Starting phenix.real_space_refine
on Fri Aug 22 21:07:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ifk_35419/08_2025/8ifk_35419.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ifk_35419/08_2025/8ifk_35419.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2025/8ifk_35419.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2025/8ifk_35419.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2025/8ifk_35419.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2025/8ifk_35419.cif"
  }
  resolution = 2.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.227
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      41      5.49       5
     Mg      1      5.21       5
     S      21      5.16       5
     C    4808      2.51       5
     N    1280      2.21       5
     O    1481      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7632
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3475
          Classifications: {'peptide': 414}
          Link IDs: {'PTRANS': 14, 'TRANS': 399}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3300
          Classifications: {'peptide': 409}
          Link IDs: {'PTRANS': 24, 'TRANS': 384}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 423
          Classifications: {'RNA': 20}
          Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 1, 'rna3p': 18}
    Chain: "D"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 433
          Classifications: {'DNA': 21}
          Link IDs: {'rna3p': 20}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.63, per 1000 atoms: 0.21
  Number of scatterers: 7632
  At special positions: 0
  Unit cell: (75.9, 86.9, 129.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      21     16.00
     P      41     15.00
     Mg      1     11.99
     O    1481      8.00
     N    1280      7.00
     C    4808      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 188.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 9 sheets defined
      38.5% alpha, 17.9% beta
      17 base pairs and 30 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 28
    Processing helix  chain 'A' and resid 34 through 38
      removed outlier: 3.908A  pdb=" N   PHE A  38 " --> pdb=" O   ASP A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 55
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 4.428A  pdb=" N   LYS A  70 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 89
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 4.034A  pdb=" N   ARG A 114 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 138
    Processing helix  chain 'A' and resid 146 through 158
      removed outlier: 3.665A  pdb=" N   SER A 150 " --> pdb=" O   ASP A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 203
    Processing helix  chain 'A' and resid 227 through 231
      removed outlier: 3.698A  pdb=" N   GLU A 231 " --> pdb=" O   PRO A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.851A  pdb=" N   GLU A 237 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 248
    Processing helix  chain 'A' and resid 257 through 279
      removed outlier: 3.564A  pdb=" N   LYS A 278 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASP A 279 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 302
      No H-bonds generated for 'chain 'A' and resid 300 through 302'
    Processing helix  chain 'A' and resid 353 through 366
    Processing helix  chain 'A' and resid 369 through 384
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 22 through 30
    Processing helix  chain 'B' and resid 46 through 62
      removed outlier: 3.676A  pdb=" N   LYS B  62 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 83
    Processing helix  chain 'B' and resid 87 through 89
      No H-bonds generated for 'chain 'B' and resid 87 through 89'
    Processing helix  chain 'B' and resid 115 through 129
      removed outlier: 4.215A  pdb=" N   ALA B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 214
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 248 through 264
    Processing helix  chain 'B' and resid 331 through 351
    Processing helix  chain 'B' and resid 366 through 375
    Processing helix  chain 'B' and resid 451 through 463
    Processing helix  chain 'B' and resid 477 through 491
    Processing helix  chain 'B' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33
      removed outlier: 5.924A  pdb=" N   ILE A   5 " --> pdb=" O   TRP A  33 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LYS A   4 " --> pdb=" O   LYS A  59 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   LEU A  61 " --> pdb=" O   LYS A   4 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   PHE A   6 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   VAL A  63 " --> pdb=" O   PHE A   6 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   SER A   8 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   ILE A  95 " --> pdb=" O   CYS A  58 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   PHE A  60 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   LEU A  97 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ILE A  62 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 319 through 324
      removed outlier: 4.340A  pdb=" N   TYR B 280 " --> pdb=" O   MET B 303 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   CYS B 279 " --> pdb=" O   PHE B 358 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   HIS B 360 " --> pdb=" O   CYS B 279 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   LEU B 281 " --> pdb=" O   HIS B 360 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   VAL B 357 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   VAL B 386 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   ILE B 359 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE B 388 " --> pdb=" O   ILE B 359 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   ALA B 361 " --> pdb=" O   ILE B 388 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   THR B 387 " --> pdb=" O   ILE B 445 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   ILE B 445 " --> pdb=" O   THR B 387 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   THR B 389 " --> pdb=" O   ILE B 443 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   ILE B 443 " --> pdb=" O   THR B 389 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LYS A 409 " --> pdb=" O   LYS B   2 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   LEU B   4 " --> pdb=" O   LYS A 409 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   PHE A 411 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   TYR B   6 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 314
      removed outlier: 6.574A  pdb=" N   LEU A 402 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210
    Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286
    Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 305
    Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 20
    Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 95
      removed outlier: 6.704A  pdb=" N   SER B  41 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   LYS B  94 " --> pdb=" O   SER B  41 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   VAL B  43 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   GLY B  42 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ILE B 142 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   VAL B  44 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   TRP B 139 " --> pdb=" O   GLN B 222 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   LEU B 224 " --> pdb=" O   TRP B 139 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   VAL B 141 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 425 through 426

    272 hydrogen bonds defined for protein.
