# Date 2008-01-16 Time 03:14:09 PST -0800 (1200482049.18 s)
#phil __OFF__

Command line arguments: "../1155.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26184
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1155

-------------------------------------------------------------------------------
  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: (71.655, 47.1647, 84.2302, 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: 3.26, per 1000 atoms: 1.15


================================== 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: (71.655, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.9514
Completeness in resolution range: 0.917604
Completeness with d_max=infinity: 0.914904

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1017
                             d_min =   1.9514

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: (71.655, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.9514
Completeness in resolution range: 0.917604
Completeness with d_max=infinity: 0.914904

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1022 -  4.1773 [2248/2277]  2027   221   9.8%
  bin  2:  4.1773 -  3.3273 [2140/2163]  1925   215  10.0%
  bin  3:  3.3273 -  2.9101 [2123/2148]  1903   220  10.4%
  bin  4:  2.9101 -  2.6456 [2114/2130]  1908   206   9.7%
  bin  5:  2.6456 -  2.4568 [2077/2116]  1874   203   9.8%
  bin  6:  2.4568 -  2.3125 [2082/2115]  1865   217  10.4%
  bin  7:  2.3125 -  2.1971 [2073/2109]  1864   209  10.1%
  bin  8:  2.1971 -  2.1017 [2043/2085]  1843   200   9.8%
  bin  9:  2.1017 -  2.0210 [2019/2120]  1818   201  10.0%
  bin 10:  2.0210 -  1.9514 [ 670/2085]   603    67  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1155/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:
        1.54 -     2.21: 25
        2.21 -     2.88: 1288
        2.88 -     3.56: 4502
        3.56 -     4.23: 9212
        4.23 -     4.90: 13367
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.542 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.573 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.810 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.843 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28389 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_1155/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1155/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 = 71.655 47.16465 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4869   r_free= 0.4915   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.289683                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6600 0.99   1453  166 0.4004 0.3974      6.6097      6.6021|
|  2:  4.6600 -  3.7169 0.99   1397  151 0.4052 0.4199         6.8      6.8613|
|  3:  3.7169 -  3.2524 0.99   1371  150 0.4540 0.4319      6.6809      6.6943|
|  4:  3.2524 -  2.9575 0.99   1372  155 0.4766 0.5042      6.5133      6.5232|
|  5:  2.9575 -  2.7469 0.98   1351  149 0.5190 0.5255      6.3705      6.3554|
|  6:  2.7469 -  2.5858 0.99   1353  153 0.5187 0.5468      6.2809      6.2408|
|  7:  2.5858 -  2.4568 0.99   1340  141 0.5282 0.4534      6.2459      6.1782|
|  8:  2.4568 -  2.3503 0.99   1338  156 0.5389 0.5416      6.1513      6.1799|
|  9:  2.3503 -  2.2601 0.99   1340  150 0.5333 0.5262      6.1482      6.1125|
| 10:  2.2601 -  2.1824 0.98   1326  151 0.5244 0.5228      6.0659      6.0973|
| 11:  2.1824 -  2.1143 0.98   1325  134 0.5228 0.5946      6.0327       6.025|
| 12:  2.1143 -  2.0540 1.00   1322  153 0.5464 0.5632      5.9421      5.9732|
| 13:  2.0540 -  2.0001 0.78   1060  128 0.5355 0.5025      5.8633      5.8265|
| 14:  2.0001 -  1.9514 0.21    282   22 0.5628 0.6163      5.8073      5.8896|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1022 -  4.6600  1453   166  0.69  34.91   0.79     0.72      73203.12|
|  2:  4.6600 -  3.7169  1397   151  0.68  37.21   0.87     0.75     115575.99|
|  3:  3.7169 -  3.2524  1371   150  0.54  48.39   0.82     0.67     129448.57|
|  4:  3.2524 -  2.9575  1372   155  0.42  57.96   0.79     0.55     121055.03|
|  5:  2.9575 -  2.7469  1351   149  0.33  65.01   0.73     0.42      96042.45|
|  6:  2.7469 -  2.5858  1353   153  0.34  64.55   0.73     0.42      79008.73|
|  7:  2.5858 -  2.4568  1340   141  0.35  64.07   0.72     0.39      65249.07|
|  8:  2.4568 -  2.3503  1338   156  0.34  64.69   0.71     0.42      60147.44|
|  9:  2.3503 -  2.2601  1340   150  0.30  67.64   0.74     0.36      56482.57|
| 10:  2.2601 -  2.1824  1326   151  0.26  70.46   0.75     0.33      55671.04|
| 11:  2.1824 -  2.1143  1325   134  0.22  73.92   0.76     0.27      52275.50|
| 12:  2.1143 -  2.0540  1322   153  0.18  77.01   0.72     0.24      49490.44|
| 13:  2.0540 -  2.0001  1060   128  0.17  77.67   0.72     0.22      42252.34|
| 14:  2.0001 -  1.9514   282    22  0.17  77.03   0.69     0.22      34618.23|
|alpha:            min =        0.22 max =            0.75 mean =         0.45|
|beta:             min =    34618.23 max =       129448.57 mean =     76840.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.49|
|phase err.(test): min =        0.00 max =           89.94 mean =        61.65|
|-----------------------------------------------------------------------------|

============================== 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 = 17.364178             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.024   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.668481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.467   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      713 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1495 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2650 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3951 |
| 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:     6612 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7731 |
|-----------------------------------------------------------------------------|
|-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 |       53.645 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.012 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.885)------------------------------------------|
|    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 = 11.885)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4924   r_free= 0.4973   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.291055                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4803   r_free= 0.4790   ksol= 0.30   Bsol= 20.00   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.26,7.09,8.55,0.00,0.00,0.00); trace/3= 7.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.00 A                  |
| x-ray target function (ml) for work reflections: 5.843590                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.560751             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.038   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.394323              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.713   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4803      final r-factor (work) = 0.4118          |
| start r-factor (free) = 0.4790      final r-factor (free) = 0.4474          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.2672 = 13.56 * 0.50 * 6.2861 + 1.00 * 53.6454                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.2867 = 13.56 * 0.50 * 5.7726 + 1.00 * 0.1460                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4118      final r-factor (work) = 0.3736          |
| start r-factor (free) = 0.4474      final r-factor (free) = 0.4331          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0633 = 1.39 * 1.00 * 5.7726 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6096 = 1.39 * 1.00 * 6.1609 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.885)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.45   14.87    None  None   None       |
|    all(noH): 2823   0      0.00    90.45   14.87    None  None   None       |
|    Sol.    : 438    0      0.00    90.45   27.46    None  None   None       |
|    Mac.    : 2385   0      0.00    88.04   12.56    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 -   9.045: 1114   |   5:    45.224 -  54.269:   52        |
|      1:     9.045 -  18.090:  831   |   6:    54.269 -  63.313:   20        |
|      2:    18.090 -  27.134:  441   |   7:    63.313 -  72.358:    9        |
|      3:    27.134 -  36.179:  239   |   8:    72.358 -  81.403:    7        |
