# Date 2008-01-16 Time 00:33:27 PST -0800 (1200472407.33 s)
#phil __OFF__

Command line arguments: "../53.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32345
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 53

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 46.6953, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8562 1.95093
Completeness in resolution range: 0.92672
Completeness with d_max=infinity: 0.923922

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8562
                             d_min =   1.9509

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8562 1.95093
Completeness in resolution range: 0.92672
Completeness with d_max=infinity: 0.923922

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8566 -  4.1750 [2220/2248]  1995   225  10.1%
  bin  2:  4.1750 -  3.3260 [2136/2155]  1922   214  10.0%
  bin  3:  3.3260 -  2.9092 [2108/2129]  1903   205   9.7%
  bin  4:  2.9092 -  2.6448 [2080/2104]  1868   212  10.2%
  bin  5:  2.6448 -  2.4562 [2075/2095]  1861   214  10.3%
  bin  6:  2.4562 -  2.3119 [2056/2103]  1858   198   9.6%
  bin  7:  2.3119 -  2.1965 [2047/2080]  1847   200   9.8%
  bin  8:  2.1965 -  2.1012 [2072/2106]  1857   215  10.4%
  bin  9:  2.1012 -  2.0205 [1971/2048]  1782   189   9.6%
  bin 10:  2.0205 -  1.9509 [ 824/2070]   737    87  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_53/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.03 -     1.80: 12
        1.80 -     2.58: 80
        2.58 -     3.35: 4073
        3.35 -     4.13: 9497
        4.13 -     4.90: 14966
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.030 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.101 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.311 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.425 3.040 -x+1,y-1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.434 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28623 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_53/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_53/model_refine_001.geo

CPU time processing inputs: 9.25


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 46.69535 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4925   r_free= 0.4863   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.292402                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8566 -  4.6568 0.99   1443  159 0.3997 0.3836      6.6093      6.6128|
|  2:  4.6568 -  3.7152 0.99   1394  155 0.3989 0.4543      6.7655      6.8713|
|  3:  3.7152 -  3.2512 0.99   1353  154 0.4719 0.4223      6.6937      6.6813|
|  4:  3.2512 -  2.9565 0.99   1357  144 0.4919 0.5007      6.5312      6.5006|
|  5:  2.9565 -  2.7460 0.99   1338  153 0.5104 0.5166      6.3629      6.4354|
|  6:  2.7460 -  2.5850 0.98   1339  150 0.5285 0.5120      6.2956      6.1999|
|  7:  2.5850 -  2.4562 0.99   1325  155 0.5262 0.5355       6.235      6.1548|
|  8:  2.4562 -  2.3497 0.98   1339  143 0.5330 0.4976      6.1719      6.1676|
|  9:  2.3497 -  2.2595 0.98   1328  140 0.5487 0.5230      6.1394      6.1847|
| 10:  2.2595 -  2.1818 0.98   1315  145 0.5450 0.5351      6.0977      6.1226|
| 11:  2.1818 -  2.1138 0.99   1314  157 0.5358 0.4955      6.0109       6.012|
| 12:  2.1138 -  2.0535 0.98   1319  143 0.5381 0.5395      5.9605      5.9451|
| 13:  2.0535 -  1.9996 0.84   1126  115 0.5573 0.4976      5.8991      5.8422|
| 14:  1.9996 -  1.9509 0.27    340   46 0.5227 0.5815       5.895      5.7665|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8566 -  4.6568  1443   159  0.68  35.74   0.79     0.71      76745.22|
|  2:  4.6568 -  3.7152  1394   155  0.66  38.30   0.89     0.73     120192.66|
|  3:  3.7152 -  3.2512  1353   154  0.55  47.91   0.82     0.67     128522.96|
|  4:  3.2512 -  2.9565  1357   144  0.43  57.59   0.78     0.53     118257.03|
|  5:  2.9565 -  2.7460  1338   153  0.32  66.07   0.73     0.40      95397.02|
|  6:  2.7460 -  2.5850  1339   150  0.25  70.99   0.71     0.30      85275.87|
|  7:  2.5850 -  2.4562  1325   155  0.27  69.82   0.73     0.32      73665.36|
|  8:  2.4562 -  2.3497  1339   143  0.31  66.91   0.72     0.37      62809.25|
|  9:  2.3497 -  2.2595  1328   140  0.35  63.76   0.72     0.44      55987.22|
| 10:  2.2595 -  2.1818  1315   145  0.36  63.23   0.74     0.43      47353.21|
| 11:  2.1818 -  2.1138  1314   157  0.31  66.64   0.73     0.41      49130.54|
| 12:  2.1138 -  2.0535  1319   143  0.28  69.28   0.75     0.37      45113.03|
| 13:  2.0535 -  1.9996  1126   115  0.26  70.56   0.71     0.36      40808.88|
| 14:  1.9996 -  1.9509   340    46  0.32  65.88   0.77     0.35      30676.85|
|alpha:            min =        0.30 max =            0.73 mean =         0.47|
|beta:             min =    30676.85 max =       128522.96 mean =     76758.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.99 mean =        60.24|
|phase err.(test): min =        0.00 max =           89.98 mean =        60.78|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.538291             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.856   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.456562              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.910   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.132 -  1.508:        9 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.508 -  1.885:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.885 -  2.262:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.262 -  2.639:      640 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.639 -  3.016:     1456 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.016 -  3.393:     2587 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.393 -  3.769:     3982 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.769 -  4.146:     5192 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.146 -  4.523:     6705 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.523 -  4.900:     7898 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.318 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.132 |       3.114 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.614)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.614)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4983   r_free= 0.4931   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.293128                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4840   r_free= 0.4811   ksol= 0.33   Bsol= 4.83   scale= 1.001    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.31,7.68,11.05,0.00,0.00,0.00); trace/3= 9.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.285322                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.376808             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.464   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.485856              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.219   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4840      final r-factor (work) = 0.4115          |
| start r-factor (free) = 0.4811      final r-factor (free) = 0.4317          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 98.5274 = 14.38 * 0.50 * 6.2892 + 1.00 * 53.3182                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.8737 = 14.38 * 0.50 * 6.2220 + 1.00 * 0.1474                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4115      final r-factor (work) = 0.3666          |
| start r-factor (free) = 0.4317      final r-factor (free) = 0.4203          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2594 = 1.49 * 1.00 * 6.2220 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1430 = 1.49 * 1.00 * 6.1402 + 1.00 * 0.0195                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.614)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.54   14.66    None  None   None       |
|    all(noH): 2823   0      0.00    79.54   14.66    None  None   None       |
|    Sol.    : 438    0      0.00    79.54   26.81    None  None   None       |
|    Mac.    : 2385   0      0.00    71.13   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.954: 1060   |   5:    39.768 -  47.721:   86        |
|      1:     7.954 -  15.907:  746   |   6:    47.721 -  55.675:   41        |
|      2:    15.907 -  23.861:  473   |   7:    55.675 -  63.628:   22        |
|      3:    23.861 -  31.814:  249   |   8:    63.628 -  71.582:   10        |