    750 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      40 hydrogen bonds
      80 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      30 stacking parallelities
  Total time for adding SS restraints: 1.15

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1143
        1.30 -     1.43: 2327
        1.43 -     1.56: 4319
        1.56 -     1.69: 80
        1.69 -     1.81: 32
  Bond restraints: 7901
  Sorted by residual:
  bond pdb=" C   PRO B 319 "
       pdb=" O   PRO B 319 "
    ideal  model  delta    sigma   weight residual
    1.234  1.178  0.056 1.14e-02 7.69e+03 2.38e+01
  bond pdb=" C   VAL B 278 "
       pdb=" O   VAL B 278 "
    ideal  model  delta    sigma   weight residual
    1.237  1.189  0.048 1.11e-02 8.12e+03 1.86e+01
  bond pdb=" C   GLU B 436 "
       pdb=" O   GLU B 436 "
    ideal  model  delta    sigma   weight residual
    1.242  1.202  0.039 1.00e-02 1.00e+04 1.56e+01
  bond pdb=" C   MET B 435 "
       pdb=" O   MET B 435 "
    ideal  model  delta    sigma   weight residual
    1.234  1.186  0.048 1.23e-02 6.61e+03 1.52e+01
  bond pdb=" C   TYR A 210 "
       pdb=" O   TYR A 210 "
    ideal  model  delta    sigma   weight residual
    1.235  1.194  0.042 1.13e-02 7.83e+03 1.37e+01
  ... (remaining 7896 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 10475
        1.74 -     3.47: 295
        3.47 -     5.21: 57
        5.21 -     6.94: 19
        6.94 -     8.68: 7
  Bond angle restraints: 10853
  Sorted by residual:
  angle pdb=" CA  TYR A 210 "
        pdb=" C   TYR A 210 "
        pdb=" O   TYR A 210 "
      ideal   model   delta    sigma   weight residual
     120.33  113.09    7.24 1.08e+00 8.57e-01 4.49e+01
  angle pdb=" C   ILE A 208 "
        pdb=" N   ARG A 209 "
        pdb=" CA  ARG A 209 "
      ideal   model   delta    sigma   weight residual
     121.24  112.72    8.52 1.44e+00 4.82e-01 3.50e+01
  angle pdb=" C   PRO B 438 "
        pdb=" CA  PRO B 438 "
        pdb=" CB  PRO B 438 "
      ideal   model   delta    sigma   weight residual
     111.21  103.77    7.44 1.33e+00 5.65e-01 3.13e+01
  angle pdb=" C   ARG A  54 "
        pdb=" CA  ARG A  54 "
        pdb=" CB  ARG A  54 "
      ideal   model   delta    sigma   weight residual
     110.90  102.22    8.68 1.58e+00 4.01e-01 3.02e+01
  angle pdb=" CA  LYS B 211 "
        pdb=" C   LYS B 211 "
        pdb=" O   LYS B 211 "
      ideal   model   delta    sigma   weight residual
     120.55  114.74    5.81 1.06e+00 8.90e-01 3.00e+01
  ... (remaining 10848 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 3839
       17.68 -    35.35: 543
       35.35 -    53.03: 205
       53.03 -    70.70: 79
       70.70 -    88.38: 23
  Dihedral angle restraints: 4689
    sinusoidal: 2274
      harmonic: 2415
  Sorted by residual:
  dihedral pdb=" O4'   G C  20 "
           pdb=" C1'   G C  20 "
           pdb=" N9    G C  20 "
           pdb=" C4    G C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -169.38   63.38     1      1.70e+01 3.46e-03 1.83e+01
  dihedral pdb=" C   ARG A 209 "
           pdb=" N   ARG A 209 "
           pdb=" CA  ARG A 209 "
           pdb=" CB  ARG A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.69   -9.91     0      2.50e+00 1.60e-01 1.57e+01
  dihedral pdb=" CA  TRP A 219 "
           pdb=" C   TRP A 219 "
           pdb=" N   GLU A 220 "
           pdb=" CA  GLU A 220 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.50  -17.50     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 4686 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1022
       0.063 -    0.126: 142
       0.126 -    0.189: 18
       0.189 -    0.252: 6
       0.252 -    0.314: 4
  Chirality restraints: 1192
  Sorted by residual:
  chirality pdb=" CA  ILE B 274 "
            pdb=" N   ILE B 274 "
            pdb=" C   ILE B 274 "
            pdb=" CB  ILE B 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.75   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CA  ARG A 209 "
            pdb=" N   ARG A 209 "
            pdb=" C   ARG A 209 "
            pdb=" CB  ARG A 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" CA  CYS A  58 "
            pdb=" N   CYS A  58 "
            pdb=" C   CYS A  58 "
            pdb=" CB  CYS A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 1189 not shown)

  Planarity restraints: 1218
