Starting phenix.real_space_refine
on Wed May 14 04:31:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bw3_44947/05_2025/9bw3_44947.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bw3_44947/05_2025/9bw3_44947.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bw3_44947/05_2025/9bw3_44947.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bw3_44947/05_2025/9bw3_44947.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bw3_44947/05_2025/9bw3_44947.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bw3_44947/05_2025/9bw3_44947.cif"
  }
  resolution = 2.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.127
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: 6
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     Mg      2      5.21       5
     S      60      5.16       5
     C    7264      2.51       5
     N    1888      2.21       5
     O    2214      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11440
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5554
          Classifications: {'peptide': 683}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665}
    Chain: "B"
      Number of atoms: 5554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5554
          Classifications: {'peptide': 683}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665}
    Chain: "C"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 105
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
    Chain: "D"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 105
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
    Chain: "A"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 61
          Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 61
          Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 7.13, per 1000 atoms: 0.62
  Number of scatterers: 11440
  At special positions: 0
  Unit cell: (90.958, 81.76, 132.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      60     16.00
     P      12     15.00
     Mg      2     11.99
     O    2214      8.00
     N    1888      7.00
     C    7264      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.99
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2652

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 10 sheets defined
      53.7% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
    Processing helix  chain 'A' and resid 27 through 41
      removed outlier: 3.554A  pdb=" N   GLU A  31 " --> pdb=" O   ASP A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 61
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 4.075A  pdb=" N   LEU A  69 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 87
      removed outlier: 4.057A  pdb=" N   LYS A  87 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 104
      removed outlier: 3.705A  pdb=" N   ALA A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 133 through 146
    Processing helix  chain 'A' and resid 152 through 159
    Processing helix  chain 'A' and resid 178 through 195
    Processing helix  chain 'A' and resid 222 through 237
      removed outlier: 3.873A  pdb=" N   VAL A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
      removed outlier: 3.793A  pdb=" N   GLN A 242 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 264
    Processing helix  chain 'A' and resid 285 through 294
      removed outlier: 3.639A  pdb=" N   VAL A 289 " --> pdb=" O   PRO A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 311
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 318 through 329
      removed outlier: 6.056A  pdb=" N   ASP A 324 " --> pdb=" O   ASN A 320 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   LYS A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 354
    Processing helix  chain 'A' and resid 361 through 366
    Processing helix  chain 'A' and resid 416 through 423
    Processing helix  chain 'A' and resid 424 through 442
    Processing helix  chain 'A' and resid 448 through 459
    Processing helix  chain 'A' and resid 467 through 474
    Processing helix  chain 'A' and resid 481 through 511
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 528 through 534
    Processing helix  chain 'A' and resid 540 through 547
      removed outlier: 3.520A  pdb=" N   PHE A 547 " --> pdb=" O   ILE A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 569
    Processing helix  chain 'A' and resid 583 through 589
      removed outlier: 4.274A  pdb=" N   VAL A 587 " --> pdb=" O   SER A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 632
    Processing helix  chain 'A' and resid 633 through 646
    Processing helix  chain 'A' and resid 663 through 677
    Processing helix  chain 'B' and resid 7 through 15
    Processing helix  chain 'B' and resid 27 through 41
      removed outlier: 3.548A  pdb=" N   GLU B  31 " --> pdb=" O   ASP B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 61
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 3.950A  pdb=" N   LEU B  69 " --> pdb=" O   GLU B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 87
      removed outlier: 3.960A  pdb=" N   LYS B  87 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 104
      removed outlier: 3.721A  pdb=" N   ALA B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 133 through 146
