Starting phenix.real_space_refine
on Wed Sep 17 05:16:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xmf_38475/09_2025/8xmf_38475.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xmf_38475/09_2025/8xmf_38475.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xmf_38475/09_2025/8xmf_38475.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xmf_38475/09_2025/8xmf_38475.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xmf_38475/09_2025/8xmf_38475.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xmf_38475/09_2025/8xmf_38475.map"
  }
  resolution = 3.64
  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=  -0.002 sd=   0.060
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      8      6.06       5
     S      52      5.16       5
     C    3245      2.51       5
     N     780      2.21       5
     O     844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 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: 4929
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2365
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 61
    Chain: "A"
      Number of atoms: 2357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2357
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 71
    Chain: "B"
      Number of atoms: 121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 121
          Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 10
    Chain: "A"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 86
          Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 10

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2274  SG  CYS B 433      47.132  34.125  96.780  1.00159.45           S
  ATOM   2359  SG  CYS B 446      45.358  32.849  87.669  1.00120.18           S
  ATOM   2365  SG  CYS B 447      45.777  37.314  87.705  1.00125.67           S
  ATOM   4652  SG  CYS A 437      23.534  28.522  91.663  1.00150.23           S
  ATOM   2298  SG  CYS B 437      53.483  28.164  92.832  1.00147.75           S
  ATOM   4628  SG  CYS A 433      29.856  22.059  96.573  1.00150.75           S
  ATOM   4716  SG  CYS A 446      31.375  22.860  86.211  1.00121.94           S
  ATOM   4722  SG  CYS A 447      30.698  18.796  88.022  1.00131.94           S

  Time building chain proxies: 1.66, per 1000 atoms: 0.34
  Number of scatterers: 4929
  At special positions: 0
  Unit cell: (77.376, 56.576, 121.472, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      8     29.99
     S      52     16.00
     O     844      8.00
     N     780      7.00
     C    3245      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 276 " - pdb=" SG  CYS A 282 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 211.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS A 408 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A 413 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS B 437 "
      pdb="  ZN A 602 "
        pdb="ZN    ZN A 602 " - pdb=" ND1 HIS A 387 "
        pdb="ZN    ZN A 602 " - pdb=" NE2 HIS A 370 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS A 433 "
      pdb="  ZN A 603 "
        pdb="ZN    ZN A 603 " - pdb=" NE2 HIS A 373 "
        pdb="ZN    ZN A 603 " - pdb=" SG  CYS A 447 "
        pdb="ZN    ZN A 603 " - pdb=" SG  CYS A 446 "
      pdb="  ZN A 604 "
        pdb="ZN    ZN A 604 " - pdb=" NE2 HIS A  43 "
        pdb="ZN    ZN A 604 " - pdb=" NE2 HIS A 251 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 433 "
        pdb="ZN    ZN B 601 " - pdb=" NE2 HIS B 370 "
        pdb="ZN    ZN B 601 " - pdb=" ND1 HIS B 387 "
      pdb="  ZN B 602 "
        pdb="ZN    ZN B 602 " - pdb=" NE2 HIS B 373 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 447 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 446 "
      pdb="  ZN B 603 "
        pdb="ZN    ZN B 603 " - pdb=" NE2 HIS B 251 "
        pdb="ZN    ZN B 603 " - pdb=" NE2 HIS B  43 "
      pdb="  ZN B 604 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS A 437 "
        pdb="ZN    ZN B 604 " - pdb=" ND1 HIS B 408 "
        pdb="ZN    ZN B 604 " - pdb=" ND1 HIS B 413 "


  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1208

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 3 sheets defined
      63.7% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'B' and resid 11 through 33
      removed outlier: 4.145A  pdb=" N   LEU B  17 " --> pdb=" O   CYS B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 62
    Processing helix  chain 'B' and resid 76 through 106
    Processing helix  chain 'B' and resid 112 through 133
      removed outlier: 3.507A  pdb=" N   VAL B 116 " --> pdb=" O   GLN B 112 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   CYS B 132 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU B 133 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 273
    Processing helix  chain 'B' and resid 291 through 298
      removed outlier: 4.161A  pdb=" N   VAL B 295 " --> pdb=" O   CYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 344
      removed outlier: 4.095A  pdb=" N   VAL B 323 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      Proline residue:  B 334  - end of helix
