Starting phenix.real_space_refine
on Tue Mar  3 23:27:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7shl_25128/03_2026/7shl_25128.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7shl_25128/03_2026/7shl_25128.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7shl_25128/03_2026/7shl_25128.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7shl_25128/03_2026/7shl_25128.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7shl_25128/03_2026/7shl_25128.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7shl_25128/03_2026/7shl_25128.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      69      5.16       5
     C    5890      2.51       5
     N    1527      2.21       5
     O    1720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9207
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 645, 5291
          Classifications: {'peptide': 645}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 627}
    Chain: "B"
      Number of atoms: 770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 770
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 8, 'TRANS': 88}
    Chain: "C"
      Number of atoms: 773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 773
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 92}
    Chain: "L"
      Number of atoms: 2228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2228
          Classifications: {'peptide': 282}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 264}
    Chain: "R"
      Number of atoms: 144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 144
          Classifications: {'peptide': 16}
          Link IDs: {'TRANS': 15}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8610  SG  CYS L 356      45.750  26.931 137.545  1.00322.01           S
  ATOM   8624  SG  CYS L 358      47.077  24.154 139.782  1.00323.88           S
  ATOM   8937  SG  CYS L 400      49.431  25.769 137.231  1.00324.29           S
  ATOM   8964  SG  CYS L 404      46.670  23.617 136.020  1.00365.62           S

  Time building chain proxies: 2.33, per 1000 atoms: 0.25
  Number of scatterers: 9207
  At special positions: 0
  Unit cell: (113.025, 100.65, 180.675, 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      69     16.00
     O    1720      8.00
     N    1527      7.00
     C    5890      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 339.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN L 500 "
        pdb="ZN    ZN L 500 " - pdb=" SG  CYS L 404 "
        pdb="ZN    ZN L 500 " - pdb=" SG  CYS L 400 "
        pdb="ZN    ZN L 500 " - pdb=" SG  CYS L 356 "
        pdb="ZN    ZN L 500 " - pdb=" SG  CYS L 358 "
      Number of angles added : 6


  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2200

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      53.0% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 26
      removed outlier: 3.863A  pdb=" N   THR A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS A  16 " --> pdb=" O   GLU A  12 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   MET A  26 " --> pdb=" O   LYS A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 47
    Processing helix  chain 'A' and resid 53 through 78
    Processing helix  chain 'A' and resid 82 through 105
    Processing helix  chain 'A' and resid 105 through 112
    Processing helix  chain 'A' and resid 138 through 151
    Processing helix  chain 'A' and resid 152 through 154
      No H-bonds generated for 'chain 'A' and resid 152 through 154'
    Processing helix  chain 'A' and resid 155 through 172
    Processing helix  chain 'A' and resid 177 through 193
      removed outlier: 3.970A  pdb=" N   PHE A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   VAL A 189 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 207
    Processing helix  chain 'A' and resid 207 through 230
    Processing helix  chain 'A' and resid 231 through 254
    Processing helix  chain 'A' and resid 255 through 257
      No H-bonds generated for 'chain 'A' and resid 255 through 257'
    Processing helix  chain 'A' and resid 258 through 266
      removed outlier: 3.899A  pdb=" N   ILE A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 287
      removed outlier: 3.603A  pdb=" N   GLU A 281 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   HIS A 283 " --> pdb=" O   HIS A 279 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   ASN A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG A 287 " --> pdb=" O   HIS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 304
      removed outlier: 3.733A  pdb=" N   ALA A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 328
      removed outlier: 4.515A  pdb=" N   HIS A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   MET A 311 " --> pdb=" O   GLY A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 333
      No H-bonds generated for 'chain 'A' and resid 331 through 333'
    Processing helix  chain 'A' and resid 334 through 357
    Processing helix  chain 'A' and resid 361 through 377
    Processing helix  chain 'A' and resid 386 through 400
    Processing helix  chain 'A' and resid 407 through 424