|      4:    36.179 -  45.224:  107   |   9:    81.403 -  90.448:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3736 r_free = 0.4331             target_work(ml) = 6.142         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3731 r_free = 0.4333             target_work(ml) = 6.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3731   r_free= 0.4333   ksol= 0.30   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.26,7.09,8.55,0.00,0.00,0.00); trace/3= 7.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.141527                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3712   r_free= 0.4312   ksol= 0.31   Bsol= 37.52   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.45,3.76,5.66,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.142294                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.516917              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.299  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.673075              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.593  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3712      final r-factor (work) = 0.3000          |
| start r-factor (free) = 0.4312      final r-factor (free) = 0.3674          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.2816 = 7.52 * 0.50 * 6.1556 + 1.00 * 0.1460                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8766 = 7.52 * 0.50 * 6.0644 + 1.00 * 0.0838                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3000      final r-factor (work) = 0.2815          |
| start r-factor (free) = 0.3674      final r-factor (free) = 0.3461          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1008 = 0.67 * 1.00 * 6.0644 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0279 = 0.67 * 1.00 * 5.9653 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.885)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.53   14.92    None  None   None       |
|    all(noH): 2823   0      0.00    87.53   14.92    None  None   None       |
|    Sol.    : 438    0      0.00    87.53   32.11    None  None   None       |
|    Mac.    : 2385   0      0.00    84.71   11.76    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 -   8.753: 1184   |   5:    43.767 -  52.520:   52        |
|      1:     8.753 -  17.507:  784   |   6:    52.520 -  61.274:   30        |
|      2:    17.507 -  26.260:  356   |   7:    61.274 -  70.027:   14        |
|      3:    26.260 -  35.014:  239   |   8:    70.027 -  78.780:    6        |
|      4:    35.014 -  43.767:  154   |   9:    78.780 -  87.534:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2815 r_free = 0.3461             target_work(ml) = 5.943         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2812 r_free = 0.3458             target_work(ml) = 5.942         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2812   r_free= 0.3458   ksol= 0.31   Bsol= 37.52   scale= 1.063   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.45,3.76,5.66,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.942375                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2798   r_free= 0.3421   ksol= 0.32   Bsol= 37.52   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.12,3.36,0.00,0.00,0.00); trace/3= 2.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.940655                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.114408              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.352  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.807758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.114  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2798      final r-factor (work) = 0.2185          |
| start r-factor (free) = 0.3421      final r-factor (free) = 0.2828          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3567 = 4.11 * 0.50 * 5.9659 + 1.00 * 0.0838                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1013 = 4.11 * 0.50 * 5.8492 + 1.00 * 0.0683                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2185      final r-factor (work) = 0.2001          |
| start r-factor (free) = 0.2828      final r-factor (free) = 0.2698          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.4365 = 2.81 * 1.00 * 5.8492 + 1.00 * 0.0133                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.0139 = 2.81 * 1.00 * 5.6971 + 1.00 * 0.0179                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.885)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.47   15.87    None  None   None       |
|    all(noH): 2823   0      0.00    99.47   15.87    None  None   None       |
|    Sol.    : 438    0      0.72    99.47   40.82    None  None   None       |
|    Mac.    : 2385   0      0.00    98.35   11.29    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 -   9.947: 1400   |   5:    49.736 -  59.683:   90        |
|      1:     9.947 -  19.894:  733   |   6:    59.683 -  69.630:   60        |
|      2:    19.894 -  29.841:  246   |   7:    69.630 -  79.577:   12        |
|      3:    29.841 -  39.789:  136   |   8:    79.577 -  89.524:   10        |
|      4:    39.789 -  49.736:  133   |   9:    89.524 -  99.471:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2001 r_free = 0.2698             target_work(ml) = 5.675         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2000 r_free = 0.2699             target_work(ml) = 5.675         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2000   r_free= 0.2699   ksol= 0.32   Bsol= 37.52   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.12,3.36,0.00,0.00,0.00); trace/3= 2.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.674502                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1997   r_free= 0.2696   ksol= 0.32   Bsol= 47.91   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,1.29,1.84,0.00,0.00,0.00); trace/3= 1.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.674438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.050687              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.745  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.178744              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.756  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1997      final r-factor (work) = 0.1650          |
| start r-factor (free) = 0.2696      final r-factor (free) = 0.2258          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7642 = 3.05 * 0.50 * 5.7009 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6032 = 3.05 * 0.50 * 5.6020 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1650      final r-factor (work) = 0.1537          |
| start r-factor (free) = 0.2258      final r-factor (free) = 0.2140          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.8251 = 3.18 * 1.00 * 5.6020 + 1.00 * 0.0177                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.4092 = 3.18 * 1.00 * 5.4716 + 1.00 * 0.0163                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.885)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.96  15.74    None  None   None       |
|    all(noH): 2823   0      0.00    105.96  15.74    None  None   None       |
|    Sol.    : 438    0      3.15    103.96  42.88    None  None   None       |
|    Mac.    : 2385   0      0.00    105.96  10.75    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 -  10.596: 1585   |   5:    52.979 -  63.575:   90        |
|      1:    10.596 -  21.192:  632   |   6:    63.575 -  74.171:   58        |
|      2:    21.192 -  31.788:  189   |   7:    74.171 -  84.767:   10        |
|      3:    31.788 -  42.384:  125   |   8:    84.767 -  95.363:    6        |
|      4:    42.384 -  52.979:  124   |   9:    95.363 - 105.959:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1537 r_free = 0.2140             target_work(ml) = 5.445         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1536 r_free = 0.2139             target_work(ml) = 5.444         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1536   r_free= 0.2139   ksol= 0.32   Bsol= 47.91   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,1.29,1.84,0.00,0.00,0.00); trace/3= 1.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.444385                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1542   r_free= 0.2139   ksol= 0.32   Bsol= 47.91   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,1.06,1.36,0.00,0.00,0.00); trace/3= 1.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.445070                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.370657              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.238  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.429201              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.040  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1542      final r-factor (work) = 0.1321          |
