# Date 2008-01-16 Time 02:33:56 PST -0800 (1200479636.91 s)
#phil __OFF__

Command line arguments: "../886.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25287
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 886

-------------------------------------------------------------------------------
  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: (70.9525, 46.4607, 86.822, 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: (70.9525, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.98286
Completeness in resolution range: 0.956261
Completeness with d_max=infinity: 0.953375

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1235
                             d_min =   1.9829

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: (70.9525, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.98286
Completeness in resolution range: 0.956261
Completeness with d_max=infinity: 0.953375

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1239 -  4.2434 [2153/2178]  1938   215  10.0%
  bin  2:  4.2434 -  3.3805 [2053/2073]  1848   205  10.0%
  bin  3:  3.3805 -  2.9568 [2058/2077]  1849   209  10.2%
  bin  4:  2.9568 -  2.6881 [2006/2036]  1809   197   9.8%
  bin  5:  2.6881 -  2.4964 [2023/2042]  1824   199   9.8%
  bin  6:  2.4964 -  2.3498 [1998/2023]  1791   207  10.4%
  bin  7:  2.3498 -  2.2325 [1980/2008]  1784   196   9.9%
  bin  8:  2.2325 -  2.1356 [1992/2028]  1796   196   9.8%
  bin  9:  2.1356 -  2.0536 [1960/2002]  1759   201  10.3%
  bin 10:  2.0536 -  1.9829 [1366/2018]  1232   134   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_886/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: 0.14 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:
        1.81 -     2.42: 17
        2.42 -     3.04: 2176
        3.04 -     3.66: 4679
        3.66 -     4.28: 9027
        4.28 -     4.90: 12289
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.293 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28183 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_886/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_886/model_refine_001.geo

CPU time processing inputs: 9.64


============================ 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 = 70.9525 46.4607 86.82195 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: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4439   r_free= 0.4288   ksol= 0.00   Bsol= 0.00   scale= 0.815    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.239368                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7332 0.99   1397  155 0.3753 0.3558      6.5487      6.4915|
|  2:  4.7332 -  3.7761 0.99   1346  152 0.3370 0.3373      6.6779       6.658|
|  3:  3.7761 -  3.3045 0.99   1319  141 0.3783 0.3440       6.563      6.5606|
|  4:  3.3045 -  3.0049 0.99   1312  152 0.4235 0.3823      6.4762         6.4|
|  5:  3.0049 -  2.7910 0.99   1306  147 0.4695 0.4416      6.3285      6.3329|
|  6:  2.7910 -  2.6273 0.99   1302  136 0.4653 0.4992      6.2368       6.168|
|  7:  2.6273 -  2.4964 0.99   1286  142 0.5040 0.4875      6.2236      6.2308|
|  8:  2.4964 -  2.3881 0.98   1274  145 0.4990 0.4448      6.1547      6.1421|
|  9:  2.3881 -  2.2965 0.98   1262  147 0.4722 0.4942       6.083      6.1286|
| 10:  2.2965 -  2.2175 1.00   1300  144 0.5119 0.4508      6.1001      6.0353|
| 11:  2.2175 -  2.1484 0.98   1276  137 0.5059 0.4819      6.0165      6.0066|
| 12:  2.1484 -  2.0871 0.98   1249  139 0.5064 0.5361      5.9734      6.0216|
| 13:  2.0871 -  2.0323 0.99   1286  141 0.5054 0.4825      5.8653       5.794|
| 14:  2.0323 -  1.9829 0.55    715   81 0.5211 0.5149      5.8636      5.7771|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7332  1397   155  0.73  31.63   0.80     0.77      61155.89|
|  2:  4.7332 -  3.7761  1346   152  0.78  28.34   0.90     0.83      75684.31|
|  3:  3.7761 -  3.3045  1319   141  0.70  35.16   0.88     0.80      78663.43|
|  4:  3.3045 -  3.0049  1312   152  0.64  40.21   0.82     0.72      71016.24|
|  5:  3.0049 -  2.7910  1306   147  0.54  48.37   0.76     0.63      63229.62|
|  6:  2.7910 -  2.6273  1302   136  0.50  51.80   0.75     0.56      58331.79|
|  7:  2.6273 -  2.4964  1286   142  0.46  55.58   0.75     0.52      56481.75|
|  8:  2.4964 -  2.3881  1274   145  0.44  56.99   0.74     0.50      52281.12|
|  9:  2.3881 -  2.2965  1262   147  0.47  54.68   0.75     0.52      46221.40|
| 10:  2.2965 -  2.2175  1300   144  0.46  55.61   0.77     0.54      41331.57|
| 11:  2.2175 -  2.1484  1276   137  0.44  57.06   0.77     0.53      40063.11|
| 12:  2.1484 -  2.0871  1249   139  0.41  59.53   0.78     0.49      38788.89|
| 13:  2.0871 -  2.0323  1286   141  0.38  61.64   0.73     0.46      34196.31|
| 14:  2.0323 -  1.9829   715    81  0.43  57.51   0.73     0.47      26622.06|
|alpha:            min =        0.46 max =            0.83 mean =         0.60|
|beta:             min =    26622.06 max =        78663.43 mean =     54262.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.96 mean =        49.07|
|phase err.(test): min =        0.00 max =           89.92 mean =        49.20|
|-----------------------------------------------------------------------------|

