2.00875 (   21)

*********************** 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
  207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 179
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7185 (mp0)
REVERT: A   82 MET cc_start: 0.7514 (ppp) cc_final: 0.7308 (pp-130)
REVERT: A  186 LEU cc_start: 0.8192 (tp) cc_final: 0.7982 (tp)
REVERT: A  202 TYR cc_start: 0.7795 (t80) cc_final: 0.6978 (t80)
REVERT: A  270 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6832 (tpt)
REVERT: A  351 LEU cc_start: 0.8839 (mt) cc_final: 0.8637 (mp)
REVERT: A  419 LYS cc_start: 0.6767 (mtpp) cc_final: 0.6519 (mttm)
REVERT: L   90 GLN cc_start: 0.8463 (pp30) cc_final: 0.8152 (pp30)
  outliers start: 28
  outliers final: 18
  residues processed: 187
  average time/residue: 0.4694
  time to fit residues: 95.6591
Evaluate side-chains
  190 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 171
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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 A residue  401 HIS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  170 SER
Chi-restraints excluded: chain H residue  174 THR
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
Chi-restraints excluded: chain L residue   92 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 83 optimal weight:    0.4980
   chunk 64 optimal weight:    0.0060
   chunk 17 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 44 optimal weight:    0.2980
   chunk 118 optimal weight:    4.9990
   chunk 87 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.4596

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.161420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.137048 restraints weight = 16600.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.43
r_work: 0.3736 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10018  Z= 0.136
  Angle     :  0.568   6.903  13639  Z= 0.295
  Chirality :  0.043   0.209   1474
  Planarity :  0.005   0.093   1751
  Dihedral  :  5.175  57.283   1484
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.15 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.17 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.24), residues: 1206
  helix:  1.05 (0.28), residues: 374
  sheet:  1.16 (0.35), residues: 250
  loop : -1.10 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 177 
 TYR   0.016   0.001   TYR A 385 
 PHE   0.015   0.001   PHE A 400 
 TRP   0.010   0.001   TRP B 353 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9997)
  covalent geometry    : angle       0.56266 (13593)
  SS BOND              : bond        0.00254 (   11)
  SS BOND              : angle       0.59317 (   22)
  hydrogen bonds       : bond        0.04249 (  399)
  hydrogen bonds       : angle       4.80028 ( 1130)
  metal coordination   : bond        0.00321 (    2)
  link_BETA1-4         : bond        0.00238 (    1)
  link_BETA1-4         : angle       1.19087 (    3)
  link_NAG-ASN         : bond        0.00273 (    7)
  link_NAG-ASN         : angle       1.98810 (   21)

*********************** 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
  203 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7257 (mp0)
REVERT: A  186 LEU cc_start: 0.8191 (tp) cc_final: 0.7990 (tp)
REVERT: A  202 TYR cc_start: 0.7844 (t80) cc_final: 0.7033 (t80)
REVERT: A  270 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6819 (tpt)
REVERT: A  351 LEU cc_start: 0.8844 (mt) cc_final: 0.8628 (mp)
REVERT: A  479 GLU cc_start: 0.7776 (tt0) cc_final: 0.7429 (mt-10)
  outliers start: 25
  outliers final: 19
  residues processed: 185
  average time/residue: 0.4331
  time to fit residues: 87.8205
Evaluate side-chains
  199 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  162 LEU
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  458 LYS
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
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  178 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
Chi-restraints excluded: chain L residue   92 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 93 optimal weight:    0.2980
   chunk 94 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 103 optimal weight:    0.5980
   chunk 75 optimal weight:    0.2980
   chunk 50 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4144 r_free = 0.4144 target = 0.161425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.135678 restraints weight = 22325.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 2.90
r_work: 0.3702 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10018  Z= 0.140
  Angle     :  0.576   6.818  13639  Z= 0.298
  Chirality :  0.043   0.206   1474
  Planarity :  0.005   0.093   1751
  Dihedral  :  5.106  54.355   1484
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.23 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.55 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.25), residues: 1206
  helix:  1.04 (0.28), residues: 374
  sheet:  1.17 (0.35), residues: 250
  loop : -1.10 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 177 
 TYR   0.016   0.001   TYR A 385 
 PHE   0.015   0.001   PHE A 400 
 TRP   0.010   0.001   TRP B 353 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9997)
  covalent geometry    : angle       0.57091 (13593)
  SS BOND              : bond        0.00281 (   11)
  SS BOND              : angle       0.66655 (   22)
  hydrogen bonds       : bond        0.04237 (  399)
  hydrogen bonds       : angle       4.76858 ( 1130)
  metal coordination   : bond        0.00298 (    2)
  link_BETA1-4         : bond        0.00296 (    1)
  link_BETA1-4         : angle       1.23506 (    3)
  link_NAG-ASN         : bond        0.00261 (    7)
  link_NAG-ASN         : angle       1.98266 (   21)