| start r-factor (free) = 0.2139      final r-factor (free) = 0.1862          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0195 = 4.37 * 0.50 * 5.4735 + 1.00 * 0.0582                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8442 = 4.37 * 0.50 * 5.3862 + 1.00 * 0.0736                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1321      final r-factor (work) = 0.1258          |
| start r-factor (free) = 0.1862      final r-factor (free) = 0.1781          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7143 = 1.43 * 1.00 * 5.3862 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5726 = 1.43 * 1.00 * 5.2886 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.885)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.97  15.30    None  None   None       |
|    all(noH): 2823   0      0.00    114.97  15.30    None  None   None       |
|    Sol.    : 438    0      3.74    106.04  42.25    None  None   None       |
|    Mac.    : 2385   0      0.00    114.97  10.35    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 -  11.497: 1761   |   5:    57.483 -  68.980:   68        |
|      1:    11.497 -  22.993:  549   |   6:    68.980 -  80.477:   38        |
|      2:    22.993 -  34.490:  152   |   7:    80.477 -  91.973:   12        |
|      3:    34.490 -  45.987:  135   |   8:    91.973 - 103.470:    3        |
|      4:    45.987 -  57.483:  102   |   9:   103.470 - 114.967:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1258 r_free = 0.1781             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1257 r_free = 0.1778             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1257   r_free= 0.1778   ksol= 0.32   Bsol= 47.91   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,1.06,1.36,0.00,0.00,0.00); trace/3= 1.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.262281                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6600 0.99   1453  166 0.0962 0.1322       5.383      5.5969|
|  2:  4.6600 -  3.7169 0.99   1397  151 0.0898 0.1222      5.4805      5.7489|
|  3:  3.7169 -  3.2524 0.99   1371  150 0.1189 0.1853      5.5722      5.9618|
|  4:  3.2524 -  2.9575 0.99   1372  155 0.1423 0.1771      5.5655      5.7294|
|  5:  2.9575 -  2.7469 0.98   1351  149 0.1515 0.2010      5.4554      5.6509|
|  6:  2.7469 -  2.5858 0.99   1353  153 0.1460 0.2249        5.36      5.6176|
|  7:  2.5858 -  2.4568 0.99   1340  141 0.1414 0.1835      5.2936      5.4837|
|  8:  2.4568 -  2.3503 0.99   1338  156 0.1313 0.1776      5.1506      5.3186|
|  9:  2.3503 -  2.2601 0.99   1340  150 0.1274 0.2155      5.0922      5.4081|
| 10:  2.2601 -  2.1824 0.98   1326  151 0.1288 0.1947       5.074      5.3567|
| 11:  2.1824 -  2.1143 0.98   1325  134 0.1365 0.2057      5.0682      5.4045|
| 12:  2.1143 -  2.0540 1.00   1322  153 0.1327 0.2038      5.0067      5.2264|
| 13:  2.0540 -  2.0001 0.78   1060  128 0.1353 0.1943       4.884       5.098|
| 14:  2.0001 -  1.9514 0.21    282   22 0.1329 0.1783      4.7893        5.04|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1022 -  4.6600  1453   166  0.93   9.75   0.97     0.96       7917.00|
|  2:  4.6600 -  3.7169  1397   151  0.95   9.01   1.02     1.00      10425.58|
|  3:  3.7169 -  3.2524  1371   150  0.91  13.83   1.05     1.04      13229.46|
|  4:  3.2524 -  2.9575  1372   155  0.89  17.00   1.02     0.99      13392.08|
|  5:  2.9575 -  2.7469  1351   149  0.87  19.48   1.01     0.97      11533.89|
|  6:  2.7469 -  2.5858  1353   153  0.87  19.78   0.99     0.96      10080.14|
|  7:  2.5858 -  2.4568  1340   141  0.87  19.48   1.00     0.97       8714.26|
|  8:  2.4568 -  2.3503  1338   156  0.89  17.81   1.00     0.96       6448.26|
|  9:  2.3503 -  2.2601  1340   150  0.88  18.03   1.01     0.98       5841.23|
| 10:  2.2601 -  2.1824  1326   151  0.89  17.75   1.01     0.98       5699.43|
| 11:  2.1824 -  2.1143  1325   134  0.87  19.61   0.99     0.95       5808.35|
| 12:  2.1143 -  2.0540  1322   153  0.87  19.40   1.01     1.00       5376.28|
| 13:  2.0540 -  2.0001  1060   128  0.87  19.83   1.00     0.97       4206.67|
| 14:  2.0001 -  1.9514   282    22  0.87  19.01   0.99     0.97       3407.93|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3407.93 max =        13392.08 mean =      8378.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.89|
|phase err.(test): min =        0.00 max =           89.94 mean =        16.19|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1262   r_free= 0.1783   ksol= 0.32   Bsol= 50.65   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.04,-0.13,0.17,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264601                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1262   r_free= 0.1783   ksol= 0.32   Bsol= 50.65   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.04,-0.13,0.17,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264601                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6600 0.99   1453  166 0.0979 0.1331      5.3944      5.6173|
|  2:  4.6600 -  3.7169 0.99   1397  151 0.0913 0.1229      5.4933      5.7613|
|  3:  3.7169 -  3.2524 0.99   1371  150 0.1192 0.1854      5.5782        5.96|
|  4:  3.2524 -  2.9575 0.99   1372  155 0.1429 0.1764      5.5664      5.7253|
|  5:  2.9575 -  2.7469 0.98   1351  149 0.1516 0.2002      5.4552      5.6498|
|  6:  2.7469 -  2.5858 0.99   1353  153 0.1461 0.2249      5.3597      5.6169|
|  7:  2.5858 -  2.4568 0.99   1340  141 0.1412 0.1837      5.2926      5.4841|
|  8:  2.4568 -  2.3503 0.99   1338  156 0.1312 0.1778      5.1504      5.3205|
|  9:  2.3503 -  2.2601 0.99   1340  150 0.1271 0.2155      5.0921      5.4085|
| 10:  2.2601 -  2.1824 0.98   1326  151 0.1287 0.1945      5.0742       5.356|
| 11:  2.1824 -  2.1143 0.98   1325  134 0.1365 0.2056      5.0681      5.4049|
| 12:  2.1143 -  2.0540 1.00   1322  153 0.1326 0.2039      5.0065      5.2268|
| 13:  2.0540 -  2.0001 0.78   1060  128 0.1354 0.1943       4.884      5.0977|
| 14:  2.0001 -  1.9514 0.21    282   22 0.1328 0.1784       4.789      5.0411|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1022 -  4.6600  1453   166  0.93   9.94   0.97     0.95       8154.86|
|  2:  4.6600 -  3.7169  1397   151  0.94   9.20   1.02     1.00      10711.63|
|  3:  3.7169 -  3.2524  1371   150  0.91  13.93   1.05     1.04      13438.56|
|  4:  3.2524 -  2.9575  1372   155  0.89  17.03   1.02     0.99      13379.46|
|  5:  2.9575 -  2.7469  1351   149  0.87  19.46   1.01     0.97      11506.75|
|  6:  2.7469 -  2.5858  1353   153  0.87  19.79   0.99     0.96      10072.80|
|  7:  2.5858 -  2.4568  1340   141  0.87  19.46   1.00     0.97       8705.93|
|  8:  2.4568 -  2.3503  1338   156  0.89  17.84   1.00     0.96       6460.84|
|  9:  2.3503 -  2.2601  1340   150  0.88  18.06   1.01     0.98       5851.21|
| 10:  2.2601 -  2.1824  1326   151  0.89  17.78   1.01     0.98       5710.01|
| 11:  2.1824 -  2.1143  1325   134  0.87  19.61   0.99     0.95       5805.93|
| 12:  2.1143 -  2.0540  1322   153  0.87  19.40   1.01     1.00       5376.35|
| 13:  2.0540 -  2.0001  1060   128  0.87  19.83   1.00     0.98       4206.98|
| 14:  2.0001 -  1.9514   282    22  0.87  19.01   0.99     0.97       3406.22|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3406.22 max =        13438.56 mean =      8435.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.93|
|phase err.(test): min =        0.00 max =           89.89 mean =        16.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.885)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.19    116.16  16.49    None  None   None       |
|    all(noH): 2823   0      1.19    116.16  16.49    None  None   None       |
|    Sol.    : 438    0      4.93    107.23  43.44    None  None   None       |
|    Mac.    : 2385   0      1.19    116.16  11.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.190 -  12.687: 1761   |   5:    58.674 -  70.170:   68        |
|      1:    12.687 -  24.184:  549   |   6:    70.170 -  81.667:   38        |
|      2:    24.184 -  35.680:  152   |   7:    81.667 -  93.164:   12        |
|      3:    35.680 -  47.177:  135   |   8:    93.164 - 104.660:    3        |
|      4:    47.177 -  58.674:  102   |   9:   104.660 - 116.157:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 348         
Filter by distance & map next to the model:
   mapped sites are within: 0.640 - 5.871
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 345 from: 348
   mapped sites are within: 0.708 - 5.871

peak=    9.184 closest distance to " CB  VAL A 230 " =    1.412
peak=    8.825 closest distance to " CG2 VAL A 296 " =    1.424
peak=    7.308 closest distance to " O   HOH Z  37 " =    1.689
peak=    7.186 closest distance to " CG  ARG A 138 " =    1.222
peak=    6.735 closest distance to " O   HOH Z 279 " =    1.321
peak=    6.613 closest distance to " NH2BARG A 102 " =    1.071
peak=    6.295 closest distance to " O   HOH Z 120 " =    1.195
peak=    6.154 closest distance to " O   HOH Z 277 " =    1.517
peak=    6.112 closest distance to " NH2 ARG A  56 " =    2.251
peak=    6.033 closest distance to " O   HOH Z 291 " =    1.348
peak=    5.855 closest distance to " O   HOH Z 278 " =    1.336
peak=    5.672 closest distance to " O   HOH Z 178 " =    1.112
peak=    5.658 closest distance to " O   HOH Z 199 " =    1.194
peak=    5.493 closest distance to " CD1AILE A 234 " =    1.111
peak=    5.465 closest distance to " O   HOH Z 117 " =    1.105
peak=    5.414 closest distance to " CD2 LEU A   5 " =    1.163
peak=    5.362 closest distance to " O   HOH Z 186 " =    1.518
peak=    5.321 closest distance to " CG  LEU A   5 " =    1.311
peak=    5.114 closest distance to " O   HOH Z 246 " =    1.502
peak=    5.111 closest distance to " O   HOH Z 316 " =    0.980
peak=    5.014 closest distance to " O   HOH Z 127 " =    1.345
peak=    4.937 closest distance to " CB  PRO A  54 " =    0.924
peak=    4.897 closest distance to " O   HOH Z 411 " =    3.566
peak=    4.874 closest distance to " O   HOH Z 132 " =    1.901
peak=    4.847 closest distance to " O   HOH Z 183 " =    1.456
peak=    4.832 closest distance to " O   HOH Z 124 " =    1.437
peak=    4.828 closest distance to " O   HOH Z  92 " =    1.203
peak=    4.766 closest distance to " O   HOH Z 260 " =    1.382
peak=    4.748 closest distance to " O   HOH Z 202 " =    1.543
peak=    4.738 closest distance to " CB  GLN A 223 " =    1.569
peak=    4.718 closest distance to " O   HOH Z  97 " =    1.880
peak=    4.683 closest distance to " O   HOH Z 374 " =    1.165
peak=    4.650 closest distance to " O   HOH Z  61 " =    1.397
peak=    4.626 closest distance to " O   HOH Z 144 " =    1.639
peak=    4.614 closest distance to " O   HOH Z 134 " =    1.503
peak=    4.612 closest distance to " O   HOH Z 112 " =    1.438
peak=    4.581 closest distance to " CB  ASN A 148 " =    1.245
peak=    4.502 closest distance to " CB  SER A  63 " =    1.349
peak=    4.455 closest distance to " O   HOH Z 236 " =    1.953
peak=    4.403 closest distance to " O   HOH Z 126 " =    1.584
peak=    4.402 closest distance to " O   HOH Z 394 " =    1.544
peak=    4.372 closest distance to " O   HOH Z  48 " =    1.926
peak=    4.371 closest distance to " O   HOH Z 243 " =    1.147
peak=    4.368 closest distance to " O   HOH Z 389 " =    1.932
peak=    4.355 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.347 closest distance to " O   HOH Z 263 " =    1.518
peak=    4.335 closest distance to " CG2 THR A 221 " =    0.998
peak=    4.327 closest distance to " CD2 LEU A 228 " =    1.268
peak=    4.317 closest distance to " NH1 ARG A 138 " =    1.107
peak=    4.311 closest distance to " O   HOH Z 272 " =    2.048
peak=    4.293 closest distance to " OD2 ASP A 286 " =    2.867
peak=    4.285 closest distance to " O   HOH Z 284 " =    2.972
peak=    4.278 closest distance to " CA  ALA A  21 " =    1.275
peak=    4.276 closest distance to " O   HOH Z 427 " =    3.266
peak=    4.251 closest distance to " CG  PRO A 198 " =    1.381
peak=    4.243 closest distance to " O   HOH Z  11 " =    1.243
peak=    4.242 closest distance to " NE2 GLN A  11 " =    1.118
peak=    4.235 closest distance to " OD1 ASN A 217 " =    1.683
peak=    4.206 closest distance to " CB  VAL A 202 " =    1.693
peak=    4.204 closest distance to " CB  VAL A 230 " =    1.225
peak=    4.195 closest distance to " O   HOH Z 182 " =    1.232
peak=    4.185 closest distance to " O   HOH Z  63 " =    1.334
peak=    4.182 closest distance to " O   HOH Z 155 " =    1.785
peak=    4.165 closest distance to " O   HOH Z  58 " =    1.572
peak=    4.131 closest distance to " CG  PRO A  54 " =    1.239
peak=    4.129 closest distance to " CB  TYR A 169 " =    0.925
peak=    4.121 closest distance to " O   HOH Z 221 " =    1.480
peak=    4.095 closest distance to " O   HOH Z 298 " =    1.971
peak=    4.092 closest distance to " O   HOH Z  80 " =    1.988
peak=    4.090 closest distance to " CD  ARG A 138 " =    0.959
peak=    4.090 closest distance to " O   HOH Z 193 " =    1.768
peak=    4.087 closest distance to " OE1 GLN A  58 " =    5.631
peak=    4.086 closest distance to " O   HOH Z 138 " =    1.010
peak=    4.078 closest distance to " O   HOH Z 371 " =    3.265
peak=    4.066 closest distance to " CG  LEU A 228 " =    1.156
peak=    4.056 closest distance to " CD1 LEU A 300 " =    1.183
peak=    4.043 closest distance to " O   ASP A 132 " =    3.754
peak=    4.034 closest distance to " O   HOH Z 189 " =    2.632
peak=    4.025 closest distance to " O   HOH Z 221 " =    1.232
peak=    4.013 closest distance to " O   HOH Z 369 " =    1.985
peak=    4.011 closest distance to " CG  PRO A 243 " =    1.270
peak=    4.011 closest distance to " O   HOH Z  97 " =    1.374
peak=    4.004 closest distance to " CD  LYS A 119 " =    1.220
peak=    3.994 closest distance to " CB  VAL A 265 " =    1.255
peak=    3.992 closest distance to " NH1 ARG A  56 " =    1.114
peak=    3.963 closest distance to " O   HOH Z  78 " =    2.163
peak=    3.963 closest distance to " O   HOH Z 193 " =    1.565
peak=    3.951 closest distance to " CB  LEU A 228 " =    1.290
peak=    3.941 closest distance to " CB  TRP A 179 " =    1.354
peak=    3.937 closest distance to " O   HOH Z 303 " =    2.192
peak=    3.933 closest distance to " CG  PRO A 213 " =    1.238
peak=    3.933 closest distance to " O   HOH Z 316 " =    2.214
peak=    3.927 closest distance to " CG  PRO A 280 " =    0.856
peak=    3.907 closest distance to " O   HOH Z 118 " =    1.965
peak=    3.893 closest distance to " O   HOH Z 368 " =    2.158
peak=    3.874 closest distance to " O   HOH Z 425 " =    1.429
peak=    3.873 closest distance to " O   HOH Z 192 " =    1.238
peak=    3.872 closest distance to " CB  ARG A 275 " =    0.932
peak=    3.863 closest distance to " O   HOH Z 136 " =    1.392
peak=    3.842 closest distance to " O   PRO A 198 " =    1.455
peak=    3.829 closest distance to " CB  SER A   3 " =    1.525
peak=    3.825 closest distance to " O   HOH Z   4 " =    1.555
peak=    3.820 closest distance to " CA  ASN A  74 " =    1.369
peak=    3.819 closest distance to " O   HOH Z 163 " =    1.634
peak=    3.817 closest distance to " CB  GLU A 128 " =    1.296
peak=    3.813 closest distance to " O   HOH Z 128 " =    1.974
peak=    3.812 closest distance to " O   HOH Z 217 " =    1.794
peak=    3.804 closest distance to " O   SER A  87 " =    2.361
peak=    3.800 closest distance to " CA  THR A 221 " =    0.928
peak=    3.795 closest distance to " O   HOH Z 423 " =    1.967
peak=    3.764 closest distance to " CA  ALA A 160 " =    0.815
peak=    3.753 closest distance to " O   HOH Z 133 " =    2.113
peak=    3.753 closest distance to " O   HOH Z 276 " =    1.436
peak=    3.750 closest distance to " O   HOH Z 326 " =    1.378
peak=    3.748 closest distance to " NZ  LYS A 117 " =    3.193
peak=    3.747 closest distance to " O   HOH Z  44 " =    2.506
peak=    3.736 closest distance to " O   HOH Z   3 " =    1.441
peak=    3.735 closest distance to " CA  LEU A 282 " =    1.188
peak=    3.734 closest distance to " O   HOH Z 184 " =    1.524
peak=    3.729 closest distance to " O   HOH Z 410 " =    1.483
peak=    3.729 closest distance to " CB  LEU A 255 " =    0.854
peak=    3.726 closest distance to " CB  ARG A  56 " =    1.109
peak=    3.720 closest distance to " CA  TYR A  30 " =    1.037
peak=    3.719 closest distance to " CB  ASP A 124 " =    0.859
peak=    3.718 closest distance to " O   HOH Z 271 " =    2.057
peak=    3.718 closest distance to " O   HOH Z  63 " =    2.112
peak=    3.717 closest distance to " O   GLN A 278 " =    1.126
peak=    3.716 closest distance to " O   HOH Z 207 " =    2.351
peak=    3.710 closest distance to " O   HOH Z  53 " =    2.567
peak=    3.708 closest distance to " O   HOH Z  68 " =    1.557
peak=    3.701 closest distance to " O   HOH Z  15 " =    2.228
peak=    3.694 closest distance to " OD1 ASN A  69 " =    2.532