|      4:    31.814 -  39.768:  134   |   9:    71.582 -  79.535:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3666 r_free = 0.4203             target_work(ml) = 6.123         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3669 r_free = 0.4211             target_work(ml) = 6.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3669   r_free= 0.4211   ksol= 0.33   Bsol= 4.83   scale= 1.127    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.31,7.68,11.05,0.00,0.00,0.00); trace/3= 9.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.122631                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3624   r_free= 0.4166   ksol= 0.34   Bsol= 34.40   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.94,3.45,6.58,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.123163                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.959139              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.827   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.574578              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.411  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3624      final r-factor (work) = 0.2822          |
| start r-factor (free) = 0.4166      final r-factor (free) = 0.3375          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4986 = 6.96 * 0.50 * 6.1362 + 1.00 * 0.1474                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0454 = 6.96 * 0.50 * 6.0228 + 1.00 * 0.0885                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2822      final r-factor (work) = 0.2577          |
| start r-factor (free) = 0.3375      final r-factor (free) = 0.3207          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4800 = 0.57 * 1.00 * 6.0228 + 1.00 * 0.0194                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3928 = 0.57 * 1.00 * 5.8824 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.614)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.42   14.42    None  None   None       |
|    all(noH): 2823   0      0.00    78.42   14.42    None  None   None       |
|    Sol.    : 438    0      0.00    78.42   32.67    None  None   None       |
|    Mac.    : 2385   0      0.00    73.28   11.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.842: 1129   |   5:    39.212 -  47.054:   77        |
|      1:     7.842 -  15.685:  778   |   6:    47.054 -  54.896:   58        |
|      2:    15.685 -  23.527:  367   |   7:    54.896 -  62.739:   28        |
|      3:    23.527 -  31.369:  216   |   8:    62.739 -  70.581:   12        |
|      4:    31.369 -  39.212:  151   |   9:    70.581 -  78.423:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2577 r_free = 0.3207             target_work(ml) = 5.857         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2575 r_free = 0.3206             target_work(ml) = 5.857         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2575   r_free= 0.3206   ksol= 0.34   Bsol= 34.40   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.94,3.45,6.58,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.857223                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2556   r_free= 0.3199   ksol= 0.32   Bsol= 34.40   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,2.26,4.44,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.856364                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.174180              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.765   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.881567              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.776  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2556      final r-factor (work) = 0.1879          |
| start r-factor (free) = 0.3199      final r-factor (free) = 0.2393          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3088 = 5.17 * 0.50 * 5.8832 + 1.00 * 0.0885                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9159 = 5.17 * 0.50 * 5.7364 + 1.00 * 0.0753                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1879      final r-factor (work) = 0.1669          |
| start r-factor (free) = 0.2393      final r-factor (free) = 0.2242          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0700 = 0.88 * 1.00 * 5.7364 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8848 = 0.88 * 1.00 * 5.5248 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.614)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.40   14.77    None  None   None       |
|    all(noH): 2823   0      0.00    82.40   14.77    None  None   None       |
|    Sol.    : 438    0      0.72    82.40   39.25    None  None   None       |
|    Mac.    : 2385   0      0.00    76.70   10.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.240: 1283   |   5:    41.202 -  49.442:   84        |
|      1:     8.240 -  16.481:  799   |   6:    49.442 -  57.682:   87        |
|      2:    16.481 -  24.721:  254   |   7:    57.682 -  65.922:   44        |
|      3:    24.721 -  32.961:  113   |   8:    65.922 -  74.163:   17        |
|      4:    32.961 -  41.202:  133   |   9:    74.163 -  82.403:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1669 r_free = 0.2242             target_work(ml) = 5.490         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1667 r_free = 0.2240             target_work(ml) = 5.490         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1667   r_free= 0.2240   ksol= 0.32   Bsol= 34.40   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,2.26,4.44,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.489773                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1655   r_free= 0.2238   ksol= 0.32   Bsol= 47.79   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.52,1.26,3.20,0.00,0.00,0.00); trace/3= 1.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.487634                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.924660              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.739  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.411463              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.550   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1655      final r-factor (work) = 0.1383          |
| start r-factor (free) = 0.2238      final r-factor (free) = 0.1917          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1661 = 2.92 * 0.50 * 5.5328 + 1.00 * 0.0753                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9913 = 2.92 * 0.50 * 5.4205 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1383      final r-factor (work) = 0.1328          |
| start r-factor (free) = 0.1917      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2446 = 0.41 * 1.00 * 5.4205 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2039 = 0.41 * 1.00 * 5.3187 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.614)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.70   14.45    None  None   None       |
|    all(noH): 2823   0      0.00    86.70   14.45    None  None   None       |
|    Sol.    : 438    0      2.31    84.36   39.28    None  None   None       |
|    Mac.    : 2385   0      0.00    86.70   9.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.670: 1430   |   5:    43.351 -  52.021:  110        |
|      1:     8.670 -  17.340:  748   |   6:    52.021 -  60.691:   65        |
|      2:    17.340 -  26.011:  196   |   7:    60.691 -  69.362:   32        |
|      3:    26.011 -  34.681:  119   |   8:    69.362 -  78.032:   19        |
|      4:    34.681 -  43.351:  100   |   9:    78.032 -  86.702:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1328 r_free = 0.1827             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1325 r_free = 0.1823             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1823   ksol= 0.32   Bsol= 47.79   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.52,1.26,3.20,0.00,0.00,0.00); trace/3= 1.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.292833                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1825   ksol= 0.32   Bsol= 47.79   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,1.07,2.84,0.00,0.00,0.00); trace/3= 1.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.293416                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.521223              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.618  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.325953              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.676   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1825      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4289 = 3.52 * 0.50 * 5.3187 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3187 = 3.52 * 0.50 * 5.2515 + 1.00 * 0.0729                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1194      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1689      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7389 = 0.33 * 1.00 * 5.2515 + 1.00 * 0.0272                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7077 = 0.33 * 1.00 * 5.2062 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.614)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.86   14.08    None  None   None       |