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 437 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   VAL B 437 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   VAL B 437 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PRO B 438 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  49 "    0.015 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   ILE A  49 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ILE A  49 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A  50 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 321 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.21e+00
        pdb=" C   TYR B 321 "    0.046 2.00e-02 2.50e+03
        pdb=" O   TYR B 321 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ASN B 322 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1215 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.38: 36
        2.38 -     3.01: 4009
        3.01 -     3.64: 12781
        3.64 -     4.27: 20625
        4.27 -     4.90: 32431
  Nonbonded interactions: 69882
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 321 "
            pdb=" OD1 ASN B 322 "
     model   vdw
     1.744 3.040
  nonbonded pdb=" O   ILE B 507 "
            pdb="MG    MG B 601 "
     model   vdw
     1.831 2.170
  nonbonded pdb=" OP2   A C   1 "
            pdb="MG    MG B 601 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" ND2 ASN B 468 "
            pdb="MG    MG B 601 "
     model   vdw
     2.020 2.250
  nonbonded pdb=" NH1 ARG B 275 "
            pdb=" OD2 ASP B 458 "
     model   vdw
     2.075 3.120
  ... (remaining 69877 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.420
  Find NCS groups from input model:        0.030
  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:6.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7901  Z= 0.262
  Angle     :  0.729   8.679  10853  Z= 0.451
  Chirality :  0.049   0.314   1192
  Planarity :  0.006   0.076   1218
  Dihedral  : 20.290  88.377   3123
  Min Nonbonded Distance : 1.744

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 24.32 %
    Favored  : 71.33 %
  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: -0.23 (0.28), residues: 803
  helix:  0.58 (0.31), residues: 281
  sheet: -0.37 (0.36), residues: 171
  loop : -0.50 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 250 
 TYR   0.028   0.002   TYR A 210 
 PHE   0.012   0.002   PHE A 343 
 TRP   0.034   0.002   TRP B 320 
 HIS   0.003   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 7901)
  covalent geometry    : angle       0.72914 (10853)
  hydrogen bonds       : bond        0.12223 (  312)
  hydrogen bonds       : angle       5.77242 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6395 (tm-30)
REVERT: B  270 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7832 (ptpp)
  outliers start: 32
  outliers final: 26
  residues processed: 134
  average time/residue: 0.5261
  time to fit residues: 74.3909
Evaluate side-chains
  126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LYS
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   58 CYS
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  211 LYS
Chi-restraints excluded: chain B residue  270 LYS
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  493 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
B 296 ASN
B 322 ASN
B 371 ASN
B 382 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.180737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.153050 restraints weight = 7226.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 1.33
r_work: 0.3754 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.0769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7901  Z= 0.153
  Angle     :  0.565   5.638  10853  Z= 0.305
  Chirality :  0.042   0.159   1192
  Planarity :  0.004   0.048   1218
  Dihedral  : 17.283  80.407   1466
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.28 %
    Favored  : 73.64 %
  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: -0.25 (0.28), residues: 803
  helix:  0.60 (0.30), residues: 291
  sheet: -0.51 (0.37), residues: 165
  loop : -0.52 (0.30), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  71 
 TYR   0.010   0.001   TYR A 330 
 PHE   0.014   0.001   PHE B  78 
 TRP   0.021   0.002   TRP A 219 
 HIS   0.002   0.001   HIS B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7901)
  covalent geometry    : angle       0.56481 (10853)
  hydrogen bonds       : bond        0.04074 (  312)
  hydrogen bonds       : angle       4.97019 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6627 (mptm)
REVERT: A  136 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6944 (mm-30)