      removed outlier: 3.578A  pdb=" N   VAL A 411 " --> pdb=" O   THR A 407 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR A 420 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL A 421 " --> pdb=" O   SER A 417 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   TYR A 424 " --> pdb=" O   THR A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 446
      removed outlier: 4.269A  pdb=" N   PHE A 431 " --> pdb=" O   ASP A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 466
      removed outlier: 3.839A  pdb=" N   GLU A 454 " --> pdb=" O   SER A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 469
      No H-bonds generated for 'chain 'A' and resid 467 through 469'
    Processing helix  chain 'A' and resid 470 through 497
      removed outlier: 3.618A  pdb=" N   TYR A 477 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR A 478 " --> pdb=" O   HIS A 474 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   ALA A 484 " --> pdb=" O   MET A 480 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   ASP A 485 " --> pdb=" O   SER A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 548
      removed outlier: 3.729A  pdb=" N   GLU A 534 " --> pdb=" O   PRO A 530 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   LYS A 535 " --> pdb=" O   GLN A 531 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   SER A 536 " --> pdb=" O   GLU A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 591
    Processing helix  chain 'A' and resid 596 through 604
    Processing helix  chain 'A' and resid 606 through 620
      removed outlier: 3.502A  pdb=" N   LEU A 610 " --> pdb=" O   ASN A 606 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   VAL A 620 " --> pdb=" O   SER A 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 36
      removed outlier: 3.904A  pdb=" N   LEU B  27 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 37
    Processing helix  chain 'C' and resid 39 through 47
    Processing helix  chain 'C' and resid 66 through 83
      removed outlier: 4.154A  pdb=" N   LYS C  72 " --> pdb=" O   HIS C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 111
    Processing helix  chain 'L' and resid 170 through 174
      removed outlier: 3.786A  pdb=" N   LEU L 174 " --> pdb=" O   MET L 171 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 215 through 225
      removed outlier: 3.925A  pdb=" N   THR L 220 " --> pdb=" O   LEU L 217 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   THR L 221 " --> pdb=" O   CYS L 218 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU L 222 " --> pdb=" O   SER L 219 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ARG L 223 " --> pdb=" O   THR L 220 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR L 225 " --> pdb=" O   LEU L 222 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 240 through 246
    Processing helix  chain 'L' and resid 264 through 269
      removed outlier: 4.312A  pdb=" N   GLY L 267 " --> pdb=" O   PHE L 264 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 287 through 292
    Processing helix  chain 'L' and resid 321 through 334
    Processing helix  chain 'L' and resid 343 through 352
    Processing helix  chain 'L' and resid 375 through 378
      No H-bonds generated for 'chain 'L' and resid 375 through 378'
    Processing helix  chain 'L' and resid 401 through 415
      removed outlier: 3.737A  pdb=" N   GLN L 407 " --> pdb=" O   THR L 403 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   PHE L 408 " --> pdb=" O   CYS L 404 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 506 through 508
      removed outlier: 6.369A  pdb=" N   VAL R  24 " --> pdb=" O   LYS A 565 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   LYS A 565 " --> pdb=" O   VAL R  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 511 through 513
    Processing sheet with id=AA3, first strand: chain 'A' and resid 593 through 595
    Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 44
      removed outlier: 3.769A  pdb=" N   ALA B  78 " --> pdb=" O   LYS B  43 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   THR B  13 " --> pdb=" O   ILE C  30 " (cutoff:3.500A)
      removed outlier: 8.703A  pdb=" N   LYS C  32 " --> pdb=" O   THR B  13 " (cutoff:3.500A)
      removed outlier: 9.057A  pdb=" N   PHE B  15 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 135 through 138
      removed outlier: 3.627A  pdb=" N   LEU L 203 " --> pdb=" O   SER L 228 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASP L 230 " --> pdb=" O   LEU L 203 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU L 229 " --> pdb=" O   SER L 251 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LYS L 253 " --> pdb=" O   LEU L 229 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 274 through 276
      removed outlier: 7.098A  pdb=" N   LEU L 275 " --> pdb=" O   ASP L 298 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   GLU L 295 " --> pdb=" O   THR L 381 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   VAL L 383 " --> pdb=" O   GLU L 295 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU L 297 " --> pdb=" O   VAL L 383 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 313 through 314
      removed outlier: 3.661A  pdb=" N   ASP L 313 " --> pdb=" O   GLN L 368 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLN L 368 " --> pdb=" O   ASP L 313 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 354 through 355

    453 hydrogen bonds defined for protein.