|    all(noH): 2823   0      0.00    87.86   14.08    None  None   None       |
|    Sol.    : 438    0      2.97    82.32   38.11    None  None   None       |
|    Mac.    : 2385   0      0.00    87.86   9.67     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.786: 1478   |   5:    43.931 -  52.717:  101        |
|      1:     8.786 -  17.572:  737   |   6:    52.717 -  61.503:   57        |
|      2:    17.572 -  26.358:  182   |   7:    61.503 -  70.289:   32        |
|      3:    26.358 -  35.144:  125   |   8:    70.289 -  79.075:   13        |
|      4:    35.144 -  43.931:   94   |   9:    79.075 -  87.861:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1653             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1652             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1652   ksol= 0.32   Bsol= 47.79   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,1.07,2.84,0.00,0.00,0.00); trace/3= 1.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195322                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8566 -  4.6568 0.99   1443  159 0.1001 0.1370      5.4229      5.6281|
|  2:  4.6568 -  3.7152 0.99   1394  155 0.0862 0.1144      5.4674      5.6665|
|  3:  3.7152 -  3.2512 0.99   1353  154 0.1129 0.1580      5.5286      5.8618|
|  4:  3.2512 -  2.9565 0.99   1357  144 0.1294 0.1791      5.4778      5.6914|
|  5:  2.9565 -  2.7460 0.99   1338  153 0.1405 0.1520       5.381      5.5135|
|  6:  2.7460 -  2.5850 0.98   1339  150 0.1291 0.2151      5.2459      5.5538|
|  7:  2.5850 -  2.4562 0.99   1325  155 0.1334 0.1811      5.2131      5.3813|
|  8:  2.4562 -  2.3497 0.98   1339  143 0.1237 0.1789      5.1183      5.3668|
|  9:  2.3497 -  2.2595 0.98   1328  140 0.1246 0.1932      5.0749      5.3859|
| 10:  2.2595 -  2.1818 0.98   1315  145 0.1169 0.1711      4.9823      5.2063|
| 11:  2.1818 -  2.1138 0.99   1314  157 0.1217 0.1908      4.9547      5.3105|
| 12:  2.1138 -  2.0535 0.98   1319  143 0.1216 0.1735      4.9243      5.1504|
| 13:  2.0535 -  1.9996 0.84   1126  115 0.1129 0.1659      4.7798      4.9491|
| 14:  1.9996 -  1.9509 0.27    340   46 0.0937 0.1631      4.6163      4.9372|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8566 -  4.6568  1443   159  0.93  10.17   0.98     0.95       8436.63|
|  2:  4.6568 -  3.7152  1394   155  0.95   8.70   1.02     1.01      10019.54|
|  3:  3.7152 -  3.2512  1353   154  0.93  12.38   1.03     1.03      11656.78|
|  4:  3.2512 -  2.9565  1357   144  0.91  14.72   1.02     1.01      10962.09|
|  5:  2.9565 -  2.7460  1338   153  0.89  17.34   1.00     0.97       9662.77|
|  6:  2.7460 -  2.5850  1339   150  0.89  17.12   0.98     0.94       7423.84|
|  7:  2.5850 -  2.4562  1325   155  0.89  17.11   0.99     0.94       6860.20|
|  8:  2.4562 -  2.3497  1339   143  0.90  16.33   1.00     0.98       5950.96|
|  9:  2.3497 -  2.2595  1328   140  0.89  17.25   1.00     0.96       5564.03|
| 10:  2.2595 -  2.1818  1315   145  0.90  16.43   1.01     0.97       4735.73|
| 11:  2.1818 -  2.1138  1314   157  0.89  17.74   1.01     0.97       4764.37|
| 12:  2.1138 -  2.0535  1319   143  0.89  17.30   1.01     1.00       4420.10|
| 13:  2.0535 -  1.9996  1126   115  0.90  16.55   0.99     0.97       3349.38|
| 14:  1.9996 -  1.9509   340    46  0.93  11.90   0.99     0.96       2213.79|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2213.79 max =        11656.78 mean =      7200.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.17|
|phase err.(test): min =        0.00 max =           89.30 mean =        14.62|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1652   ksol= 0.32   Bsol= 49.16   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,-0.32,1.49,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195362                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1652   ksol= 0.32   Bsol= 49.16   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,-0.32,1.49,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195362                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8566 -  4.6568 0.99   1443  159 0.1001 0.1370      5.4237      5.6284|
|  2:  4.6568 -  3.7152 0.99   1394  155 0.0861 0.1143      5.4673      5.6662|
|  3:  3.7152 -  3.2512 0.99   1353  154 0.1129 0.1580      5.5284      5.8619|
|  4:  3.2512 -  2.9565 0.99   1357  144 0.1294 0.1791      5.4778      5.6913|
|  5:  2.9565 -  2.7460 0.99   1338  153 0.1405 0.1520       5.381      5.5134|
|  6:  2.7460 -  2.5850 0.98   1339  150 0.1290 0.2151      5.2459      5.5538|
|  7:  2.5850 -  2.4562 0.99   1325  155 0.1335 0.1811      5.2132      5.3815|
|  8:  2.4562 -  2.3497 0.98   1339  143 0.1237 0.1789      5.1183      5.3667|
|  9:  2.3497 -  2.2595 0.98   1328  140 0.1246 0.1931      5.0749       5.386|
| 10:  2.2595 -  2.1818 0.98   1315  145 0.1169 0.1712      4.9823      5.2065|
| 11:  2.1818 -  2.1138 0.99   1314  157 0.1217 0.1908      4.9547      5.3106|
| 12:  2.1138 -  2.0535 0.98   1319  143 0.1216 0.1735      4.9242      5.1503|
| 13:  2.0535 -  1.9996 0.84   1126  115 0.1129 0.1659      4.7797      4.9488|
| 14:  1.9996 -  1.9509 0.27    340   46 0.0937 0.1629      4.6163      4.9367|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8566 -  4.6568  1443   159  0.93  10.18   0.98     0.95       8448.02|
|  2:  4.6568 -  3.7152  1394   155  0.95   8.70   1.02     1.01      10019.38|
|  3:  3.7152 -  3.2512  1353   154  0.93  12.38   1.03     1.03      11652.80|
|  4:  3.2512 -  2.9565  1357   144  0.91  14.71   1.02     1.01      10961.83|
|  5:  2.9565 -  2.7460  1338   153  0.89  17.33   1.00     0.98       9661.80|
|  6:  2.7460 -  2.5850  1339   150  0.89  17.12   0.98     0.94       7424.40|
|  7:  2.5850 -  2.4562  1325   155  0.89  17.11   0.99     0.94       6862.21|
|  8:  2.4562 -  2.3497  1339   143  0.90  16.33   1.00     0.98       5951.19|
|  9:  2.3497 -  2.2595  1328   140  0.89  17.25   1.00     0.96       5565.13|
| 10:  2.2595 -  2.1818  1315   145  0.90  16.43   1.01     0.98       4734.93|
| 11:  2.1818 -  2.1138  1314   157  0.89  17.74   1.01     0.97       4765.31|
| 12:  2.1138 -  2.0535  1319   143  0.89  17.30   1.01     1.01       4419.84|
| 13:  2.0535 -  1.9996  1126   115  0.90  16.55   0.99     0.97       3347.79|
| 14:  1.9996 -  1.9509   340    46  0.93  11.90   0.99     0.96       2211.94|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2211.94 max =        11652.80 mean =      7201.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.17|
|phase err.(test): min =        0.00 max =           89.30 mean =        14.62|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.614)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.38    89.24   15.46    None  None   None       |
|    all(noH): 2823   0      1.38    89.24   15.46    None  None   None       |
|    Sol.    : 438    0      4.34    83.69   39.49    None  None   None       |
|    Mac.    : 2385   0      1.38    89.24   11.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.375 -  10.161: 1478   |   5:    45.306 -  54.092:  101        |
|      1:    10.161 -  18.947:  737   |   6:    54.092 -  62.878:   57        |
|      2:    18.947 -  27.733:  182   |   7:    62.878 -  71.664:   32        |
|      3:    27.733 -  36.519:  125   |   8:    71.664 -  80.450:   13        |
|      4:    36.519 -  45.306:   94   |   9:    80.450 -  89.236:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.540 - 4.268
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 308
   mapped sites are within: 0.718 - 4.268

peak=   10.905 closest distance to " CB  VAL A 230 " =    1.486
peak=    9.592 closest distance to " CB  VAL A 296 " =    1.563
peak=    5.818 closest distance to " CD2 LEU A   5 " =    1.157