============================== 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 = 8.402902              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.222   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.760791              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.725   (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 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      686 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1489 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2630 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3930 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5029 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6574 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7671 |
|-----------------------------------------------------------------------------|
|-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 |       53.901 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.693 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    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 = 11.967)------------------------------------------|
|    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: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4516   r_free= 0.4349   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.244081                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4362   r_free= 0.4151   ksol= 0.35   Bsol= 18.82   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.94,8.97,8.48,0.00,0.00,0.00); trace/3= 8.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.234166                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.606657              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.027   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.729164              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.873   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4362      final r-factor (work) = 0.3317          |
| start r-factor (free) = 0.4151      final r-factor (free) = 0.3472          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.6558 = 7.61 * 0.50 * 6.2458 + 1.00 * 53.9009                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3166 = 7.61 * 0.50 * 6.0989 + 1.00 * 0.1205                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3317      final r-factor (work) = 0.2719          |
| start r-factor (free) = 0.3472      final r-factor (free) = 0.3142          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4618 = 0.73 * 1.00 * 6.0989 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3435 = 0.73 * 1.00 * 5.9389 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.15   11.42    None  None   None       |
|    all(noH): 2823   0      0.00    73.15   11.42    None  None   None       |
|    Sol.    : 438    0      0.00    73.15   27.98    None  None   None       |
|    Mac.    : 2385   0      0.00    60.17   8.38     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 -   7.316: 1351   |   5:    36.577 -  43.893:   80        |
|      1:     7.316 -  14.631:  732   |   6:    43.893 -  51.208:   37        |
|      2:    14.631 -  21.947:  315   |   7:    51.208 -  58.524:   17        |
|      3:    21.947 -  29.262:  176   |   8:    58.524 -  65.839:    9        |
|      4:    29.262 -  36.577:  105   |   9:    65.839 -  73.155:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2719 r_free = 0.3142             target_work(ml) = 5.892         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2713 r_free = 0.3143             target_work(ml) = 5.891         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2713   r_free= 0.3143   ksol= 0.35   Bsol= 18.82   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.94,8.97,8.48,0.00,0.00,0.00); trace/3= 8.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.890647                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2662   r_free= 0.3086   ksol= 0.34   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.39,4.70,5.13,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.888818                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.082605              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.337   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.354952              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.840  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2662      final r-factor (work) = 0.1869          |
| start r-factor (free) = 0.3086      final r-factor (free) = 0.2314          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2813 = 3.08 * 0.50 * 5.9439 + 1.00 * 0.1200                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8873 = 3.08 * 0.50 * 5.7269 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1869      final r-factor (work) = 0.1712          |
| start r-factor (free) = 0.2314      final r-factor (free) = 0.2184          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0457 = 0.35 * 1.00 * 5.7269 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9730 = 0.35 * 1.00 * 5.5274 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.86   11.43    None  None   None       |
|    all(noH): 2823   0      0.00    73.86   11.43    None  None   None       |
|    Sol.    : 438    0      0.00    73.86   31.09    None  None   None       |
|    Mac.    : 2385   0      0.00    61.28   7.82     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:     0.000 -   7.386: 1495   |   5:    36.929 -  44.314:   91        |
|      1:     7.386 -  14.772:  665   |   6:    44.314 -  51.700:   44        |
|      2:    14.772 -  22.157:  226   |   7:    51.700 -  59.086:   20        |
|      3:    22.157 -  29.543:  121   |   8:    59.086 -  66.472:    8        |
|      4:    29.543 -  36.929:  151   |   9:    66.472 -  73.857:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1712 r_free = 0.2184             target_work(ml) = 5.499         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1711 r_free = 0.2184             target_work(ml) = 5.499         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1711   r_free= 0.2184   ksol= 0.34   Bsol= 50.00   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.39,4.70,5.13,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.499387                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1704   r_free= 0.2173   ksol= 0.34   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,3.14,4.32,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.500503                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.661110              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.684  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 7.715235              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.258  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1704      final r-factor (work) = 0.1311          |
| start r-factor (free) = 0.2173      final r-factor (free) = 0.1780          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1891 = 3.66 * 0.50 * 5.5331 + 1.00 * 0.0604                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9297 = 3.66 * 0.50 * 5.3862 + 1.00 * 0.0701                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1311      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1780      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 41.5665 = 7.72 * 1.00 * 5.3862 + 1.00 * 0.0110                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 40.4961 = 7.72 * 1.00 * 5.2469 + 1.00 * 0.0148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.52   12.44    None  None   None       |
|    all(noH): 2823   0      0.00    83.52   12.44    None  None   None       |
|    Sol.    : 438    0      0.29    83.52   36.77    None  None   None       |
|    Mac.    : 2385   0      0.00    77.20   7.97     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 -   8.352: 1666   |   5:    41.761 -  50.113:   81        |
|      1:     8.352 -  16.704:  564   |   6:    50.113 -  58.465:   81        |
|      2:    16.704 -  25.057:  167   |   7:    58.465 -  66.818:   34        |
|      3:    25.057 -  33.409:  115   |   8:    66.818 -  75.170:   15        |
|      4:    33.409 -  41.761:   95   |   9:    75.170 -  83.522:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1219 r_free = 0.1697             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1699             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1699   ksol= 0.34   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,3.14,4.32,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.220956                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1697   ksol= 0.33   Bsol= 52.98   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.97,2.80,4.16,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.219574                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.610390              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.159  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.165237              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.005  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2944 = 1.61 * 0.50 * 5.2463 + 1.00 * 0.0701                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2526 = 1.61 * 0.50 * 5.2143 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1195      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8763 = 0.17 * 1.00 * 5.2143 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8784 = 0.17 * 1.00 * 5.2181 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.20   11.62    None  None   None       |