REVERT: A  315 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8133 (mppt)
REVERT: A  352 LYS cc_start: 0.7537 (mmtm) cc_final: 0.7281 (mmtt)
REVERT: B  355 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7797 (ttpp)
  outliers start: 30
  outliers final: 10
  residues processed: 134
  average time/residue: 0.5103
  time to fit residues: 72.4877
Evaluate side-chains
  112 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  315 LYS
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  355 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0020
   chunk 78 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9996

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
A 163 GLN
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
B 296 ASN
B 371 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.177320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.148862 restraints weight = 7113.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 1.30
r_work: 0.3702 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3602 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7901  Z= 0.203
  Angle     :  0.586   5.639  10853  Z= 0.317
  Chirality :  0.044   0.157   1192
  Planarity :  0.004   0.041   1218
  Dihedral  : 16.937  76.897   1420
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 23.51 %
    Favored  : 72.69 %
  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: -0.39 (0.28), residues: 803
  helix:  0.58 (0.30), residues: 291
  sheet: -0.79 (0.35), residues: 176
  loop : -0.55 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  71 
 TYR   0.012   0.001   TYR A 210 
 PHE   0.017   0.002   PHE A 343 
 TRP   0.023   0.002   TRP A 219 
 HIS   0.003   0.001   HIS A 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 7901)
  covalent geometry    : angle       0.58642 (10853)
  hydrogen bonds       : bond        0.04132 (  312)
  hydrogen bonds       : angle       5.05999 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  136 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6989 (mm-30)
REVERT: A  280 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7693 (mptp)
REVERT: B  322 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.6285 (m-40)
REVERT: B  355 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7815 (ttpp)
  outliers start: 28
  outliers final: 13
  residues processed: 128
  average time/residue: 0.5818
  time to fit residues: 78.2649
Evaluate side-chains
  118 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain B residue  428 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0970
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
B 296 ASN
B 371 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.180434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.154165 restraints weight = 7236.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 1.35
r_work: 0.3723 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3618 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7901  Z= 0.145
  Angle     :  0.541   5.440  10853  Z= 0.293
  Chirality :  0.042   0.157   1192
  Planarity :  0.004   0.038   1218
  Dihedral  : 16.943  73.949   1420
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 22.69 %
    Favored  : 72.42 %
  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: -0.23 (0.28), residues: 803
  helix:  0.78 (0.30), residues: 290
  sheet: -0.65 (0.37), residues: 168
  loop : -0.57 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.010   0.001   TYR A 210 
 PHE   0.015   0.002   PHE B  78 
 TRP   0.022   0.002   TRP A 219 
 HIS   0.003   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7901)
  covalent geometry    : angle       0.54106 (10853)
  hydrogen bonds       : bond        0.03647 (  312)
  hydrogen bonds       : angle       4.88558 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  136 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6896 (mm-30)
REVERT: A  352 LYS cc_start: 0.7604 (mmtm) cc_final: 0.7279 (mmtt)
REVERT: B  322 ASN cc_start: 0.6421 (OUTLIER) cc_final: 0.6060 (m-40)
  outliers start: 36
  outliers final: 15
  residues processed: 134
  average time/residue: 0.5642
  time to fit residues: 79.7210
Evaluate side-chains
  119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  160 HIS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  428 LYS
Chi-restraints excluded: chain B residue  435 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0970
   chunk 64 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0980
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0870