peak=    5.779 closest distance to " NE2 GLN A  11 " =    1.161
peak=    5.761 closest distance to " O   HOH Z 188 " =    1.702
peak=    5.555 closest distance to " CG  LEU A   5 " =    1.205
peak=    5.512 closest distance to " CG  PRO A  54 " =    1.339
peak=    5.483 closest distance to " CD1AILE A 234 " =    1.000
peak=    5.329 closest distance to " O   HOH Z 248 " =    1.425
peak=    5.319 closest distance to " NH2AARG A 145 " =    1.098
peak=    5.307 closest distance to " O   HOH Z 232 " =    2.347
peak=    5.240 closest distance to " CB  GLN A 223 " =    1.507
peak=    5.229 closest distance to " CG  LEU A 228 " =    1.198
peak=    5.121 closest distance to " CB  ARG A 275 " =    0.947
peak=    5.092 closest distance to " O   HOH Z  43 " =    1.494
peak=    4.992 closest distance to " O   HOH Z 403 " =    1.701
peak=    4.890 closest distance to " O   HOH Z 130 " =    1.073
peak=    4.865 closest distance to " NH2 ARG A  56 " =    2.060
peak=    4.851 closest distance to " O   HOH Z 142 " =    1.667
peak=    4.664 closest distance to " O   HOH Z   9 " =    1.295
peak=    4.619 closest distance to " O   HOH Z 193 " =    1.932
peak=    4.542 closest distance to " O   HOH Z 238 " =    1.337
peak=    4.498 closest distance to " O   HOH Z   3 " =    2.167
peak=    4.469 closest distance to " CB  ASN A 142 " =    1.112
peak=    4.448 closest distance to " O   SER A  87 " =    2.350
peak=    4.435 closest distance to " O   HOH Z 406 " =    1.463
peak=    4.423 closest distance to " O   HOH Z 272 " =    1.887
peak=    4.422 closest distance to " O   HOH Z 126 " =    1.629
peak=    4.421 closest distance to " CG  GLN A  58 " =    1.033
peak=    4.414 closest distance to " CZ  PHE A 218 " =    1.202
peak=    4.409 closest distance to " O   HOH Z 124 " =    1.299
peak=    4.397 closest distance to " CB  GLN A 183 " =    1.239
peak=    4.389 closest distance to " O   HOH Z 251 " =    1.708
peak=    4.388 closest distance to " O   HOH Z 143 " =    1.578
peak=    4.378 closest distance to " O   HOH Z 402 " =    1.424
peak=    4.366 closest distance to " CG2 ILE A 234 " =    1.066
peak=    4.347 closest distance to " O   HOH Z 375 " =    0.986
peak=    4.344 closest distance to " NH2AARG A 190 " =    2.012
peak=    4.335 closest distance to " O   HOH Z  78 " =    1.662
peak=    4.333 closest distance to " CD2 TRP A 179 " =    1.393
peak=    4.328 closest distance to " O   HOH Z 369 " =    2.414
peak=    4.317 closest distance to " O   HOH Z  85 " =    1.582
peak=    4.314 closest distance to " O   HOH Z 255 " =    1.045
peak=    4.295 closest distance to " CB  VAL A 230 " =    1.226
peak=    4.288 closest distance to " O   HOH Z 346 " =    1.579
peak=    4.239 closest distance to " CB  ASN A 148 " =    1.354
peak=    4.203 closest distance to " CB  ALA A   9 " =    1.626
peak=    4.188 closest distance to " CB  ARG A  79 " =    1.533
peak=    4.167 closest distance to " O   HOH Z 265 " =    2.095
peak=    4.156 closest distance to " CB  SER A  26 " =    1.793
peak=    4.143 closest distance to " CB  VAL A 265 " =    1.380
peak=    4.100 closest distance to " O   HOH Z 261 " =    2.286
peak=    4.096 closest distance to " O   HOH Z 427 " =    2.860
peak=    4.081 closest distance to " O   HOH Z 107 " =    0.789
peak=    4.050 closest distance to " CA  ALA A  51 " =    0.966
peak=    4.045 closest distance to " CG  PRO A 243 " =    1.193
peak=    4.044 closest distance to " CD  LYS A  76 " =    1.665
peak=    4.036 closest distance to " O   HOH Z 422 " =    2.449
peak=    4.012 closest distance to " O   HOH Z 359 " =    1.474
peak=    4.012 closest distance to " O   HOH Z 303 " =    2.149
peak=    4.011 closest distance to " CD  ARG A 269 " =    1.020
peak=    4.009 closest distance to " CB  PRO A  54 " =    0.920
peak=    4.003 closest distance to " O   HOH Z 112 " =    1.146
peak=    4.000 closest distance to " O   HOH Z  61 " =    1.818
peak=    3.998 closest distance to " O   HOH Z 236 " =    1.399
peak=    3.997 closest distance to " O   HOH Z 126 " =    1.818
peak=    3.994 closest distance to " O   HOH Z 287 " =    1.908
peak=    3.994 closest distance to " O   HOH Z  95 " =    1.220
peak=    3.990 closest distance to " O   HOH Z 417 " =    1.132
peak=    3.983 closest distance to " N   ASN A  39 " =    1.274
peak=    3.969 closest distance to " CA  TYR A  30 " =    1.065
peak=    3.952 closest distance to " CB  GLU A 152 " =    1.208
peak=    3.944 closest distance to " O   HOH Z   9 " =    2.009
peak=    3.943 closest distance to " O   HOH Z  69 " =    2.097
peak=    3.942 closest distance to " CB  VAL A 202 " =    1.600
peak=    3.937 closest distance to " CG  LEU A 167 " =    1.295
peak=    3.932 closest distance to " CG AARG A 275 " =    1.247
peak=    3.921 closest distance to " O   HOH Z 246 " =    1.110
peak=    3.902 closest distance to " CB  SER A  63 " =    1.144
peak=    3.902 closest distance to " O   HOH Z 126 " =    1.849
peak=    3.900 closest distance to " O   HOH Z  80 " =    1.667
peak=    3.899 closest distance to " O   HOH Z  69 " =    0.823
peak=    3.877 closest distance to " O   HOH Z  59 " =    1.849
peak=    3.876 closest distance to " CG2 VAL A 257 " =    0.823
peak=    3.865 closest distance to " O   HOH Z 425 " =    1.401
peak=    3.863 closest distance to " O   HOH Z 188 " =    2.310
peak=    3.858 closest distance to " OG ASER A 258 " =    2.959
peak=    3.854 closest distance to " CB  GLN A  88 " =    1.259
peak=    3.851 closest distance to " O   HOH Z  97 " =    1.331
peak=    3.851 closest distance to " CB  ASN A 110 " =    1.088
peak=    3.849 closest distance to " CB  GLU A 277 " =    3.582
peak=    3.849 closest distance to " O   HOH Z 368 " =    2.187
peak=    3.836 closest distance to " O   HOH Z 213 " =    1.970
peak=    3.832 closest distance to " O   HOH Z  88 " =    2.601
peak=    3.828 closest distance to " O   HOH Z 234 " =    3.557
peak=    3.828 closest distance to " O   HOH Z  49 " =    1.022
peak=    3.828 closest distance to " N   PHE A 130 " =    1.344
peak=    3.819 closest distance to " CA  GLY A 241 " =    4.076
peak=    3.818 closest distance to " CD  LYS A 166 " =    1.321
peak=    3.811 closest distance to " N   ASP A 162 " =    1.216
peak=    3.809 closest distance to " O   HOH Z 130 " =    2.464
peak=    3.806 closest distance to " O   HOH Z  30 " =    1.480
peak=    3.794 closest distance to " O   HOH Z 203 " =    1.313
peak=    3.792 closest distance to " CB  ARG A 190 " =    1.780
peak=    3.773 closest distance to " CA  PHE A 283 " =    1.181
peak=    3.762 closest distance to " O   HOH Z 128 " =    2.127
peak=    3.756 closest distance to " O   HOH Z  76 " =    1.080
peak=    3.738 closest distance to " CG2 ILE A 120 " =    1.360
peak=    3.720 closest distance to " O   HOH Z 286 " =    2.405
peak=    3.719 closest distance to " O   HOH Z 365 " =    2.560
peak=    3.718 closest distance to " NH2AARG A 190 " =    2.078
peak=    3.715 closest distance to " ND2 ASN A 187 " =    1.623
peak=    3.713 closest distance to " O   HOH Z  10 " =    1.763
peak=    3.710 closest distance to " CA  ASN A 217 " =    1.171
peak=    3.708 closest distance to " O   HOH Z  88 " =    3.366
peak=    3.708 closest distance to " O   HOH Z 423 " =    1.837
peak=    3.685 closest distance to " CG  PRO A 213 " =    1.159
peak=    3.682 closest distance to " CB  THR A  31 " =    1.616
peak=    3.671 closest distance to " NZ  LYS A 117 " =    2.728
peak=    3.667 closest distance to " CB  ALA A 248 " =    1.403
peak=    3.667 closest distance to " O   PRO A 198 " =    1.576
peak=    3.664 closest distance to " O   HOH Z  44 " =    2.005
peak=    3.663 closest distance to " O   HOH Z  40 " =    1.688
peak=    3.663 closest distance to " CD2 LEU A 228 " =    1.289
peak=    3.653 closest distance to " CB  ARG A  79 " =    1.019
peak=    3.648 closest distance to " O   HOH Z 329 " =    4.060
peak=    3.641 closest distance to " CB AVAL A  41 " =    1.193
peak=    3.636 closest distance to " ND2 ASN A 249 " =    0.889
peak=    3.636 closest distance to " O   HOH Z 298 " =    1.694
peak=    3.627 closest distance to " NH1 ARG A 138 " =    1.116
peak=    3.626 closest distance to " CD2 TYR A 186 " =    1.102
peak=    3.591 closest distance to " CB  TYR A 169 " =    0.773
peak=    3.588 closest distance to " O   HOH Z 117 " =    1.087
peak=    3.586 closest distance to " O   HOH Z 410 " =    3.076
peak=    3.585 closest distance to " CB  ASP A 191 " =    1.165
peak=    3.585 closest distance to " CB  THR A  52 " =    0.955
