Starting phenix.real_space_refine
on Wed Sep 17 21:12:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bw3_44947/09_2025/9bw3_44947.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bw3_44947/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bw3_44947/09_2025/9bw3_44947.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bw3_44947/09_2025/9bw3_44947.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bw3_44947/09_2025/9bw3_44947.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bw3_44947/09_2025/9bw3_44947.map"
  }
  resolution = 2.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.127
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.94, per 1000 atoms: 0.26
  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: 0.84
  Conformation dependent library (CDL) restraints added in 575.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.41
  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: 2.11

  Time building geometry restraints manager: 1.11 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: 0.02
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:             1.510
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.060
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.060
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.003   0.000   ARG A 331 
 TYR   0.010   0.001   TYR B 101 
 PHE   0.015   0.001   PHE A 487 
 TRP   0.007   0.001   TRP A   9 
 HIS   0.003   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 (11688)
  covalent geometry    : angle       0.42284 (15774)
  hydrogen bonds       : bond        0.14600 (  538)
  hydrogen bonds       : angle       6.27045 ( 1554)
  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  : 0.457 
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: 0.6417
  time to fit residues: 115.3469
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  : 0.476 
-------------------------------------------------------------------------------
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 98 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.0050
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    2.8002

-------------------------------------------------------------------------------
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 232 ASN
B  14 ASN
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 = 0.3771 r_free = 0.3771 target = 0.153743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.123469 restraints weight = 11034.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.40
r_work: 0.3298 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.0999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  11689  Z= 0.302
  Angle     :  0.644   6.462  15774  Z= 0.351
  Chirality :  0.048   0.172   1678
  Planarity :  0.005   0.049   2012
  Dihedral  : 11.136 177.020   1634
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.85 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.21), residues: 1382
  helix:  1.04 (0.19), residues: 660
  sheet:  0.32 (0.41), residues: 126
  loop :  0.34 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 331 
 TYR   0.018   0.002   TYR B 574 
 PHE   0.026   0.003   PHE A 100 
 TRP   0.012   0.003   TRP A 558 
 HIS   0.007   0.002   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 (11688)
  covalent geometry    : angle       0.64410 (15774)
  hydrogen bonds       : bond        0.05162 (  538)
  hydrogen bonds       : angle       5.74489 ( 1554)
  Misc. bond           : bond        0.00133 (    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: 36
    poor density    : 164
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  294 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7631 (mt-10)
REVERT: A  315 ASP cc_start: 0.8256 (p0) cc_final: 0.8047 (p0)
REVERT: A  317 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8642 (mtp)
REVERT: A  336 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8560 (ttmt)
REVERT: B   52 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7608 (tmtm)
  outliers start: 36
  outliers final: 18
  residues processed: 186
  average time/residue: 0.6494
  time to fit residues: 129.4601
Evaluate side-chains
  178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 SER
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  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 A residue  599 GLU
Chi-restraints excluded: chain A residue  634 MET
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 129 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 106 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 135 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   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 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 = 0.3788 r_free = 0.3788 target = 0.155701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.125066 restraints weight = 11146.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.47
r_work: 0.3329 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11689  Z= 0.137
  Angle     :  0.499   5.621  15774  Z= 0.274
  Chirality :  0.041   0.152   1678
  Planarity :  0.003   0.045   2012
  Dihedral  : 10.502 172.870   1633
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.67 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.22), residues: 1382
  helix:  1.26 (0.20), residues: 662
  sheet:  0.30 (0.42), residues: 126
  loop :  0.36 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 235 
 TYR   0.012   0.001   TYR B 574 
 PHE   0.019   0.002   PHE A  74 
 TRP   0.009   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11688)
  covalent geometry    : angle       0.49932 (15774)
  hydrogen bonds       : bond        0.03872 (  538)
  hydrogen bonds       : angle       5.29728 ( 1554)
  Misc. bond           : bond        0.00042 (    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
  209 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 176