    Processing helix  chain 'B' and resid 152 through 159
    Processing helix  chain 'B' and resid 178 through 195
    Processing helix  chain 'B' and resid 222 through 237
      removed outlier: 3.779A  pdb=" N   VAL B 226 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 242
    Processing helix  chain 'B' and resid 257 through 264
    Processing helix  chain 'B' and resid 285 through 295
      removed outlier: 3.573A  pdb=" N   VAL B 289 " --> pdb=" O   PRO B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 311
    Processing helix  chain 'B' and resid 313 through 317
    Processing helix  chain 'B' and resid 318 through 329
      removed outlier: 5.841A  pdb=" N   ASP B 324 " --> pdb=" O   ASN B 320 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   LYS B 325 " --> pdb=" O   GLU B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 354
    Processing helix  chain 'B' and resid 361 through 367
      removed outlier: 4.174A  pdb=" N   VAL B 367 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 423
    Processing helix  chain 'B' and resid 424 through 443
    Processing helix  chain 'B' and resid 448 through 459
    Processing helix  chain 'B' and resid 467 through 474
    Processing helix  chain 'B' and resid 481 through 511
    Processing helix  chain 'B' and resid 520 through 525
    Processing helix  chain 'B' and resid 528 through 534
    Processing helix  chain 'B' and resid 540 through 547
      removed outlier: 3.566A  pdb=" N   PHE B 547 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 569
    Processing helix  chain 'B' and resid 583 through 589
      removed outlier: 4.403A  pdb=" N   VAL B 587 " --> pdb=" O   SER B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 632
    Processing helix  chain 'B' and resid 633 through 646
    Processing helix  chain 'B' and resid 663 through 677
    Processing helix  chain 'C' and resid 316 through 321
    Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151
      removed outlier: 6.889A  pdb=" N   GLY A 462 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   ASN A 410 " --> pdb=" O   GLY A 462 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   GLY A 464 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   GLY A 412 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   MET A 466 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   LEU A 414 " --> pdb=" O   MET A 466 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151
      removed outlier: 3.736A  pdb=" N   CYS A 409 " --> pdb=" O   CYS A 170 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   CYS A 170 " --> pdb=" O   CYS A 409 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301
    Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606
    Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
      removed outlier: 5.890A  pdb=" N   ASN B 410 " --> pdb=" O   GLY B 462 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   GLY B 464 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   GLY B 412 " --> pdb=" O   GLY B 464 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   MET B 466 " --> pdb=" O   GLY B 412 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   LEU B 414 " --> pdb=" O   MET B 466 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408
      removed outlier: 6.456A  pdb=" N   GLY B 247 " --> pdb=" O   SER B 279 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   GLY B 281 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ALA B 249 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   VAL B 283 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   LEU B 251 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301
    Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606
    Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659

    540 hydrogen bonds defined for protein.
    1554 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: 3.40

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3676
        1.34 -     1.46: 2718
        1.46 -     1.58: 5162
        1.58 -     1.69: 20
        1.69 -     1.81: 112
  Bond restraints: 11688
  Sorted by residual:
  bond pdb=" CA  MET A 240 "
       pdb=" CB  MET A 240 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.013 1.69e-02 3.50e+03 6.03e-01
  bond pdb=" C3' ATP B 803 "
       pdb=" C4' ATP B 803 "
    ideal  model  delta    sigma   weight residual
    1.526  1.519  0.007 1.10e-02 8.26e+03 4.62e-01
  bond pdb=" C3' ATP A 803 "
       pdb=" C4' ATP A 803 "
    ideal  model  delta    sigma   weight residual
    1.526  1.520  0.006 1.10e-02 8.26e+03 3.39e-01
  bond pdb=" C2' ATP A 803 "
       pdb=" C3' ATP A 803 "
    ideal  model  delta    sigma   weight residual
    1.531  1.524  0.007 1.20e-02 6.94e+03 3.14e-01
  bond pdb=" CA  MET A 240 "
       pdb=" C   MET A 240 "
    ideal  model  delta    sigma   weight residual
    1.523  1.531 -0.007 1.34e-02 5.57e+03 3.02e-01
  ... (remaining 11683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 15468
        1.19 -     2.38: 234
        2.38 -     3.57: 55
        3.57 -     4.76: 5
        4.76 -     5.95: 12
  Bond angle restraints: 15774
  Sorted by residual:
  angle pdb=" C3' ATP B 803 "
        pdb=" C4' ATP B 803 "