peak=    3.580 closest distance to " O   HOH Z 299 " =    4.103
peak=    3.575 closest distance to " CA  ILE A 234 " =    1.030
peak=    3.566 closest distance to " O   HOH Z 389 " =    1.462
peak=    3.563 closest distance to " O   HOH Z 273 " =    3.068
peak=    3.561 closest distance to " O   ASP A 124 " =    1.235
peak=    3.553 closest distance to " CB  ARG A 156 " =    1.276
peak=    3.553 closest distance to " O   HOH Z 132 " =    2.272
peak=    3.537 closest distance to " O   HOH Z 132 " =    2.712
peak=    3.532 closest distance to " O   HOH Z 272 " =    2.158
peak=    3.532 closest distance to " O   HOH Z 350 " =    1.743
peak=    3.532 closest distance to " CA  ASP A 162 " =    0.970
peak=    3.528 closest distance to " O   HOH Z 128 " =    1.923
peak=    3.528 closest distance to " CA  ALA A 129 " =    1.525
peak=    3.526 closest distance to " CB  SER A   3 " =    1.217
peak=    3.526 closest distance to " O   HOH Z 380 " =    1.536
peak=    3.523 closest distance to " O   HOH Z 141 " =    1.692
peak=    3.521 closest distance to " O   HOH Z 214 " =    2.689
peak=    3.520 closest distance to " O   HOH Z  78 " =    2.026
peak=    3.506 closest distance to " CG  MET A 185 " =    1.174
peak=    3.498 closest distance to " O   HOH Z  92 " =    2.163
peak=    3.492 closest distance to " O   HOH Z   1 " =    1.772
peak=    3.492 closest distance to " CG AARG A 102 " =    1.043
peak=    3.491 closest distance to " NE AARG A 145 " =    0.886
peak=    3.479 closest distance to " CA  ASN A 215 " =    0.966
peak=    3.471 closest distance to " N   ARG A 156 " =    1.319
peak=    3.463 closest distance to " O   HOH Z 193 " =    1.504
peak=    3.457 closest distance to " OE1 GLU A   2 " =    2.061
peak=    3.455 closest distance to " CB  ALA A 114 " =    1.248
peak=    3.455 closest distance to " O  BHOH Z 338 " =    2.416
peak=    3.451 closest distance to " O   HOH Z 258 " =    1.780
peak=    3.451 closest distance to " CA  ASP A 149 " =    1.149
peak=    3.451 closest distance to " CG1 ILE A  49 " =    1.510
peak=    3.447 closest distance to " CZ  PHE A  38 " =    1.030
peak=    3.444 closest distance to " O   HOH Z 337 " =    2.004
peak=    3.436 closest distance to " O   HOH Z 156 " =    3.133
peak=    3.436 closest distance to " O   ASN A  74 " =    1.423
peak=    3.435 closest distance to " CB  TRP A 266 " =    1.125
peak=    3.433 closest distance to " O   HOH Z 109 " =    1.427
peak=    3.432 closest distance to " O   HOH Z 200 " =    1.990
peak=    3.421 closest distance to " O   HOH Z 385 " =    3.851
peak=    3.411 closest distance to " O   HOH Z 334 " =    1.359
peak=    3.410 closest distance to " CA  ARG A  36 " =    0.997
peak=    3.410 closest distance to " O   HOH Z 144 " =    1.623
peak=    3.409 closest distance to " CE  LYS A  76 " =    0.911
peak=    3.407 closest distance to " O   HOH Z 123 " =    1.143
peak=    3.405 closest distance to " O   HOH Z 415 " =    3.418
peak=    3.397 closest distance to " O   HOH Z 284 " =    2.949
peak=    3.395 closest distance to " O   HOH Z 365 " =    1.508
peak=    3.394 closest distance to " O   HOH Z 130 " =    1.971
peak=    3.388 closest distance to " O   HOH Z 128 " =    2.047
peak=    3.380 closest distance to " CE3 TRP A 150 " =    1.069
peak=    3.374 closest distance to " O   HOH Z 425 " =    1.977
peak=    3.360 closest distance to " CD1 ILE A  33 " =    1.672
peak=    3.358 closest distance to " CE1 TYR A 186 " =    1.205
peak=    3.356 closest distance to " CG  PRO A 280 " =    0.858
peak=    3.354 closest distance to " O   HOH Z 371 " =    2.657
peak=    3.350 closest distance to " O   HOH Z 171 " =    3.666
peak=    3.341 closest distance to " CG  PRO A 198 " =    1.289
peak=    3.341 closest distance to " CB  SER A 212 " =    1.448
peak=    3.340 closest distance to " O   HOH Z 263 " =    1.783
peak=    3.336 closest distance to " CG2 VAL A 197 " =    1.125
peak=    3.336 closest distance to " O   HOH Z 193 " =    1.374
peak=    3.332 closest distance to " N   SER A 135 " =    1.327
peak=    3.326 closest distance to " CD1 ILE A 199 " =    1.299
peak=    3.323 closest distance to " O   HOH Z 352 " =    1.337
peak=    3.322 closest distance to " CG  GLN A  88 " =    1.119
peak=    3.320 closest distance to " NE  ARG A  56 " =    3.490
peak=    3.314 closest distance to " NH1AARG A 275 " =    0.979
peak=    3.313 closest distance to " O   HOH Z 250 " =    1.383
peak=    3.309 closest distance to " CB  ALA A 295 " =    1.370
peak=    3.307 closest distance to " O   HOH Z 405 " =    1.223
peak=    3.305 closest distance to " O   HOH Z 353 " =    2.562
peak=    3.304 closest distance to " OG1 THR A 264 " =    0.718
peak=    3.301 closest distance to " CB  ASN A 215 " =    1.065
peak=    3.300 closest distance to " CA  ASN A 127 " =    1.019
peak=    3.295 closest distance to " CA  ARG A 195 " =    1.182
peak=    3.295 closest distance to " CA  GLY A 267 " =    0.936
peak=    3.291 closest distance to " O   HOH Z 388 " =    2.289
peak=    3.290 closest distance to " NE2 GLN A  73 " =    1.362
peak=    3.290 closest distance to " O   HOH Z 254 " =    1.385
peak=    3.287 closest distance to " CB  SER A 273 " =    0.881
peak=    3.286 closest distance to " O   ASN A 284 " =    1.700
peak=    3.286 closest distance to " O   HOH Z 421 " =    2.227
peak=    3.284 closest distance to " CB  TRP A 179 " =    1.324
peak=    3.281 closest distance to " CB  PHE A 204 " =    1.005
peak=    3.281 closest distance to " O   HOH Z  41 " =    2.024
peak=    3.279 closest distance to " O   HOH Z 361 " =    3.579
peak=    3.278 closest distance to " O   HOH Z 249 " =    1.103
peak=    3.274 closest distance to " O   HOH Z 293 " =    1.869
peak=    3.272 closest distance to " CG  GLU A  37 " =    0.879
peak=    3.267 closest distance to " CG2 ILE A  20 " =    1.600
peak=    3.265 closest distance to " O   HOH Z 392 " =    2.667
peak=    3.264 closest distance to " O   HOH Z  97 " =    1.877
peak=    3.264 closest distance to " O   THR A 182 " =    1.445
peak=    3.264 closest distance to " CB  LYS A 117 " =    1.233
peak=    3.261 closest distance to " OG  SER A  62 " =    2.756
peak=    3.260 closest distance to " CB  VAL A 268 " =    0.859
peak=    3.257 closest distance to " CA  TYR A 116 " =    1.462
peak=    3.251 closest distance to " OG BSER A 164 " =    2.123
peak=    3.248 closest distance to " CA  LYS A 290 " =    1.230
peak=    3.246 closest distance to " O   HOH Z 357 " =    2.047
peak=    3.244 closest distance to " O   HOH Z 325 " =    2.155
peak=    3.242 closest distance to " OD1 ASN A  69 " =    2.432
peak=    3.238 closest distance to " O   HOH Z  50 " =    1.763
peak=    3.237 closest distance to " CG  ARG A  66 " =    3.110
peak=    3.236 closest distance to " O   HOH Z 118 " =    1.644
peak=    3.236 closest distance to " O   HOH Z  68 " =    2.128
peak=    3.231 closest distance to " NH2AARG A 275 " =    3.384
peak=    3.231 closest distance to " NZ  LYS A 117 " =    1.126
peak=    3.225 closest distance to " O   HOH Z 196 " =    0.995
peak=    3.225 closest distance to " O   GLY A  23 " =    2.570
peak=    3.223 closest distance to " CA  LEU A 282 " =    1.245
peak=    3.223 closest distance to " OG1 THR A 221 " =    1.396
peak=    3.222 closest distance to " O   HOH Z 173 " =    2.086
peak=    3.221 closest distance to " CG  LYS A 289 " =    1.437
peak=    3.221 closest distance to " O   HOH Z  85 " =    1.782
peak=    3.219 closest distance to " O   GLY A  91 " =    1.570
peak=    3.218 closest distance to " NE2 GLN A 223 " =    1.737
peak=    3.217 closest distance to " CD2 LEU A 297 " =    1.025
peak=    3.215 closest distance to " O   HOH Z 129 " =    1.070
peak=    3.213 closest distance to " NH1 ARG A  66 " =    1.438
peak=    3.211 closest distance to " O   HOH Z 435 " =    2.023
peak=    3.210 closest distance to " CE  LYS A 119 " =    1.138
peak=    3.208 closest distance to " CB  ASP A 124 " =    0.866
peak=    3.208 closest distance to " O   HOH Z 100 " =    0.758
peak=    3.204 closest distance to " CB  ASN A  39 " =    0.838
peak=    3.201 closest distance to " O   HOH Z 298 " =    4.268
peak=    3.193 closest distance to " CG2 THR A 221 " =    1.134
peak=    3.192 closest distance to " O   HOH Z  28 " =    1.689
peak=    3.190 closest distance to " CB  GLU A 128 " =    0.923
peak=    3.190 closest distance to " CB  PRO A  90 " =    1.178
peak=    3.189 closest distance to " O   HOH Z  59 " =    1.827
peak=    3.186 closest distance to " NH2BARG A 190 " =    1.736