|    all(noH): 2823   0      0.00    76.20   11.62    None  None   None       |
|    Sol.    : 438    0      1.59    76.20   33.17    None  None   None       |
|    Mac.    : 2385   0      0.00    75.08   7.66     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 -   7.621: 1616   |   5:    38.102 -  45.723:   82        |
|      1:     7.621 -  15.241:  613   |   6:    45.723 -  53.343:   66        |
|      2:    15.241 -  22.861:  166   |   7:    53.343 -  60.964:   33        |
|      3:    22.861 -  30.482:  116   |   8:    60.964 -  68.584:   14        |
|      4:    30.482 -  38.102:  110   |   9:    68.584 -  76.204:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1212 r_free = 0.1640             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1211 r_free = 0.1638             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1638   ksol= 0.33   Bsol= 52.98   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.97,2.80,4.16,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.203747                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1637   ksol= 0.33   Bsol= 52.98   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.78,2.59,4.04,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.203667                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.442823              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.963  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.820030              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.028   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0355 = 3.44 * 0.50 * 5.2174 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9741 = 3.44 * 0.50 * 5.1691 + 1.00 * 0.0760                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2505 = 0.82 * 1.00 * 5.1691 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2479 = 0.82 * 1.00 * 5.1415 + 1.00 * 0.0317                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.16   11.94    None  None   None       |
|    all(noH): 2823   0      0.00    81.16   11.94    None  None   None       |
|    Sol.    : 438    0      1.37    78.89   34.75    None  None   None       |
|    Mac.    : 2385   0      0.00    81.16   7.75     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 -   8.116: 1671   |   5:    40.579 -  48.695:   81        |
|      1:     8.116 -  16.232:  579   |   6:    48.695 -  56.811:   72        |
|      2:    16.232 -  24.347:  148   |   7:    56.811 -  64.926:   23        |
|      3:    24.347 -  32.463:  116   |   8:    64.926 -  73.042:   17        |
|      4:    32.463 -  40.579:  111   |   9:    73.042 -  81.158:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1582             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1101 r_free = 0.1583             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1583   ksol= 0.33   Bsol= 52.98   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.78,2.59,4.04,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143918                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7332 0.99   1397  155 0.0979 0.1315      5.3776      5.5339|
|  2:  4.7332 -  3.7761 0.99   1346  152 0.0844 0.1139      5.4306      5.6289|
|  3:  3.7761 -  3.3045 0.99   1319  141 0.1058 0.1512      5.4718       5.856|
|  4:  3.3045 -  3.0049 0.99   1312  152 0.1178 0.1669      5.4432      5.6037|
|  5:  3.0049 -  2.7910 0.99   1306  147 0.1317 0.1704      5.3206      5.5711|
|  6:  2.7910 -  2.6273 0.99   1302  136 0.1168 0.1835      5.1832      5.4492|
|  7:  2.6273 -  2.4964 0.99   1286  142 0.1266 0.1622      5.1681      5.3577|
|  8:  2.4964 -  2.3881 0.98   1274  145 0.1142 0.1723       5.067      5.3382|
|  9:  2.3881 -  2.2965 0.98   1262  147 0.1184 0.1814      5.0553      5.3284|
| 10:  2.2965 -  2.2175 1.00   1300  144 0.1090 0.1701      4.9552      5.2155|
| 11:  2.2175 -  2.1484 0.98   1276  137 0.1136 0.1808      4.9537      5.2836|
| 12:  2.1484 -  2.0871 0.98   1249  139 0.1090 0.1777      4.8765       5.201|
| 13:  2.0871 -  2.0323 0.99   1286  141 0.1120 0.1659      4.7792       5.026|
| 14:  2.0323 -  1.9829 0.55    715   81 0.0968 0.1606      4.6552      4.8803|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7332  1397   155  0.94   9.23   0.98     0.95       7211.92|
|  2:  4.7332 -  3.7761  1346   152  0.95   8.06   1.01     1.00       9146.65|
|  3:  3.7761 -  3.3045  1319   141  0.93  11.43   1.02     1.02      10420.03|
|  4:  3.3045 -  3.0049  1312   152  0.92  13.68   1.01     0.98      10411.16|
|  5:  3.0049 -  2.7910  1306   147  0.90  15.97   0.99     0.97       8365.05|
|  6:  2.7910 -  2.6273  1302   136  0.90  16.04   0.98     0.95       6914.03|
|  7:  2.6273 -  2.4964  1286   142  0.91  15.53   0.98     0.95       6165.55|
|  8:  2.4964 -  2.3881  1274   145  0.91  15.48   0.98     0.96       5386.56|
|  9:  2.3881 -  2.2965  1262   147  0.91  15.83   1.00     0.96       5288.86|
| 10:  2.2965 -  2.2175  1300   144  0.90  16.17   0.99     0.96       4549.79|
| 11:  2.2175 -  2.1484  1276   137  0.90  16.55   0.99     0.95       4516.49|
| 12:  2.1484 -  2.0871  1249   139  0.91  15.37   1.01     1.00       4045.02|
| 13:  2.0871 -  2.0323  1286   141  0.90  16.74   1.00     0.97       3387.10|
| 14:  2.0323 -  1.9829   715    81  0.92  14.20   0.98     0.95       2619.72|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2619.72 max =        10420.03 mean =      6474.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.73 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.67|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1583   ksol= 0.33   Bsol= 56.26   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,-0.56,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143972                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1583   ksol= 0.33   Bsol= 56.26   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,-0.56,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143972                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7332 0.99   1397  155 0.0979 0.1316      5.3781      5.5347|
|  2:  4.7332 -  3.7761 0.99   1346  152 0.0844 0.1139      5.4309      5.6288|
|  3:  3.7761 -  3.3045 0.99   1319  141 0.1058 0.1512      5.4718      5.8562|
|  4:  3.3045 -  3.0049 0.99   1312  152 0.1178 0.1669      5.4432      5.6038|
|  5:  3.0049 -  2.7910 0.99   1306  147 0.1317 0.1704      5.3205      5.5707|
|  6:  2.7910 -  2.6273 0.99   1302  136 0.1168 0.1834      5.1831      5.4492|
|  7:  2.6273 -  2.4964 0.99   1286  142 0.1266 0.1623      5.1682       5.358|
|  8:  2.4964 -  2.3881 0.98   1274  145 0.1142 0.1722       5.067      5.3381|
|  9:  2.3881 -  2.2965 0.98   1262  147 0.1184 0.1813      5.0553      5.3282|
| 10:  2.2965 -  2.2175 1.00   1300  144 0.1090 0.1702      4.9553      5.2158|
| 11:  2.2175 -  2.1484 0.98   1276  137 0.1136 0.1807      4.9538      5.2835|
| 12:  2.1484 -  2.0871 0.98   1249  139 0.1090 0.1777      4.8764      5.2009|
| 13:  2.0871 -  2.0323 0.99   1286  141 0.1120 0.1658      4.7791      5.0255|
| 14:  2.0323 -  1.9829 0.55    715   81 0.0968 0.1606       4.655      4.8801|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7332  1397   155  0.94   9.23   0.98     0.95       7221.55|
|  2:  4.7332 -  3.7761  1346   152  0.95   8.06   1.01     1.00       9154.56|
|  3:  3.7761 -  3.3045  1319   141  0.93  11.43   1.03     1.02      10422.81|
|  4:  3.3045 -  3.0049  1312   152  0.92  13.69   1.01     0.98      10410.62|
|  5:  3.0049 -  2.7910  1306   147  0.90  15.97   1.00     0.97       8362.78|
|  6:  2.7910 -  2.6273  1302   136  0.90  16.04   0.98     0.96       6912.98|
|  7:  2.6273 -  2.4964  1286   142  0.91  15.53   0.99     0.96       6166.25|
|  8:  2.4964 -  2.3881  1274   145  0.91  15.48   0.99     0.97       5386.64|
|  9:  2.3881 -  2.2965  1262   147  0.91  15.83   1.01     0.97       5289.14|
| 10:  2.2965 -  2.2175  1300   144  0.90  16.17   1.00     0.97       4550.44|
| 11:  2.2175 -  2.1484  1276   137  0.90  16.55   1.00     0.95       4516.98|
| 12:  2.1484 -  2.0871  1249   139  0.91  15.37   1.02     1.01       4044.86|
| 13:  2.0871 -  2.0323  1286   141  0.90  16.73   1.00     0.98       3385.81|
| 14:  2.0323 -  1.9829   715    81  0.92  14.20   0.99     0.96       2618.02|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2618.02 max =        10422.81 mean =      6475.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.73 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.27    84.43   15.21    None  None   None       |
|    all(noH): 2823   0      3.27    84.43   15.21    None  None   None       |
|    Sol.    : 438    0      4.65    82.16   38.02    None  None   None       |
|    Mac.    : 2385   0      3.27    84.43   11.02    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:     3.271 -  11.387: 1671   |   5:    43.850 -  51.966:   81        |
|      1:    11.387 -  19.503:  579   |   6:    51.966 -  60.081:   72        |
|      2:    19.503 -  27.618:  148   |   7:    60.081 -  68.197:   23        |
|      3:    27.618 -  35.734:  116   |   8:    68.197 -  76.313:   17        |
|      4:    35.734 -  43.850:  111   |   9:    76.313 -  84.429:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.360 - 4.748
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 297
   mapped sites are within: 0.720 - 4.748