    1299 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: 1.53

  Time building geometry restraints manager: 0.99 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: 2958
        1.34 -     1.46: 2025
        1.46 -     1.58: 4306
        1.58 -     1.70: 0
        1.70 -     1.82: 108
  Bond restraints: 9397
  Sorted by residual:
  bond pdb=" CA  ASN L 281 "
       pdb=" CB  ASN L 281 "
    ideal  model  delta    sigma   weight residual
    1.523  1.542 -0.019 1.27e-02 6.20e+03 2.12e+00
  bond pdb=" CB  GLN L 348 "
       pdb=" CG  GLN L 348 "
    ideal  model  delta    sigma   weight residual
    1.520  1.482  0.038 3.00e-02 1.11e+03 1.63e+00
  bond pdb=" CA  LYS A 117 "
       pdb=" C   LYS A 117 "
    ideal  model  delta    sigma   weight residual
    1.523  1.505  0.018 1.56e-02 4.11e+03 1.31e+00
  bond pdb=" N   ILE L 314 "
       pdb=" CA  ILE L 314 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.017 1.57e-02 4.06e+03 1.17e+00
  bond pdb=" CB  LYS B  11 "
       pdb=" CG  LYS B  11 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.00e+00
  ... (remaining 9392 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 12293
        1.55 -     3.11: 326
        3.11 -     4.66: 61
        4.66 -     6.21: 18
        6.21 -     7.76: 6
  Bond angle restraints: 12704
  Sorted by residual:
  angle pdb=" N   ILE L 314 "
        pdb=" CA  ILE L 314 "
        pdb=" C   ILE L 314 "
      ideal   model   delta    sigma   weight residual
     106.21  109.98   -3.77 1.07e+00 8.73e-01 1.24e+01
  angle pdb=" CB  LYS B  11 "
        pdb=" CG  LYS B  11 "
        pdb=" CD  LYS B  11 "
      ideal   model   delta    sigma   weight residual
     111.30  118.35   -7.05 2.30e+00 1.89e-01 9.39e+00
  angle pdb=" CB  ARG C  82 "
        pdb=" CG  ARG C  82 "
        pdb=" CD  ARG C  82 "
      ideal   model   delta    sigma   weight residual
     111.30  118.32   -7.02 2.30e+00 1.89e-01 9.31e+00
  angle pdb=" N   LYS A 615 "
        pdb=" CA  LYS A 615 "
        pdb=" CB  LYS A 615 "
      ideal   model   delta    sigma   weight residual
     110.12  114.24   -4.12 1.47e+00 4.63e-01 7.84e+00
  angle pdb=" CB  LYS A 615 "
        pdb=" CG  LYS A 615 "
        pdb=" CD  LYS A 615 "
      ideal   model   delta    sigma   weight residual
     111.30  117.67   -6.37 2.30e+00 1.89e-01 7.68e+00
  ... (remaining 12699 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 5123
       17.38 -    34.77: 526
       34.77 -    52.15: 79
       52.15 -    69.54: 8
       69.54 -    86.92: 11
  Dihedral angle restraints: 5747
    sinusoidal: 2366
      harmonic: 3381
  Sorted by residual:
  dihedral pdb=" CA  TYR A 253 "
           pdb=" C   TYR A 253 "
           pdb=" N   LEU A 254 "
           pdb=" CA  LEU A 254 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.54  -17.46     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  ARG B  37 "
           pdb=" C   ARG B  37 "
           pdb=" N   PRO B  38 "
           pdb=" CA  PRO B  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.74  -17.26     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  MET A 576 "
           pdb=" C   MET A 576 "
           pdb=" N   VAL A 577 "
           pdb=" CA  VAL A 577 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.17  -16.83     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 5744 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 957
       0.036 -    0.072: 360
       0.072 -    0.108: 90
       0.108 -    0.144: 24
       0.144 -    0.180: 4
  Chirality restraints: 1435
  Sorted by residual:
  chirality pdb=" CB  THR L 308 "
            pdb=" CA  THR L 308 "
            pdb=" OG1 THR L 308 "
            pdb=" CG2 THR L 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.12e-01
  chirality pdb=" CB  THR C  57 "
            pdb=" CA  THR C  57 "
            pdb=" OG1 THR C  57 "
            pdb=" CG2 THR C  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.73e-01
  chirality pdb=" CA  ILE A 593 "
            pdb=" N   ILE A 593 "
            pdb=" C   ILE A 593 "
            pdb=" CB  ILE A 593 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.68e-01
  ... (remaining 1432 not shown)

  Planarity restraints: 1615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY L 393 "   -0.035 5.00e-02 4.00e+02   5.37e-02 4.62e+00
        pdb=" N   PRO L 394 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO L 394 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO L 394 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN L 348 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.11e+00
        pdb=" CD  GLN L 348 "    0.035 2.00e-02 2.50e+03
        pdb=" OE1 GLN L 348 "   -0.013 2.00e-02 2.50e+03
        pdb=" NE2 GLN L 348 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE L 342 "    0.025 5.00e-02 4.00e+02   3.76e-02 2.27e+00
        pdb=" N   PRO L 343 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO L 343 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO L 343 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1612 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 170
        2.65 -     3.21: 9239
        3.21 -     3.77: 15113
        3.77 -     4.34: 20217
        4.34 -     4.90: 32093
  Nonbonded interactions: 76832
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 611 "
            pdb=" NZ  LYS A 615 "
     model   vdw
     2.087 3.120
  nonbonded pdb=" O   LEU A 226 "
            pdb=" OG  SER A 230 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OG1 THR C  57 "
            pdb=" OE1 GLU C  59 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O   GLY A 183 "
            pdb=" OG  SER A 187 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OG  SER B  95 "