   chunk 29 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.3556

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

Flipped N/Q/H residues before XYZ refinement:
A  56 ASN
A 156 GLN
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
B 296 ASN
B 371 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.181910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.155599 restraints weight = 7271.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.38
r_work: 0.3753 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7901  Z= 0.127
  Angle     :  0.529   6.745  10853  Z= 0.285
  Chirality :  0.041   0.152   1192
  Planarity :  0.004   0.037   1218
  Dihedral  : 16.823  72.307   1416
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 23.78 %
    Favored  : 72.55 %
  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: -0.12 (0.28), residues: 803
  helix:  0.86 (0.31), residues: 290
  sheet: -0.46 (0.38), residues: 161
  loop : -0.58 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 250 
 TYR   0.010   0.001   TYR A 210 
 PHE   0.013   0.001   PHE B  78 
 TRP   0.022   0.002   TRP A 219 
 HIS   0.003   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7901)
  covalent geometry    : angle       0.52857 (10853)
  hydrogen bonds       : bond        0.03433 (  312)
  hydrogen bonds       : angle       4.76068 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  136 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6918 (mm-30)
REVERT: A  227 LEU cc_start: 0.8364 (mt) cc_final: 0.8116 (mp)
REVERT: B   58 ASP cc_start: 0.7969 (m-30) cc_final: 0.7761 (m-30)
REVERT: B  322 ASN cc_start: 0.6375 (OUTLIER) cc_final: 0.6024 (m-40)
REVERT: B  355 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7860 (tttp)
  outliers start: 27
  outliers final: 14
  residues processed: 129
  average time/residue: 0.5403
  time to fit residues: 73.7636
Evaluate side-chains
  120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain A residue  160 HIS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain B residue  435 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 50 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
A 340 HIS
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
B 371 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.180922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.154410 restraints weight = 7194.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 1.37
r_work: 0.3728 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3624 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7901  Z= 0.149
  Angle     :  0.536   5.387  10853  Z= 0.289
  Chirality :  0.042   0.154   1192
  Planarity :  0.004   0.038   1218
  Dihedral  : 16.755  72.124   1415
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 23.91 %
    Favored  : 72.28 %
  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: -0.11 (0.28), residues: 803
  helix:  0.87 (0.31), residues: 290
  sheet: -0.59 (0.38), residues: 168
  loop : -0.49 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 250 
 TYR   0.009   0.001   TYR A 330 
 PHE   0.014   0.002   PHE B  78 
 TRP   0.021   0.002   TRP A 219 
 HIS   0.004   0.001   HIS A 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7901)
  covalent geometry    : angle       0.53621 (10853)
  hydrogen bonds       : bond        0.03521 (  312)
  hydrogen bonds       : angle       4.78634 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B  355 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7846 (tttp)
  outliers start: 28
  outliers final: 12
  residues processed: 132
  average time/residue: 0.5093
  time to fit residues: 71.1013
Evaluate side-chains
  120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  160 HIS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  355 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0050
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 56 optimal weight:    0.1980
   chunk 65 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
B 371 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.181406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.154941 restraints weight = 7259.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 1.38
r_work: 0.3745 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3642 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7901  Z= 0.138
  Angle     :  0.537   7.499  10853  Z= 0.288
  Chirality :  0.041   0.155   1192
  Planarity :  0.004   0.040   1218