        pdb=" O4' ATP B 803 "
      ideal   model   delta    sigma   weight residual
     105.22  101.89    3.33 1.30e+00 5.94e-01 6.60e+00
  angle pdb=" N   ASP D 317 "
        pdb=" CA  ASP D 317 "
        pdb=" CB  ASP D 317 "
      ideal   model   delta    sigma   weight residual
     113.65  110.21    3.44 1.47e+00 4.63e-01 5.48e+00
  angle pdb=" C3' ATP A 803 "
        pdb=" C4' ATP A 803 "
        pdb=" C5' ATP A 803 "
      ideal   model   delta    sigma   weight residual
     115.19  111.22    3.97 1.76e+00 3.23e-01 5.09e+00
  angle pdb=" C3' ATP B 803 "
        pdb=" C4' ATP B 803 "
        pdb=" C5' ATP B 803 "
      ideal   model   delta    sigma   weight residual
     115.19  111.33    3.86 1.76e+00 3.23e-01 4.81e+00
  angle pdb=" C2' ATP B 803 "
        pdb=" C3' ATP B 803 "
        pdb=" O3' ATP B 803 "
      ideal   model   delta    sigma   weight residual
     111.83  106.03    5.80 2.67e+00 1.40e-01 4.73e+00
  ... (remaining 15769 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.31: 6763
       34.31 -    68.63: 272
       68.63 -   102.94: 35
      102.94 -   137.25: 0
      137.25 -   171.56: 2
  Dihedral angle restraints: 7072
    sinusoidal: 2948
      harmonic: 4124
  Sorted by residual:
  dihedral pdb=" C2  TTP A 801 "
           pdb=" C1' TTP A 801 "
           pdb=" N1  TTP A 801 "
           pdb=" O4' TTP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  130.12  171.56     1      2.00e+01 2.50e-03 4.77e+01
  dihedral pdb=" C2  TTP B 801 "
           pdb=" C1' TTP B 801 "
           pdb=" N1  TTP B 801 "
           pdb=" O4' TTP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  135.73  165.95     1      2.00e+01 2.50e-03 4.73e+01
  dihedral pdb=" C5' TTP B 801 "
           pdb=" O5' TTP B 801 "
           pdb=" PA  TTP B 801 "
           pdb=" O3A TTP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.97 -105.64  -74.39     1      2.00e+01 2.50e-03 1.75e+01
  ... (remaining 7069 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1471
       0.056 -    0.112: 183
       0.112 -    0.169: 18
       0.169 -    0.225: 0
       0.225 -    0.281: 6
  Chirality restraints: 1678
  Sorted by residual:
  chirality pdb=" C2' ATP A 803 "
            pdb=" C1' ATP A 803 "
            pdb=" C3' ATP A 803 "
            pdb=" O2' ATP A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.96    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" C2' ATP B 803 "
            pdb=" C1' ATP B 803 "
            pdb=" C3' ATP B 803 "
            pdb=" O2' ATP B 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.96    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" C3' ATP B 803 "
            pdb=" C2' ATP B 803 "
            pdb=" C4' ATP B 803 "
            pdb=" O3' ATP B 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.91    0.28 2.00e-01 2.50e+01 1.93e+00
  ... (remaining 1675 not shown)

  Planarity restraints: 2012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B   6 "    0.036 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO B   7 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B   7 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B   7 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  37 "   -0.007 2.00e-02 2.50e+03   1.43e-02 2.05e+00
        pdb=" C   PHE B  37 "    0.025 2.00e-02 2.50e+03
        pdb=" O   PHE B  37 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL B  38 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  37 "   -0.007 2.00e-02 2.50e+03   1.33e-02 1.77e+00
        pdb=" C   PHE A  37 "    0.023 2.00e-02 2.50e+03
        pdb=" O   PHE A  37 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL A  38 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2009 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 112
        2.51 -     3.11: 8797
        3.11 -     3.71: 19496
        3.71 -     4.30: 30010
        4.30 -     4.90: 47556
  Nonbonded interactions: 105971
  Sorted by model distance:
  nonbonded pdb=" O1B TTP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.919 2.170
  nonbonded pdb=" O2A TTP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.928 2.170
  nonbonded pdb=" O   PRO B 616 "
            pdb=" OH  TYR B 626 "
     model   vdw
     1.993 3.040
  nonbonded pdb=" OG1 THR A 663 "
            pdb=" OE2 GLU C 313 "
     model   vdw
     2.018 3.040
  nonbonded pdb=" OH  TYR B  64 "
            pdb=" OE2 GLU B 116 "
     model   vdw
     2.021 3.040
  ... (remaining 105966 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.43 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     27.510
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:10.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
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      :  0.008   0.834  11689  Z= 0.777
  Angle     :  0.423   5.947  15774  Z= 0.233
  Chirality :  0.041   0.281   1678
  Planarity :  0.003   0.055   2012
  Dihedral  : 17.839 171.565   4420
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 22.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 18.10 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.22), residues: 1382
  helix:  1.67 (0.20), residues: 668
  sheet:  0.46 (0.39), residues: 146