            pdb=" OD2 ASP C  25 "
     model   vdw
     2.211 3.040
  ... (remaining 76827 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.150
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9401  Z= 0.145
  Angle     :  0.648   7.763  12710  Z= 0.345
  Chirality :  0.041   0.180   1435
  Planarity :  0.004   0.054   1615
  Dihedral  : 14.140  86.922   3547
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.26), residues: 1128
  helix:  0.89 (0.23), residues: 542
  sheet: -0.79 (0.58), residues: 85
  loop : -0.70 (0.30), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  82 
 TYR   0.022   0.002   TYR A 596 
 PHE   0.014   0.001   PHE A  64 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.005   0.001   HIS A 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9397)
  covalent geometry    : angle       0.64603 (12704)
  hydrogen bonds       : bond        0.14244 (  453)
  hydrogen bonds       : angle       6.39800 ( 1299)
  metal coordination   : bond        0.00330 (    4)
  metal coordination   : angle       2.22791 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 MET cc_start: 0.8713 (mpp) cc_final: 0.8177 (mpp)
REVERT: A  476 MET cc_start: 0.8306 (mtp) cc_final: 0.7916 (mtm)
REVERT: A  553 LEU cc_start: 0.8800 (mt) cc_final: 0.8589 (mp)
REVERT: A  582 MET cc_start: 0.8862 (mtm) cc_final: 0.8635 (mtt)
REVERT: B   41 ASP cc_start: 0.7808 (m-30) cc_final: 0.7573 (m-30)
REVERT: B   68 ARG cc_start: 0.7796 (tpt170) cc_final: 0.7551 (tpt170)
REVERT: L  300 PHE cc_start: 0.7339 (p90) cc_final: 0.6951 (p90)
REVERT: L  324 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7292 (tp30)
REVERT: L  366 PHE cc_start: 0.8544 (p90) cc_final: 0.8061 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0939
  time to fit residues: 21.0686
Evaluate side-chains
  122 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.3342

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

Flipped N/Q/H residues before XYZ refinement:
A 474 HIS
A 547 HIS
A 641 ASN
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.099616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.067594 restraints weight = 31964.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.068665 restraints weight = 17152.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.069538 restraints weight = 11669.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.070161 restraints weight = 9356.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.070539 restraints weight = 8178.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9401  Z= 0.163
  Angle     :  0.635   6.412  12710  Z= 0.328
  Chirality :  0.042   0.226   1435
  Planarity :  0.004   0.045   1615
  Dihedral  :  4.495  20.591   1224
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.45 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.26), residues: 1128
  helix:  1.01 (0.23), residues: 555
  sheet: -1.10 (0.55), residues: 95
  loop : -0.40 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  82 
 TYR   0.021   0.002   TYR A 596 
 PHE   0.023   0.002   PHE A 543 
 TRP   0.012   0.001   TRP A 555 
 HIS   0.004   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9397)
  covalent geometry    : angle       0.63090 (12704)
  hydrogen bonds       : bond        0.04369 (  453)
  hydrogen bonds       : angle       5.13607 ( 1299)
  metal coordination   : bond        0.00651 (    4)
  metal coordination   : angle       3.48524 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 GLU cc_start: 0.7703 (tp30) cc_final: 0.7413 (tp30)
REVERT: A  566 MET cc_start: -0.1315 (OUTLIER) cc_final: -0.1550 (mmp)
REVERT: A  582 MET cc_start: 0.8882 (mtm) cc_final: 0.8556 (mtt)
REVERT: B   41 ASP cc_start: 0.7863 (m-30) cc_final: 0.7409 (m-30)
REVERT: B   45 TYR cc_start: 0.6802 (m-80) cc_final: 0.6511 (m-80)
REVERT: L  300 PHE cc_start: 0.7206 (p90) cc_final: 0.6832 (p90)
REVERT: L  366 PHE cc_start: 0.8507 (p90) cc_final: 0.8012 (p90)
  outliers start: 12
  outliers final: 7
  residues processed: 143
  average time/residue: 0.1036
  time to fit residues: 20.5622
Evaluate side-chains
  134 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain L residue  298 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 73 optimal weight:    6.9990
   chunk 105 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0470
   chunk 79 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.101233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.070469 restraints weight = 31660.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.071475 restraints weight = 17137.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.072402 restraints weight = 11056.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.072778 restraints weight = 8779.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.073186 restraints weight = 7793.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9401  Z= 0.123
  Angle     :  0.586   8.256  12710  Z= 0.301
  Chirality :  0.041   0.183   1435
  Planarity :  0.004   0.050   1615
  Dihedral  :  4.337  20.058   1224
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.42 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.26), residues: 1128
  helix:  1.18 (0.23), residues: 553
  sheet: -1.08 (0.61), residues: 81
  loop : -0.42 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  96 
 TYR   0.019   0.001   TYR A 477 
 PHE   0.021   0.001   PHE A 543 
 TRP   0.006   0.001   TRP A  91 
 HIS   0.003   0.001   HIS L 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9397)
  covalent geometry    : angle       0.58372 (12704)
  hydrogen bonds       : bond        0.03927 (  453)