    Processing helix  chain 'B' and resid 352 through 362
    Processing helix  chain 'B' and resid 399 through 410
      removed outlier: 3.658A  pdb=" N   HIS B 410 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 33
      removed outlier: 3.842A  pdb=" N   LEU A  17 " --> pdb=" O   CYS A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 63
      removed outlier: 4.131A  pdb=" N   ARG A  63 " --> pdb=" O   ARG A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 75
      No H-bonds generated for 'chain 'A' and resid 73 through 75'
    Processing helix  chain 'A' and resid 76 through 106
    Processing helix  chain 'A' and resid 112 through 133
    Processing helix  chain 'A' and resid 245 through 273
    Processing helix  chain 'A' and resid 291 through 298
    Processing helix  chain 'A' and resid 315 through 344
      Proline residue:  A 334  - end of helix
    Processing helix  chain 'A' and resid 352 through 362
    Processing helix  chain 'A' and resid 392 through 394
      No H-bonds generated for 'chain 'A' and resid 392 through 394'
    Processing helix  chain 'A' and resid 395 through 410
      removed outlier: 3.666A  pdb=" N   VAL A 399 " --> pdb=" O   SER A 395 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   HIS A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 444
    Processing sheet with id=AA1, first strand: chain 'B' and resid 370 through 378
      removed outlier: 5.483A  pdb=" N   GLU B 371 " --> pdb=" O   HIS B 387 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   HIS B 387 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ARG B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   GLN B 418 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ALA B 386 " --> pdb=" O   GLN B 418 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 376
      removed outlier: 6.518A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   LYS A 389 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   GLU A 371 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   HIS A 387 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 414 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 376
      removed outlier: 6.518A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   LYS A 389 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   GLU A 371 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   HIS A 387 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   GLN A 418 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA A 386 " --> pdb=" O   GLN A 418 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   GLU A 420 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ILE A 388 " --> pdb=" O   GLU A 420 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    954 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: 0.74

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 833
        1.33 -     1.45: 1184
        1.45 -     1.57: 2937
        1.57 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 5026
  Sorted by residual:
  bond pdb=" CA  GLU A 420 "
       pdb=" C   GLU A 420 "
    ideal  model  delta    sigma   weight residual
    1.525  1.475  0.050 1.29e-02 6.01e+03 1.52e+01
  bond pdb=" CA  GLU A 420 "
       pdb=" CB  GLU A 420 "
    ideal  model  delta    sigma   weight residual
    1.525  1.481  0.044 1.29e-02 6.01e+03 1.19e+01
  bond pdb=" CAX Y01 A 606 "
       pdb=" OAF Y01 A 606 "
    ideal  model  delta    sigma   weight residual
    1.247  1.308 -0.061 2.00e-02 2.50e+03 9.39e+00
  bond pdb=" CAX Y01 B 606 "
       pdb=" OAH Y01 B 606 "
    ideal  model  delta    sigma   weight residual
    1.248  1.309 -0.061 2.00e-02 2.50e+03 9.18e+00
  bond pdb=" CAX Y01 B 607 "
       pdb=" OAH Y01 B 607 "
    ideal  model  delta    sigma   weight residual
    1.248  1.308 -0.060 2.00e-02 2.50e+03 9.10e+00
  ... (remaining 5021 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 6589
        1.53 -     3.06: 219
        3.06 -     4.58: 50
        4.58 -     6.11: 11
        6.11 -     7.64: 4
  Bond angle restraints: 6873
  Sorted by residual:
  angle pdb=" N   LYS A 444 "
        pdb=" CA  LYS A 444 "
        pdb=" C   LYS A 444 "
      ideal   model   delta    sigma   weight residual
     111.07  107.17    3.90 1.07e+00 8.73e-01 1.33e+01
  angle pdb=" N   GLU B 420 "
        pdb=" CA  GLU B 420 "
        pdb=" C   GLU B 420 "
      ideal   model   delta    sigma   weight residual
     107.69  100.85    6.84 2.01e+00 2.48e-01 1.16e+01
  angle pdb=" CA  PRO A 290 "
        pdb=" C   PRO A 290 "
        pdb=" O   PRO A 290 "
      ideal   model   delta    sigma   weight residual
     121.34  118.15    3.19 1.14e+00 7.69e-01 7.84e+00
  angle pdb=" N   GLN B 440 "
        pdb=" CA  GLN B 440 "
        pdb=" C   GLN B 440 "
      ideal   model   delta    sigma   weight residual
     108.76  113.41   -4.65 1.69e+00 3.50e-01 7.56e+00
  angle pdb=" C   PHE A 287 "
        pdb=" CA  PHE A 287 "
        pdb=" CB  PHE A 287 "
      ideal   model   delta    sigma   weight residual
     108.76  112.27   -3.51 1.37e+00 5.33e-01 6.55e+00