peak=   11.011 closest distance to " CB  VAL A 230 " =    1.479
peak=    6.556 closest distance to " CG2 VAL A 296 " =    1.068
peak=    6.087 closest distance to " NH2 ARG A  56 " =    2.201
peak=    5.910 closest distance to " CG  LEU A   5 " =    1.177
peak=    5.824 closest distance to " NE2 GLN A  11 " =    1.179
peak=    5.800 closest distance to " CD2 LEU A   5 " =    1.250
peak=    5.713 closest distance to " O   HOH Z 144 " =    1.984
peak=    5.591 closest distance to " CG  LEU A 228 " =    1.120
peak=    5.452 closest distance to " O   HOH Z 232 " =    2.332
peak=    5.420 closest distance to " CG  PRO A  54 " =    1.271
peak=    5.074 closest distance to " CB  GLN A 183 " =    1.226
peak=    4.998 closest distance to " CB  GLN A 223 " =    1.474
peak=    4.973 closest distance to " CB  VAL A 296 " =    1.105
peak=    4.883 closest distance to " O   HOH Z 427 " =    2.854
peak=    4.734 closest distance to " CB  SER A  63 " =    1.298
peak=    4.625 closest distance to " O   HOH Z   9 " =    1.400
peak=    4.608 closest distance to " CB  PRO A  54 " =    0.961
peak=    4.588 closest distance to " O   HOH Z 126 " =    1.993
peak=    4.534 closest distance to " O   HOH Z 425 " =    1.450
peak=    4.518 closest distance to " O   HOH Z 369 " =    2.134
peak=    4.510 closest distance to " O   HOH Z  55 " =    2.423
peak=    4.475 closest distance to " CB  ASN A 148 " =    1.343
peak=    4.435 closest distance to " C   PRO A 198 " =    1.556
peak=    4.428 closest distance to " CB  VAL A 230 " =    1.156
peak=    4.351 closest distance to " CB  GLU A 152 " =    1.247
peak=    4.330 closest distance to " O   HOH Z 298 " =    1.817
peak=    4.327 closest distance to " O   HOH Z 272 " =    1.858
peak=    4.314 closest distance to " O   HOH Z 209 " =    2.290
peak=    4.290 closest distance to " O   HOH Z 193 " =    1.819
peak=    4.287 closest distance to " O   HOH Z 346 " =    1.618
peak=    4.268 closest distance to " O   HOH Z  61 " =    1.644
peak=    4.247 closest distance to " CB  ARG A  79 " =    1.498
peak=    4.233 closest distance to " CB  TRP A 266 " =    1.009
peak=    4.231 closest distance to " O   HOH Z 236 " =    2.119
peak=    4.214 closest distance to " CD2 LEU A 228 " =    1.159
peak=    4.207 closest distance to " O   SER A  87 " =    2.320
peak=    4.204 closest distance to " O   HOH Z 303 " =    2.142
peak=    4.190 closest distance to " CB  SER A   3 " =    1.353
peak=    4.170 closest distance to " O   HOH Z 316 " =    3.033
peak=    4.155 closest distance to " CB  ARG A 275 " =    0.910
peak=    4.127 closest distance to " O   HOH Z 368 " =    2.142
peak=    4.107 closest distance to " CG  PRO A 213 " =    1.163
peak=    4.089 closest distance to " O   HOH Z  78 " =    1.685
peak=    4.079 closest distance to " CA  TYR A  30 " =    1.010
peak=    4.078 closest distance to " CD  ARG A  66 " =    2.423
peak=    4.074 closest distance to " O   HOH Z 193 " =    1.648
peak=    4.071 closest distance to " O   HOH Z 234 " =    3.760
peak=    4.065 closest distance to " ND2 ASN A 187 " =    1.478
peak=    4.059 closest distance to " CB  VAL A 265 " =    1.320
peak=    4.045 closest distance to " OD1 ASN A  69 " =    2.626
peak=    4.037 closest distance to " O   HOH Z 158 " =    3.164
peak=    3.983 closest distance to " O   HOH Z   2 " =    1.510
peak=    3.979 closest distance to " CG  LEU A 167 " =    1.220
peak=    3.978 closest distance to " O   HOH Z 261 " =    2.091
peak=    3.975 closest distance to " O   HOH Z 411 " =    3.709
peak=    3.961 closest distance to " O   HOH Z 389 " =    1.938
peak=    3.955 closest distance to " O   HOH Z  30 " =    1.565
peak=    3.938 closest distance to " CD  ARG A 159 " =    0.720
peak=    3.928 closest distance to " CB  ASN A 142 " =    1.026
peak=    3.923 closest distance to " CB  ASP A 140 " =    0.942
peak=    3.920 closest distance to " CZ  PHE A 218 " =    1.083
peak=    3.918 closest distance to " CB  GLU A 128 " =    1.061
peak=    3.907 closest distance to " NH2AARG A 190 " =    1.814
peak=    3.881 closest distance to " N   PHE A 130 " =    1.249
peak=    3.874 closest distance to " O   HOH Z 203 " =    1.741
peak=    3.847 closest distance to " CG  PRO A 243 " =    1.108
peak=    3.838 closest distance to " CA  ALA A  51 " =    0.974
peak=    3.829 closest distance to " O   HOH Z 403 " =    1.655
peak=    3.826 closest distance to " O   HOH Z   1 " =    1.843
peak=    3.818 closest distance to " CG  PRO A 198 " =    1.187
peak=    3.817 closest distance to " OG  SER A  97 " =    2.928
peak=    3.814 closest distance to " CB BVAL A  41 " =    1.208
peak=    3.813 closest distance to " CB  ARG A 190 " =    1.507
peak=    3.789 closest distance to " O   HOH Z  88 " =    3.256
peak=    3.785 closest distance to " O   HOH Z  10 " =    1.749
peak=    3.784 closest distance to " O   HOH Z 214 " =    2.095
peak=    3.777 closest distance to " O   HOH Z 193 " =    1.952
peak=    3.776 closest distance to " CB  SER A 216 " =    0.858
peak=    3.774 closest distance to " CB  ASN A  39 " =    0.918
peak=    3.773 closest distance to " NH1AARG A 145 " =    1.101
peak=    3.766 closest distance to " O   HOH Z 126 " =    1.735
peak=    3.766 closest distance to " CB  GLU A 277 " =    3.576
peak=    3.744 closest distance to " O   HOH Z  43 " =    1.853
peak=    3.737 closest distance to " O   HOH Z 248 " =    1.640
peak=    3.733 closest distance to " O   HOH Z 286 " =    2.432
peak=    3.703 closest distance to " CB  LEU A 228 " =    1.242
peak=    3.693 closest distance to " CB  SER A 212 " =    1.225
peak=    3.689 closest distance to " OG BSER A 164 " =    2.221
peak=    3.683 closest distance to " CA  THR A 264 " =    0.756
peak=    3.681 closest distance to " CD1 ILE A  33 " =    1.711
peak=    3.679 closest distance to " CB  VAL A 202 " =    1.589
peak=    3.670 closest distance to " CA  LYS A 117 " =    1.181
peak=    3.670 closest distance to " CE  LYS A  76 " =    0.870
peak=    3.653 closest distance to " O   HOH Z  78 " =    2.111
peak=    3.648 closest distance to " O   HOH Z   1 " =    1.772
peak=    3.641 closest distance to " CB  THR A  82 " =    1.328
peak=    3.636 closest distance to " CB  ALA A   9 " =    1.611
peak=    3.636 closest distance to " O   HOH Z 371 " =    2.878
peak=    3.631 closest distance to " ND1 HIS A  86 " =    1.759
peak=    3.627 closest distance to " CG2 VAL A 257 " =    0.884
peak=    3.624 closest distance to " CG  GLN A  88 " =    1.092
peak=    3.623 closest distance to " CB  GLN A  88 " =    1.272
peak=    3.618 closest distance to " CB  TRP A 179 " =    1.486
peak=    3.618 closest distance to " NZ  LYS A 117 " =    3.110
peak=    3.615 closest distance to " CG1 ILE A  49 " =    1.463
peak=    3.610 closest distance to " CB  ASN A 187 " =    1.054
peak=    3.610 closest distance to " O   HOH Z 280 " =    3.004
peak=    3.602 closest distance to " O   HOH Z 437 " =    1.712
peak=    3.598 closest distance to " O   HOH Z 128 " =    2.101
peak=    3.586 closest distance to " CG2 THR A 221 " =    1.088
peak=    3.583 closest distance to " CD2 TRP A 179 " =    1.342
peak=    3.580 closest distance to " CB  MET A  40 " =    0.863
peak=    3.579 closest distance to " CA  ALA A 291 " =    0.903
peak=    3.576 closest distance to " CA  ASN A 215 " =    1.178
peak=    3.575 closest distance to " O   HOH Z  97 " =    1.989
peak=    3.574 closest distance to " O   HOH Z 133 " =    1.669
peak=    3.573 closest distance to " CB  LEU A 143 " =    1.174
peak=    3.571 closest distance to " O   HOH Z 423 " =    2.647
peak=    3.568 closest distance to " O   HOH Z   9 " =    1.932
peak=    3.562 closest distance to " CG1BVAL A  72 " =    1.623
peak=    3.562 closest distance to " CB  HIS A 108 " =    0.803
peak=    3.558 closest distance to " O   HOH Z 147 " =    1.738
peak=    3.553 closest distance to " O   HOH Z 409 " =    2.918
peak=    3.550 closest distance to " O   HOH Z  61 " =    1.555
peak=    3.545 closest distance to " O   HOH Z 422 " =    2.635
peak=    3.542 closest distance to " O   HOH Z 366 " =    2.900
peak=    3.542 closest distance to " CE1 TYR A 186 " =    1.333
peak=    3.536 closest distance to " O   HOH Z 148 " =    3.413
peak=    3.536 closest distance to " CG  MET A 185 " =    1.269
peak=    3.529 closest distance to " CB  THR A 157 " =    1.177
peak=    3.529 closest distance to " OE2 GLU A  53 " =    1.983
peak=    3.529 closest distance to " CA  TYR A 116 " =    1.386
peak=    3.524 closest distance to " O   HOH Z 273 " =    2.807
peak=    3.516 closest distance to " CA  ARG A 195 " =    1.222
peak=    3.515 closest distance to " O   MET A 105 " =    1.795
peak=    3.510 closest distance to " O   HOH Z 368 " =    3.628
peak=    3.506 closest distance to " O   HOH Z 250 " =    1.319
peak=    3.501 closest distance to " CB  ARG A 139 " =    0.981
peak=    3.501 closest distance to " O   HOH Z   7 " =    1.325
peak=    3.499 closest distance to " O   HOH Z 197 " =    3.265
peak=    3.495 closest distance to " CA  SER A  87 " =    0.933
peak=    3.489 closest distance to " O   HOH Z 180 " =    2.110
peak=    3.484 closest distance to " OD2 ASP A 286 " =    2.818
peak=    3.483 closest distance to " CB  ASN A 110 " =    1.186
peak=    3.478 closest distance to " CD  LYS A 166 " =    1.343
peak=    3.474 closest distance to " O   HOH Z 305 " =    3.467
peak=    3.473 closest distance to " O   HOH Z 263 " =    1.662