  hydrogen bonds       : angle       4.88442 ( 1299)
  metal coordination   : bond        0.00342 (    4)
  metal coordination   : angle       2.47012 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8921 (mm)
REVERT: A  566 MET cc_start: -0.1176 (OUTLIER) cc_final: -0.1545 (mmp)
REVERT: A  582 MET cc_start: 0.8780 (mtm) cc_final: 0.8502 (mtt)
REVERT: B   41 ASP cc_start: 0.7822 (m-30) cc_final: 0.7416 (m-30)
REVERT: B   45 TYR cc_start: 0.6698 (m-80) cc_final: 0.6443 (m-80)
REVERT: B   70 GLN cc_start: 0.7722 (mp10) cc_final: 0.7118 (mp10)
REVERT: L  300 PHE cc_start: 0.7166 (p90) cc_final: 0.6758 (p90)
REVERT: L  366 PHE cc_start: 0.8523 (p90) cc_final: 0.8012 (p90)
  outliers start: 15
  outliers final: 3
  residues processed: 155
  average time/residue: 0.0979
  time to fit residues: 21.2990
Evaluate side-chains
  134 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain L residue  298 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 58 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0670
   chunk 1 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.2922

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

Flipped N/Q/H residues before XYZ refinement:
A 474 HIS
A 488 ASN
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.099401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.068518 restraints weight = 31681.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.069730 restraints weight = 17103.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.070288 restraints weight = 11022.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.070875 restraints weight = 8697.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.071416 restraints weight = 7537.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9401  Z= 0.151
  Angle     :  0.608   9.477  12710  Z= 0.308
  Chirality :  0.042   0.186   1435
  Planarity :  0.004   0.050   1615
  Dihedral  :  4.345  20.638   1224
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.81 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.26), residues: 1128
  helix:  1.09 (0.22), residues: 558
  sheet: -1.12 (0.60), residues: 81
  loop : -0.42 (0.30), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 334 
 TYR   0.015   0.002   TYR A 477 
 PHE   0.020   0.001   PHE A 543 
 TRP   0.011   0.001   TRP A  14 
 HIS   0.004   0.001   HIS A 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9397)
  covalent geometry    : angle       0.60607 (12704)
  hydrogen bonds       : bond        0.03941 (  453)
  hydrogen bonds       : angle       4.81211 ( 1299)
  metal coordination   : bond        0.00377 (    4)
  metal coordination   : angle       2.54119 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8278 (mpp)
REVERT: A  297 MET cc_start: 0.8709 (tpp) cc_final: 0.8370 (tpp)
REVERT: A  582 MET cc_start: 0.8838 (mtm) cc_final: 0.8539 (mtt)
REVERT: B   22 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8058 (m)
REVERT: C   32 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8085 (mmtm)
REVERT: L  176 LYS cc_start: 0.8107 (mppt) cc_final: 0.7568 (tptp)
REVERT: L  300 PHE cc_start: 0.7224 (p90) cc_final: 0.6884 (p90)
REVERT: L  366 PHE cc_start: 0.8489 (p90) cc_final: 0.8047 (p90)
  outliers start: 24
  outliers final: 13
  residues processed: 153
  average time/residue: 0.1010
  time to fit residues: 21.2744
Evaluate side-chains
  141 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  615 LYS
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain L residue  221 THR
Chi-restraints excluded: chain L residue  298 ASP
Chi-restraints excluded: chain R residue   24 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 104 optimal weight:    0.8980
   chunk 84 optimal weight:   20.0000
   chunk 17 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 83 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0030
   chunk 20 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
A 474 HIS
A 590 ASN
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.100064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.068590 restraints weight = 31534.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.069672 restraints weight = 16798.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.070406 restraints weight = 11253.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.070925 restraints weight = 9009.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.070925 restraints weight = 7850.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9401  Z= 0.128
  Angle     :  0.614  11.638  12710  Z= 0.306
  Chirality :  0.042   0.224   1435
  Planarity :  0.004   0.055   1615
  Dihedral  :  4.275  19.829   1224
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.44 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.26), residues: 1128
  helix:  1.15 (0.22), residues: 557
  sheet: -1.12 (0.61), residues: 81
  loop : -0.40 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 334 
 TYR   0.019   0.001   TYR A 477 
 PHE   0.019   0.001   PHE A 543 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.006   0.001   HIS A 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9397)
  covalent geometry    : angle       0.61245 (12704)
  hydrogen bonds       : bond        0.03774 (  453)
  hydrogen bonds       : angle       4.77369 ( 1299)
  metal coordination   : bond        0.00250 (    4)
  metal coordination   : angle       2.34801 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 MET cc_start: 0.8710 (mpp) cc_final: 0.8460 (mpp)
REVERT: A  236 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8311 (mpp)
REVERT: A  285 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8973 (mm)