  ... (remaining 6868 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.86: 2995
       26.86 -    53.71: 160
       53.71 -    80.57: 15
       80.57 -   107.43: 19
      107.43 -   134.28: 15
  Dihedral angle restraints: 3204
    sinusoidal: 1357
      harmonic: 1847
  Sorted by residual:
  dihedral pdb=" CB  CYS B 276 "
           pdb=" SG  CYS B 276 "
           pdb=" SG  CYS B 282 "
           pdb=" CB  CYS B 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.81   55.19     1      1.00e+01 1.00e-02 4.12e+01
  dihedral pdb=" CB  CYS A 276 "
           pdb=" SG  CYS A 276 "
           pdb=" SG  CYS A 282 "
           pdb=" CB  CYS A 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.38   45.62     1      1.00e+01 1.00e-02 2.89e+01
  dihedral pdb=" OAJ AV0 B 605 "
           pdb=" CBN AV0 B 605 "
           pdb=" CCD AV0 B 605 "
           pdb=" OBZ AV0 B 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.90  -69.38  134.28     1      3.00e+01 1.11e-03 1.81e+01
  ... (remaining 3201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 731
       0.052 -    0.104: 126
       0.104 -    0.156: 15
       0.156 -    0.208: 2
       0.208 -    0.260: 3
  Chirality restraints: 877
  Sorted by residual:
  chirality pdb=" CA  GLU B 371 "
            pdb=" N   GLU B 371 "
            pdb=" C   GLU B 371 "
            pdb=" CB  GLU B 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  CYS A 291 "
            pdb=" N   CYS A 291 "
            pdb=" C   CYS A 291 "
            pdb=" CB  CYS A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CCV AV0 A 605 "
            pdb=" CCR AV0 A 605 "
            pdb=" CCT AV0 A 605 "
            pdb=" OAU AV0 A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.50    0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 874 not shown)

  Planarity restraints: 814
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 284 "   -0.047 5.00e-02 4.00e+02   7.23e-02 8.36e+00
        pdb=" N   PRO A 285 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 285 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 285 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  43 "   -0.020 2.00e-02 2.50e+03   1.79e-02 4.81e+00
        pdb=" CG  HIS B  43 "    0.025 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  43 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  43 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  43 "    0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  43 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 289 "    0.034 5.00e-02 4.00e+02   5.23e-02 4.37e+00
        pdb=" N   PRO A 290 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 290 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 290 "    0.029 5.00e-02 4.00e+02
  ... (remaining 811 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 47
        2.57 -     3.15: 4237
        3.15 -     3.73: 7826
        3.73 -     4.32: 9483
        4.32 -     4.90: 15716
  Nonbonded interactions: 37309
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  47 "
            pdb="ZN    ZN B 603 "
     model   vdw
     1.982 2.230
  nonbonded pdb=" OD1 ASP B 255 "
            pdb="ZN    ZN B 603 "
     model   vdw
     1.986 2.230
  nonbonded pdb=" OD2 ASP A  47 "
            pdb="ZN    ZN A 604 "
     model   vdw
     1.987 2.230
  nonbonded pdb=" OE2 GLU A 371 "
            pdb="ZN    ZN A 603 "
     model   vdw
     1.992 2.230
  nonbonded pdb=" OD2 ASP A 255 "
            pdb="ZN    ZN A 604 "
     model   vdw
     1.992 2.230
  ... (remaining 37304 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 11 through 280 or (resid 281 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 282 through 442 or (resid 443 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 444 through 606))
  selection = (chain 'B' and (resid 11 through 305 or (resid 306 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 307 through 349 or (resid 350 through 352 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 353 through 360 \ 
 or (resid 361 and (name N or name CA or name C or name O or name CB )) or resid \ 
 362 through 606))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.200
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.860
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
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      :  0.015   0.283   5050  Z= 0.546
  Angle     :  0.693   7.640   6877  Z= 0.365
  Chirality :  0.042   0.260    877
  Planarity :  0.005   0.072    814
  Dihedral  : 19.980 134.282   1990
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.35 (0.35), residues: 620
  helix:  2.05 (0.26), residues: 378
  sheet:  0.32 (0.89), residues: 42
  loop : -1.29 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  30 
 TYR   0.009   0.001   TYR B 396 
 PHE   0.026   0.001   PHE B 294 
 TRP   0.010   0.001   TRP A 312 
 HIS   0.015   0.001   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 5026)
  covalent geometry    : angle       0.69236 ( 6873)
  SS BOND              : bond        0.00619 (    2)
  SS BOND              : angle       1.12772 (    4)