*********************** 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
  205 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 179
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7075 (mp0)
REVERT: A  202 TYR cc_start: 0.7694 (t80) cc_final: 0.6894 (t80)
REVERT: H   86 LEU cc_start: 0.8859 (mt) cc_final: 0.8644 (mp)
  outliers start: 26
  outliers final: 19
  residues processed: 186
  average time/residue: 0.4389
  time to fit residues: 89.6038
Evaluate side-chains
  192 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 173
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0170
   chunk 73 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.6418

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.160671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.135834 restraints weight = 17816.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 2.54
r_work: 0.3711 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3562 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3563
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10018  Z= 0.169
  Angle     :  0.596   6.815  13639  Z= 0.309
  Chirality :  0.044   0.210   1474
  Planarity :  0.005   0.096   1751
  Dihedral  :  5.095  54.640   1484
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.73 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 13.02 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.24), residues: 1206
  helix:  1.00 (0.28), residues: 374
  sheet:  1.11 (0.35), residues: 250
  loop : -1.15 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 177 
 TYR   0.019   0.002   TYR A 385 
 PHE   0.018   0.001   PHE A 400 
 TRP   0.011   0.001   TRP B 353 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 9997)
  covalent geometry    : angle       0.59102 (13593)
  SS BOND              : bond        0.00316 (   11)
  SS BOND              : angle       0.66087 (   22)
  hydrogen bonds       : bond        0.04547 (  399)
  hydrogen bonds       : angle       4.83142 ( 1130)
  metal coordination   : bond        0.00371 (    2)
  link_BETA1-4         : bond        0.00316 (    1)
  link_BETA1-4         : angle       1.34605 (    3)
  link_NAG-ASN         : bond        0.00242 (    7)
  link_NAG-ASN         : angle       2.05066 (   21)

*********************** 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
  200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 172
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 ASN cc_start: 0.7448 (t0) cc_final: 0.7223 (t0)
REVERT: A  202 TYR cc_start: 0.7848 (t80) cc_final: 0.7042 (t80)
REVERT: A  408 MET cc_start: 0.8455 (mmt) cc_final: 0.8049 (mmt)
REVERT: H   86 LEU cc_start: 0.8885 (mt) cc_final: 0.8663 (mp)
  outliers start: 28
  outliers final: 22
  residues processed: 181
  average time/residue: 0.4294
  time to fit residues: 85.5491
Evaluate side-chains
  191 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
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  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0970
   chunk 76 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 118 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 110 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0970
   overall best weight:    0.4576