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A   61 ASN cc_start: 0.7747 (m110) cc_final: 0.7216 (m-40)
REVERT: A   66 GLU cc_start: 0.7179 (tp30) cc_final: 0.6869 (tp30)
REVERT: A  294 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7569 (mt-10)
REVERT: A  659 LYS cc_start: 0.7403 (mttt) cc_final: 0.6896 (mmpt)
REVERT: B   52 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7515 (tmtm)
REVERT: B  267 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.6408 (tp)
REVERT: B  315 ASP cc_start: 0.8019 (p0) cc_final: 0.7763 (p0)
  outliers start: 33
  outliers final: 17
  residues processed: 194
  average time/residue: 0.6405
  time to fit residues: 133.3390
Evaluate side-chains
  177 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 SER
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  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  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  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 C residue  316 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 10 optimal weight:    0.3980
   chunk 87 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 123 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  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 = 0.3826 r_free = 0.3826 target = 0.158681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.129050 restraints weight = 11128.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.41
r_work: 0.3371 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: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1373

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     :  0.483   5.824  15774  Z= 0.264
  Chirality :  0.041   0.136   1678
  Planarity :  0.003   0.044   2012
  Dihedral  : 10.138 170.703   1631
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.23 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.22), residues: 1382
  helix:  1.35 (0.20), residues: 664
  sheet:  0.14 (0.41), residues: 134
  loop :  0.45 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 331 
 TYR   0.019   0.001   TYR A  57 
 PHE   0.018   0.002   PHE B 261 
 TRP   0.010   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (11688)
  covalent geometry    : angle       0.48322 (15774)
  hydrogen bonds       : bond        0.03641 (  538)
  hydrogen bonds       : angle       5.14000 ( 1554)
  Misc. bond           : bond        0.00028 (    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
  202 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 172
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A   61 ASN cc_start: 0.7718 (m110) cc_final: 0.7163 (m-40)
REVERT: A   66 GLU cc_start: 0.7193 (tp30) cc_final: 0.6885 (tp30)
REVERT: A  294 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7551 (mt-10)
REVERT: A  336 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8361 (ttmt)
REVERT: A  599 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8231 (mt-10)
REVERT: A  659 LYS cc_start: 0.7403 (mttt) cc_final: 0.6909 (mmpt)
REVERT: B   52 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7589 (tmtm)
REVERT: B  315 ASP cc_start: 0.8036 (p0) cc_final: 0.7498 (p0)
REVERT: B  658 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8287 (mt)
  outliers start: 30
  outliers final: 12
  residues processed: 190
  average time/residue: 0.6498
  time to fit residues: 132.2523
Evaluate side-chains
  178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
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  336 LYS
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  599 GLU
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  121 ARG
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 67 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 118 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3829 r_free = 0.3829 target = 0.158924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128975 restraints weight = 11026.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.41
r_work: 0.3370 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    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 = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1427

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= 0.135
  Angle     :  0.488   6.775  15774  Z= 0.267
  Chirality :  0.041   0.136   1678
  Planarity :  0.003   0.039   2012
  Dihedral  :  9.994 171.011   1623
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.40 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.22), residues: 1382
  helix:  1.36 (0.20), residues: 664
  sheet:  0.05 (0.42), residues: 134
  loop :  0.45 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 331 
 TYR   0.012   0.001   TYR A 574 
 PHE   0.018   0.002   PHE B 261 
 TRP   0.010   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (11688)
  covalent geometry    : angle       0.48841 (15774)
  hydrogen bonds       : bond        0.03647 (  538)
  hydrogen bonds       : angle       5.12701 ( 1554)
  Misc. bond           : bond        0.00027 (    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
  200 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 168
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A   61 ASN cc_start: 0.7692 (m110) cc_final: 0.7144 (m-40)
REVERT: A   66 GLU cc_start: 0.7247 (tp30) cc_final: 0.6955 (tp30)
REVERT: A  131 ASN cc_start: 0.8021 (t0) cc_final: 0.7706 (t0)
REVERT: A  256 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8232 (ttp80)
REVERT: A  294 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7514 (mt-10)
REVERT: A  336 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8396 (ttmt)
REVERT: A  402 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8003 (mp0)
REVERT: A  599 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8237 (mt-10)
REVERT: A  659 LYS cc_start: 0.7421 (mttt) cc_final: 0.6938 (mmpt)
REVERT: B   52 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7681 (tmtm)