  loop :  0.54 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A   9 
 HIS   0.003   0.001   HIS A 568 
 PHE   0.015   0.001   PHE A 487 
 TYR   0.010   0.001   TYR B 101 
 ARG   0.003   0.000   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14600 (  538)
  hydrogen bonds       : angle       6.27045 ( 1554)
  covalent geometry    : bond        0.00192 (11688)
  covalent geometry    : angle       0.42284 (15774)
  Misc. bond           : bond        0.83368 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 1.166 
Fit side-chains
REVERT: A  315 ASP cc_start: 0.8093 (p0) cc_final: 0.7834 (p0)
  outliers start: 10
  outliers final: 7
  residues processed: 167
  average time/residue: 1.3229
  time to fit residues: 238.6057
Evaluate side-chains
  158 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 151
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  581 THR
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  352 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0870
   chunk 55 optimal weight:    6.9990
   chunk 108 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 125 optimal weight:    3.9990
   overall best weight:    1.5564

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
A  34 HIS
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  14 ASN
B  34 HIS
B 320 ASN
** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.155942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.125798 restraints weight = 10920.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.41
r_work: 0.3332 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.0942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11689  Z= 0.202
  Angle     :  0.559   5.584  15774  Z= 0.306
  Chirality :  0.044   0.169   1678
  Planarity :  0.004   0.049   2012
  Dihedral  : 10.729 175.717   1634
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.10 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.22), residues: 1382
  helix:  1.30 (0.20), residues: 662
  sheet:  0.45 (0.42), residues: 126
  loop :  0.45 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A   9 
 HIS   0.005   0.001   HIS B 372 
 PHE   0.022   0.002   PHE A 100 
 TYR   0.016   0.002   TYR A 606 
 ARG   0.007   0.001   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04566 (  538)
  hydrogen bonds       : angle       5.53621 ( 1554)
  covalent geometry    : bond        0.00459 (11688)
  covalent geometry    : angle       0.55869 (15774)
  Misc. bond           : bond        0.00135 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 169
  time to evaluate  : 1.361 
Fit side-chains
REVERT: A  209 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8226 (ttpt)
REVERT: A  294 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7678 (mt-10)
REVERT: A  336 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8479 (ttmt)
REVERT: A  348 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7925 (ttp)
REVERT: B   52 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7508 (tmtm)
  outliers start: 31
  outliers final: 19
  residues processed: 187
  average time/residue: 1.4170
  time to fit residues: 285.8901
Evaluate side-chains
  181 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  312 GLN
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain A residue  634 MET
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   10 ILE
Chi-restraints excluded: chain B residue   52 LYS
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  584 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 127 optimal weight:    0.7980
   chunk 70 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 115 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  44 ASN
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
B 109 ASN
B 320 ASN
B 668 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.156485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.125423 restraints weight = 11151.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 1.49
r_work: 0.3335 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11689  Z= 0.131
  Angle     :  0.488   5.848  15774  Z= 0.268
  Chirality :  0.041   0.140   1678
  Planarity :  0.003   0.046   2012
  Dihedral  : 10.266 172.106   1632
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.58 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.22), residues: 1382
  helix:  1.37 (0.20), residues: 664
  sheet:  0.30 (0.42), residues: 126
  loop :  0.46 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.018   0.002   PHE B 261 
 TYR   0.012   0.001   TYR B 574 
 ARG   0.005   0.000   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03731 (  538)
  hydrogen bonds       : angle       5.21412 ( 1554)
  covalent geometry    : bond        0.00288 (11688)
  covalent geometry    : angle       0.48837 (15774)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 1.413 
Fit side-chains
REVERT: A   61 ASN cc_start: 0.7739 (m110) cc_final: 0.7228 (m-40)
REVERT: A   66 GLU cc_start: 0.7236 (tp30) cc_final: 0.6903 (tp30)
REVERT: A  209 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8224 (ttpt)
REVERT: A  294 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7586 (mt-10)
REVERT: A  659 LYS cc_start: 0.7422 (mttt) cc_final: 0.6918 (mmpt)