REVERT: A  476 MET cc_start: 0.8361 (mtp) cc_final: 0.7808 (mtm)
REVERT: A  582 MET cc_start: 0.8855 (mtm) cc_final: 0.8571 (mtt)
REVERT: B   22 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8104 (m)
REVERT: L  176 LYS cc_start: 0.8138 (mppt) cc_final: 0.7566 (tptp)
REVERT: L  300 PHE cc_start: 0.7283 (p90) cc_final: 0.6879 (p90)
REVERT: L  366 PHE cc_start: 0.8460 (p90) cc_final: 0.8037 (p90)
  outliers start: 21
  outliers final: 13
  residues processed: 149
  average time/residue: 0.0946
  time to fit residues: 19.7032
Evaluate side-chains
  148 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  615 LYS
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain L residue  298 ASP
Chi-restraints excluded: chain R residue   24 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0270
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0980
   chunk 67 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 108 optimal weight:    9.9990
   chunk 36 optimal weight:    0.7980
   chunk 100 optimal weight:    0.0980
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.3838

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

Flipped N/Q/H residues before XYZ refinement:
** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN
L 184 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.101424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.070598 restraints weight = 32217.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.071735 restraints weight = 17510.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.072408 restraints weight = 11163.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.073173 restraints weight = 8758.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.073604 restraints weight = 7401.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9401  Z= 0.114
  Angle     :  0.619  12.360  12710  Z= 0.305
  Chirality :  0.042   0.238   1435
  Planarity :  0.004   0.060   1615
  Dihedral  :  4.241  18.535   1224
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.40 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.26), residues: 1128
  helix:  1.15 (0.23), residues: 560
  sheet: -0.96 (0.62), residues: 81
  loop : -0.34 (0.31), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  63 
 TYR   0.016   0.001   TYR A 477 
 PHE   0.018   0.001   PHE A 543 
 TRP   0.006   0.001   TRP A 147 
 HIS   0.003   0.001   HIS L 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9397)
  covalent geometry    : angle       0.61769 (12704)
  hydrogen bonds       : bond        0.03604 (  453)
  hydrogen bonds       : angle       4.65716 ( 1299)
  metal coordination   : bond        0.00203 (    4)
  metal coordination   : angle       2.16096 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 MET cc_start: 0.8629 (mpp) cc_final: 0.8329 (mpp)
REVERT: A  236 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8282 (mpp)
REVERT: A  297 MET cc_start: 0.8671 (tpp) cc_final: 0.8385 (tpp)
REVERT: A  476 MET cc_start: 0.8220 (mtp) cc_final: 0.7636 (mtm)
REVERT: A  582 MET cc_start: 0.8827 (mtm) cc_final: 0.8555 (mtt)
REVERT: B   51 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8474 (tt)
REVERT: L  176 LYS cc_start: 0.8138 (mppt) cc_final: 0.7561 (tptp)
REVERT: L  300 PHE cc_start: 0.7229 (p90) cc_final: 0.6794 (p90)
REVERT: L  366 PHE cc_start: 0.8486 (p90) cc_final: 0.8159 (p90)
  outliers start: 19
  outliers final: 13
  residues processed: 156
  average time/residue: 0.1047
  time to fit residues: 22.7458
Evaluate side-chains
  146 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  615 LYS
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain L residue  221 THR
Chi-restraints excluded: chain L residue  298 ASP
Chi-restraints excluded: chain R residue   24 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 86 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 43 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 87 optimal weight:    0.2980
   chunk 57 optimal weight:    6.9990
   chunk 107 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 474 HIS
A 547 HIS
** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.100672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.069372 restraints weight = 31575.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.070598 restraints weight = 17067.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.071331 restraints weight = 11366.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.071802 restraints weight = 9109.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.072364 restraints weight = 8126.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9401  Z= 0.128
  Angle     :  0.637   9.363  12710  Z= 0.314
  Chirality :  0.044   0.283   1435
  Planarity :  0.004   0.058   1615
  Dihedral  :  4.294  19.612   1224
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.26 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.26), residues: 1128
  helix:  1.19 (0.22), residues: 553
  sheet: -1.00 (0.61), residues: 81
  loop : -0.48 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  63 
 TYR   0.015   0.001   TYR A 477 
 PHE   0.018   0.001   PHE L 289 
 TRP   0.008   0.001   TRP R  35 
 HIS   0.003   0.001   HIS L 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9397)
  covalent geometry    : angle       0.63495 (12704)
  hydrogen bonds       : bond        0.03655 (  453)
  hydrogen bonds       : angle       4.68850 ( 1299)
  metal coordination   : bond        0.00216 (    4)
  metal coordination   : angle       2.15795 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8285 (mpp)
REVERT: A  297 MET cc_start: 0.8724 (tpp) cc_final: 0.8447 (tpp)
REVERT: A  582 MET cc_start: 0.8829 (mtm) cc_final: 0.8598 (mtt)