peak=    3.469 closest distance to " O   HOH Z 126 " =    1.455
peak=    3.460 closest distance to " NE2 HIS A 207 " =    1.459
peak=    3.460 closest distance to " O   HOH Z  58 " =    1.560
peak=    3.454 closest distance to " O   HOH Z 130 " =    2.117
peak=    3.450 closest distance to " O   HOH Z 353 " =    2.631
peak=    3.449 closest distance to " O   HOH Z  59 " =    1.833
peak=    3.448 closest distance to " CD1 LEU A 228 " =    2.032
peak=    3.443 closest distance to " O   HOH Z 380 " =    1.685
peak=    3.443 closest distance to " O   ALA A 158 " =    1.425
peak=    3.442 closest distance to " CB  ASN A 224 " =    0.998
peak=    3.440 closest distance to " O   HOH Z 213 " =    2.124
peak=    3.440 closest distance to " CG1 VAL A 153 " =    0.953
peak=    3.432 closest distance to " NH2 ARG A 156 " =    1.100
peak=    3.431 closest distance to " CB  ARG A  79 " =    0.889
peak=    3.431 closest distance to " O   HOH Z  40 " =    1.887
peak=    3.430 closest distance to " O   HOH Z 109 " =    2.501
peak=    3.428 closest distance to " O   HOH Z   3 " =    1.868
peak=    3.418 closest distance to " O   HOH Z 171 " =    3.883
peak=    3.413 closest distance to " CA  ALA A  21 " =    1.161
peak=    3.410 closest distance to " O  BHOH Z 338 " =    2.416
peak=    3.410 closest distance to " CG1 ILE A  33 " =    1.272
peak=    3.408 closest distance to " CD2 LEU A 255 " =    1.628
peak=    3.401 closest distance to " CB  LYS A 117 " =    1.213
peak=    3.399 closest distance to " N   SER A 135 " =    1.320
peak=    3.397 closest distance to " CA  LYS A 290 " =    1.327
peak=    3.396 closest distance to " CA  ALA A 158 " =    1.198
peak=    3.386 closest distance to " O   HOH Z  68 " =    2.115
peak=    3.386 closest distance to " O   HOH Z  21 " =    1.688
peak=    3.383 closest distance to " O   HOH Z 145 " =    3.677
peak=    3.379 closest distance to " O   HOH Z  63 " =    1.345
peak=    3.378 closest distance to " CD BLYS A 290 " =    1.120
peak=    3.375 closest distance to " CG  GLN A 278 " =    1.335
peak=    3.370 closest distance to " O   HOH Z 303 " =    3.008
peak=    3.369 closest distance to " OG  SER A  62 " =    2.910
peak=    3.367 closest distance to " O   HOH Z 285 " =    2.709
peak=    3.365 closest distance to " O   HOH Z 175 " =    2.158
peak=    3.365 closest distance to " CD1 LEU A 300 " =    1.140
peak=    3.364 closest distance to " CB  GLU A  46 " =    0.984
peak=    3.363 closest distance to " O   HOH Z  85 " =    2.073
peak=    3.355 closest distance to " O   HOH Z 435 " =    2.004
peak=    3.352 closest distance to " O   ALA A 291 " =    1.558
peak=    3.349 closest distance to " O   HOH Z 299 " =    4.184
peak=    3.343 closest distance to " CA  THR A 221 " =    0.935
peak=    3.342 closest distance to " N   ASN A 127 " =    1.287
peak=    3.338 closest distance to " CG1 ILE A 151 " =    1.084
peak=    3.335 closest distance to " CG BARG A 102 " =    1.870
peak=    3.332 closest distance to " O   HOH Z 132 " =    2.552
peak=    3.326 closest distance to " O   LYS A 290 " =    2.437
peak=    3.324 closest distance to " O   HOH Z 419 " =    1.845
peak=    3.324 closest distance to " CE3 TRP A 150 " =    0.953
peak=    3.322 closest distance to " O   HOH Z 329 " =    3.976
peak=    3.322 closest distance to " O   HOH Z 291 " =    1.600
peak=    3.319 closest distance to " CG2 ILE A  20 " =    1.502
peak=    3.319 closest distance to " O   HOH Z 133 " =    2.514
peak=    3.316 closest distance to " OG  SER A  62 " =    2.969
peak=    3.314 closest distance to " CB  ALA A 291 " =    1.428
peak=    3.309 closest distance to " CA  GLY A 267 " =    0.956
peak=    3.304 closest distance to " O   HOH Z 260 " =    1.449
peak=    3.302 closest distance to " O   HOH Z 344 " =    3.040
peak=    3.299 closest distance to " O   HOH Z 345 " =    3.493
peak=    3.299 closest distance to " CA  ASP A 162 " =    1.029
peak=    3.294 closest distance to " O   HOH Z 425 " =    2.049
peak=    3.292 closest distance to " O   HOH Z 423 " =    1.695
peak=    3.292 closest distance to " CA  SER A 146 " =    1.733
peak=    3.290 closest distance to " CG  ARG A 138 " =    1.214
peak=    3.285 closest distance to " CB  TRP A 150 " =    1.357
peak=    3.284 closest distance to " OE2 GLU A   2 " =    1.792
peak=    3.283 closest distance to " O   HOH Z 172 " =    3.214
peak=    3.283 closest distance to " O   HOH Z 271 " =    2.128
peak=    3.282 closest distance to " ND1 HIS A  81 " =    1.741
peak=    3.282 closest distance to " CA  ARG A  36 " =    1.083
peak=    3.281 closest distance to " CB  ALA A 104 " =    0.732
peak=    3.280 closest distance to " O   HOH Z 290 " =    1.047
peak=    3.276 closest distance to " CA  ASN A  74 " =    1.291
peak=    3.276 closest distance to " C   ALA A 299 " =    0.965
peak=    3.269 closest distance to " N   VAL A 126 " =    1.344
peak=    3.268 closest distance to " O   PRO A  90 " =    1.475
peak=    3.264 closest distance to " CD2 TYR A 186 " =    1.073
peak=    3.263 closest distance to " CA  TYR A  30 " =    1.056
peak=    3.262 closest distance to " CB  ALA A  34 " =    1.043
peak=    3.261 closest distance to " O   HOH Z 116 " =    1.698
peak=    3.260 closest distance to " CG BARG A 275 " =    1.478
peak=    3.259 closest distance to " O   HOH Z 227 " =    1.748
peak=    3.259 closest distance to " CB  VAL A 250 " =    1.078
peak=    3.255 closest distance to " CE  LYS A  48 " =    1.166
peak=    3.254 closest distance to " O   HOH Z 184 " =    1.411
peak=    3.254 closest distance to " OG  SER A  22 " =    2.903
peak=    3.250 closest distance to " O   HOH Z  53 " =    2.523
peak=    3.249 closest distance to " CB  ALA A 248 " =    0.986
peak=    3.249 closest distance to " O   HOH Z 188 " =    1.980
peak=    3.247 closest distance to " O   HOH Z 313 " =    1.558
peak=    3.245 closest distance to " O   HOH Z 128 " =    1.860
peak=    3.240 closest distance to " CB  ARG A 138 " =    0.966
peak=    3.239 closest distance to " CA  LEU A 282 " =    1.114
peak=    3.237 closest distance to " O   HOH Z 392 " =    1.319
peak=    3.235 closest distance to " CB  GLN A 103 " =    1.111
peak=    3.234 closest distance to " O   HOH Z  88 " =    2.777
peak=    3.223 closest distance to " O   HOH Z  44 " =    2.841
peak=    3.219 closest distance to " CB  VAL A 268 " =    0.866
peak=    3.212 closest distance to " O   HOH Z 329 " =    2.882
peak=    3.207 closest distance to " CG  GLN A  89 " =    1.445
peak=    3.204 closest distance to " N   ARG A 156 " =    1.294
peak=    3.201 closest distance to " O   HOH Z 189 " =    2.983
peak=    3.197 closest distance to " CB  ILE A 120 " =    1.418
peak=    3.195 closest distance to " CG  MET A 185 " =    1.039
peak=    3.192 closest distance to " CB  THR A  31 " =    1.633
peak=    3.186 closest distance to " O   HOH Z 303 " =    1.862
peak=    3.185 closest distance to " ND2 ASN A 249 " =    0.845
peak=    3.184 closest distance to " O   HOH Z 273 " =    1.623
peak=    3.184 closest distance to " CB  GLN A  89 " =    1.267
peak=    3.183 closest distance to " N   ALA A 256 " =    1.080
peak=    3.182 closest distance to " O   HOH Z 371 " =    3.329
peak=    3.179 closest distance to " O   HOH Z 325 " =    2.327
peak=    3.174 closest distance to " N   GLN A 278 " =    1.206
peak=    3.169 closest distance to " O   HOH Z 302 " =    1.807
peak=    3.167 closest distance to " CB  ALA A   1 " =    4.748
peak=    3.164 closest distance to " O   HOH Z   2 " =    1.512
peak=    3.156 closest distance to " CA  ILE A 234 " =    0.949
peak=    3.154 closest distance to " CB  TYR A 116 " =    0.901
peak=    3.152 closest distance to " CG  ARG A 159 " =    0.963
peak=    3.152 closest distance to " NZ  LYS A  48 " =    1.353
peak=    3.152 closest distance to " O   HOH Z  88 " =    3.285
peak=    3.146 closest distance to " ND2 ASN A 110 " =    1.673
peak=    3.142 closest distance to " CA  MET A 105 " =    0.958
peak=    3.134 closest distance to " O   HOH Z 112 " =    1.627
peak=    3.125 closest distance to " O   TYR A 116 " =    1.292
peak=    3.123 closest distance to " O   HOH Z 124 " =    2.011
peak=    3.118 closest distance to " NH2BARG A 145 " =    1.958
peak=    3.115 closest distance to " CD1 ILE A 106 " =    0.954
peak=    3.111 closest distance to " O   HOH Z 154 " =    2.231
peak=    3.104 closest distance to " CB  ALA A 227 " =    1.000
peak=    3.101 closest distance to " O   HOH Z 423 " =    1.512
peak=    3.098 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.096 closest distance to " O   HOH Z 251 " =    1.547
peak=    3.090 closest distance to " CB  SER A 245 " =    3.170
peak=    3.090 closest distance to " CA  VAL A  41 " =    0.859
peak=    3.090 closest distance to " CB  PHE A 283 " =    0.722
peak=    3.083 closest distance to " O   HOH Z 294 " =    1.501
peak=    3.078 closest distance to " O   HOH Z 187 " =    2.297
peak=    3.071 closest distance to " O   HOH Z 383 " =    2.274
peak=    3.064 closest distance to " CG2 ILE A 234 " =    0.879
peak=    3.060 closest distance to " CD1 LEU A  96 " =    0.737
peak=    3.059 closest distance to " O   HOH Z 213 " =    1.964
peak=    3.059 closest distance to " OG  SER A 206 " =    1.221
peak=    3.055 closest distance to " O   HOH Z  29 " =    2.376
peak=    3.049 closest distance to " CA  ARG A 102 " =    1.158
peak=    3.044 closest distance to " O   TRP A 274 " =    1.826