  Dihedral  : 16.740  72.232   1415
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 24.73 %
    Favored  : 72.15 %
  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: -0.04 (0.28), residues: 803
  helix:  0.93 (0.31), residues: 290
  sheet: -0.57 (0.38), residues: 168
  loop : -0.45 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 250 
 TYR   0.009   0.001   TYR A 330 
 PHE   0.013   0.001   PHE B  78 
 TRP   0.021   0.002   TRP A 219 
 HIS   0.002   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7901)
  covalent geometry    : angle       0.53653 (10853)
  hydrogen bonds       : bond        0.03410 (  312)
  hydrogen bonds       : angle       4.73155 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A   17 PHE cc_start: 0.8527 (t80) cc_final: 0.8322 (t80)
REVERT: A   51 LYS cc_start: 0.5729 (tptt) cc_final: 0.5403 (tppp)
REVERT: A  227 LEU cc_start: 0.8373 (mt) cc_final: 0.8136 (mt)
REVERT: A  287 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8330 (mmm)
REVERT: A  406 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7501 (mmtt)
REVERT: B   58 ASP cc_start: 0.7989 (m-30) cc_final: 0.7755 (m-30)
REVERT: B  355 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7868 (tttp)
  outliers start: 23
  outliers final: 11
  residues processed: 129
  average time/residue: 0.5216
  time to fit residues: 71.1100
Evaluate side-chains
  123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   58 CYS
Chi-restraints excluded: chain A residue  160 HIS
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  355 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0000
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
B 296 ASN
B 371 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.181186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.154658 restraints weight = 7259.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 1.37
r_work: 0.3731 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3626 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7901  Z= 0.149
  Angle     :  0.542   6.408  10853  Z= 0.291
  Chirality :  0.042   0.153   1192
  Planarity :  0.004   0.044   1218
  Dihedral  : 16.695  72.423   1414
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 25.00 %
    Favored  : 71.74 %
  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: -0.00 (0.28), residues: 803
  helix:  1.01 (0.31), residues: 284
  sheet: -0.56 (0.38), residues: 168
  loop : -0.44 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 250 
 TYR   0.009   0.001   TYR A 330 
 PHE   0.014   0.002   PHE B  78 
 TRP   0.021   0.002   TRP A 219 
 HIS   0.002   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7901)
  covalent geometry    : angle       0.54220 (10853)
  hydrogen bonds       : bond        0.03461 (  312)
  hydrogen bonds       : angle       4.76713 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.5598 (tptt) cc_final: 0.5273 (tppp)
REVERT: A   92 MET cc_start: 0.6496 (ttt) cc_final: 0.6225 (ttm)
REVERT: A  287 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8329 (mmm)
REVERT: A  352 LYS cc_start: 0.7497 (mmtm) cc_final: 0.7101 (mmmt)
REVERT: B   58 ASP cc_start: 0.7971 (m-30) cc_final: 0.7744 (m-30)
REVERT: B  355 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7777 (ttpp)
  outliers start: 24
  outliers final: 12
  residues processed: 128
  average time/residue: 0.5700
  time to fit residues: 77.1029
Evaluate side-chains
  121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   58 CYS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  355 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 23 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    0.2980
   chunk 66 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
B 296 ASN
B 371 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.181431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.154988 restraints weight = 7195.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 1.36
r_work: 0.3733 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7901  Z= 0.150
  Angle     :  0.547   6.034  10853  Z= 0.294
  Chirality :  0.042   0.155   1192
  Planarity :  0.004   0.042   1218
  Dihedral  : 16.701  72.732   1414
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 25.41 %
    Favored  : 71.88 %
  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:  0.02 (0.28), residues: 803
  helix:  0.99 (0.31), residues: 284
  sheet: -0.41 (0.39), residues: 161
  loop : -0.48 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  71 