peak=    3.183 closest distance to " CB  SER A  97 " =    1.012
peak=    3.183 closest distance to " CB  SER A  62 " =    1.064
peak=    3.183 closest distance to " O   HOH Z 322 " =    1.897
peak=    3.176 closest distance to " CG BARG A 102 " =    1.803
peak=    3.176 closest distance to " CB  ASN A  45 " =    1.113
peak=    3.164 closest distance to " O   HOH Z 305 " =    3.488
peak=    3.160 closest distance to " O   HOH Z 344 " =    1.433
peak=    3.159 closest distance to " CD  ARG A 195 " =    0.871
peak=    3.151 closest distance to " O   HOH Z   1 " =    1.889
peak=    3.150 closest distance to " O   HOH Z 368 " =    3.476
peak=    3.149 closest distance to " O   HOH Z 199 " =    2.345
peak=    3.145 closest distance to " O   HOH Z 172 " =    3.491
peak=    3.144 closest distance to " O   HOH Z 371 " =    1.395
peak=    3.135 closest distance to " CB  LEU A 300 " =    0.947
peak=    3.123 closest distance to " CG2 THR A 220 " =    0.723
peak=    3.117 closest distance to " OG ASER A  99 " =    1.350
peak=    3.117 closest distance to " CA  ARG A 159 " =    1.073
peak=    3.116 closest distance to " O   HOH Z  94 " =    2.125
peak=    3.115 closest distance to " CA  TRP A 150 " =    0.863
peak=    3.115 closest distance to " CA  VAL A 125 " =    1.046
peak=    3.106 closest distance to " CB  ALA A 233 " =    1.326
peak=    3.103 closest distance to " O   HOH Z 140 " =    1.498
peak=    3.100 closest distance to " CA  TYR A 214 " =    1.168
peak=    3.100 closest distance to " O   HOH Z 403 " =    1.500
peak=    3.098 closest distance to " NE1 TRP A  92 " =    1.330
peak=    3.096 closest distance to " O   HOH Z 152 " =    1.654
peak=    3.093 closest distance to " CG  GLN A  55 " =    2.400
peak=    3.090 closest distance to " OG BSER A 210 " =    1.494
peak=    3.084 closest distance to " O   HOH Z 394 " =    3.643
peak=    3.073 closest distance to " CB  SER A 216 " =    0.819
peak=    3.068 closest distance to " CB  ARG A 219 " =    0.989
peak=    3.051 closest distance to " CA  SER A  87 " =    0.968

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.521 - 5.638
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.776 - 5.638

peak=   -4.880 closest distance to " O   HOH Z 193 " =    0.856
peak=   -4.800 closest distance to " O   HOH Z 203 " =    1.289
peak=   -4.667 closest distance to " C   HIS A 108 " =    1.173
peak=   -4.619 closest distance to " CG  GLN A  58 " =    0.945
peak=   -4.493 closest distance to " O   HOH Z  69 " =    1.470
peak=   -4.472 closest distance to " O   HOH Z 211 " =    1.033
peak=   -4.450 closest distance to " OG BSER A 134 " =    1.341
peak=   -4.435 closest distance to " CD  ARG A  14 " =    3.120
peak=   -4.116 closest distance to " O   PRO A 163 " =    2.025
peak=   -4.097 closest distance to " O   HOH Z 394 " =    1.502
peak=   -4.097 closest distance to " CG  GLN A 223 " =    2.141
peak=   -4.095 closest distance to " CD  ARG A 156 " =    2.017
peak=   -4.067 closest distance to " O   PRO A 198 " =    1.243
peak=   -3.970 closest distance to " O   HOH Z 290 " =    1.149
peak=   -3.936 closest distance to " OH  TYR A 172 " =    1.751
peak=   -3.922 closest distance to " O   HOH Z 116 " =    1.447
peak=   -3.914 closest distance to " CD1 ILE A 263 " =    2.723
peak=   -3.899 closest distance to " CD1 LEU A 101 " =    2.341
peak=   -3.897 closest distance to " O   HOH Z 131 " =    4.138
peak=   -3.887 closest distance to " CE  MET A 105 " =    2.378
peak=   -3.841 closest distance to " OG  SER A  97 " =    2.303
peak=   -3.838 closest distance to " O   HOH Z 267 " =    5.468
peak=   -3.835 closest distance to " O   HOH Z 100 " =    0.842
peak=   -3.821 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.787 closest distance to " CG2 VAL A 202 " =    2.716
peak=   -3.777 closest distance to " O   VAL A  67 " =    2.500
peak=   -3.765 closest distance to " CB  ALA A  43 " =    2.442
peak=   -3.752 closest distance to " CB  ASP A 132 " =    2.383
peak=   -3.746 closest distance to " CD2 TYR A 293 " =    1.959
peak=   -3.745 closest distance to " NE2 GLN A  88 " =    1.218
peak=   -3.736 closest distance to " OG  SER A  87 " =    1.485
peak=   -3.721 closest distance to " CB  SER A 210 " =    1.183
peak=   -3.710 closest distance to " O   HOH Z 216 " =    1.259
peak=   -3.688 closest distance to " CE BMET A  47 " =    1.417
peak=   -3.687 closest distance to " O   HOH Z 166 " =    1.988
peak=   -3.685 closest distance to " O   HOH Z 351 " =    1.596
peak=   -3.678 closest distance to " O   ASN A 187 " =    1.594
peak=   -3.671 closest distance to " CB  PHE A 192 " =    1.995
peak=   -3.665 closest distance to " O   ALA A 227 " =    1.379
peak=   -3.659 closest distance to " OD1 ASN A 301 " =    1.950
peak=   -3.654 closest distance to " CA  VAL A  67 " =    2.937
peak=   -3.653 closest distance to " CD1 ILE A 199 " =    2.310
peak=   -3.647 closest distance to " CG2 ILE A  49 " =    2.843
peak=   -3.642 closest distance to " O   HOH Z 281 " =    3.104
peak=   -3.641 closest distance to " CD1 LEU A 255 " =    2.717
peak=   -3.631 closest distance to " OXT GLY A 302 " =    2.945
peak=   -3.628 closest distance to " N   PHE A  59 " =    2.020
peak=   -3.619 closest distance to " ND2 ASN A 249 " =    2.266
peak=   -3.584 closest distance to " O   HOH Z 371 " =    2.359
peak=   -3.565 closest distance to " O   HOH Z 109 " =    0.776
peak=   -3.563 closest distance to " O   HOH Z  11 " =    1.750
peak=   -3.549 closest distance to " CA  GLY A 241 " =    2.430
peak=   -3.530 closest distance to " O   VAL A 189 " =    2.591
peak=   -3.530 closest distance to " OE1 GLN A 183 " =    1.546
peak=   -3.525 closest distance to " CA  ASP A 298 " =    1.075
peak=   -3.488 closest distance to " O   HOH Z 252 " =    3.791
peak=   -3.484 closest distance to " CD  PRO A 243 " =    2.034
peak=   -3.463 closest distance to " CG2 VAL A 296 " =    2.012
peak=   -3.460 closest distance to " O   VAL A 174 " =    2.229
peak=   -3.460 closest distance to " CG1 VAL A 112 " =    2.794
peak=   -3.458 closest distance to " O   HOH Z 295 " =    1.657
peak=   -3.455 closest distance to " O   HOH Z 387 " =    2.376
peak=   -3.446 closest distance to " O   PHE A 218 " =    1.565
peak=   -3.441 closest distance to " CB  ALA A  51 " =    1.906
peak=   -3.440 closest distance to " NE2 GLN A  11 " =    1.737
peak=   -3.431 closest distance to " O   HOH Z 169 " =    0.983
peak=   -3.423 closest distance to " O   HOH Z 191 " =    5.638
peak=   -3.422 closest distance to " N   ASP A 286 " =    2.148
peak=   -3.420 closest distance to " CB  PRO A 163 " =    2.445
peak=   -3.415 closest distance to " N   ALA A 226 " =    1.906
peak=   -3.409 closest distance to " ND2 ASN A 173 " =    1.411
peak=   -3.405 closest distance to " CZ  PHE A  38 " =    2.340
peak=   -3.401 closest distance to " CB  GLN A  55 " =    1.367
peak=   -3.400 closest distance to " O   HOH Z 174 " =    3.832
peak=   -3.398 closest distance to " SG BCYS A 201 " =    2.289
peak=   -3.396 closest distance to " N   ALA A 248 " =    1.606
peak=   -3.395 closest distance to " O   HOH Z 404 " =    1.423
peak=   -3.393 closest distance to " O   HOH Z 352 " =    1.503
peak=   -3.390 closest distance to " CG  LEU A   5 " =    0.917
peak=   -3.389 closest distance to " O   HOH Z 134 " =    3.598
peak=   -3.378 closest distance to " O   SER A  95 " =    1.604
peak=   -3.376 closest distance to " O   HOH Z 423 " =    2.252
peak=   -3.375 closest distance to " CB  ALA A 131 " =    2.041
peak=   -3.372 closest distance to " O   SER A 146 " =    1.351
peak=   -3.372 closest distance to " NH2AARG A 275 " =    4.657
peak=   -3.362 closest distance to " OG BSER A 210 " =    1.625
peak=   -3.358 closest distance to " O   HOH Z 301 " =    2.433
peak=   -3.353 closest distance to " CB  ALA A 248 " =    2.307
peak=   -3.352 closest distance to " O   HOH Z 377 " =    2.152
peak=   -3.352 closest distance to " CG  TRP A 266 " =    1.933
peak=   -3.351 closest distance to " O   HOH Z 114 " =    3.243
peak=   -3.350 closest distance to " CG  ASP A 231 " =    0.803
peak=   -3.349 closest distance to " CB  ALA A 161 " =    2.419
peak=   -3.347 closest distance to " CD  PRO A 213 " =    2.033
peak=   -3.338 closest distance to " O   HOH Z 236 " =    1.550
peak=   -3.333 closest distance to " O   HOH Z 119 " =    2.185
peak=   -3.332 closest distance to " NE2 GLN A  88 " =    2.037
peak=   -3.331 closest distance to " N   ASN A 127 " =    1.318
peak=   -3.327 closest distance to " OD2 ASP A 191 " =    1.333