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.752 - 5.469
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 208
   mapped sites are within: 0.752 - 5.469

peak=   -4.743 closest distance to " CG2 VAL A 230 " =    0.836
peak=   -4.533 closest distance to " CD  ARG A 156 " =    2.032
peak=   -4.461 closest distance to " CD  ARG A  14 " =    3.239
peak=   -4.380 closest distance to " CB  PRO A 243 " =    2.631
peak=   -4.206 closest distance to " O   HOH Z 266 " =    5.277
peak=   -4.155 closest distance to " OG BSER A 134 " =    1.253
peak=   -4.110 closest distance to " O   VAL A  67 " =    2.563
peak=   -4.096 closest distance to " CG  GLN A 223 " =    2.111
peak=   -4.093 closest distance to " O   HOH Z 231 " =    1.798
peak=   -4.062 closest distance to " O   HOH Z  52 " =    1.407
peak=   -4.020 closest distance to " N   ALA A  43 " =    2.548
peak=   -4.006 closest distance to " O   HOH Z 435 " =    2.855
peak=   -3.933 closest distance to " CB  PRO A 163 " =    2.463
peak=   -3.926 closest distance to " CB  ALA A 161 " =    2.606
peak=   -3.906 closest distance to " O   HOH Z 290 " =    1.250
peak=   -3.870 closest distance to " CG1 VAL A 112 " =    2.581
peak=   -3.867 closest distance to " CB  PRO A 280 " =    2.163
peak=   -3.858 closest distance to " CE2 TYR A  30 " =    2.714
peak=   -3.825 closest distance to " CB  ALA A  43 " =    2.541
peak=   -3.818 closest distance to " O   HOH Z 351 " =    1.577
peak=   -3.817 closest distance to " CA  GLY A 241 " =    2.294
peak=   -3.816 closest distance to " CG2 VAL A 296 " =    1.107
peak=   -3.812 closest distance to " CD  GLN A  58 " =    1.016
peak=   -3.808 closest distance to " CG1 VAL A 112 " =    2.781
peak=   -3.800 closest distance to " O   GLY A  80 " =    2.482
peak=   -3.800 closest distance to " O   HOH Z 359 " =    3.297
peak=   -3.789 closest distance to " O   HOH Z 185 " =    2.208
peak=   -3.787 closest distance to " CZ3 TRP A 179 " =    1.190
peak=   -3.786 closest distance to " C   HIS A 108 " =    1.259
peak=   -3.776 closest distance to " O   PRO A 198 " =    1.216
peak=   -3.754 closest distance to " OG  SER A  97 " =    2.230
peak=   -3.733 closest distance to " OG  SER A  87 " =    1.396
peak=   -3.725 closest distance to " O   HOH Z 389 " =    2.040
peak=   -3.722 closest distance to " CB  PHE A 192 " =    1.832
peak=   -3.720 closest distance to " CD2 LEU A 237 " =    2.836
peak=   -3.716 closest distance to " N   THR A 157 " =    1.436
peak=   -3.706 closest distance to " O   VAL A  67 " =    2.744
peak=   -3.692 closest distance to " CG1 VAL A 296 " =    1.403
peak=   -3.686 closest distance to " O   ARG A 145 " =    1.540
peak=   -3.680 closest distance to " O   VAL A 189 " =    2.590
peak=   -3.676 closest distance to " O   HOH Z 166 " =    2.258
peak=   -3.669 closest distance to " CA  GLY A 203 " =    2.382
peak=   -3.668 closest distance to " CB  ALA A 248 " =    2.074
peak=   -3.667 closest distance to " O   HOH Z 394 " =    1.511
peak=   -3.654 closest distance to " CB  ALA A 248 " =    2.423
peak=   -3.638 closest distance to " NH2 ARG A  79 " =    1.986
peak=   -3.628 closest distance to " O   PRO A 163 " =    2.039
peak=   -3.617 closest distance to " O   HOH Z  73 " =    2.170
peak=   -3.614 closest distance to " CD1 LEU A 228 " =    2.281
peak=   -3.611 closest distance to " O   HOH Z  11 " =    1.956
peak=   -3.599 closest distance to " O   HOH Z 140 " =    1.423
peak=   -3.596 closest distance to " OXT GLY A 302 " =    3.074
peak=   -3.591 closest distance to " O   HOH Z 350 " =    1.700
peak=   -3.589 closest distance to " CG  TRP A 266 " =    1.746
peak=   -3.585 closest distance to " ND2 ASN A  45 " =    1.513
peak=   -3.572 closest distance to " O   HOH Z  44 " =    2.242
peak=   -3.560 closest distance to " CB  ALA A 291 " =    2.426
peak=   -3.553 closest distance to " C   ALA A 158 " =    1.391
peak=   -3.552 closest distance to " C   LEU A 222 " =    0.807
peak=   -3.551 closest distance to " CD1 LEU A 101 " =    2.356
peak=   -3.533 closest distance to " OD1 ASN A 187 " =    1.572
peak=   -3.529 closest distance to " N   ALA A 226 " =    2.144
peak=   -3.527 closest distance to " CB  VAL A 230 " =    1.042
peak=   -3.508 closest distance to " O   PRO A 198 " =    1.396
peak=   -3.503 closest distance to " O   HOH Z 103 " =    1.778
peak=   -3.502 closest distance to " CE BMET A  47 " =    1.613
peak=   -3.501 closest distance to " O   HOH Z 114 " =    2.992
peak=   -3.498 closest distance to " CA  ASP A  27 " =    2.425
peak=   -3.492 closest distance to " O   HOH Z  60 " =    2.240
peak=   -3.491 closest distance to " CG  PRO A 163 " =    2.525
peak=   -3.477 closest distance to " NH2AARG A 275 " =    5.307
peak=   -3.474 closest distance to " O   HOH Z 211 " =    1.439
peak=   -3.469 closest distance to " OH  TYR A 214 " =    1.207
peak=   -3.466 closest distance to " O   HOH Z 198 " =    2.237
peak=   -3.465 closest distance to " O   HOH Z  51 " =    1.127
peak=   -3.463 closest distance to " CG  ASP A 231 " =    0.752
peak=   -3.458 closest distance to " O   HOH Z 111 " =    2.072
peak=   -3.455 closest distance to " CG1 VAL A 250 " =    2.743
peak=   -3.450 closest distance to " O   HOH Z  38 " =    1.698
peak=   -3.450 closest distance to " CE2 PHE A 218 " =    2.494
peak=   -3.448 closest distance to " CD  LYS A 289 " =    2.488
peak=   -3.447 closest distance to " O   HOH Z 407 " =    3.165
peak=   -3.445 closest distance to " O   HOH Z 166 " =    2.052
peak=   -3.445 closest distance to " N   ASP A 171 " =    2.398
peak=   -3.439 closest distance to " CD2 LEU A   5 " =    1.115
peak=   -3.430 closest distance to " O   HOH Z 166 " =    1.418
peak=   -3.415 closest distance to " O   HOH Z 231 " =    1.210
peak=   -3.405 closest distance to " CA  ASP A 298 " =    1.040
peak=   -3.400 closest distance to " O   HOH Z  43 " =    1.733
peak=   -3.399 closest distance to " O   HOH Z 281 " =    2.647
peak=   -3.398 closest distance to " CG1 VAL A 197 " =    2.268
peak=   -3.398 closest distance to " O   GLY A  17 " =    1.275
peak=   -3.396 closest distance to " O   HOH Z 426 " =    1.675
peak=   -3.396 closest distance to " OD1 ASN A 148 " =    1.473
peak=   -3.394 closest distance to " O   HOH Z 191 " =    5.437
peak=   -3.391 closest distance to " CB  ALA A 291 " =    2.152
peak=   -3.390 closest distance to " C   MET A 188 " =    1.430
peak=   -3.389 closest distance to " ND2 ASN A 249 " =    2.474
peak=   -3.375 closest distance to " N   THR A 235 " =    1.224
peak=   -3.372 closest distance to " O   SER A  22 " =    2.216
peak=   -3.370 closest distance to " O   HOH Z 313 " =    1.552
peak=   -3.367 closest distance to " CD  ARG A 139 " =    1.608