  hydrogen bonds       : bond        0.08781 (  316)
  hydrogen bonds       : angle       4.22056 (  954)
  metal coordination   : bond        0.21669 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.184 
Fit side-chains
REVERT: B   99 GLU cc_start: 0.8673 (tp30) cc_final: 0.8400 (tp30)
REVERT: B  103 ARG cc_start: 0.9084 (ttm-80) cc_final: 0.8783 (ttm110)
REVERT: B  355 ASN cc_start: 0.8121 (t0) cc_final: 0.7864 (t0)
REVERT: B  360 LEU cc_start: 0.9467 (mm) cc_final: 0.9245 (mm)
REVERT: B  408 HIS cc_start: 0.9138 (t70) cc_final: 0.8489 (t70)
REVERT: A   41 SER cc_start: 0.9339 (p) cc_final: 0.8660 (p)
REVERT: A   59 ARG cc_start: 0.8428 (ttm170) cc_final: 0.7961 (tpm170)
REVERT: A   99 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7773 (mm-30)
REVERT: A  294 PHE cc_start: 0.8003 (t80) cc_final: 0.7623 (t80)
REVERT: A  380 SER cc_start: 0.9221 (t) cc_final: 0.8934 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0719
  time to fit residues: 18.2746
Evaluate side-chains
  168 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 61 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 413 HIS
A 108 HIS
A 127 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.178748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.129199 restraints weight = 7371.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.134597 restraints weight = 4075.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.137978 restraints weight = 2898.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.140140 restraints weight = 2383.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.141217 restraints weight = 2120.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.028   1.961   5050  Z= 0.933
  Angle     :  0.667   8.349   6877  Z= 0.321
  Chirality :  0.044   0.364    877
  Planarity :  0.004   0.046    814
  Dihedral  : 13.302 102.409   1019
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 20.72 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.48 (0.35), residues: 620
  helix:  2.10 (0.26), residues: 378
  sheet: -0.00 (0.88), residues: 42
  loop : -1.04 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 246 
 TYR   0.014   0.001   TYR A 270 
 PHE   0.016   0.001   PHE B  19 
 TRP   0.014   0.001   TRP B 273 
 HIS   0.004   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 5026)
  covalent geometry    : angle       0.66722 ( 6873)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       0.45789 (    4)
  hydrogen bonds       : bond        0.03779 (  316)
  hydrogen bonds       : angle       3.76797 (  954)
  metal coordination   : bond        0.41816 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 189
  time to evaluate  : 0.221 
Fit side-chains
REVERT: B  246 ARG cc_start: 0.6731 (mmm160) cc_final: 0.6415 (mmm160)
REVERT: B  320 LEU cc_start: 0.9148 (tp) cc_final: 0.8886 (tp)
REVERT: B  355 ASN cc_start: 0.8166 (t0) cc_final: 0.7912 (t0)
REVERT: A   59 ARG cc_start: 0.8469 (ttm170) cc_final: 0.7950 (tpm170)
REVERT: A   99 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8184 (tp30)
REVERT: A  294 PHE cc_start: 0.8135 (t80) cc_final: 0.7641 (t80)
REVERT: A  380 SER cc_start: 0.9272 (t) cc_final: 0.8992 (t)
  outliers start: 19
  outliers final: 16
  residues processed: 191
  average time/residue: 0.0741
  time to fit residues: 18.2052
Evaluate side-chains
  187 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 171
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 56 optimal weight:    0.0370
   chunk 15 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 59 optimal weight:    0.2980
   chunk 37 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 GLN
A 362 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.181699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.132499 restraints weight = 7212.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.137899 restraints weight = 4031.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.141477 restraints weight = 2895.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.143741 restraints weight = 2381.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.144836 restraints weight = 2110.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5050  Z= 0.124
  Angle     :  0.609   8.500   6877  Z= 0.297
  Chirality :  0.040   0.240    877
  Planarity :  0.004   0.033    814
  Dihedral  : 10.125  93.164   1019
  Min Nonbonded Distance : 1.728

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 25.55 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.48 (0.35), residues: 620
  helix:  2.13 (0.26), residues: 378
  sheet: -0.12 (0.90), residues: 42
  loop : -1.06 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 103 
 TYR   0.006   0.001   TYR B 396 
 PHE   0.018   0.001   PHE B 287 
 TRP   0.015   0.001   TRP B 273 
 HIS   0.008   0.001   HIS B 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5026)
  covalent geometry    : angle       0.60868 ( 6873)
  SS BOND              : bond        0.00151 (    2)
  SS BOND              : angle       0.27896 (    4)
  hydrogen bonds       : bond        0.03556 (  316)
  hydrogen bonds       : angle       3.58915 (  954)