peak=   -3.321 closest distance to " O   HOH Z 359 " =    2.966
peak=   -3.319 closest distance to " O   HOH Z 198 " =    0.973
peak=   -3.315 closest distance to " OG  SER A  87 " =    1.272
peak=   -3.313 closest distance to " CG  PHE A 283 " =    2.595
peak=   -3.312 closest distance to " ND2 ASN A 209 " =    1.929
peak=   -3.312 closest distance to " NH2 ARG A  79 " =    2.052
peak=   -3.311 closest distance to " O   HOH Z 107 " =    1.021
peak=   -3.310 closest distance to " O   SER A 276 " =    1.620
peak=   -3.307 closest distance to " O   TRP A  70 " =    1.569
peak=   -3.305 closest distance to " CD2 PHE A 225 " =    1.042
peak=   -3.304 closest distance to " ND2 ASN A 187 " =    1.656
peak=   -3.303 closest distance to " O   HOH Z 372 " =    2.283
peak=   -3.296 closest distance to " O   HOH Z  60 " =    1.416
peak=   -3.294 closest distance to " O   HOH Z  11 " =    2.059
peak=   -3.294 closest distance to " O   HOH Z 398 " =    1.396
peak=   -3.293 closest distance to " O   GLY A  80 " =    2.558
peak=   -3.290 closest distance to " NE2 GLN A  55 " =    1.527
peak=   -3.288 closest distance to " O   HOH Z 232 " =    1.577
peak=   -3.288 closest distance to " CG2 THR A  18 " =    2.862
peak=   -3.287 closest distance to " O   HOH Z 244 " =    1.989
peak=   -3.286 closest distance to " OE2 GLU A 152 " =    1.343
peak=   -3.286 closest distance to " O   ALA A   7 " =    1.545
peak=   -3.284 closest distance to " O   HOH Z 429 " =    1.521
peak=   -3.280 closest distance to " CB  ALA A 248 " =    2.075
peak=   -3.277 closest distance to " O   HOH Z 286 " =    1.635
peak=   -3.276 closest distance to " CA  GLY A 133 " =    1.929
peak=   -3.276 closest distance to " O   HOH Z 313 " =    1.288
peak=   -3.275 closest distance to " O   HOH Z 421 " =    3.074
peak=   -3.274 closest distance to " O   HOH Z 162 " =    2.898
peak=   -3.273 closest distance to " ND2 ASN A  45 " =    1.302
peak=   -3.272 closest distance to " CG  ARG A  66 " =    2.185
peak=   -3.269 closest distance to " NE  ARG A 259 " =    1.042
peak=   -3.267 closest distance to " O   HOH Z 437 " =    1.492
peak=   -3.264 closest distance to " O   HOH Z 427 " =    1.482
peak=   -3.260 closest distance to " CB  HIS A  86 " =    1.096
peak=   -3.259 closest distance to " O   HOH Z 313 " =    1.679
peak=   -3.256 closest distance to " O   HOH Z  89 " =    2.653
peak=   -3.256 closest distance to " O   HOH Z 102 " =    1.809
peak=   -3.249 closest distance to " O   HOH Z  52 " =    1.579
peak=   -3.248 closest distance to " O   HOH Z 388 " =    2.262
peak=   -3.247 closest distance to " CE3 TRP A 150 " =    2.075
peak=   -3.245 closest distance to " C   MET A 188 " =    1.416
peak=   -3.245 closest distance to " O   HOH Z  68 " =    1.333
peak=   -3.243 closest distance to " N   SER A 276 " =    1.389
peak=   -3.236 closest distance to " O   HOH Z 215 " =    1.482
peak=   -3.236 closest distance to " O   HOH Z 140 " =    1.577
peak=   -3.235 closest distance to " O   HOH Z 165 " =    1.942
peak=   -3.235 closest distance to " O   HOH Z 113 " =    1.657
peak=   -3.233 closest distance to " O   HOH Z  73 " =    2.535
peak=   -3.232 closest distance to " CA  GLY A  98 " =    1.926
peak=   -3.230 closest distance to " CA  GLY A 203 " =    2.473
peak=   -3.228 closest distance to " CE  MET A 113 " =    2.773
peak=   -3.225 closest distance to " ND2 ASN A 252 " =    1.956
peak=   -3.218 closest distance to " CG  GLN A 103 " =    2.392
peak=   -3.215 closest distance to " O   HOH Z 111 " =    4.394
peak=   -3.212 closest distance to " C   LEU A 222 " =    1.243
peak=   -3.209 closest distance to " O   SER A  87 " =    2.104
peak=   -3.208 closest distance to " O   ILE A  49 " =    1.724
peak=   -3.206 closest distance to " CD  LYS A 289 " =    2.308
peak=   -3.206 closest distance to " CB  SER A 245 " =    2.061
peak=   -3.204 closest distance to " O   HOH Z 407 " =    2.636
peak=   -3.202 closest distance to " O   TRP A  92 " =    1.947
peak=   -3.194 closest distance to " O   SER A 135 " =    1.589
peak=   -3.189 closest distance to " OE1 GLN A  88 " =    1.092
peak=   -3.188 closest distance to " O   HOH Z 137 " =    1.750
peak=   -3.188 closest distance to " CG  LEU A 228 " =    1.020
peak=   -3.187 closest distance to " NH2 ARG A  66 " =    1.191
peak=   -3.181 closest distance to " O   HOH Z 250 " =    1.624
peak=   -3.179 closest distance to " O   HOH Z 414 " =    2.537
peak=   -3.177 closest distance to " OH  TYR A 169 " =    0.908
peak=   -3.174 closest distance to " O   HOH Z 185 " =    2.138
peak=   -3.166 closest distance to " CG2 VAL A 189 " =    1.999
peak=   -3.165 closest distance to " N   HIS A 115 " =    2.219
peak=   -3.163 closest distance to " CG2 ILE A 151 " =    2.507
peak=   -3.156 closest distance to " CA  GLY A  57 " =    2.121
peak=   -3.153 closest distance to " OG1 THR A  52 " =    2.576
peak=   -3.148 closest distance to " O   HOH Z 345 " =    2.008
peak=   -3.136 closest distance to " O   HOH Z 431 " =    2.057
peak=   -3.134 closest distance to " CE1 TYR A 247 " =    2.506
peak=   -3.132 closest distance to " CA  GLY A  23 " =    1.808
peak=   -3.127 closest distance to " CG  LEU A  83 " =    2.151
peak=   -3.125 closest distance to " NZ  LYS A 166 " =    1.855
peak=   -3.124 closest distance to " O   ASN A 252 " =    1.281
peak=   -3.114 closest distance to " CG1 VAL A 125 " =    1.994
peak=   -3.112 closest distance to " O   HOH Z 140 " =    0.979
peak=   -3.100 closest distance to " O   LYS A  76 " =    1.780
peak=   -3.092 closest distance to " O   GLY A  80 " =    2.538
peak=   -3.089 closest distance to " C   ASP A 124 " =    1.956
peak=   -3.085 closest distance to " O   TYR A  15 " =    1.955
peak=   -3.079 closest distance to " O   PRO A 198 " =    1.291
peak=   -3.078 closest distance to " N   ALA A 244 " =    1.482
peak=   -3.060 closest distance to " O   HOH Z 166 " =    2.179
peak=   -3.056 closest distance to " O   HOH Z 340 " =    1.217
peak=   -3.056 closest distance to " N   GLY A 196 " =    1.754
peak=   -3.047 closest distance to " O   HOH Z 227 " =    1.761
peak=   -3.044 closest distance to " CD2 PHE A  61 " =    2.698
peak=   -3.041 closest distance to " O   HOH Z 297 " =    2.660
peak=   -3.036 closest distance to " SG BCYS A 201 " =    2.510
peak=   -3.028 closest distance to " O   ALA A 292 " =    2.076
peak=   -3.021 closest distance to " O   ILE A 106 " =    0.982

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.4925 0.4863   6.292402e+00   6.287306e+00
   1_bss:  0.4840 0.4811   6.285322e+00   6.280447e+00
   1_xyz:  0.4115 0.4317   6.193764e+00   6.230358e+00
   1_adp:  0.3666 0.4203   6.123295e+00   6.207407e+00
   1_occ:  0.3669 0.4211   6.122631e+00   6.208643e+00
   2_bss:  0.3624 0.4166   6.123163e+00   6.209637e+00
   2_xyz:  0.2822 0.3375   5.921112e+00   6.072019e+00
   2_adp:  0.2577 0.3207   5.857238e+00   6.023365e+00
   2_occ:  0.2575 0.3206   5.857223e+00   6.023036e+00
   3_bss:  0.2556 0.3199   5.856364e+00   6.022030e+00
   3_xyz:  0.1879 0.2393   5.581252e+00   5.781563e+00
   3_adp:  0.1669 0.2242   5.490093e+00   5.713268e+00
   3_occ:  0.1667 0.2240   5.489773e+00   5.713618e+00
   4_bss:  0.1655 0.2238   5.487634e+00   5.711160e+00
   4_xyz:  0.1383 0.1917   5.335136e+00   5.572455e+00
   4_adp:  0.1328 0.1827   5.294062e+00   5.524400e+00
   4_occ:  0.1325 0.1823   5.292833e+00   5.523881e+00
   5_bss:  0.1327 0.1825   5.293416e+00   5.524474e+00
   5_xyz:  0.1194 0.1689   5.212314e+00   5.456191e+00
   5_adp:  0.1175 0.1653   5.195843e+00   5.436239e+00
   5_occ:  0.1174 0.1652   5.195322e+00   5.435983e+00
   5_bss:  0.1174 0.1652   5.195362e+00   5.435981e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.333   4.827   8.307   7.677  11.047   0.000   0.000   0.000
   1_xyz:  0.333   4.827   8.307   7.677  11.047   0.000   0.000   0.000
   1_adp:  0.333   4.827   8.307   7.677  11.047   0.000   0.000   0.000
   1_occ:  0.333   4.827   8.307   7.677  11.047   0.000   0.000   0.000
   2_bss:  0.337  34.401   3.944   3.445   6.579   0.000   0.000   0.000
   2_xyz:  0.337  34.401   3.944   3.445   6.579   0.000   0.000   0.000
   2_adp:  0.337  34.401   3.944   3.445   6.579   0.000   0.000   0.000
   2_occ:  0.337  34.401   3.944   3.445   6.579   0.000   0.000   0.000
   3_bss:  0.321  34.401   1.935   2.257   4.439   0.000   0.000   0.000
   3_xyz:  0.321  34.401   1.935   2.257   4.439   0.000   0.000   0.000
   3_adp:  0.321  34.401   1.935   2.257   4.439   0.000   0.000   0.000