peak=   -3.366 closest distance to " CZ2 TRP A 274 " =    0.907
peak=   -3.366 closest distance to " O   HOH Z 198 " =    1.533
peak=   -3.359 closest distance to " O   HOH Z   2 " =    1.919
peak=   -3.358 closest distance to " CA  ASP A  27 " =    2.683
peak=   -3.339 closest distance to " CD1 LEU A 101 " =    2.816
peak=   -3.338 closest distance to " N   SER A 276 " =    1.350
peak=   -3.335 closest distance to " O   HOH Z 417 " =    2.982
peak=   -3.333 closest distance to " O   HOH Z 275 " =    1.450
peak=   -3.329 closest distance to " O   HOH Z 389 " =    1.453
peak=   -3.329 closest distance to " CG  MET A 105 " =    0.954
peak=   -3.328 closest distance to " CD  PRO A 213 " =    2.111
peak=   -3.327 closest distance to " NH2BARG A 275 " =    1.619
peak=   -3.327 closest distance to " CZ  PHE A 192 " =    2.860
peak=   -3.320 closest distance to " O   HOH Z 243 " =    1.994
peak=   -3.315 closest distance to " O   HOH Z  90 " =    2.872
peak=   -3.312 closest distance to " O   SER A 210 " =    1.911
peak=   -3.310 closest distance to " CD1 ILE A 199 " =    2.525
peak=   -3.310 closest distance to " O   HOH Z 134 " =    3.567
peak=   -3.310 closest distance to " CA  GLY A 241 " =    3.136
peak=   -3.305 closest distance to " O   HOH Z 345 " =    2.216
peak=   -3.305 closest distance to " N   ALA A 248 " =    1.595
peak=   -3.303 closest distance to " CE  MET A 105 " =    2.288
peak=   -3.301 closest distance to " CB  TRP A  85 " =    2.596
peak=   -3.301 closest distance to " N   GLN A  58 " =    1.816
peak=   -3.300 closest distance to " CZ  PHE A  59 " =    1.523
peak=   -3.298 closest distance to " CE1 TYR A 169 " =    2.547
peak=   -3.298 closest distance to " CE3 TRP A 150 " =    2.210
peak=   -3.296 closest distance to " O   HOH Z 346 " =    1.801
peak=   -3.291 closest distance to " CD2 PHE A  61 " =    1.936
peak=   -3.281 closest distance to " CG  GLU A 152 " =    1.431
peak=   -3.279 closest distance to " NZ  LYS A 119 " =    3.456
peak=   -3.278 closest distance to " O   HOH Z 102 " =    1.546
peak=   -3.273 closest distance to " O   HOH Z 423 " =    1.144
peak=   -3.273 closest distance to " CA  GLY A  98 " =    1.932
peak=   -3.273 closest distance to " CB  ASP A 132 " =    2.344
peak=   -3.271 closest distance to " O   HOH Z 372 " =    2.445
peak=   -3.270 closest distance to " CD1 PHE A  59 " =    1.977
peak=   -3.269 closest distance to " O   HOH Z 353 " =    1.987
peak=   -3.268 closest distance to " O   HOH Z 111 " =    1.168
peak=   -3.267 closest distance to " OG BSER A 134 " =    1.696
peak=   -3.265 closest distance to " O   HOH Z 292 " =    1.760
peak=   -3.263 closest distance to " ND2 ASN A  60 " =    1.743
peak=   -3.261 closest distance to " O   HOH Z 131 " =    4.151
peak=   -3.257 closest distance to " O   GLY A  80 " =    2.605
peak=   -3.253 closest distance to " O   SER A 135 " =    1.459
peak=   -3.245 closest distance to " C   ASN A 187 " =    1.799
peak=   -3.243 closest distance to " CB  ASP A 171 " =    2.217
peak=   -3.238 closest distance to " CD2 LEU A 167 " =    1.835
peak=   -3.237 closest distance to " C   ASP A 231 " =    2.569
peak=   -3.233 closest distance to " CD2 TYR A 247 " =    2.470
peak=   -3.232 closest distance to " O   LYS A 289 " =    3.165
peak=   -3.232 closest distance to " CZ  TYR A 169 " =    1.561
peak=   -3.229 closest distance to " O   THR A  18 " =    1.595
peak=   -3.225 closest distance to " O   ALA A 161 " =    1.668
peak=   -3.214 closest distance to " OE2 GLU A 152 " =    1.179
peak=   -3.214 closest distance to " O   HOH Z 390 " =    2.340
peak=   -3.209 closest distance to " O   MET A  40 " =    2.791
peak=   -3.209 closest distance to " O   ASN A 301 " =    1.544
peak=   -3.199 closest distance to " O   PHE A 218 " =    1.569
peak=   -3.197 closest distance to " O   HOH Z 359 " =    1.680
peak=   -3.194 closest distance to " O   ARG A  24 " =    2.069
peak=   -3.190 closest distance to " O   HOH Z 410 " =    2.168
peak=   -3.187 closest distance to " CG  PHE A 283 " =    2.709
peak=   -3.183 closest distance to " CB  ALA A   9 " =    2.523
peak=   -3.182 closest distance to " C   LEU A 143 " =    1.159
peak=   -3.181 closest distance to " O   HOH Z 149 " =    2.283
peak=   -3.180 closest distance to " O   HOH Z 295 " =    1.570
peak=   -3.176 closest distance to " N   ASN A  60 " =    1.337
peak=   -3.176 closest distance to " N   ALA A 248 " =    2.439
peak=   -3.176 closest distance to " OD1 ASP A 171 " =    1.678
peak=   -3.172 closest distance to " ND2 ASN A 187 " =    1.611
peak=   -3.171 closest distance to " CG2 ILE A 263 " =    2.391
peak=   -3.171 closest distance to " OG1 THR A 178 " =    1.284
peak=   -3.167 closest distance to " O   HOH Z 139 " =    3.009
peak=   -3.166 closest distance to " CB  PRO A  54 " =    2.458
peak=   -3.165 closest distance to " O   HOH Z 176 " =    0.820
peak=   -3.163 closest distance to " CA  SER A 135 " =    1.415
peak=   -3.161 closest distance to " O   GLN A 240 " =    2.406
peak=   -3.156 closest distance to " OE1 GLN A  88 " =    1.177
peak=   -3.151 closest distance to " CG  LEU A 228 " =    0.982
peak=   -3.147 closest distance to " CG  ARG A 269 " =    2.449
peak=   -3.137 closest distance to " NE2 GLN A 194 " =    1.734
peak=   -3.135 closest distance to " CD2 TYR A 293 " =    1.984
peak=   -3.133 closest distance to " O   GLN A 240 " =    2.121
peak=   -3.129 closest distance to " O   HOH Z 371 " =    2.247
peak=   -3.126 closest distance to " O   HOH Z 189 " =    2.109
peak=   -3.122 closest distance to " CD2 PHE A 225 " =    1.099
peak=   -3.111 closest distance to " O   HOH Z 412 " =    4.341
peak=   -3.109 closest distance to " ND2 ASN A 252 " =    1.931
peak=   -3.106 closest distance to " CB  ALA A 114 " =    2.464
peak=   -3.100 closest distance to " O   HOH Z 174 " =    3.029
peak=   -3.099 closest distance to " O   ALA A  51 " =    1.368
peak=   -3.093 closest distance to " ND2BASN A 224 " =    1.569
peak=   -3.091 closest distance to " O   HOH Z  13 " =    1.849
peak=   -3.090 closest distance to " CB  TYR A  15 " =    2.177
peak=   -3.082 closest distance to " CD  GLU A 277 " =    1.240
peak=   -3.082 closest distance to " O   HOH Z 380 " =    1.340
peak=   -3.080 closest distance to " OH  TYR A 247 " =    1.866
peak=   -3.075 closest distance to " CG  LEU A 101 " =    2.356
peak=   -3.068 closest distance to " OD1 ASN A 301 " =    2.012
peak=   -3.063 closest distance to " O   HOH Z 357 " =    2.014
peak=   -3.054 closest distance to " OXT GLY A 302 " =    3.473
peak=   -3.049 closest distance to " O   HOH Z 108 " =    1.620
peak=   -3.045 closest distance to " O   HOH Z 336 " =    5.469
peak=   -3.038 closest distance to " O   HOH Z 168 " =    1.841