peak=    3.691 closest distance to " OE1 GLN A  11 " =    1.732
peak=    3.684 closest distance to " CG1 VAL A 153 " =    1.081
peak=    3.676 closest distance to " O   HOH Z 422 " =    2.646
peak=    3.673 closest distance to " O   MET A 105 " =    1.844
peak=    3.671 closest distance to " O   HOH Z 281 " =    4.044
peak=    3.658 closest distance to " O   HOH Z 227 " =    1.900
peak=    3.656 closest distance to " O   HOH Z  88 " =    3.497
peak=    3.652 closest distance to " O   HOH Z 265 " =    2.368
peak=    3.652 closest distance to " O   HOH Z 392 " =    2.499
peak=    3.646 closest distance to " CZ3 TRP A  92 " =    1.052
peak=    3.641 closest distance to " O   HOH Z 141 " =    1.534
peak=    3.638 closest distance to " O   HOH Z 180 " =    2.124
peak=    3.636 closest distance to " CB  TRP A 266 " =    1.022
peak=    3.630 closest distance to " OE1 GLN A  58 " =    1.304
peak=    3.629 closest distance to " CB  GLU A 152 " =    1.152
peak=    3.625 closest distance to " O   HOH Z 133 " =    1.794
peak=    3.624 closest distance to " O   HOH Z 345 " =    3.348
peak=    3.618 closest distance to " CD2 LEU A 255 " =    1.519
peak=    3.618 closest distance to " CG1BVAL A  72 " =    1.638
peak=    3.617 closest distance to " O   HOH Z 102 " =    1.340
peak=    3.616 closest distance to " O   GLN A  55 " =    1.521
peak=    3.613 closest distance to " O   HOH Z 232 " =    2.020
peak=    3.596 closest distance to " O   HOH Z  13 " =    1.789
peak=    3.591 closest distance to " O   HOH Z 193 " =    2.064
peak=    3.590 closest distance to " O   HOH Z 151 " =    1.723
peak=    3.579 closest distance to " O   HOH Z 261 " =    1.439
peak=    3.579 closest distance to " O   HOH Z 295 " =    1.579
peak=    3.576 closest distance to " O   HOH Z  49 " =    1.962
peak=    3.575 closest distance to " O   HOH Z 289 " =    1.515
peak=    3.565 closest distance to " CG  GLN A  88 " =    1.074
peak=    3.565 closest distance to " CB  MET A  40 " =    0.769
peak=    3.563 closest distance to " CD  LYS A 166 " =    1.544
peak=    3.555 closest distance to " O   HOH Z  30 " =    1.773
peak=    3.554 closest distance to " O   HOH Z 214 " =    1.935
peak=    3.545 closest distance to " O   ALA A 100 " =    1.853
peak=    3.543 closest distance to " CG1 ILE A  49 " =    1.595
peak=    3.542 closest distance to " O   HOH Z 203 " =    1.575
peak=    3.542 closest distance to " O   HOH Z 329 " =    3.465
peak=    3.540 closest distance to " CG  GLU A  44 " =    1.054
peak=    3.532 closest distance to " O   HOH Z 359 " =    3.757
peak=    3.530 closest distance to " NH2BARG A 190 " =    1.693
peak=    3.524 closest distance to " CG  ARG A  66 " =    2.195
peak=    3.523 closest distance to " CB  GLU A 277 " =    3.688
peak=    3.521 closest distance to " CB  ARG A 259 " =    1.822
peak=    3.518 closest distance to " O   HOH Z 437 " =    2.418
peak=    3.513 closest distance to " CG2 VAL A 174 " =    1.353
peak=    3.512 closest distance to " O   HOH Z 426 " =    3.019
peak=    3.511 closest distance to " OE1 GLN A  55 " =    1.449
peak=    3.510 closest distance to " NE2 HIS A 115 " =    0.905
peak=    3.504 closest distance to " O   HOH Z 357 " =    1.200
peak=    3.503 closest distance to " CD ALYS A 290 " =    0.931
peak=    3.500 closest distance to " O   HOH Z 189 " =    3.566
peak=    3.496 closest distance to " OG  SER A  22 " =    2.998
peak=    3.494 closest distance to " O   HOH Z  37 " =    2.553
peak=    3.490 closest distance to " CA  SER A  32 " =    1.620
peak=    3.490 closest distance to " O   ALA A 165 " =    1.245
peak=    3.484 closest distance to " O   HOH Z 214 " =    1.038
peak=    3.479 closest distance to " O   HOH Z 420 " =    2.211
peak=    3.472 closest distance to " O   HOH Z 374 " =    2.983
peak=    3.466 closest distance to " CA  ALA A 295 " =    1.067
peak=    3.465 closest distance to " O   HOH Z 426 " =    1.415
peak=    3.458 closest distance to " CB  LEU A 143 " =    0.988
peak=    3.452 closest distance to " CD2 HIS A 115 " =    0.813
peak=    3.451 closest distance to " O   HOH Z 327 " =    2.438
peak=    3.447 closest distance to " O   HOH Z 344 " =    2.814
peak=    3.442 closest distance to " C   SER A  32 " =    1.094
peak=    3.438 closest distance to " O   HOH Z 355 " =    2.007
peak=    3.424 closest distance to " O   HOH Z 132 " =    3.440
peak=    3.419 closest distance to " O   HOH Z 116 " =    1.725
peak=    3.416 closest distance to " O   HOH Z 332 " =    1.689
peak=    3.410 closest distance to " O   HOH Z 215 " =    1.462
peak=    3.407 closest distance to " O   HOH Z 374 " =    2.429
peak=    3.404 closest distance to " O   HOH Z 215 " =    1.517
peak=    3.403 closest distance to " O   HOH Z  93 " =    2.812
peak=    3.402 closest distance to " O   THR A  31 " =    1.462
peak=    3.399 closest distance to " O   HOH Z 130 " =    3.923
peak=    3.399 closest distance to " O   HOH Z  49 " =    1.232
peak=    3.398 closest distance to " O   HOH Z 236 " =    1.545
peak=    3.396 closest distance to " O   HOH Z 331 " =    1.195
peak=    3.393 closest distance to " O   HOH Z 429 " =    2.181
peak=    3.390 closest distance to " CZ  PHE A 192 " =    1.109
peak=    3.389 closest distance to " O   HOH Z 280 " =    1.461
peak=    3.383 closest distance to " CE  LYS A  76 " =    0.846
peak=    3.382 closest distance to " O   HOH Z 143 " =    1.248
peak=    3.379 closest distance to " N   LEU A 101 " =    1.254
peak=    3.378 closest distance to " O   GLY A  57 " =    2.259
peak=    3.376 closest distance to " O   HOH Z 290 " =    1.160
peak=    3.375 closest distance to " O   HOH Z 199 " =    2.993
peak=    3.372 closest distance to " O   HOH Z 407 " =    2.296
peak=    3.372 closest distance to " N   TYR A  15 " =    1.015
peak=    3.367 closest distance to " O   HOH Z 284 " =    1.428
peak=    3.358 closest distance to " O   HOH Z 149 " =    2.037
peak=    3.356 closest distance to " CG2 THR A 220 " =    1.052
peak=    3.355 closest distance to " NH2BARG A 145 " =    2.137
peak=    3.354 closest distance to " O   HOH Z 152 " =    1.547
peak=    3.353 closest distance to " O   GLY A  75 " =    3.091
peak=    3.353 closest distance to " O   HOH Z 124 " =    2.650
peak=    3.352 closest distance to " CB  MET A  47 " =    1.172
peak=    3.352 closest distance to " O   HOH Z  99 " =    2.017
peak=    3.348 closest distance to " O   HOH Z  63 " =    1.803
peak=    3.348 closest distance to " O   HOH Z 257 " =    0.975
peak=    3.347 closest distance to " CA  PHE A 283 " =    1.248
peak=    3.347 closest distance to " O   HOH Z 218 " =    4.559
peak=    3.342 closest distance to " NH1AARG A 145 " =    0.940
peak=    3.341 closest distance to " OG BSER A 258 " =    3.538
peak=    3.341 closest distance to " O   HOH Z 166 " =    1.554
peak=    3.340 closest distance to " CB  ALA A 100 " =    1.379
peak=    3.337 closest distance to " O   HOH Z 108 " =    1.767
peak=    3.337 closest distance to " O   HOH Z 392 " =    1.878
peak=    3.336 closest distance to " O   ASN A 217 " =    1.501
peak=    3.336 closest distance to " CB  LYS A 117 " =    1.117
peak=    3.336 closest distance to " CG1BVAL A 121 " =    1.210
peak=    3.333 closest distance to " O   HOH Z  68 " =    2.529
peak=    3.333 closest distance to " CA  MET A  40 " =    1.027
peak=    3.330 closest distance to " CD1 TRP A 266 " =    1.148
peak=    3.328 closest distance to " CD  ARG A 269 " =    0.839
peak=    3.324 closest distance to " CG  LEU A 167 " =    1.123
peak=    3.324 closest distance to " CB  THR A 235 " =    1.198
peak=    3.320 closest distance to " CG1 VAL A 174 " =    1.233
peak=    3.320 closest distance to " O   HOH Z  71 " =    1.227
peak=    3.312 closest distance to " O   HOH Z 407 " =    3.347
peak=    3.309 closest distance to " O   HOH Z 434 " =    1.442
peak=    3.306 closest distance to " O   SER A 164 " =    1.039
peak=    3.303 closest distance to " O   HOH Z 104 " =    3.367
peak=    3.303 closest distance to " O   HOH Z 281 " =    1.556
peak=    3.299 closest distance to " O   HOH Z 131 " =    2.417
peak=    3.298 closest distance to " O   HOH Z 204 " =    1.508
peak=    3.295 closest distance to " OG ASER A 164 " =    0.749
peak=    3.295 closest distance to " CB  THR A  31 " =    1.925
peak=    3.293 closest distance to " CA  VAL A 126 " =    1.271
peak=    3.291 closest distance to " OG BSER A 164 " =    2.119
peak=    3.291 closest distance to " O   HOH Z 126 " =    1.708
peak=    3.289 closest distance to " CB  TYR A  30 " =    1.530
peak=    3.288 closest distance to " CA  GLY A 147 " =    0.827
peak=    3.288 closest distance to " CD  ARG A  56 " =    1.249