REVERT: B   52 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7519 (tmtm)
REVERT: B  190 MET cc_start: 0.8853 (mtm) cc_final: 0.8621 (mtt)
REVERT: C  316 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7287 (ptpp)
  outliers start: 28
  outliers final: 14
  residues processed: 192
  average time/residue: 1.3681
  time to fit residues: 282.7302
Evaluate side-chains
  175 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  312 GLN
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   52 LYS
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  599 GLU
Chi-restraints excluded: chain C residue  316 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 109 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0070
   chunk 43 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  44 ASN
A 232 ASN
A 568 HIS
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
B 320 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.157849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.127802 restraints weight = 11069.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.42
r_work: 0.3354 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11689  Z= 0.158
  Angle     :  0.510   5.527  15774  Z= 0.279
  Chirality :  0.042   0.138   1678
  Planarity :  0.003   0.040   2012
  Dihedral  : 10.284 174.307   1626
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.99 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.22), residues: 1382
  helix:  1.30 (0.20), residues: 664
  sheet:  0.13 (0.41), residues: 134
  loop :  0.45 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A   9 
 HIS   0.005   0.001   HIS B 372 
 PHE   0.020   0.002   PHE B 261 
 TYR   0.018   0.002   TYR A  57 
 ARG   0.006   0.001   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03906 (  538)
  hydrogen bonds       : angle       5.24661 ( 1554)
  covalent geometry    : bond        0.00355 (11688)
  covalent geometry    : angle       0.50956 (15774)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 1.202 
Fit side-chains
REVERT: A   61 ASN cc_start: 0.7742 (m110) cc_final: 0.7228 (m-40)
REVERT: A   66 GLU cc_start: 0.7213 (tp30) cc_final: 0.6859 (tp30)
REVERT: A  209 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8202 (ttpt)
REVERT: A  256 ARG cc_start: 0.8443 (tmm160) cc_final: 0.8226 (ttp80)
REVERT: A  294 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7538 (mt-10)
REVERT: A  336 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8393 (ttmt)
REVERT: A  348 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7724 (ttp)
REVERT: A  659 LYS cc_start: 0.7543 (mttt) cc_final: 0.6972 (mmpt)
REVERT: B   52 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7562 (tmtm)
REVERT: B  658 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8321 (mt)
  outliers start: 34
  outliers final: 15
  residues processed: 186
  average time/residue: 1.3550
  time to fit residues: 271.1538
Evaluate side-chains
  178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  312 GLN
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue   52 LYS
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  599 GLU
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 113 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 120 optimal weight:    0.5980
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  44 ASN
A 232 ASN
A 568 HIS
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
B 320 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.155368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.125329 restraints weight = 11011.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.40
r_work: 0.3320 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11689  Z= 0.237
  Angle     :  0.575   6.907  15774  Z= 0.314
  Chirality :  0.045   0.159   1678
  Planarity :  0.004   0.046   2012
  Dihedral  : 10.656 175.730   1626
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.99 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.22), residues: 1382
  helix:  1.08 (0.19), residues: 660
  sheet:  0.10 (0.42), residues: 130
  loop :  0.33 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 558 
 HIS   0.006   0.001   HIS B 372 
 PHE   0.023   0.003   PHE B 261 
 TYR   0.017   0.002   TYR B 498 
 ARG   0.006   0.001   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04459 (  538)
  hydrogen bonds       : angle       5.46542 ( 1554)
  covalent geometry    : bond        0.00543 (11688)
  covalent geometry    : angle       0.57544 (15774)
  Misc. bond           : bond        0.00066 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 161
  time to evaluate  : 1.289 
Fit side-chains
REVERT: A   66 GLU cc_start: 0.7320 (tp30) cc_final: 0.6931 (tp30)
REVERT: A  294 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7550 (mt-10)
REVERT: A  315 ASP cc_start: 0.8217 (p0) cc_final: 0.7981 (p0)
REVERT: A  317 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8238 (mtt)
REVERT: A  336 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8470 (ttmt)
REVERT: A  348 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7997 (ttp)
REVERT: B   52 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7597 (tmtm)
REVERT: B   60 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6552 (mm-30)