  metal coordination   : bond        0.00938 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 184
  time to evaluate  : 0.195 
Fit side-chains
REVERT: B  246 ARG cc_start: 0.6722 (mmm160) cc_final: 0.6474 (mmm160)
REVERT: B  320 LEU cc_start: 0.9034 (tp) cc_final: 0.8771 (tp)
REVERT: B  355 ASN cc_start: 0.8155 (t0) cc_final: 0.7771 (t0)
REVERT: A   59 ARG cc_start: 0.8450 (ttm170) cc_final: 0.7967 (tpm170)
REVERT: A   99 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8163 (tp30)
REVERT: A  103 ARG cc_start: 0.8953 (ttm170) cc_final: 0.8741 (ttm110)
REVERT: A  294 PHE cc_start: 0.8021 (t80) cc_final: 0.7278 (t80)
REVERT: A  324 MET cc_start: 0.8958 (tpp) cc_final: 0.8531 (tpt)
  outliers start: 21
  outliers final: 20
  residues processed: 187
  average time/residue: 0.0711
  time to fit residues: 17.1565
Evaluate side-chains
  192 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 172
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   37 MET
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0370
   chunk 59 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.181663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.131818 restraints weight = 7210.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.137337 restraints weight = 4035.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.140798 restraints weight = 2889.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.142968 restraints weight = 2381.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.144178 restraints weight = 2120.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5050  Z= 0.124
  Angle     :  0.607   8.435   6877  Z= 0.302
  Chirality :  0.039   0.155    877
  Planarity :  0.003   0.032    814
  Dihedral  :  9.141  88.209   1019
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 27.36 %
    Favored  : 67.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.50 (0.35), residues: 620
  helix:  2.15 (0.27), residues: 378
  sheet: -0.19 (0.89), residues: 42
  loop : -1.04 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 103 
 TYR   0.014   0.001   TYR A 396 
 PHE   0.017   0.001   PHE A  19 
 TRP   0.012   0.001   TRP B 273 
 HIS   0.005   0.001   HIS B 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5026)
  covalent geometry    : angle       0.60436 ( 6873)
  SS BOND              : bond        0.00232 (    2)
  SS BOND              : angle       2.54232 (    4)
  hydrogen bonds       : bond        0.03431 (  316)
  hydrogen bonds       : angle       3.55273 (  954)
  metal coordination   : bond        0.00531 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 179
  time to evaluate  : 0.190 
Fit side-chains
REVERT: B  246 ARG cc_start: 0.6762 (mmm160) cc_final: 0.6520 (mmm160)
REVERT: B  320 LEU cc_start: 0.9038 (tp) cc_final: 0.8785 (tp)
REVERT: B  355 ASN cc_start: 0.8060 (t0) cc_final: 0.7767 (t0)
REVERT: B  362 ASN cc_start: 0.8165 (t0) cc_final: 0.7950 (t0)
REVERT: A   59 ARG cc_start: 0.8469 (ttm170) cc_final: 0.7966 (tpm170)
REVERT: A   99 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8263 (tp30)
REVERT: A  103 ARG cc_start: 0.8955 (ttm170) cc_final: 0.8701 (ttm-80)
REVERT: A  294 PHE cc_start: 0.8007 (t80) cc_final: 0.7225 (t80)
  outliers start: 26
  outliers final: 19
  residues processed: 186
  average time/residue: 0.0698
  time to fit residues: 16.9621
Evaluate side-chains
  190 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 171
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  284 ASN
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0370
   chunk 35 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 43 optimal weight:   20.0000
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.182063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.132137 restraints weight = 7364.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.137676 restraints weight = 4092.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.141163 restraints weight = 2926.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.143376 restraints weight = 2405.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.144557 restraints weight = 2138.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5050  Z= 0.121
  Angle     :  0.586   6.391   6877  Z= 0.293
  Chirality :  0.040   0.214    877
  Planarity :  0.003   0.033    814
  Dihedral  :  8.655  85.349   1019
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 27.57 %
    Favored  : 66.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.35), residues: 620
  helix:  2.17 (0.26), residues: 378
  sheet: -0.17 (0.88), residues: 42
  loop : -0.99 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 103 
 TYR   0.013   0.001   TYR A 396 
 PHE   0.016   0.001   PHE A 287 
 TRP   0.013   0.001   TRP B 273 
 HIS   0.003   0.001   HIS B 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5026)
  covalent geometry    : angle       0.58618 ( 6873)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.47364 (    4)
  hydrogen bonds       : bond        0.03360 (  316)
  hydrogen bonds       : angle       3.50483 (  954)