peak=    3.288 closest distance to " CB  ALA A 104 " =    1.093
peak=    3.287 closest distance to " O   HOH Z  33 " =    1.790
peak=    3.283 closest distance to " CG2 THR A  42 " =    0.951
peak=    3.282 closest distance to " CB  SER A 271 " =    0.957
peak=    3.277 closest distance to " O   HOH Z  40 " =    1.481
peak=    3.277 closest distance to " O   HOH Z 195 " =    1.792
peak=    3.276 closest distance to " CB  ALA A 256 " =    0.967
peak=    3.274 closest distance to " O   HOH Z  13 " =    2.162
peak=    3.273 closest distance to " O   HOH Z 272 " =    2.505
peak=    3.270 closest distance to " CD1 LEU A   5 " =    1.407
peak=    3.261 closest distance to " O   HOH Z  44 " =    1.735
peak=    3.258 closest distance to " NH1 ARG A  14 " =    1.021
peak=    3.256 closest distance to " NE BARG A 102 " =    1.251
peak=    3.247 closest distance to " O   HOH Z 406 " =    1.286
peak=    3.245 closest distance to " O   HOH Z  99 " =    2.674
peak=    3.244 closest distance to " O   HOH Z 313 " =    1.948
peak=    3.243 closest distance to " CA  ASP A 124 " =    0.708
peak=    3.242 closest distance to " NZ  LYS A 117 " =    0.967
peak=    3.240 closest distance to " O   HOH Z 377 " =    1.335
peak=    3.237 closest distance to " O   HOH Z 119 " =    2.201
peak=    3.236 closest distance to " CG1 ILE A  33 " =    1.245
peak=    3.236 closest distance to " O   GLY A  91 " =    1.153
peak=    3.233 closest distance to " O   HOH Z  21 " =    1.936
peak=    3.229 closest distance to " CA  VAL A  41 " =    0.946
peak=    3.226 closest distance to " NH2 ARG A 219 " =    1.773
peak=    3.225 closest distance to " CD  ARG A 159 " =    0.854
peak=    3.223 closest distance to " CD2 HIS A 115 " =    1.018
peak=    3.222 closest distance to " O   HOH Z 197 " =    1.344
peak=    3.220 closest distance to " CD1 ILE A 199 " =    1.052
peak=    3.220 closest distance to " O   HOH Z  78 " =    1.261
peak=    3.214 closest distance to " CD1 ILE A  33 " =    1.580
peak=    3.212 closest distance to " O   HOH Z 279 " =    2.321
peak=    3.209 closest distance to " CA  ASP A 191 " =    0.770
peak=    3.209 closest distance to " O   HOH Z 424 " =    2.726
peak=    3.206 closest distance to " O   HOH Z  43 " =    2.165
peak=    3.203 closest distance to " O   HOH Z 244 " =    1.561
peak=    3.201 closest distance to " CD  GLU A 152 " =    0.803
peak=    3.200 closest distance to " NH1BARG A 145 " =    1.274
peak=    3.198 closest distance to " N   ASN A 110 " =    1.188
peak=    3.198 closest distance to " CB  ASN A 215 " =    1.088
peak=    3.191 closest distance to " O   HOH Z  48 " =    2.171
peak=    3.187 closest distance to " CA  LYS A 117 " =    1.223
peak=    3.184 closest distance to " CG  MET A 188 " =    1.330
peak=    3.181 closest distance to " O   HOH Z 322 " =    1.245
peak=    3.181 closest distance to " CB  ASP A 140 " =    0.713
peak=    3.179 closest distance to " O   HOH Z 366 " =    3.070
peak=    3.176 closest distance to " NZ  LYS A  48 " =    1.307
peak=    3.171 closest distance to " CB  TYR A  30 " =    1.135
peak=    3.169 closest distance to " N   ASN A  39 " =    1.399
peak=    3.167 closest distance to " O   HOH Z  85 " =    1.992
peak=    3.165 closest distance to " O   HOH Z   9 " =    2.312
peak=    3.155 closest distance to " CB  ALA A 248 " =    0.983
peak=    3.154 closest distance to " CG  LYS A  76 " =    1.943
peak=    3.153 closest distance to " OE1 GLU A   2 " =    2.169
peak=    3.148 closest distance to " CB  GLN A  89 " =    1.042
peak=    3.148 closest distance to " NH1 ARG A 269 " =    0.890
peak=    3.142 closest distance to " CD  ARG A  14 " =    1.190
peak=    3.142 closest distance to " CD1 LEU A 101 " =    1.315
peak=    3.132 closest distance to " O   HOH Z 175 " =    2.376
peak=    3.132 closest distance to " CE1 PHE A 208 " =    1.039
peak=    3.129 closest distance to " CB  ASN A 170 " =    1.428
peak=    3.118 closest distance to " NE  ARG A 156 " =    1.057
peak=    3.111 closest distance to " CA  ALA A 158 " =    1.043
peak=    3.111 closest distance to " CB  ARG A 139 " =    0.904
peak=    3.110 closest distance to " CB  ALA A  34 " =    0.941
peak=    3.107 closest distance to " NE2 GLN A  89 " =    1.228
peak=    3.105 closest distance to " CB  GLN A  58 " =    0.855
peak=    3.097 closest distance to " O   SER A 164 " =    1.424
peak=    3.092 closest distance to " CG2BVAL A  41 " =    1.178
peak=    3.089 closest distance to " CB  ALA A 161 " =    0.990
peak=    3.087 closest distance to " CG  ARG A 269 " =    0.885
peak=    3.086 closest distance to " CG  GLN A  77 " =    2.171
peak=    3.082 closest distance to " CG2 ILE A 234 " =    0.854
peak=    3.079 closest distance to " O   HOH Z 368 " =    3.351
peak=    3.078 closest distance to " O   HOH Z 164 " =    2.004
peak=    3.071 closest distance to " O   VAL A 232 " =    1.963
peak=    3.052 closest distance to " OG  SER A  28 " =    1.474
peak=    3.020 closest distance to " O   HOH Z 298 " =    5.871

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.678 - 5.768
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 210
   mapped sites are within: 0.853 - 5.768

peak=   -5.062 closest distance to " CD  ARG A 138 " =    1.190
peak=   -4.864 closest distance to " CG2 VAL A 230 " =    0.972
peak=   -4.527 closest distance to " OG ASER A 134 " =    1.241
peak=   -4.346 closest distance to " O   HOH Z 231 " =    1.399
peak=   -4.320 closest distance to " O   HOH Z 266 " =    4.209
peak=   -4.284 closest distance to " O   HOH Z 166 " =    1.793
peak=   -4.238 closest distance to " N   ARG A  56 " =    1.143
peak=   -4.192 closest distance to " O   HOH Z  19 " =    1.926
peak=   -4.150 closest distance to " CG  ARG A 138 " =    0.878
peak=   -4.111 closest distance to " O   HOH Z  13 " =    1.272
peak=   -4.110 closest distance to " O   ILE A 109 " =    2.710
peak=   -4.053 closest distance to " CB  GLN A  55 " =    1.171
peak=   -4.051 closest distance to " C   ASN A 187 " =    1.825
peak=   -4.015 closest distance to " CG  ASN A  45 " =    1.805
peak=   -3.987 closest distance to " O   HOH Z 221 " =    1.316
peak=   -3.980 closest distance to " OD2 ASP A  50 " =    1.480
peak=   -3.974 closest distance to " O   HOH Z 380 " =    4.842
peak=   -3.953 closest distance to " O   HOH Z 221 " =    1.587
peak=   -3.932 closest distance to " O   HOH Z 407 " =    3.178
peak=   -3.891 closest distance to " O   HOH Z  92 " =    1.393
peak=   -3.875 closest distance to " N   GLN A  58 " =    1.657
peak=   -3.870 closest distance to " O   HOH Z  11 " =    1.590
peak=   -3.848 closest distance to " O   HOH Z 243 " =    1.590
peak=   -3.830 closest distance to " O   HOH Z 377 " =    1.607
peak=   -3.802 closest distance to " C   ALA A 158 " =    1.169
peak=   -3.785 closest distance to " CD2 LEU A 143 " =    2.505
peak=   -3.774 closest distance to " N   ALA A  43 " =    2.461
peak=   -3.760 closest distance to " CE3 TRP A 150 " =    1.919
peak=   -3.748 closest distance to " O   HOH Z 290 " =    1.014
peak=   -3.734 closest distance to " O   HOH Z 388 " =    1.661
peak=   -3.729 closest distance to " NE2 GLN A  55 " =    2.531
peak=   -3.715 closest distance to " OG BSER A 134 " =    1.355
peak=   -3.706 closest distance to " CG  MET A 105 " =    0.950
peak=   -3.671 closest distance to " NH2 ARG A  66 " =    1.672
peak=   -3.670 closest distance to " CG  GLU A 152 " =    2.415
peak=   -3.663 closest distance to " O   HOH Z 275 " =    1.777
peak=   -3.663 closest distance to " OG1 THR A  82 " =    1.652
peak=   -3.657 closest distance to " O   HOH Z  71 " =    0.853
peak=   -3.650 closest distance to " CE  MET A  93 " =    1.307
peak=   -3.647 closest distance to " CG2 VAL A 112 " =    2.542
peak=   -3.639 closest distance to " O   HOH Z 292 " =    4.404
peak=   -3.613 closest distance to " O   HOH Z  17 " =    1.282
peak=   -3.608 closest distance to " O   HOH Z 124 " =    1.340
peak=   -3.598 closest distance to " O   HOH Z 283 " =    1.771
peak=   -3.596 closest distance to " CD  ARG A 156 " =    2.109
peak=   -3.594 closest distance to " CB  ALA A 100 " =    2.051
peak=   -3.582 closest distance to " CZ  TYR A 169 " =    1.914
peak=   -3.581 closest distance to " CB  TRP A  85 " =    2.339
peak=   -3.580 closest distance to " CA  SER A 164 " =    1.941
peak=   -3.570 closest distance to " O   VAL A  67 " =    2.827
peak=   -3.568 closest distance to " OG BSER A 134 " =    1.797
peak=   -3.564 closest distance to " CD1 PHE A  59 " =    1.810
peak=   -3.563 closest distance to " CA  GLY A  98 " =    2.175
peak=   -3.559 closest distance to " NH1 ARG A  56 " =    2.364