REVERT: B  267 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6383 (tp)
REVERT: B  658 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8276 (mt)
REVERT: B  665 ARG cc_start: 0.8295 (tmt170) cc_final: 0.8091 (tmt170)
  outliers start: 32
  outliers final: 15
  residues processed: 180
  average time/residue: 1.3949
  time to fit residues: 269.5441
Evaluate side-chains
  180 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  312 GLN
Chi-restraints excluded: chain A residue  317 MET
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  584 ILE
Chi-restraints excluded: chain B residue   52 LYS
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  352 GLU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 131 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   chunk 119 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 46 optimal weight:    0.4980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  44 ASN
A 232 ASN
A 568 HIS
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
B 320 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.158475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.128622 restraints weight = 11192.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.43
r_work: 0.3370 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11689  Z= 0.128
  Angle     :  0.485   7.436  15774  Z= 0.265
  Chirality :  0.041   0.135   1678
  Planarity :  0.003   0.040   2012
  Dihedral  : 10.181 171.990   1626
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.64 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.22), residues: 1382
  helix:  1.28 (0.20), residues: 662
  sheet: -0.05 (0.42), residues: 134
  loop :  0.38 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.018   0.002   PHE B 261 
 TYR   0.015   0.001   TYR A  57 
 ARG   0.007   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03612 (  538)
  hydrogen bonds       : angle       5.14401 ( 1554)
  covalent geometry    : bond        0.00282 (11688)
  covalent geometry    : angle       0.48475 (15774)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 171
  time to evaluate  : 1.528 
Fit side-chains
REVERT: A   66 GLU cc_start: 0.7287 (tp30) cc_final: 0.6941 (tp30)
REVERT: A  294 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7559 (mt-10)
REVERT: A  315 ASP cc_start: 0.8144 (p0) cc_final: 0.7895 (p0)
REVERT: A  336 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8391 (ttmt)
REVERT: A  348 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7698 (ttp)
REVERT: A  402 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7985 (mp0)
REVERT: A  604 ARG cc_start: 0.7805 (mmt-90) cc_final: 0.7587 (mmt-90)
REVERT: A  659 LYS cc_start: 0.7400 (mttt) cc_final: 0.6941 (mmpt)
REVERT: B   52 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7681 (tmtm)
REVERT: B   60 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6587 (mm-30)
REVERT: B  267 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6454 (tp)
REVERT: B  658 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8293 (mt)
REVERT: B  665 ARG cc_start: 0.8299 (tmt170) cc_final: 0.8091 (tmt170)
  outliers start: 30
  outliers final: 13
  residues processed: 188
  average time/residue: 1.4257
  time to fit residues: 288.4585
Evaluate side-chains
  180 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   52 LYS
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  604 ARG
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 29 optimal weight:    6.9990
   chunk 108 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  44 ASN
A 232 ASN
A 568 HIS
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
B 320 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.157302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.127218 restraints weight = 11143.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.42
r_work: 0.3344 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11689  Z= 0.172
  Angle     :  0.522   7.378  15774  Z= 0.284
  Chirality :  0.042   0.141   1678
  Planarity :  0.003   0.041   2012
  Dihedral  : 10.247 175.048   1623
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.29 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.22), residues: 1382
  helix:  1.20 (0.20), residues: 662
  sheet: -0.12 (0.42), residues: 134
  loop :  0.32 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A   9 
 HIS   0.005   0.001   HIS B 372 
 PHE   0.020   0.002   PHE A  74 
 TYR   0.014   0.002   TYR A 574 
 ARG   0.006   0.001   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03961 (  538)
  hydrogen bonds       : angle       5.24892 ( 1554)
  covalent geometry    : bond        0.00390 (11688)
  covalent geometry    : angle       0.52164 (15774)
  Misc. bond           : bond        0.00025 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 1.204 
Fit side-chains
REVERT: A   66 GLU cc_start: 0.7308 (tp30) cc_final: 0.6964 (tp30)
REVERT: A  256 ARG cc_start: 0.8560 (tmt170) cc_final: 0.8275 (ttp80)
REVERT: A  315 ASP cc_start: 0.8153 (p0) cc_final: 0.7895 (p0)
REVERT: A  336 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8481 (ttmt)
REVERT: A  348 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7823 (ttp)