REVERT: L  176 LYS cc_start: 0.8080 (mppt) cc_final: 0.7535 (tptp)
REVERT: L  300 PHE cc_start: 0.7289 (p90) cc_final: 0.6911 (p90)
REVERT: L  366 PHE cc_start: 0.8480 (p90) cc_final: 0.8183 (p90)
  outliers start: 20
  outliers final: 15
  residues processed: 144
  average time/residue: 0.0956
  time to fit residues: 19.4344
Evaluate side-chains
  151 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  615 LYS
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain L residue  221 THR
Chi-restraints excluded: chain L residue  298 ASP
Chi-restraints excluded: chain R residue   24 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0980
   chunk 73 optimal weight:   10.0000
   chunk 78 optimal weight:    0.6980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 313 GLN
A 474 HIS
A 547 HIS
A 600 GLN
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.099231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.068319 restraints weight = 31694.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.069628 restraints weight = 17427.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.070383 restraints weight = 11277.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.070749 restraints weight = 8814.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.071080 restraints weight = 7890.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9401  Z= 0.155
  Angle     :  0.663  10.687  12710  Z= 0.330
  Chirality :  0.044   0.283   1435
  Planarity :  0.004   0.056   1615
  Dihedral  :  4.398  20.256   1224
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.87 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.26), residues: 1128
  helix:  1.14 (0.22), residues: 551
  sheet: -1.07 (0.61), residues: 81
  loop : -0.52 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  63 
 TYR   0.016   0.002   TYR A 477 
 PHE   0.022   0.001   PHE A 543 
 TRP   0.011   0.001   TRP A  14 
 HIS   0.006   0.001   HIS A 474 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9397)
  covalent geometry    : angle       0.66135 (12704)
  hydrogen bonds       : bond        0.03830 (  453)
  hydrogen bonds       : angle       4.76143 ( 1299)
  metal coordination   : bond        0.00282 (    4)
  metal coordination   : angle       2.37106 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8251 (mpp)
REVERT: A  278 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8075 (mm)
REVERT: A  297 MET cc_start: 0.8722 (tpp) cc_final: 0.8421 (tpt)
REVERT: A  582 MET cc_start: 0.8827 (mtm) cc_final: 0.8579 (mtt)
REVERT: B   51 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8489 (tt)
REVERT: L  176 LYS cc_start: 0.8200 (mppt) cc_final: 0.7592 (tptp)
REVERT: L  300 PHE cc_start: 0.7290 (p90) cc_final: 0.6882 (p90)
REVERT: L  366 PHE cc_start: 0.8518 (p90) cc_final: 0.8206 (p90)
  outliers start: 23
  outliers final: 18
  residues processed: 144
  average time/residue: 0.0945
  time to fit residues: 19.3585
Evaluate side-chains
  153 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  615 LYS
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain L residue  221 THR
Chi-restraints excluded: chain L residue  222 LEU
Chi-restraints excluded: chain L residue  298 ASP
Chi-restraints excluded: chain L residue  345 THR
Chi-restraints excluded: chain R residue   24 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0770
   chunk 105 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 83 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0870
   chunk 95 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
A 547 HIS
A 600 GLN
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.101724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.069795 restraints weight = 31639.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.070467 restraints weight = 17334.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.071543 restraints weight = 11366.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.071919 restraints weight = 9114.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.072535 restraints weight = 8212.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9401  Z= 0.119
  Angle     :  0.669  11.093  12710  Z= 0.329
  Chirality :  0.044   0.286   1435
  Planarity :  0.004   0.058   1615
  Dihedral  :  4.368  21.347   1224
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.64 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.26), residues: 1128
  helix:  1.21 (0.23), residues: 553
  sheet: -1.00 (0.62), residues: 81
  loop : -0.57 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  63 
 TYR   0.019   0.001   TYR A 477 
 PHE   0.017   0.001   PHE L 289 
 TRP   0.007   0.001   TRP R  35 
 HIS   0.004   0.001   HIS L 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9397)
  covalent geometry    : angle       0.66768 (12704)
  hydrogen bonds       : bond        0.03594 (  453)
  hydrogen bonds       : angle       4.71844 ( 1299)
  metal coordination   : bond        0.00206 (    4)
  metal coordination   : angle       2.17255 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9347 (mm)
REVERT: A  236 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8089 (mpp)
REVERT: A  278 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8151 (mm)
REVERT: A  297 MET cc_start: 0.8709 (tpp) cc_final: 0.8434 (mmp)
REVERT: A  476 MET cc_start: 0.8312 (mtp) cc_final: 0.7737 (mtm)
REVERT: A  582 MET cc_start: 0.8901 (mtm) cc_final: 0.8670 (mtt)
REVERT: A  642 MET cc_start: 0.8068 (mpp) cc_final: 0.7773 (mmm)
REVERT: B   51 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8405 (tt)
REVERT: L  176 LYS cc_start: 0.8047 (mppt) cc_final: 0.7527 (tptp)