peak=   -3.558 closest distance to " CB  PRO A 163 " =    2.724
peak=   -3.558 closest distance to " CD  GLN A  88 " =    0.898
peak=   -3.551 closest distance to " N   ALA A 226 " =    2.070
peak=   -3.547 closest distance to " CE1 HIS A 115 " =    1.232
peak=   -3.547 closest distance to " O   GLY A 211 " =    1.476
peak=   -3.540 closest distance to " O   HOH Z 345 " =    2.259
peak=   -3.537 closest distance to " CB  TYR A  15 " =    2.196
peak=   -3.526 closest distance to " ND2 ASN A  60 " =    1.403
peak=   -3.522 closest distance to " OG  SER A  97 " =    2.203
peak=   -3.521 closest distance to " CB  ALA A 227 " =    2.309
peak=   -3.518 closest distance to " O   ASN A 301 " =    1.550
peak=   -3.511 closest distance to " CD2 LEU A 237 " =    2.600
peak=   -3.510 closest distance to " N   GLY A  17 " =    1.519
peak=   -3.507 closest distance to " NH1AARG A 102 " =    1.074
peak=   -3.500 closest distance to " O   HOH Z 151 " =    1.336
peak=   -3.492 closest distance to " O   HOH Z  55 " =    2.631
peak=   -3.492 closest distance to " CG  GLN A 223 " =    2.427
peak=   -3.490 closest distance to " NE2 GLN A  73 " =    1.662
peak=   -3.487 closest distance to " CD2 PHE A  61 " =    1.965
peak=   -3.484 closest distance to " CD1 TRP A 179 " =    1.198
peak=   -3.481 closest distance to " OD1 ASN A 148 " =    1.630
peak=   -3.480 closest distance to " O   HOH Z 166 " =    1.594
peak=   -3.478 closest distance to " O   HOH Z  43 " =    1.734
peak=   -3.477 closest distance to " CD1 LEU A 228 " =    2.424
peak=   -3.475 closest distance to " O   HOH Z 317 " =    2.413
peak=   -3.471 closest distance to " O   HOH Z 274 " =    2.485
peak=   -3.467 closest distance to " O   HOH Z 396 " =    1.445
peak=   -3.460 closest distance to " CD2 LEU A 300 " =    2.839
peak=   -3.459 closest distance to " O   HOH Z  84 " =    1.403
peak=   -3.458 closest distance to " OD2 ASP A 171 " =    1.896
peak=   -3.456 closest distance to " O   HOH Z  52 " =    2.011
peak=   -3.451 closest distance to " CB  SER A  63 " =    3.255
peak=   -3.451 closest distance to " O   HOH Z 113 " =    1.763
peak=   -3.449 closest distance to " O   HOH Z 189 " =    2.495
peak=   -3.448 closest distance to " NH2AARG A 275 " =    5.380
peak=   -3.446 closest distance to " N   GLN A 122 " =    1.621
peak=   -3.443 closest distance to " O   HOH Z 222 " =    0.983
peak=   -3.437 closest distance to " O   HOH Z 103 " =    1.884
peak=   -3.429 closest distance to " O   HOH Z 427 " =    1.467
peak=   -3.429 closest distance to " CG  GLU A  53 " =    1.503
peak=   -3.425 closest distance to " O   HOH Z  98 " =    1.622
peak=   -3.419 closest distance to " OG  SER A 245 " =    1.262
peak=   -3.417 closest distance to " NZ  LYS A 117 " =    1.438
peak=   -3.417 closest distance to " CA  GLY A 203 " =    2.124
peak=   -3.413 closest distance to " CD  ARG A  14 " =    3.142
peak=   -3.411 closest distance to " N   SER A 276 " =    1.381
peak=   -3.408 closest distance to " O   LEU A 101 " =    1.277
peak=   -3.406 closest distance to " O   HOH Z  98 " =    1.460
peak=   -3.406 closest distance to " O   GLY A 118 " =    2.183
peak=   -3.397 closest distance to " O   HOH Z 275 " =    1.489
peak=   -3.396 closest distance to " CE  MET A 105 " =    2.288
peak=   -3.396 closest distance to " CZ  TYR A 172 " =    1.656
peak=   -3.394 closest distance to " OG  SER A  62 " =    4.570
peak=   -3.390 closest distance to " CG  ASP A 231 " =    0.857
peak=   -3.388 closest distance to " O   HOH Z 138 " =    1.071
peak=   -3.382 closest distance to " CD1 LEU A   5 " =    2.492
peak=   -3.382 closest distance to " CD  LYS A 289 " =    2.333
peak=   -3.380 closest distance to " ND1 HIS A 115 " =    1.218
peak=   -3.379 closest distance to " O   HOH Z 184 " =    1.097
peak=   -3.376 closest distance to " O   HOH Z 353 " =    2.284
peak=   -3.372 closest distance to " CE2 TYR A  30 " =    2.769
peak=   -3.360 closest distance to " O   LEU A 255 " =    1.690
peak=   -3.356 closest distance to " O   HOH Z 387 " =    3.832
peak=   -3.350 closest distance to " O   HOH Z   9 " =    2.064
peak=   -3.349 closest distance to " O   HOH Z  93 " =    2.119
peak=   -3.348 closest distance to " OD1 ASP A 200 " =    1.272
peak=   -3.343 closest distance to " CD  GLN A  88 " =    2.405
peak=   -3.339 closest distance to " OD1 ASN A 173 " =    1.218
peak=   -3.336 closest distance to " CB  CYS A 254 " =    2.323
peak=   -3.334 closest distance to " O   HOH Z 423 " =    2.123
peak=   -3.331 closest distance to " O   HOH Z 241 " =    1.263
peak=   -3.326 closest distance to " CG  ASN A 301 " =    1.885
peak=   -3.324 closest distance to " CB  ALA A  43 " =    2.420
peak=   -3.321 closest distance to " CB  ALA A  51 " =    1.842
peak=   -3.320 closest distance to " CB  GLN A  55 " =    0.988
peak=   -3.318 closest distance to " CG  GLU A 277 " =    1.176
peak=   -3.313 closest distance to " O   HOH Z  97 " =    1.215
peak=   -3.313 closest distance to " O   HOH Z 102 " =    1.143
peak=   -3.311 closest distance to " O   HOH Z 336 " =    5.487
peak=   -3.309 closest distance to " O   HOH Z 345 " =    4.715
peak=   -3.308 closest distance to " C   LEU A 143 " =    1.339
peak=   -3.304 closest distance to " O   GLY A 196 " =    1.268
peak=   -3.296 closest distance to " O   LEU A 300 " =    2.484
peak=   -3.295 closest distance to " O   VAL A 174 " =    2.136
peak=   -3.287 closest distance to " CD2 LEU A 237 " =    2.656
peak=   -3.284 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.282 closest distance to " CG2 THR A   4 " =    1.894
peak=   -3.275 closest distance to " O   HOH Z 420 " =    5.768
peak=   -3.274 closest distance to " O   HOH Z  60 " =    2.292
peak=   -3.273 closest distance to " O   HOH Z 138 " =    0.983
peak=   -3.270 closest distance to " CA  GLY A 133 " =    1.900
peak=   -3.264 closest distance to " O   HOH Z 293 " =    1.304
peak=   -3.264 closest distance to " OE2 GLU A   2 " =    1.819
peak=   -3.261 closest distance to " O   GLY A  80 " =    2.486
peak=   -3.260 closest distance to " CG  PRO A 163 " =    2.489
peak=   -3.257 closest distance to " O   HOH Z 411 " =    3.611
peak=   -3.257 closest distance to " CA  VAL A 232 " =    2.300
peak=   -3.247 closest distance to " OG  SER A  87 " =    1.254
peak=   -3.246 closest distance to " C   GLY A  23 " =    2.177
peak=   -3.245 closest distance to " OD1 ASN A 249 " =    1.424
peak=   -3.235 closest distance to " O   HOH Z  97 " =    2.233
peak=   -3.231 closest distance to " ND2BASN A 224 " =    1.691
peak=   -3.229 closest distance to " O   HOH Z 118 " =    4.599
peak=   -3.226 closest distance to " O   GLY A  57 " =    1.346
peak=   -3.225 closest distance to " O   HOH Z 186 " =    1.289
peak=   -3.223 closest distance to " CB  SER A 258 " =    2.050
peak=   -3.222 closest distance to " O   HOH Z 198 " =    2.204
peak=   -3.216 closest distance to " O   HOH Z  10 " =    1.543
peak=   -3.215 closest distance to " O   HOH Z 108 " =    2.762
peak=   -3.212 closest distance to " OG1 THR A 178 " =    1.194
peak=   -3.208 closest distance to " ND2 ASN A  45 " =    1.093
peak=   -3.207 closest distance to " CD2 TYR A 293 " =    2.213
peak=   -3.206 closest distance to " O   HOH Z 185 " =    2.153
peak=   -3.196 closest distance to " CB  ALA A 248 " =    1.903
peak=   -3.190 closest distance to " O   HOH Z 265 " =    1.584
peak=   -3.189 closest distance to " C   GLU A  46 " =    1.090
peak=   -3.189 closest distance to " O   HOH Z 236 " =    1.308
peak=   -3.187 closest distance to " CG  GLN A  58 " =    1.186
peak=   -3.186 closest distance to " O   HOH Z 378 " =    1.342
peak=   -3.185 closest distance to " CB  PRO A 243 " =    2.708
peak=   -3.183 closest distance to " O   HOH Z 134 " =    2.361
peak=   -3.183 closest distance to " CG  TYR A 172 " =    2.166
peak=   -3.181 closest distance to " CZ3 TRP A  92 " =    1.246
peak=   -3.173 closest distance to " O   HOH Z 392 " =    0.924
peak=   -3.169 closest distance to " O   HOH Z 125 " =    2.836
peak=   -3.166 closest distance to " CE  MET A 105 " =    2.205
peak=   -3.165 closest distance to " O   HOH Z 366 " =    1.694
peak=   -3.163 closest distance to " OH  TYR A 169 " =    1.076
peak=   -3.158 closest distance to " C   LEU A 101 " =    1.037
peak=   -3.157 closest distance to " CA  GLY A  35 " =    2.062
peak=   -3.157 closest distance to " O   HOH Z 252 " =    1.126
peak=   -3.154 closest distance to " OG ASER A 210 " =    1.359
peak=   -3.151 closest distance to " N   ALA A 248 " =    1.988
peak=   -3.151 closest distance to " CG  TYR A 169 " =    1.679