REVERT: A  402 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7983 (mp0)
REVERT: B   52 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7615 (tmtm)
REVERT: B  267 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6458 (tp)
REVERT: B  384 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7456 (pm20)
REVERT: B  658 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8284 (mt)
  outliers start: 28
  outliers final: 13
  residues processed: 177
  average time/residue: 1.3721
  time to fit residues: 261.1055
Evaluate side-chains
  177 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   52 LYS
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  604 ARG
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain C residue  316 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 127 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  44 ASN
A 232 ASN
A 568 HIS
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
B 320 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.158558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.128728 restraints weight = 11084.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.42
r_work: 0.3367 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3253
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3253
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11689  Z= 0.136
  Angle     :  0.492   6.524  15774  Z= 0.268
  Chirality :  0.041   0.135   1678
  Planarity :  0.003   0.040   2012
  Dihedral  : 10.048 172.592   1623
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.37 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.22), residues: 1382
  helix:  1.30 (0.20), residues: 662
  sheet: -0.14 (0.42), residues: 134
  loop :  0.33 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.018   0.002   PHE A  74 
 TYR   0.011   0.001   TYR B 574 
 ARG   0.010   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03622 (  538)
  hydrogen bonds       : angle       5.12547 ( 1554)
  covalent geometry    : bond        0.00302 (11688)
  covalent geometry    : angle       0.49194 (15774)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 1.449 
Fit side-chains
REVERT: A   66 GLU cc_start: 0.7274 (tp30) cc_final: 0.6942 (tp30)
REVERT: A  131 ASN cc_start: 0.8032 (t0) cc_final: 0.7735 (t0)
REVERT: A  256 ARG cc_start: 0.8558 (tmt170) cc_final: 0.8263 (ttp80)
REVERT: A  294 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7400 (mt-10)
REVERT: A  336 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8428 (ttmt)
REVERT: A  348 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7713 (ttp)
REVERT: A  402 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8010 (mp0)
REVERT: A  659 LYS cc_start: 0.7362 (mttt) cc_final: 0.6929 (mmpt)
REVERT: B   52 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7579 (tmtm)
REVERT: B   61 ASN cc_start: 0.7694 (m-40) cc_final: 0.7428 (m110)
REVERT: B  267 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6432 (tp)
REVERT: B  658 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8292 (mt)
  outliers start: 29
  outliers final: 14
  residues processed: 181
  average time/residue: 1.3612
  time to fit residues: 265.0792
Evaluate side-chains
  183 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   52 LYS
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  604 ARG
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain C residue  316 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 98 optimal weight:    0.0970
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  44 ASN
A 232 ASN
A 568 HIS
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.158843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.129376 restraints weight = 11082.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.40
r_work: 0.3371 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3256
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3256
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11689  Z= 0.136
  Angle     :  0.495   8.140  15774  Z= 0.269
  Chirality :  0.041   0.137   1678
  Planarity :  0.003   0.039   2012
  Dihedral  : 10.002 171.834   1623
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.61 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.22), residues: 1382
  helix:  1.31 (0.20), residues: 662
  sheet: -0.17 (0.42), residues: 134
  loop :  0.33 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.019   0.002   PHE A  74 
 TYR   0.012   0.001   TYR A 612 
 ARG   0.008   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03619 (  538)
  hydrogen bonds       : angle       5.10411 ( 1554)
  covalent geometry    : bond        0.00303 (11688)
  covalent geometry    : angle       0.49502 (15774)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 163
  time to evaluate  : 1.301 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.6535 (pt0) cc_final: 0.5788 (tp30)
REVERT: A   66 GLU cc_start: 0.7274 (tp30) cc_final: 0.6946 (tp30)
REVERT: A  294 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7404 (mt-10)
REVERT: A  336 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8429 (ttmt)
REVERT: A  348 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7710 (ttp)
REVERT: A  402 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7988 (mp0)