REVERT: B   60 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6634 (mm-30)
REVERT: B  315 ASP cc_start: 0.8060 (p0) cc_final: 0.7843 (p0)
REVERT: B  658 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8284 (mt)
  outliers start: 32
  outliers final: 14
  residues processed: 185
  average time/residue: 0.6396
  time to fit residues: 126.6156
Evaluate side-chains
  182 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 162
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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  256 ARG
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  336 LYS
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  599 GLU
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  121 ARG
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0170
   chunk 125 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 129 optimal weight:    6.9990
   overall best weight:    0.9020

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.158617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.128476 restraints weight = 11189.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.43
r_work: 0.3368 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
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 = 0.20   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: 0.8186
moved from start:          0.1506

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= 0.135
  Angle     :  0.485   5.805  15774  Z= 0.265
  Chirality :  0.041   0.137   1678
  Planarity :  0.003   0.038   2012
  Dihedral  :  9.965 171.161   1623
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.48 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.22), residues: 1382
  helix:  1.39 (0.20), residues: 662
  sheet: -0.04 (0.42), residues: 134
  loop :  0.44 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 235 
 TYR   0.012   0.001   TYR A 574 
 PHE   0.018   0.002   PHE B 261 
 TRP   0.010   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11688)
  covalent geometry    : angle       0.48520 (15774)
  hydrogen bonds       : bond        0.03627 (  538)
  hydrogen bonds       : angle       5.10280 ( 1554)
  Misc. bond           : bond        0.00036 (    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
  202 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 169
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A   61 ASN cc_start: 0.7691 (m110) cc_final: 0.7119 (m-40)
REVERT: A   66 GLU cc_start: 0.7255 (tp30) cc_final: 0.6969 (tp30)
REVERT: A  256 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8225 (ttp80)
REVERT: A  294 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7449 (mt-10)
REVERT: A  315 ASP cc_start: 0.8042 (p0) cc_final: 0.7791 (p0)
REVERT: A  336 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8425 (ttmt)
REVERT: A  348 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7708 (ttp)
REVERT: A  599 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8204 (mt-10)
REVERT: A  659 LYS cc_start: 0.7335 (mttt) cc_final: 0.6863 (mmpt)
REVERT: B   52 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7708 (tmtm)
REVERT: B   60 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6621 (mm-30)
REVERT: B  315 ASP cc_start: 0.8080 (p0) cc_final: 0.7874 (p0)
REVERT: B  658 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8272 (mt)
  outliers start: 33
  outliers final: 15
  residues processed: 186
  average time/residue: 0.6549
  time to fit residues: 130.2584
Evaluate side-chains
  184 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 163
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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  256 ARG
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  384 GLU
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  658 LEU
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  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 107 optimal weight:    4.9990
   chunk 132 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 137 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.155289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.125027 restraints weight = 11043.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.41
r_work: 0.3319 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1399

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= 0.240
  Angle     :  0.578   6.201  15774  Z= 0.315
  Chirality :  0.045   0.162   1678
  Planarity :  0.004   0.045   2012
  Dihedral  : 10.524 175.659   1623
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.48 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.22), residues: 1382
  helix:  1.07 (0.20), residues: 660
  sheet: -0.00 (0.42), residues: 130
  loop :  0.33 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 235 
 TYR   0.018   0.002   TYR B 498 
 PHE   0.023   0.003   PHE B 261 
 TRP   0.009   0.002   TRP A 558 
 HIS   0.006   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 (11688)
  covalent geometry    : angle       0.57793 (15774)
  hydrogen bonds       : bond        0.04444 (  538)
  hydrogen bonds       : angle       5.42468 ( 1554)
  Misc. bond           : bond        0.00069 (    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
  193 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 160
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   66 GLU cc_start: 0.7307 (tp30) cc_final: 0.7001 (tp30)
REVERT: A  256 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8239 (ttp80)
REVERT: A  294 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7465 (mt-10)
REVERT: A  315 ASP cc_start: 0.8193 (p0) cc_final: 0.7880 (p0)
REVERT: A  317 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7658 (mtt)
REVERT: A  336 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8499 (ttmt)
REVERT: A  348 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7937 (ttp)
REVERT: A  402 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7990 (mp0)