   3_occ:  0.321  34.401   1.935   2.257   4.439   0.000   0.000   0.000
   4_bss:  0.324  47.788   0.520   1.264   3.202   0.000   0.000   0.000
   4_xyz:  0.324  47.788   0.520   1.264   3.202   0.000   0.000   0.000
   4_adp:  0.324  47.788   0.520   1.264   3.202   0.000   0.000   0.000
   4_occ:  0.324  47.788   0.520   1.264   3.202   0.000   0.000   0.000
   5_bss:  0.321  47.788   0.157   1.066   2.839   0.000   0.000   0.000
   5_xyz:  0.321  47.788   0.157   1.066   2.839   0.000   0.000   0.000
   5_adp:  0.321  47.788   0.157   1.066   2.839   0.000   0.000   0.000
   5_occ:  0.321  47.788   0.157   1.066   2.839   0.000   0.000   0.000
   5_bss:  0.324  49.163  -1.177  -0.316   1.492  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.298 0.3900  0.4669    76760.897
   1_bss:  60.769 0.3824  0.5963    75145.523
   1_xyz:  50.218 0.5170  0.7841    56181.556
   1_adp:  46.801 0.5599  0.9117    51531.576
   1_occ:  46.897 0.5586  0.9073    51686.506
   2_bss:  46.646 0.5617  0.7868    51457.658
   2_xyz:  36.047 0.6882  0.9353    31488.865
   2_adp:  33.210 0.7213  0.9730    27602.721
   2_occ:  33.220 0.7212  0.9729    27625.975
   3_bss:  33.102 0.7226  0.9138    27514.951
   3_xyz:  23.675 0.8247  1.0028    14783.941
   3_adp:  21.681 0.8454  1.0134    12920.810
   3_occ:  21.695 0.8452  1.0131    12916.154
   4_bss:  21.577 0.8463  0.9709    12819.076
   4_xyz:  18.048 0.8801  0.9851     9424.721
   4_adp:  16.982 0.8900  0.9831     8647.641
   4_occ:  16.983 0.8900  0.9830     8644.063
   5_bss:  16.970 0.8902  0.9721     8656.843
   5_xyz:  15.538 0.9023  0.9799     7476.802
   5_adp:  15.123 0.9059  0.9781     7214.383
   5_occ:  15.118 0.9059  0.9780     7200.683
   5_bss:  15.118 0.9059  0.9788     7201.350
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3318e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3318e+01
   1_xyz:   1.729  0.013  0.106 18.310  0.007  4.105   1.4736e-01
   1_adp:   1.729  0.013  0.106 18.310  0.007  4.105   1.4736e-01
   1_occ:   1.729  0.013  0.106 18.310  0.007  4.105   1.4736e-01
   2_bss:   1.729  0.013  0.106 18.310  0.007  4.105   1.4736e-01
   2_xyz:   1.237  0.009  0.082 16.201  0.005  4.106   8.8527e-02
   2_adp:   1.237  0.009  0.082 16.201  0.005  4.106   8.8527e-02
   2_occ:   1.237  0.009  0.082 16.201  0.005  4.106   8.8527e-02
   3_bss:   1.237  0.009  0.082 16.201  0.005  4.106   8.8527e-02
   3_xyz:   1.137  0.008  0.079 15.795  0.005  4.125   7.5348e-02
   3_adp:   1.137  0.008  0.079 15.795  0.005  4.125   7.5348e-02
   3_occ:   1.137  0.008  0.079 15.795  0.005  4.125   7.5348e-02
   4_bss:   1.137  0.008  0.079 15.795  0.005  4.125   7.5348e-02
   4_xyz:   1.043  0.007  0.074 15.633  0.004  4.123   6.4803e-02
   4_adp:   1.043  0.007  0.074 15.633  0.004  4.123   6.4803e-02
   4_occ:   1.043  0.007  0.074 15.633  0.004  4.123   6.4803e-02
   5_bss:   1.043  0.007  0.074 15.633  0.004  4.123   6.4803e-02
   5_xyz:   1.121  0.008  0.082 15.816  0.004  4.112   7.2867e-02
   5_adp:   1.121  0.008  0.082 15.816  0.004  4.112   7.2867e-02
   5_occ:   1.121  0.008  0.082 15.816  0.004  4.112   7.2867e-02
   5_bss:   1.121  0.008  0.082 15.816  0.004  4.112   7.2867e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.132   6.9018e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.132   6.9018e+00
   1_xyz:  14.728  0.166  0.440 88.883  0.058  2.070   1.0076e-01
   1_adp:  14.728  0.166  0.440 88.883  0.058  2.070   1.0076e-01
   1_occ:  14.728  0.166  0.440 88.883  0.058  2.070   1.0076e-01
   2_bss:  14.728  0.166  0.440 88.883  0.058  2.070   1.0076e-01
   2_xyz:   8.442  0.094  0.296 87.098  0.039  2.186   9.2773e-02
   2_adp:   8.442  0.094  0.296 87.098  0.039  2.186   9.2773e-02
   2_occ:   8.442  0.094  0.296 87.098  0.039  2.186   9.2773e-02
   3_bss:   8.442  0.094  0.296 87.098  0.039  2.186   9.2773e-02
   3_xyz:   7.311  0.044  0.297 86.380  0.036  2.229   7.0184e-02
   3_adp:   7.311  0.044  0.297 86.380  0.036  2.229   7.0184e-02
   3_occ:   7.311  0.044  0.297 86.380  0.036  2.229   7.0184e-02
   4_bss:   7.311  0.044  0.297 86.380  0.036  2.229   7.0184e-02
   4_xyz:   8.101  0.044  0.261 87.217  0.039  2.316   4.3467e-02
   4_adp:   8.101  0.044  0.261 87.217  0.039  2.316   4.3467e-02
   4_occ:   8.101  0.044  0.261 87.217  0.039  2.316   4.3467e-02
   5_bss:   8.101  0.044  0.261 87.217  0.039  2.316   4.3467e-02
   5_xyz:   6.847  0.042  0.313 85.615  0.030  2.321   5.2836e-02
   5_adp:   6.847  0.042  0.313 85.615  0.030  2.321   5.2836e-02
   5_occ:   6.847  0.042  0.313 85.615  0.030  2.321   5.2836e-02
   5_bss:   6.847  0.042  0.313 85.615  0.030  2.321   5.2836e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  79.54   0.00  14.66  71.13   0.00  12.43  79.54   0.00  26.81
   1_occ:  79.54   0.00  14.66  71.13   0.00  12.43  79.54   0.00  26.81
   2_bss:  79.54   0.00  14.66  71.13   0.00  12.43  79.54   0.00  26.81
   2_xyz:  79.54   0.00  14.66  71.13   0.00  12.43  79.54   0.00  26.81
   2_adp:  78.42   0.00  14.42  73.28   0.00  11.07  78.42   0.00  32.67
   2_occ:  78.42   0.00  14.42  73.28   0.00  11.07  78.42   0.00  32.67
   3_bss:  78.42   0.00  14.42  73.28   0.00  11.07  78.42   0.00  32.67
   3_xyz:  78.42   0.00  14.42  73.28   0.00  11.07  78.42   0.00  32.67
   3_adp:  82.40   0.00  14.77  76.70   0.00  10.28  82.40   0.72  39.25
   3_occ:  82.40   0.00  14.77  76.70   0.00  10.28  82.40   0.72  39.25
   4_bss:  82.40   0.00  14.77  76.70   0.00  10.28  82.40   0.72  39.25
   4_xyz:  82.40   0.00  14.77  76.70   0.00  10.28  82.40   0.72  39.25
   4_adp:  86.70   0.00  14.45  86.70   0.00   9.89  84.36   2.31  39.28
   4_occ:  86.70   0.00  14.45  86.70   0.00   9.89  84.36   2.31  39.28
   5_bss:  86.70   0.00  14.45  86.70   0.00   9.89  84.36   2.31  39.28
   5_xyz:  86.70   0.00  14.45  86.70   0.00   9.89  84.36   2.31  39.28
   5_adp:  87.86   0.00  14.08  87.86   0.00   9.67  82.32   2.97  38.11
   5_occ:  87.86   0.00  14.08  87.86   0.00   9.67  82.32   2.97  38.11
   5_bss:  89.24   1.38  15.46  89.24   1.38  11.04  83.69   4.34  39.49
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.302    0.010    0.413
   1_adp:    1.302    0.010    0.413
   1_occ:    1.302    0.010    0.413
   2_bss:    1.302    0.010    0.413
   2_xyz:    1.837    0.046    0.577
   2_adp:    1.837    0.046    0.577
   2_occ:    1.837    0.046    0.577
   3_bss:    1.837    0.046    0.577
   3_xyz:    1.673    0.063    0.688
   3_adp:    1.673    0.063    0.688
   3_occ:    1.673    0.063    0.688
   4_bss:    1.673    0.063    0.688
   4_xyz:    1.802    0.044    0.728
   4_adp:    1.802    0.044    0.728
   4_occ:    1.802    0.044    0.728
   5_bss:    1.802    0.044    0.728
   5_xyz:    1.933    0.032    0.756
   5_adp:    1.933    0.032    0.756
   5_occ:    1.933    0.032    0.756
   5_bss:    1.933    0.032    0.756
------------------------------------------------------------------------

CPU time actual refinement: 341.49


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_53/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_53/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_53/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_53/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_53/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 341.34 
  Macro-tasks:
    bulk solvent and scale       = 39.33  
    individual site refinement   = 139.18 
    weights calculation          = 31.57  
    collect and process          = 6.41   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 216.61 
  Micro-tasks:
    mask                            = 2.41   
    f_calc                          = 107.23 
    alpha_beta                      = 8.18   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 117.43 
    fmodel                         = 7.60   
    r_factors                      = 0.27   
    phase_errors                   = 10.46  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 254.96 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.791 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    676 calls, 106.97 s
gradients_fft:          621 calls, 104.02 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 00:39:22 PST -0800 (1200472762.65 s)
Start R-work = 0.4925, R-free = 0.4863 (no bulk solvent and anisotropic scale)
Final R-work = 0.1359, R-free = 0.1810 (no bulk solvent and anisotropic scale)

Start R-work = 0.4840, R-free = 0.4811
Final R-work = 0.1174, R-free = 0.1652