REVERT: A  659 LYS cc_start: 0.7411 (mttt) cc_final: 0.6905 (mmpt)
REVERT: B   52 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7628 (tmtm)
REVERT: B   61 ASN cc_start: 0.7677 (m-40) cc_final: 0.7425 (m110)
REVERT: B  267 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6451 (tp)
REVERT: B  539 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7874 (mmtm)
REVERT: B  658 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8289 (mt)
  outliers start: 29
  outliers final: 15
  residues processed: 179
  average time/residue: 1.3933
  time to fit residues: 268.1153
Evaluate side-chains
  179 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 158
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain B residue   52 LYS
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  604 ARG
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain C residue  316 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 129 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 120 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 123 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  44 ASN
A 232 ASN
A 568 HIS
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
B 320 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.158921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.129586 restraints weight = 11107.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.40
r_work: 0.3378 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11689  Z= 0.131
  Angle     :  0.492   7.244  15774  Z= 0.268
  Chirality :  0.041   0.135   1678
  Planarity :  0.003   0.047   2012
  Dihedral  :  9.939 170.580   1623
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.34 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.22), residues: 1382
  helix:  1.33 (0.20), residues: 662
  sheet: -0.21 (0.42), residues: 134
  loop :  0.34 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 
 PHE   0.020   0.002   PHE A  74 
 TYR   0.018   0.001   TYR B  57 
 ARG   0.011   0.001   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  538)
  hydrogen bonds       : angle       5.07362 ( 1554)
  covalent geometry    : bond        0.00291 (11688)
  covalent geometry    : angle       0.49192 (15774)
  Misc. bond           : bond        0.00013 (    1)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 1.196 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.6490 (pt0) cc_final: 0.5825 (tp30)
REVERT: A   66 GLU cc_start: 0.7294 (tp30) cc_final: 0.6973 (tp30)
REVERT: A  294 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7412 (mt-10)
REVERT: A  336 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8430 (ttmt)
REVERT: A  348 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7700 (ttp)
REVERT: A  402 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7990 (mp0)
REVERT: A  659 LYS cc_start: 0.7440 (mttt) cc_final: 0.6971 (mmpt)
REVERT: B   52 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7685 (tmtm)
REVERT: B   60 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6606 (mm-30)
REVERT: B   61 ASN cc_start: 0.7692 (m-40) cc_final: 0.7429 (m110)
REVERT: B  267 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6465 (tp)
REVERT: B  658 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8241 (mt)
  outliers start: 22
  outliers final: 15
  residues processed: 180
  average time/residue: 1.3674
  time to fit residues: 264.8146
Evaluate side-chains
  182 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  460 SER
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain B residue   52 LYS
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  604 ARG
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain C residue  316 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 126 optimal weight:    0.6980
   chunk 65 optimal weight:    0.3980
   chunk 2 optimal weight:    0.5980
   chunk 6 optimal weight:    0.2980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A  44 ASN
A 232 ASN
A 568 HIS
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.158581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.128076 restraints weight = 11078.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.49
r_work: 0.3372 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11689  Z= 0.110
  Angle     :  0.473   8.179  15774  Z= 0.257
  Chirality :  0.040   0.134   1678
  Planarity :  0.003   0.042   2012
  Dihedral  :  9.613 166.243   1623
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 18.59 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.22), residues: 1382
  helix:  1.42 (0.20), residues: 664
  sheet: -0.27 (0.42), residues: 134
  loop :  0.39 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A   9 
 HIS   0.003   0.001   HIS B 372 
 PHE   0.019   0.001   PHE A  74 
 TYR   0.011   0.001   TYR A 612 
 ARG   0.011   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03291 (  538)
  hydrogen bonds       : angle       4.94778 ( 1554)
  covalent geometry    : bond        0.00241 (11688)
  covalent geometry    : angle       0.47321 (15774)
  Misc. bond           : bond        0.00009 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9069.67 seconds
wall clock time: 157 minutes 7.19 seconds (9427.19 seconds total)