-------------------------------------------------------------------------------
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 = 0.4141 r_free = 0.4141 target = 0.161244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.136661 restraints weight = 17570.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 2.51
r_work: 0.3724 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3575
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3575 r_free = 0.3575    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 = 0.3575 r_free = 0.3575    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3575
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10018  Z= 0.137
  Angle     :  0.581   8.304  13639  Z= 0.299
  Chirality :  0.043   0.205   1474
  Planarity :  0.005   0.094   1751
  Dihedral  :  4.939  54.089   1484
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.32 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.50 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.24), residues: 1206
  helix:  1.04 (0.28), residues: 374
  sheet:  1.15 (0.35), residues: 250
  loop : -1.13 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 177 
 TYR   0.015   0.001   TYR A 385 
 PHE   0.014   0.001   PHE A 400 
 TRP   0.010   0.001   TRP B 353 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9997)
  covalent geometry    : angle       0.57535 (13593)
  SS BOND              : bond        0.00242 (   11)
  SS BOND              : angle       0.67204 (   22)
  hydrogen bonds       : bond        0.04212 (  399)
  hydrogen bonds       : angle       4.78047 ( 1130)
  metal coordination   : bond        0.00278 (    2)
  link_BETA1-4         : bond        0.00246 (    1)
  link_BETA1-4         : angle       1.23745 (    3)
  link_NAG-ASN         : bond        0.00241 (    7)
  link_NAG-ASN         : angle       2.01849 (   21)

*********************** 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
  201 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: A  202 TYR cc_start: 0.7830 (t80) cc_final: 0.6992 (t80)
REVERT: A  306 ARG cc_start: 0.8000 (tpt90) cc_final: 0.7665 (tpt90)
REVERT: A  369 PHE cc_start: 0.8407 (t80) cc_final: 0.8160 (t80)
REVERT: A  408 MET cc_start: 0.8437 (mmt) cc_final: 0.8050 (mmt)
REVERT: H   86 LEU cc_start: 0.8880 (mt) cc_final: 0.8679 (mp)
  outliers start: 25
  outliers final: 22
  residues processed: 181
  average time/residue: 0.4114
  time to fit residues: 82.1227
Evaluate side-chains
  196 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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  433 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Chi-restraints excluded: chain L residue   92 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0980
   chunk 70 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   chunk 52 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 116 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.161336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.137376 restraints weight = 16144.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 2.33
r_work: 0.3744 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3613 r_free = 0.3613    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3613 r_free = 0.3613    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10018  Z= 0.133
  Angle     :  0.582   9.162  13639  Z= 0.302
  Chirality :  0.043   0.202   1474
  Planarity :  0.005   0.093   1751
  Dihedral  :  4.799  53.824   1484
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.48 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.97 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.25), residues: 1206
  helix:  1.13 (0.28), residues: 374
  sheet:  1.13 (0.35), residues: 252
  loop : -1.09 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 559 
 TYR   0.014   0.001   TYR A 385 
 PHE   0.013   0.001   PHE A 400 
 TRP   0.009   0.001   TRP B 353 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9997)
  covalent geometry    : angle       0.57708 (13593)
  SS BOND              : bond        0.00228 (   11)
  SS BOND              : angle       0.54428 (   22)
  hydrogen bonds       : bond        0.04160 (  399)
  hydrogen bonds       : angle       4.73665 ( 1130)
  metal coordination   : bond        0.00268 (    2)
  link_BETA1-4         : bond        0.00315 (    1)
  link_BETA1-4         : angle       1.24098 (    3)
  link_NAG-ASN         : bond        0.00241 (    7)
  link_NAG-ASN         : angle       2.03039 (   21)

*********************** 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
  199 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 176
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  202 TYR cc_start: 0.7793 (t80) cc_final: 0.6998 (t80)
REVERT: A  369 PHE cc_start: 0.8369 (t80) cc_final: 0.8123 (t80)
REVERT: A  408 MET cc_start: 0.8373 (mmt) cc_final: 0.7985 (mmt)
REVERT: A  431 ASP cc_start: 0.7393 (p0) cc_final: 0.7120 (p0)
REVERT: A  479 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7518 (pt0)
  outliers start: 23
  outliers final: 20
  residues processed: 180
  average time/residue: 0.4224
  time to fit residues: 83.6767
Evaluate side-chains
  196 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 175
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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  479 GLU
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0060
   chunk 34 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0170
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.4434