  metal coordination   : bond        0.00372 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 0.133 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.7722 (tpt170) cc_final: 0.7486 (tpt90)
REVERT: B  246 ARG cc_start: 0.6742 (mmm160) cc_final: 0.6536 (mmm160)
REVERT: B  320 LEU cc_start: 0.9028 (tp) cc_final: 0.8772 (tp)
REVERT: B  355 ASN cc_start: 0.8022 (t0) cc_final: 0.7801 (t0)
REVERT: B  404 LYS cc_start: 0.8816 (tptp) cc_final: 0.8307 (tptt)
REVERT: A   59 ARG cc_start: 0.8478 (ttm170) cc_final: 0.7970 (tpm170)
REVERT: A   99 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8226 (tp30)
REVERT: A  103 ARG cc_start: 0.8990 (ttm170) cc_final: 0.8717 (ttm110)
REVERT: A  324 MET cc_start: 0.8947 (tpp) cc_final: 0.8657 (ttt)
  outliers start: 28
  outliers final: 22
  residues processed: 183
  average time/residue: 0.0704
  time to fit residues: 16.7273
Evaluate side-chains
  192 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  284 ASN
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0670
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.3324

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
B 362 ASN
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.178719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.127989 restraints weight = 7296.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.133209 restraints weight = 4170.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.136567 restraints weight = 3030.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.138362 restraints weight = 2510.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.139816 restraints weight = 2260.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5050  Z= 0.166
  Angle     :  0.623   6.420   6877  Z= 0.316
  Chirality :  0.040   0.181    877
  Planarity :  0.003   0.035    814
  Dihedral  :  8.612  86.107   1019
  Min Nonbonded Distance : 1.814

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 28.17 %
    Favored  : 65.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.42 (0.35), residues: 620
  helix:  2.09 (0.26), residues: 378
  sheet: -0.41 (0.87), residues: 42
  loop : -1.04 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 103 
 TYR   0.013   0.001   TYR A 396 
 PHE   0.017   0.001   PHE A  19 
 TRP   0.012   0.001   TRP B 273 
 HIS   0.003   0.001   HIS A 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 5026)
  covalent geometry    : angle       0.62273 ( 6873)
  SS BOND              : bond        0.00585 (    2)
  SS BOND              : angle       0.95972 (    4)
  hydrogen bonds       : bond        0.03646 (  316)
  hydrogen bonds       : angle       3.57613 (  954)
  metal coordination   : bond        0.00395 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 173
  time to evaluate  : 0.258 
Fit side-chains
REVERT: B  246 ARG cc_start: 0.6778 (mmm160) cc_final: 0.6513 (mmm160)
REVERT: B  320 LEU cc_start: 0.9088 (tp) cc_final: 0.8811 (tp)
REVERT: B  355 ASN cc_start: 0.8109 (t0) cc_final: 0.7828 (t0)
REVERT: A   59 ARG cc_start: 0.8487 (ttm170) cc_final: 0.7947 (tpm170)
  outliers start: 33
  outliers final: 28
  residues processed: 181
  average time/residue: 0.0740
  time to fit residues: 17.3627
Evaluate side-chains
  194 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  362 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  284 ASN
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 48 optimal weight:    0.2980
   chunk 14 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0060
   chunk 18 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
B 362 ASN
A  85 ASN
A 284 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.179636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.130235 restraints weight = 7336.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.135564 restraints weight = 4096.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.138894 restraints weight = 2941.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.140996 restraints weight = 2429.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.142167 restraints weight = 2170.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5050  Z= 0.126
  Angle     :  0.607   6.832   6877  Z= 0.309
  Chirality :  0.039   0.150    877
  Planarity :  0.003   0.034    814
  Dihedral  :  8.353  83.266   1019
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 28.97 %
    Favored  : 64.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.47 (0.34), residues: 620
  helix:  2.16 (0.27), residues: 378
  sheet: -0.11 (0.87), residues: 40
  loop : -1.14 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 361 
 TYR   0.011   0.001   TYR A 396 
 PHE   0.015   0.001   PHE B 287 
 TRP   0.016   0.001   TRP B 273 
 HIS   0.003   0.001   HIS B 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5026)
  covalent geometry    : angle       0.60689 ( 6873)
  SS BOND              : bond        0.00293 (    2)
  SS BOND              : angle       0.62367 (    4)
  hydrogen bonds       : bond        0.03485 (  316)
  hydrogen bonds       : angle       3.54497 (  954)
  metal coordination   : bond        0.00285 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 0.204 