 TYR   0.009   0.001   TYR A 210 
 PHE   0.014   0.002   PHE B  78 
 TRP   0.021   0.002   TRP A 219 
 HIS   0.002   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7901)
  covalent geometry    : angle       0.54722 (10853)
  hydrogen bonds       : bond        0.03465 (  312)
  hydrogen bonds       : angle       4.76655 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.5757 (tptt) cc_final: 0.5385 (tppp)
REVERT: A   92 MET cc_start: 0.6371 (ttt) cc_final: 0.6072 (ttm)
REVERT: A  287 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8331 (mmm)
REVERT: A  352 LYS cc_start: 0.7516 (mmtm) cc_final: 0.7100 (mmmt)
REVERT: B   58 ASP cc_start: 0.7992 (m-30) cc_final: 0.7749 (m-30)
REVERT: B  355 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7827 (ttpp)
  outliers start: 20
  outliers final: 12
  residues processed: 121
  average time/residue: 0.5274
  time to fit residues: 67.5815
Evaluate side-chains
  119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   58 CYS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  355 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
B 296 ASN
B 371 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.176165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.147122 restraints weight = 7240.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 1.33
r_work: 0.3682 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3581 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   7901  Z= 0.244
  Angle     :  0.627   9.619  10853  Z= 0.335
  Chirality :  0.046   0.187   1192
  Planarity :  0.005   0.041   1218
  Dihedral  : 16.813  75.844   1414
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 25.82 %
    Favored  : 71.60 %
  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: -0.24 (0.28), residues: 803
  helix:  0.72 (0.30), residues: 284
  sheet: -0.63 (0.37), residues: 171
  loop : -0.51 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 250 
 TYR   0.014   0.002   TYR B  37 
 PHE   0.019   0.002   PHE A 343 
 TRP   0.021   0.002   TRP A  33 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 7901)
  covalent geometry    : angle       0.62677 (10853)
  hydrogen bonds       : bond        0.04089 (  312)
  hydrogen bonds       : angle       5.01490 (  830)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  161 ASP cc_start: 0.6240 (p0) cc_final: 0.6029 (p0)
REVERT: A  280 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7671 (mptp)
REVERT: B   58 ASP cc_start: 0.8129 (m-30) cc_final: 0.7892 (m-30)
REVERT: B  355 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7844 (ttpp)
  outliers start: 19
  outliers final: 12
  residues processed: 125
  average time/residue: 0.5120
  time to fit residues: 67.8226
Evaluate side-chains
  123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   58 CYS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  243 ARG
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  355 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0170
   chunk 74 optimal weight:    0.0670
   chunk 11 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0370
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.2834

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
A 286 GLN
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
B 296 ASN
B 371 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.183305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.157184 restraints weight = 7251.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 1.37
r_work: 0.3771 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7901  Z= 0.122
  Angle     :  0.540   7.056  10853  Z= 0.290
  Chirality :  0.041   0.150   1192
  Planarity :  0.004   0.047   1218
  Dihedral  : 16.842  72.360   1414
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 26.77 %
    Favored  : 71.47 %
  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: -0.08 (0.28), residues: 803
  helix:  0.95 (0.31), residues: 284
  sheet: -0.56 (0.38), residues: 168
  loop : -0.52 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  71 
 TYR   0.009   0.001   TYR A 210 
 PHE   0.014   0.001   PHE B  78 
 TRP   0.023   0.002   TRP A 219 
 HIS   0.003   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7901)
  covalent geometry    : angle       0.53953 (10853)
  hydrogen bonds       : bond        0.03363 (  312)
  hydrogen bonds       : angle       4.73225 (  830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2820.91 seconds
wall clock time: 48 minutes 43.55 seconds (2923.55 seconds total)