REVERT: L  300 PHE cc_start: 0.7260 (p90) cc_final: 0.6895 (p90)
REVERT: L  366 PHE cc_start: 0.8391 (p90) cc_final: 0.8147 (p90)
  outliers start: 21
  outliers final: 13
  residues processed: 150
  average time/residue: 0.0813
  time to fit residues: 17.4504
Evaluate side-chains
  150 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  615 LYS
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain L residue  221 THR
Chi-restraints excluded: chain L residue  298 ASP
Chi-restraints excluded: chain L residue  345 THR
Chi-restraints excluded: chain R residue   24 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0770
   chunk 21 optimal weight:    0.5980
   chunk 108 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 12 optimal weight:    8.9990
   chunk 105 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 547 HIS
A 600 GLN
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.101016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.070372 restraints weight = 31618.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.071563 restraints weight = 16727.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.072235 restraints weight = 11239.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.073123 restraints weight = 8918.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.073230 restraints weight = 7548.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9401  Z= 0.129
  Angle     :  0.682  10.909  12710  Z= 0.339
  Chirality :  0.045   0.286   1435
  Planarity :  0.004   0.057   1615
  Dihedral  :  4.383  21.428   1224
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.93 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.26), residues: 1128
  helix:  1.22 (0.23), residues: 553
  sheet: -0.78 (0.58), residues: 91
  loop : -0.55 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  63 
 TYR   0.019   0.001   TYR A 477 
 PHE   0.020   0.001   PHE A 543 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.003   0.001   HIS L 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9397)
  covalent geometry    : angle       0.68143 (12704)
  hydrogen bonds       : bond        0.03701 (  453)
  hydrogen bonds       : angle       4.70110 ( 1299)
  metal coordination   : bond        0.00221 (    4)
  metal coordination   : angle       1.86600 (    6)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8094 (mpp)
REVERT: A  278 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8155 (mm)
REVERT: A  285 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8043 (tp)
REVERT: A  297 MET cc_start: 0.8679 (tpp) cc_final: 0.8432 (mmp)
REVERT: A  476 MET cc_start: 0.8305 (mtp) cc_final: 0.7755 (mtm)
REVERT: A  566 MET cc_start: -0.1507 (OUTLIER) cc_final: -0.1932 (mmp)
REVERT: A  582 MET cc_start: 0.8854 (mtm) cc_final: 0.8608 (mtt)
REVERT: A  642 MET cc_start: 0.8013 (mpp) cc_final: 0.7716 (mmm)
REVERT: B   51 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8408 (tt)
REVERT: L  176 LYS cc_start: 0.8177 (mppt) cc_final: 0.7581 (tptp)
REVERT: L  300 PHE cc_start: 0.7238 (p90) cc_final: 0.6816 (p90)
REVERT: L  366 PHE cc_start: 0.8396 (p90) cc_final: 0.8115 (p90)
REVERT: L  370 ILE cc_start: 0.7869 (mp) cc_final: 0.7427 (tp)
  outliers start: 21
  outliers final: 14
  residues processed: 148
  average time/residue: 0.0888
  time to fit residues: 18.5537
Evaluate side-chains
  153 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  492 ASN
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  615 LYS
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain L residue  221 THR
Chi-restraints excluded: chain L residue  298 ASP
Chi-restraints excluded: chain L residue  345 THR
Chi-restraints excluded: chain R residue   24 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 35 optimal weight:    0.0170
   chunk 59 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   chunk 105 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0050
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.4832

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

Flipped N/Q/H residues before XYZ refinement:
A 547 HIS
A 600 GLN
** B  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.101679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.071031 restraints weight = 31123.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.072069 restraints weight = 16276.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.072840 restraints weight = 10626.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.073466 restraints weight = 8397.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.073733 restraints weight = 7215.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9401  Z= 0.124
  Angle     :  0.692  10.441  12710  Z= 0.341
  Chirality :  0.044   0.268   1435
  Planarity :  0.004   0.086   1615
  Dihedral  :  4.377  20.943   1224
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.31 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.26), residues: 1128
  helix:  1.21 (0.23), residues: 551
  sheet: -0.93 (0.62), residues: 81
  loop : -0.60 (0.30), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 290 
 TYR   0.018   0.001   TYR A 477 
 PHE   0.019   0.001   PHE L 289 
 TRP   0.008   0.001   TRP R  35 
 HIS   0.003   0.001   HIS L 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9397)
  covalent geometry    : angle       0.69062 (12704)
  hydrogen bonds       : bond        0.03659 (  453)
  hydrogen bonds       : angle       4.70417 ( 1299)
  metal coordination   : bond        0.00186 (    4)
  metal coordination   : angle       1.92210 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2553.72 seconds
wall clock time: 44 minutes 29.93 seconds (2669.93 seconds total)