================= 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    :  0.4439 0.4288   6.239368e+00   6.215420e+00
   1_bss:  0.4362 0.4151   6.234166e+00   6.204226e+00
   1_xyz:  0.3317 0.3472   6.048280e+00   6.083140e+00
   1_adp:  0.2719 0.3142   5.891527e+00   5.997371e+00
   1_occ:  0.2713 0.3143   5.890647e+00   5.998522e+00
   2_bss:  0.2662 0.3086   5.888818e+00   5.994503e+00
   2_xyz:  0.1869 0.2314   5.575536e+00   5.741413e+00
   2_adp:  0.1712 0.2184   5.499365e+00   5.682661e+00
   2_occ:  0.1711 0.2184   5.499387e+00   5.683153e+00
   3_bss:  0.1704 0.2173   5.500503e+00   5.682936e+00
   3_xyz:  0.1311 0.1780   5.280224e+00   5.503238e+00
   3_adp:  0.1219 0.1697   5.220910e+00   5.456458e+00
   3_occ:  0.1219 0.1699   5.220956e+00   5.456604e+00
   4_bss:  0.1219 0.1697   5.219574e+00   5.455421e+00
   4_xyz:  0.1195 0.1669   5.208022e+00   5.444756e+00
   4_adp:  0.1212 0.1640   5.204517e+00   5.424966e+00
   4_occ:  0.1211 0.1638   5.203747e+00   5.423766e+00
   5_bss:  0.1211 0.1637   5.203667e+00   5.423663e+00
   5_xyz:  0.1122 0.1581   5.150713e+00   5.393228e+00
   5_adp:  0.1102 0.1582   5.144350e+00   5.396309e+00
   5_occ:  0.1101 0.1583   5.143918e+00   5.395987e+00
   5_bss:  0.1101 0.1583   5.143972e+00   5.396004e+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:  0.349  18.818   7.940   8.974   8.482   0.000   0.000   0.000
   1_xyz:  0.349  18.818   7.940   8.974   8.482   0.000   0.000   0.000
   1_adp:  0.349  18.818   7.940   8.974   8.482   0.000   0.000   0.000
   1_occ:  0.349  18.818   7.940   8.974   8.482   0.000   0.000   0.000
   2_bss:  0.344  50.001   4.392   4.697   5.129   0.000   0.000   0.000
   2_xyz:  0.344  50.001   4.392   4.697   5.129   0.000   0.000   0.000
   2_adp:  0.344  50.001   4.392   4.697   5.129   0.000   0.000   0.000
   2_occ:  0.344  50.001   4.392   4.697   5.129   0.000   0.000   0.000
   3_bss:  0.344  50.001   3.221   3.142   4.322   0.000   0.000   0.000
   3_xyz:  0.344  50.001   3.221   3.142   4.322   0.000   0.000   0.000
   3_adp:  0.344  50.001   3.221   3.142   4.322   0.000   0.000   0.000
   3_occ:  0.344  50.001   3.221   3.142   4.322   0.000   0.000   0.000
   4_bss:  0.330  52.985   2.969   2.799   4.156   0.000   0.000   0.000
   4_xyz:  0.330  52.985   2.969   2.799   4.156   0.000   0.000   0.000
   4_adp:  0.330  52.985   2.969   2.799   4.156   0.000   0.000   0.000
   4_occ:  0.330  52.985   2.969   2.799   4.156   0.000   0.000   0.000
   5_bss:  0.332  52.985   2.777   2.591   4.045   0.000   0.000   0.000
   5_xyz:  0.332  52.985   2.777   2.591   4.045   0.000   0.000   0.000
   5_adp:  0.332  52.985   2.777   2.591   4.045   0.000   0.000   0.000
   5_occ:  0.332  52.985   2.777   2.591   4.045   0.000   0.000   0.000
   5_bss:  0.332  56.256  -0.344  -0.565   0.908   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.079 0.5328  0.6033    54262.506
   1_bss:  49.112 0.5305  0.7702    52055.770
   1_xyz:  38.204 0.6631  0.9325    34064.877
   1_adp:  32.025 0.7358  1.0327    26186.209
   1_occ:  32.088 0.7350  1.0307    26238.879
   2_bss:  31.788 0.7382  0.9062    25841.256
   2_xyz:  22.518 0.8367  0.9892    13503.351
   2_adp:  20.685 0.8555  1.0009    11890.594
   2_occ:  20.701 0.8553  1.0006    11891.834
   3_bss:  20.686 0.8555  0.9590    11904.145
   3_xyz:  16.599 0.8927  0.9856     8092.536
   3_adp:  15.589 0.9016  0.9866     7365.442
   3_occ:  15.593 0.9016  0.9864     7365.822
   4_bss:  15.578 0.9017  0.9770     7340.757
   4_xyz:  15.208 0.9052  0.9759     7119.840
   4_adp:  14.700 0.9096  0.9773     6886.884
   4_occ:  14.679 0.9098  0.9774     6867.361
   5_bss:  14.675 0.9098  0.9715     6865.713
   5_xyz:  14.122 0.9141  0.9749     6464.567
   5_adp:  14.197 0.9135  0.9712     6480.508
   5_occ:  14.189 0.9135  0.9711     6474.622
   5_bss:  14.191 0.9135  0.9758     6475.897
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3901e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3901e+01
   1_xyz:   1.530  0.012  0.101 18.167  0.006  4.121   1.2047e-01
   1_adp:   1.530  0.012  0.101 18.167  0.006  4.121   1.2047e-01
   1_occ:   1.530  0.012  0.101 18.167  0.006  4.121   1.2047e-01
   2_bss:   1.530  0.012  0.101 18.167  0.006  4.121   1.2047e-01
   2_xyz:   0.959  0.006  0.071 16.213  0.004  4.122   6.0449e-02
   2_adp:   0.959  0.006  0.071 16.213  0.004  4.122   6.0449e-02
   2_occ:   0.959  0.006  0.071 16.213  0.004  4.122   6.0449e-02
   3_bss:   0.959  0.006  0.071 16.213  0.004  4.122   6.0449e-02
   3_xyz:   1.084  0.008  0.087 15.971  0.004  4.132   7.0052e-02
   3_adp:   1.084  0.008  0.087 15.971  0.004  4.132   7.0052e-02
   3_occ:   1.084  0.008  0.087 15.971  0.004  4.132   7.0052e-02
   4_bss:   1.084  0.008  0.087 15.971  0.004  4.132   7.0052e-02
   4_xyz:   0.912  0.006  0.073 15.660  0.003  4.133   5.4128e-02
   4_adp:   0.912  0.006  0.073 15.660  0.003  4.133   5.4128e-02
   4_occ:   0.912  0.006  0.073 15.660  0.003  4.133   5.4128e-02
   5_bss:   0.912  0.006  0.073 15.660  0.003  4.133   5.4128e-02
   5_xyz:   1.107  0.010  0.092 15.680  0.004  4.113   7.5994e-02
   5_adp:   1.107  0.010  0.092 15.680  0.004  4.113   7.5994e-02
   5_occ:   1.107  0.010  0.092 15.680  0.004  4.113   7.5994e-02
   5_bss:   1.107  0.010  0.092 15.680  0.004  4.113   7.5994e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9887e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9887e+00
   1_xyz:  12.131  0.150  0.415 87.751  0.032  2.252   8.8553e-02
   1_adp:  12.131  0.150  0.415 87.751  0.032  2.252   8.8553e-02
   1_occ:  12.131  0.150  0.415 87.751  0.032  2.252   8.8553e-02
   2_bss:  12.131  0.150  0.415 87.751  0.032  2.252   8.8553e-02
   2_xyz:   6.959  0.054  0.248 89.369  0.044  2.363   4.8007e-02
   2_adp:   6.959  0.054  0.248 89.369  0.044  2.363   4.8007e-02
   2_occ:   6.959  0.054  0.248 89.369  0.044  2.363   4.8007e-02
   3_bss:   6.959  0.054  0.248 89.369  0.044  2.363   4.8007e-02
   3_xyz:   9.561  0.073  0.519 82.998  0.026  2.276   5.0982e-02
   3_adp:   9.561  0.073  0.519 82.998  0.026  2.276   5.0982e-02
   3_occ:   9.561  0.073  0.519 82.998  0.026  2.276   5.0982e-02
   4_bss:   9.561  0.073  0.519 82.998  0.026  2.276   5.0982e-02
   4_xyz:   7.642  0.043  0.403 83.157  0.037  2.390   2.9330e-02
   4_adp:   7.642  0.043  0.403 83.157  0.037  2.390   2.9330e-02
   4_occ:   7.642  0.043  0.403 83.157  0.037  2.390   2.9330e-02
   5_bss:   7.642  0.043  0.403 83.157  0.037  2.390   2.9330e-02
   5_xyz:   7.247  0.052  0.642 84.345  0.040  2.218   6.0127e-02
   5_adp:   7.247  0.052  0.642 84.345  0.040  2.218   6.0127e-02
   5_occ:   7.247  0.052  0.642 84.345  0.040  2.218   6.0127e-02
   5_bss:   7.247  0.052  0.642 84.345  0.040  2.218   6.0127e-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:  73.15   0.00  11.42  60.17   0.00   8.38  73.15   0.00  27.98
   1_occ:  73.15   0.00  11.42  60.17   0.00   8.38  73.15   0.00  27.98
   2_bss:  73.15   0.00  11.42  60.17   0.00   8.38  73.15   0.00  27.98
   2_xyz:  73.15   0.00  11.42  60.17   0.00   8.38  73.15   0.00  27.98
   2_adp:  73.86   0.00  11.43  61.28   0.00   7.82  73.86   0.00  31.09
   2_occ:  73.86   0.00  11.43  61.28   0.00   7.82  73.86   0.00  31.09
   3_bss:  73.86   0.00  11.43  61.28   0.00   7.82  73.86   0.00  31.09
   3_xyz:  73.86   0.00  11.43  61.28   0.00   7.82  73.86   0.00  31.09
   3_adp:  83.52   0.00  12.44  77.20   0.00   7.97  83.52   0.29  36.77
   3_occ:  83.52   0.00  12.44  77.20   0.00   7.97  83.52   0.29  36.77
   4_bss:  83.52   0.00  12.44  77.20   0.00   7.97  83.52   0.29  36.77
   4_xyz:  83.52   0.00  12.44  77.20   0.00   7.97  83.52   0.29  36.77
   4_adp:  76.20   0.00  11.62  75.08   0.00   7.66  76.20   1.59  33.17
   4_occ:  76.20   0.00  11.62  75.08   0.00   7.66  76.20   1.59  33.17
   5_bss:  76.20   0.00  11.62  75.08   0.00   7.66  76.20   1.59  33.17
   5_xyz:  76.20   0.00  11.62  75.08   0.00   7.66  76.20   1.59  33.17
   5_adp:  81.16   0.00  11.94  81.16   0.00   7.75  78.89   1.37  34.75
   5_occ:  81.16   0.00  11.94  81.16   0.00   7.75  78.89   1.37  34.75
   5_bss:  84.43   3.27  15.21  84.43   3.27  11.02  82.16   4.65  38.02
------------------------------------------------------------------------
 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:    1.192    0.010    0.401
   1_adp:    1.192    0.010    0.401
   1_occ:    1.192    0.010    0.401
   2_bss:    1.192    0.010    0.401
   2_xyz:    1.387    0.036    0.506
   2_adp:    1.387    0.036    0.506
   2_occ:    1.387    0.036    0.506
   3_bss:    1.387    0.036    0.506
   3_xyz:    1.459    0.036    0.564
   3_adp:    1.459    0.036    0.564
   3_occ:    1.459    0.036    0.564
   4_bss:    1.459    0.036    0.564
   4_xyz:    1.633    0.048    0.574
   4_adp:    1.633    0.048    0.574
   4_occ:    1.633    0.048    0.574
   5_bss:    1.633    0.048    0.574
   5_xyz:    1.660    0.041    0.586
   5_adp:    1.660    0.041    0.586
   5_occ:    1.660    0.041    0.586
   5_bss:    1.660    0.041    0.586
------------------------------------------------------------------------

CPU time actual refinement: 322.75


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_886/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_886/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_886/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_886/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_886/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.60 
  Macro-tasks:
    bulk solvent and scale       = 42.36  
    individual site refinement   = 126.38 
    weights calculation          = 32.41  
    collect and process          = 6.54   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 207.80 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 97.90  
    alpha_beta                      = 8.34   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 106.71 
    fmodel                         = 7.45   
    r_factors                      = 0.21   
    phase_errors                   = 10.64  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 234.40 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.624 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    628 calls, 97.57 s
gradients_fft:          572 calls, 94.16 s

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

# Date 2008-01-16 Time 02:39:32 PST -0800 (1200479972.08 s)
Start R-work = 0.4439, R-free = 0.4288 (no bulk solvent and anisotropic scale)
Final R-work = 0.1276, R-free = 0.1753 (no bulk solvent and anisotropic scale)

Start R-work = 0.4362, R-free = 0.4151
Final R-work = 0.1101, R-free = 0.1583