REVERT: B   52 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7584 (tmtm)
REVERT: B   60 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6553 (mm-30)
REVERT: B  315 ASP cc_start: 0.8188 (p0) cc_final: 0.7924 (p0)
REVERT: B  384 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.7443 (pm20)
REVERT: B  632 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7962 (mtt)
REVERT: B  658 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8287 (mt)
  outliers start: 33
  outliers final: 16
  residues processed: 177
  average time/residue: 0.6460
  time to fit residues: 122.4365
Evaluate side-chains
  178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
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  256 ARG
Chi-restraints excluded: chain A residue  273 VAL
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  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  584 ILE
Chi-restraints excluded: chain A residue  590 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  121 ARG
Chi-restraints excluded: chain B residue  216 VAL
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  632 MET
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 135 optimal weight:    0.2980
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 HIS
B 320 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.158542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.128605 restraints weight = 11092.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.42
r_work: 0.3373 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
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 = 0.15   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 = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3253
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11689  Z= 0.129
  Angle     :  0.488   7.653  15774  Z= 0.267
  Chirality :  0.041   0.136   1678
  Planarity :  0.003   0.041   2012
  Dihedral  : 10.078 171.885   1623
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.13 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.22), residues: 1382
  helix:  1.30 (0.20), residues: 662
  sheet: -0.11 (0.42), residues: 134
  loop :  0.37 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 235 
 TYR   0.019   0.001   TYR B  57 
 PHE   0.018   0.002   PHE B 261 
 TRP   0.010   0.002   TRP A   9 
 HIS   0.004   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (11688)
  covalent geometry    : angle       0.48833 (15774)
  hydrogen bonds       : bond        0.03598 (  538)
  hydrogen bonds       : angle       5.12118 ( 1554)
  Misc. bond           : bond        0.00028 (    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
  188 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 161
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A   66 GLU cc_start: 0.7277 (tp30) cc_final: 0.6997 (tp30)
REVERT: A  256 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8237 (ttp80)
REVERT: A  294 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7377 (mt-10)
REVERT: A  315 ASP cc_start: 0.8081 (p0) cc_final: 0.7808 (p0)
REVERT: A  348 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7689 (ttp)
REVERT: A  402 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7974 (mp0)
REVERT: A  599 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8206 (mt-10)
REVERT: A  659 LYS cc_start: 0.7316 (mttt) cc_final: 0.6898 (mmpt)
REVERT: B   52 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7577 (tmtm)
REVERT: B   60 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6652 (mm-30)
REVERT: B  315 ASP cc_start: 0.8143 (p0) cc_final: 0.7935 (p0)
REVERT: B  632 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8038 (mtt)
REVERT: B  658 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8248 (mt)
  outliers start: 27
  outliers final: 13
  residues processed: 174
  average time/residue: 0.6647
  time to fit residues: 123.6670
Evaluate side-chains
  179 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
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  256 ARG
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  348 MET
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 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  121 ARG
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  632 MET
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 100 optimal weight:    0.5980
   chunk 115 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.157418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.127850 restraints weight = 10985.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.39
r_work: 0.3349 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1501

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= 0.162
  Angle     :  0.519   7.712  15774  Z= 0.282
  Chirality :  0.042   0.141   1678
  Planarity :  0.003   0.045   2012
  Dihedral  : 10.216 174.623   1623
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.29 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.22), residues: 1382
  helix:  1.23 (0.20), residues: 662
  sheet: -0.17 (0.42), residues: 134
  loop :  0.35 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 235 
 TYR   0.014   0.001   TYR A 612 
 PHE   0.019   0.002   PHE B 261 
 TRP   0.010   0.002   TRP A   9 
 HIS   0.005   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (11688)
  covalent geometry    : angle       0.51879 (15774)
  hydrogen bonds       : bond        0.03870 (  538)
  hydrogen bonds       : angle       5.19617 ( 1554)
  Misc. bond           : bond        0.00031 (    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
  194 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 162
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A   66 GLU cc_start: 0.7281 (tp30) cc_final: 0.6995 (tp30)
REVERT: A  256 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8260 (ttp80)
REVERT: A  294 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7379 (mt-10)
REVERT: A  315 ASP cc_start: 0.8117 (p0) cc_final: 0.7823 (p0)