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

Flipped N/Q/H residues before XYZ refinement:
H  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.161243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.136623 restraints weight = 18031.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 2.54
r_work: 0.3725 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10018  Z= 0.136
  Angle     :  0.580   9.191  13639  Z= 0.301
  Chirality :  0.044   0.201   1474
  Planarity :  0.005   0.093   1751
  Dihedral  :  4.711  53.764   1484
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.48 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 14.73 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.25), residues: 1206
  helix:  1.12 (0.28), residues: 374
  sheet:  1.11 (0.35), residues: 250
  loop : -1.09 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 559 
 TYR   0.016   0.001   TYR A 385 
 PHE   0.013   0.001   PHE A 400 
 TRP   0.013   0.001   TRP A 477 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9997)
  covalent geometry    : angle       0.57465 (13593)
  SS BOND              : bond        0.00244 (   11)
  SS BOND              : angle       0.56074 (   22)
  hydrogen bonds       : bond        0.04150 (  399)
  hydrogen bonds       : angle       4.73019 ( 1130)
  metal coordination   : bond        0.00257 (    2)
  link_BETA1-4         : bond        0.00278 (    1)
  link_BETA1-4         : angle       1.23533 (    3)
  link_NAG-ASN         : bond        0.00227 (    7)
  link_NAG-ASN         : angle       2.05934 (   21)

********************** 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
  202 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 180
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.7447 (mp0) cc_final: 0.7058 (mp0)
REVERT: A  202 TYR cc_start: 0.7648 (t80) cc_final: 0.6870 (t80)
REVERT: A  369 PHE cc_start: 0.8230 (t80) cc_final: 0.8003 (t80)
REVERT: A  383 MET cc_start: 0.7904 (mtp) cc_final: 0.7526 (mtp)
REVERT: A  408 MET cc_start: 0.8232 (mmt) cc_final: 0.7814 (mmt)
REVERT: A  431 ASP cc_start: 0.7105 (p0) cc_final: 0.6828 (p0)
REVERT: H   83 MET cc_start: 0.7252 (mtm) cc_final: 0.7040 (mtp)
  outliers start: 22
  outliers final: 20
  residues processed: 186
  average time/residue: 0.4272
  time to fit residues: 87.8522
Evaluate side-chains
  195 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 175
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   85 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  433 VAL
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  174 THR
Chi-restraints excluded: chain H residue  178 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   17 ASP
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0570
   chunk 11 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0570
   chunk 100 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.4616

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.161215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.137198 restraints weight = 16114.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3840 rms_B_bonded: 2.34
r_work: 0.3741 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3598 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10018  Z= 0.139
  Angle     :  0.596  11.018  13639  Z= 0.307
  Chirality :  0.044   0.201   1474
  Planarity :  0.005   0.093   1751
  Dihedral  :  4.699  53.705   1484
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.56 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.83 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.24), residues: 1206
  helix:  1.11 (0.28), residues: 374
  sheet:  1.12 (0.34), residues: 250
  loop : -1.11 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 559 
 TYR   0.016   0.001   TYR A 385 
 PHE   0.014   0.001   PHE A 400 
 TRP   0.009   0.001   TRP A 477 
 HIS   0.007   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9997)
  covalent geometry    : angle       0.59034 (13593)
  SS BOND              : bond        0.00238 (   11)
  SS BOND              : angle       0.75462 (   22)
  hydrogen bonds       : bond        0.04166 (  399)
  hydrogen bonds       : angle       4.72887 ( 1130)
  metal coordination   : bond        0.00280 (    2)
  link_BETA1-4         : bond        0.00259 (    1)
  link_BETA1-4         : angle       1.23371 (    3)
  link_NAG-ASN         : bond        0.00220 (    7)
  link_NAG-ASN         : angle       2.10863 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4800.93 seconds
wall clock time: 82 minutes 19.17 seconds (4939.17 seconds total)