Fit side-chains
REVERT: B   99 GLU cc_start: 0.8647 (tp30) cc_final: 0.8392 (tp30)
REVERT: B  102 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: B  246 ARG cc_start: 0.6770 (mmm160) cc_final: 0.6514 (mmm160)
REVERT: B  320 LEU cc_start: 0.9021 (tp) cc_final: 0.8741 (tp)
REVERT: B  355 ASN cc_start: 0.8098 (t0) cc_final: 0.7810 (t0)
REVERT: B  404 LYS cc_start: 0.8837 (tptp) cc_final: 0.8288 (tptt)
REVERT: A   59 ARG cc_start: 0.8485 (ttm170) cc_final: 0.7963 (tpm170)
REVERT: A  103 ARG cc_start: 0.8950 (ttm170) cc_final: 0.8710 (ttm110)
  outliers start: 33
  outliers final: 27
  residues processed: 187
  average time/residue: 0.0723
  time to fit residues: 17.5898
Evaluate side-chains
  196 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  362 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 17 optimal weight:    8.9990
   chunk 58 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0970
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
B 345 GLN
B 362 ASN
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  85 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.179714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.129901 restraints weight = 7283.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.135193 restraints weight = 4072.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.138571 restraints weight = 2938.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.140416 restraints weight = 2432.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.141991 restraints weight = 2180.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5050  Z= 0.135
  Angle     :  0.611   7.154   6877  Z= 0.310
  Chirality :  0.040   0.187    877
  Planarity :  0.003   0.033    814
  Dihedral  :  8.280  81.886   1019
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 30.18 %
    Favored  : 63.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.42 (0.34), residues: 620
  helix:  2.12 (0.26), residues: 378
  sheet: -0.22 (0.86), residues: 40
  loop : -1.14 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 103 
 TYR   0.010   0.001   TYR A 396 
 PHE   0.021   0.001   PHE A  19 
 TRP   0.025   0.002   TRP A 273 
 HIS   0.003   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5026)
  covalent geometry    : angle       0.61111 ( 6873)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.50424 (    4)
  hydrogen bonds       : bond        0.03543 (  316)
  hydrogen bonds       : angle       3.56703 (  954)
  metal coordination   : bond        0.00308 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B  246 ARG cc_start: 0.6766 (mmm160) cc_final: 0.6536 (mmm160)
REVERT: B  320 LEU cc_start: 0.9035 (tp) cc_final: 0.8756 (tp)
REVERT: B  355 ASN cc_start: 0.8089 (t0) cc_final: 0.7808 (t0)
REVERT: B  404 LYS cc_start: 0.8828 (tptp) cc_final: 0.8277 (tptt)
REVERT: A   59 ARG cc_start: 0.8496 (ttm170) cc_final: 0.7956 (tpm170)
REVERT: A  103 ARG cc_start: 0.8976 (ttm170) cc_final: 0.8743 (ttm110)
  outliers start: 30
  outliers final: 26
  residues processed: 170
  average time/residue: 0.0764
  time to fit residues: 16.7118
Evaluate side-chains
  187 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 161
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   44 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  362 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 38 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0060
   chunk 23 optimal weight:    0.9980
   chunk 17 optimal weight:    0.1980
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
B 362 ASN
** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  85 ASN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.179871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.130854 restraints weight = 7318.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.136117 restraints weight = 4090.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.139583 restraints weight = 2949.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.141766 restraints weight = 2427.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.143011 restraints weight = 2159.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5050  Z= 0.124
  Angle     :  0.604   7.368   6877  Z= 0.307
  Chirality :  0.040   0.186    877
  Planarity :  0.003   0.033    814
  Dihedral  :  8.179  81.017   1019
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 30.58 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.39 (0.34), residues: 620
  helix:  2.10 (0.26), residues: 378
  sheet: -0.24 (0.86), residues: 40
  loop : -1.16 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  30 
 TYR   0.010   0.001   TYR A 396 
 PHE   0.016   0.001   PHE B 287 
 TRP   0.019   0.002   TRP A 273 
 HIS   0.003   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5026)
  covalent geometry    : angle       0.60425 ( 6873)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       0.42674 (    4)
  hydrogen bonds       : bond        0.03455 (  316)
  hydrogen bonds       : angle       3.55186 (  954)