REVERT: A  317 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7605 (mtt)
REVERT: A  348 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7743 (ttp)
REVERT: A  402 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7973 (mp0)
REVERT: A  599 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8183 (mt-10)
REVERT: B   52 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7587 (tmtm)
REVERT: B   60 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6625 (mm-30)
REVERT: B  267 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6618 (tp)
REVERT: B  315 ASP cc_start: 0.8092 (p0) cc_final: 0.7855 (p0)
REVERT: B  384 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7408 (pm20)
REVERT: B  632 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7989 (mtt)
REVERT: B  658 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8263 (mt)
  outliers start: 32
  outliers final: 15
  residues processed: 178
  average time/residue: 0.6732
  time to fit residues: 128.2648
Evaluate side-chains
  184 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 159
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
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  256 ARG
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  317 MET
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  384 GLU
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  494 MET
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 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  121 ARG
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  632 MET
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 118 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.157561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127911 restraints weight = 11100.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.40
r_work: 0.3356 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3243
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11689  Z= 0.153
  Angle     :  0.510   7.516  15774  Z= 0.278
  Chirality :  0.041   0.138   1678
  Planarity :  0.003   0.041   2012
  Dihedral  : 10.157 174.419   1623
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.22), residues: 1382
  helix:  1.25 (0.20), residues: 662
  sheet: -0.17 (0.42), residues: 134
  loop :  0.35 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 235 
 TYR   0.013   0.001   TYR A 612 
 PHE   0.020   0.002   PHE A  74 
 TRP   0.010   0.002   TRP A   9 
 HIS   0.005   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (11688)
  covalent geometry    : angle       0.51036 (15774)
  hydrogen bonds       : bond        0.03777 (  538)
  hydrogen bonds       : angle       5.17055 ( 1554)
  Misc. bond           : bond        0.00028 (    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
  191 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A   66 GLU cc_start: 0.7272 (tp30) cc_final: 0.6990 (tp30)
REVERT: A  256 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8258 (ttp80)
REVERT: A  294 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7341 (mt-10)
REVERT: A  315 ASP cc_start: 0.8102 (p0) cc_final: 0.7809 (p0)
REVERT: A  317 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7578 (mtt)
REVERT: A  336 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8471 (ttmt)
REVERT: A  348 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7732 (ttp)
REVERT: A  402 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7978 (mp0)
REVERT: A  599 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8168 (mt-10)
REVERT: A  659 LYS cc_start: 0.7393 (mttt) cc_final: 0.6886 (mmpt)
REVERT: B   52 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7589 (tmtm)
REVERT: B   60 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6641 (mm-30)
REVERT: B  267 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6611 (tp)
REVERT: B  315 ASP cc_start: 0.8138 (p0) cc_final: 0.7921 (p0)
REVERT: B  632 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8012 (mtt)
REVERT: B  658 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8273 (mt)
  outliers start: 26
  outliers final: 15
  residues processed: 179
  average time/residue: 0.6511
  time to fit residues: 124.6273
Evaluate side-chains
  186 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
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  256 ARG
Chi-restraints excluded: chain A residue  273 VAL
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  384 GLU
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 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  121 ARG
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  632 MET
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.157577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.127952 restraints weight = 11114.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.40
r_work: 0.3356 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3243
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11689  Z= 0.151
  Angle     :  0.509   7.339  15774  Z= 0.278
  Chirality :  0.041   0.140   1678
  Planarity :  0.003   0.044   2012
  Dihedral  : 10.102 174.124   1623
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.21 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.22), residues: 1382
  helix:  1.26 (0.20), residues: 662
  sheet: -0.19 (0.42), residues: 134
  loop :  0.34 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 235 
 TYR   0.013   0.001   TYR A 612 
 PHE   0.021   0.002   PHE A  74 
 TRP   0.010   0.002   TRP A   9 
 HIS   0.005   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (11688)
  covalent geometry    : angle       0.50949 (15774)
  hydrogen bonds       : bond        0.03766 (  538)
  hydrogen bonds       : angle       5.15623 ( 1554)
  Misc. bond           : bond        0.00021 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4489.40 seconds
wall clock time: 77 minutes 24.68 seconds (4644.68 seconds total)