  metal coordination   : bond        0.00286 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 167
  time to evaluate  : 0.203 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.8313 (tpt90) cc_final: 0.8091 (tpt90)
REVERT: B  246 ARG cc_start: 0.6745 (mmm160) cc_final: 0.6513 (mmm160)
REVERT: B  320 LEU cc_start: 0.9009 (tp) cc_final: 0.8727 (tp)
REVERT: B  355 ASN cc_start: 0.8068 (t0) cc_final: 0.7787 (t0)
REVERT: B  404 LYS cc_start: 0.8816 (tptp) cc_final: 0.8261 (tptt)
REVERT: A   59 ARG cc_start: 0.8480 (ttm170) cc_final: 0.7957 (tpm170)
REVERT: A  103 ARG cc_start: 0.8971 (ttm170) cc_final: 0.8757 (ttm110)
REVERT: A  324 MET cc_start: 0.8913 (tpp) cc_final: 0.8634 (ttt)
  outliers start: 29
  outliers final: 25
  residues processed: 175
  average time/residue: 0.0713
  time to fit residues: 16.1601
Evaluate side-chains
  189 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  362 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
B 362 ASN
A  85 ASN
A 345 GLN
** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.180286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.130935 restraints weight = 7407.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.136240 restraints weight = 4139.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.139629 restraints weight = 2977.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.141744 restraints weight = 2461.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.142811 restraints weight = 2197.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5050  Z= 0.128
  Angle     :  0.610   7.463   6877  Z= 0.311
  Chirality :  0.040   0.188    877
  Planarity :  0.003   0.033    814
  Dihedral  :  8.126  80.370   1019
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 31.39 %
    Favored  : 62.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.40 (0.34), residues: 620
  helix:  2.14 (0.26), residues: 376
  sheet: -0.24 (0.87), residues: 40
  loop : -1.20 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  30 
 TYR   0.009   0.001   TYR A 396 
 PHE   0.022   0.001   PHE A  19 
 TRP   0.017   0.001   TRP A 273 
 HIS   0.002   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5026)
  covalent geometry    : angle       0.60987 ( 6873)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       0.43181 (    4)
  hydrogen bonds       : bond        0.03456 (  316)
  hydrogen bonds       : angle       3.56711 (  954)
  metal coordination   : bond        0.00286 (   22)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 168
  time to evaluate  : 0.199 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.8344 (tpt90) cc_final: 0.8077 (tpt90)
REVERT: B  320 LEU cc_start: 0.9005 (tp) cc_final: 0.8729 (tp)
REVERT: B  355 ASN cc_start: 0.8068 (t0) cc_final: 0.7788 (t0)
REVERT: B  404 LYS cc_start: 0.8814 (tptp) cc_final: 0.8269 (tptt)
REVERT: A   59 ARG cc_start: 0.8483 (ttm170) cc_final: 0.7948 (tpm170)
REVERT: A  103 ARG cc_start: 0.8974 (ttm170) cc_final: 0.8765 (ttm110)
REVERT: A  324 MET cc_start: 0.8894 (tpp) cc_final: 0.8637 (ttt)
  outliers start: 29
  outliers final: 27
  residues processed: 177
  average time/residue: 0.0762
  time to fit residues: 17.3711
Evaluate side-chains
  192 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  104 PHE
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  362 ASN
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  109 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 37 optimal weight:    0.2980
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 362 ASN
A  85 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.180927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.131757 restraints weight = 7280.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.137040 restraints weight = 4139.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.140441 restraints weight = 2990.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.142288 restraints weight = 2470.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.143772 restraints weight = 2219.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5050  Z= 0.128
  Angle     :  0.617   7.336   6877  Z= 0.312
  Chirality :  0.040   0.174    877
  Planarity :  0.003   0.039    814
  Dihedral  :  8.101  80.169   1019
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 31.59 %
    Favored  : 62.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.38 (0.34), residues: 620
  helix:  2.15 (0.26), residues: 376
  sheet: -0.25 (0.87), residues: 40
  loop : -1.24 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  30 
 TYR   0.008   0.001   TYR A 396 
 PHE   0.016   0.001   PHE B 287 
 TRP   0.028   0.002   TRP A 273 
 HIS   0.005   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5026)
  covalent geometry    : angle       0.61696 ( 6873)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.43024 (    4)
  hydrogen bonds       : bond        0.03434 (  316)
  hydrogen bonds       : angle       3.58011 (  954)
  metal coordination   : bond        0.00287 (   22)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1209.08 seconds
wall clock time: 21 minutes 30.12 seconds (1290.12 seconds total)