peak=   -3.150 closest distance to " O   HOH Z 239 " =    1.500
peak=   -3.144 closest distance to " O   HOH Z 246 " =    1.299
peak=   -3.141 closest distance to " CD1 ILE A  33 " =    2.149
peak=   -3.133 closest distance to " CA  ASN A 142 " =    1.277
peak=   -3.131 closest distance to " C   SER A 206 " =    1.396
peak=   -3.127 closest distance to " OE1 GLU A 277 " =    2.130
peak=   -3.122 closest distance to " CD  ARG A 139 " =    1.586
peak=   -3.121 closest distance to " OE1 GLN A  88 " =    0.927
peak=   -3.117 closest distance to " O   HOH Z  92 " =    2.430
peak=   -3.099 closest distance to " NH1BARG A 190 " =    2.218
peak=   -3.091 closest distance to " O   HOH Z 325 " =    1.562
peak=   -3.082 closest distance to " CG  ARG A 269 " =    2.223
peak=   -3.073 closest distance to " CG1 VAL A 296 " =    1.531
peak=   -3.072 closest distance to " OD2 ASP A  65 " =    1.513
peak=   -3.066 closest distance to " N   LEU A 261 " =    1.055
peak=   -3.056 closest distance to " O   SER A 135 " =    1.495
peak=   -3.055 closest distance to " CD2 LEU A   5 " =    0.896
peak=   -3.052 closest distance to " NE1 TRP A 150 " =    2.168
peak=   -3.040 closest distance to " OG ASER A 258 " =    2.862
peak=   -3.020 closest distance to " CD1 TYR A 186 " =    1.949

================= 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    :  0.4869 0.4915   6.289683e+00   6.288112e+00
   1_bss:  0.4803 0.4790   5.843590e+00   5.835803e+00
   1_xyz:  0.4118 0.4474   6.203078e+00   6.244812e+00
   1_adp:  0.3736 0.4331   6.141971e+00   6.225771e+00
   1_occ:  0.3731 0.4333   6.141527e+00   6.225906e+00
   2_bss:  0.3712 0.4312   6.142294e+00   6.224459e+00
   2_xyz:  0.3000 0.3674   5.989173e+00   6.130538e+00
   2_adp:  0.2815 0.3461   5.943284e+00   6.096002e+00
   2_occ:  0.2812 0.3458   5.942375e+00   6.095569e+00
   3_bss:  0.2798 0.3421   5.940655e+00   6.091316e+00
   3_xyz:  0.2185 0.2828   5.735768e+00   5.928795e+00
   3_adp:  0.2001 0.2698   5.674505e+00   5.890030e+00
   3_occ:  0.2000 0.2699   5.674502e+00   5.890062e+00
   4_bss:  0.1997 0.2696   5.674438e+00   5.889610e+00
   4_xyz:  0.1650 0.2258   5.498612e+00   5.730322e+00
   4_adp:  0.1537 0.2140   5.444889e+00   5.680739e+00
   4_occ:  0.1536 0.2139   5.444385e+00   5.680356e+00
   5_bss:  0.1542 0.2139   5.445070e+00   5.680166e+00
   5_xyz:  0.1321 0.1862   5.305438e+00   5.551502e+00
   5_adp:  0.1258 0.1781   5.262924e+00   5.509122e+00
   5_occ:  0.1257 0.1778   5.262281e+00   5.508553e+00
   5_bss:  0.1262 0.1783   5.264601e+00   5.510818e+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:  0.300  20.000   8.257   7.094   8.552   0.000   0.000   0.000
   1_xyz:  0.300  20.000   8.257   7.094   8.552   0.000   0.000   0.000
   1_adp:  0.300  20.000   8.257   7.094   8.552   0.000   0.000   0.000
   1_occ:  0.300  20.000   8.257   7.094   8.552   0.000   0.000   0.000
   2_bss:  0.307  37.518   4.448   3.762   5.659   0.000   0.000   0.000
   2_xyz:  0.307  37.518   4.448   3.762   5.659   0.000   0.000   0.000
   2_adp:  0.307  37.518   4.448   3.762   5.659   0.000   0.000   0.000
   2_occ:  0.307  37.518   4.448   3.762   5.659   0.000   0.000   0.000
   3_bss:  0.317  37.518   2.321   2.118   3.357   0.000   0.000   0.000
   3_xyz:  0.317  37.518   2.321   2.118   3.357   0.000   0.000   0.000
   3_adp:  0.317  37.518   2.321   2.118   3.357   0.000   0.000   0.000
   3_occ:  0.317  37.518   2.321   2.118   3.357   0.000   0.000   0.000
   4_bss:  0.324  47.912   1.424   1.291   1.836   0.000   0.000   0.000
   4_xyz:  0.324  47.912   1.424   1.291   1.836   0.000   0.000   0.000
   4_adp:  0.324  47.912   1.424   1.291   1.836   0.000   0.000   0.000
   4_occ:  0.324  47.912   1.424   1.291   1.836   0.000   0.000   0.000
   5_bss:  0.324  47.912   1.153   1.056   1.362   0.000   0.000   0.000
   5_xyz:  0.324  47.912   1.153   1.056   1.362   0.000   0.000   0.000
   5_adp:  0.324  47.912   1.153   1.056   1.362   0.000   0.000   0.000
   5_occ:  0.324  47.912   1.153   1.056   1.362   0.000   0.000   0.000
   5_bss:  0.320  50.651  -0.037  -0.134   0.171   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.504 0.3736  0.4469    76833.323
   1_bss:  62.368 0.3598  0.5283    74034.120
   1_xyz:  56.240 0.4372  0.6279    61201.581
   1_adp:  52.005 0.4920  0.7762    55952.310
   1_occ:  52.059 0.4914  0.7748    56143.703
   2_bss:  51.853 0.4939  0.6996    55871.148
   2_xyz:  41.194 0.6266  0.8831    39416.549
   2_adp:  38.329 0.6611  0.9342    35298.610
   2_occ:  38.278 0.6617  0.9346    35210.573
   3_bss:  38.003 0.6647  0.8731    34716.621
   3_xyz:  29.428 0.7627  0.9671    21783.626
   3_adp:  27.679 0.7819  0.9738    19680.228
   3_occ:  27.687 0.7819  0.9735    19691.063
   4_bss:  27.595 0.7830  0.9384    19679.459
   4_xyz:  22.488 0.8363  0.9741    13438.676
   4_adp:  20.991 0.8517  0.9742    12113.578
   4_occ:  20.972 0.8519  0.9743    12095.469
   5_bss:  20.944 0.8521  0.9630    12070.573
   5_xyz:  17.910 0.8806  0.9801     9147.029
   5_adp:  16.841 0.8906  0.9797     8391.094
   5_occ:  16.819 0.8908  0.9797     8377.589
   5_bss:  16.863 0.8905  0.9794     8434.166
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3645e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3645e+01
   1_xyz:   1.714  0.013  0.108 18.284  0.007  4.109   1.4601e-01
   1_adp:   1.714  0.013  0.108 18.284  0.007  4.109   1.4601e-01
   1_occ:   1.714  0.013  0.108 18.284  0.007  4.109   1.4601e-01
   2_bss:   1.714  0.013  0.108 18.284  0.007  4.109   1.4601e-01
   2_xyz:   1.151  0.008  0.079 16.186  0.005  4.108   8.3751e-02
   2_adp:   1.151  0.008  0.079 16.186  0.005  4.108   8.3751e-02
   2_occ:   1.151  0.008  0.079 16.186  0.005  4.108   8.3751e-02
   3_bss:   1.151  0.008  0.079 16.186  0.005  4.108   8.3751e-02
   3_xyz:   1.092  0.007  0.077 15.306  0.005  4.126   6.8316e-02
   3_adp:   1.092  0.007  0.077 15.306  0.005  4.126   6.8316e-02
   3_occ:   1.092  0.007  0.077 15.306  0.005  4.126   6.8316e-02
   4_bss:   1.092  0.007  0.077 15.306  0.005  4.126   6.8316e-02
   4_xyz:   0.969  0.006  0.070 15.211  0.004  4.114   5.8190e-02
   4_adp:   0.969  0.006  0.070 15.211  0.004  4.114   5.8190e-02
   4_occ:   0.969  0.006  0.070 15.211  0.004  4.114   5.8190e-02
   5_bss:   0.969  0.006  0.070 15.211  0.004  4.114   5.8190e-02
   5_xyz:   1.148  0.008  0.084 15.445  0.004  4.120   7.3588e-02
   5_adp:   1.148  0.008  0.084 15.445  0.004  4.120   7.3588e-02
   5_occ:   1.148  0.008  0.084 15.445  0.004  4.120   7.3588e-02
   5_bss:   1.148  0.008  0.084 15.445  0.004  4.120   7.3588e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9531e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9531e+00
   1_xyz:  14.842  0.170  0.455 85.014  0.051  2.187   9.9879e-02
   1_adp:  14.842  0.170  0.455 85.014  0.051  2.187   9.9879e-02
   1_occ:  14.842  0.170  0.455 85.014  0.051  2.187   9.9879e-02
   2_bss:  14.842  0.170  0.455 85.014  0.051  2.187   9.9879e-02
   2_xyz:   8.192  0.082  0.266 82.192  0.031  2.011   5.7766e-02
   2_adp:   8.192  0.082  0.266 82.192  0.031  2.011   5.7766e-02
   2_occ:   8.192  0.082  0.266 82.192  0.031  2.011   5.7766e-02
   3_bss:   8.192  0.082  0.266 82.192  0.031  2.011   5.7766e-02
   3_xyz:   7.853  0.072  0.276 75.964  0.049  2.320   6.2018e-02
   3_adp:   7.853  0.072  0.276 75.964  0.049  2.320   6.2018e-02
   3_occ:   7.853  0.072  0.276 75.964  0.049  2.320   6.2018e-02
   4_bss:   7.853  0.072  0.276 75.964  0.049  2.320   6.2018e-02
   4_xyz:   8.459  0.044  0.238 87.315  0.033  2.423   3.7586e-02
   4_adp:   8.459  0.044  0.238 87.315  0.033  2.423   3.7586e-02
   4_occ:   8.459  0.044  0.238 87.315  0.033  2.423   3.7586e-02
   5_bss:   8.459  0.044  0.238 87.315  0.033  2.423   3.7586e-02
   5_xyz:   8.192  0.065  0.444 82.432  0.030  2.302   5.0228e-02
   5_adp:   8.192  0.065  0.444 82.432  0.030  2.302   5.0228e-02
   5_occ:   8.192  0.065  0.444 82.432  0.030  2.302   5.0228e-02
   5_bss:   8.192  0.065  0.444 82.432  0.030  2.302   5.0228e-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:  90.45   0.00  14.87  88.04   0.00  12.56  90.45   0.00  27.46
   1_occ:  90.45   0.00  14.87  88.04   0.00  12.56  90.45   0.00  27.46
   2_bss:  90.45   0.00  14.87  88.04   0.00  12.56  90.45   0.00  27.46
   2_xyz:  90.45   0.00  14.87  88.04   0.00  12.56  90.45   0.00  27.46
   2_adp:  87.53   0.00  14.92  84.71   0.00  11.76  87.53   0.00  32.11
   2_occ:  87.53   0.00  14.92  84.71   0.00  11.76  87.53   0.00  32.11
   3_bss:  87.53   0.00  14.92  84.71   0.00  11.76  87.53   0.00  32.11
   3_xyz:  87.53   0.00  14.92  84.71   0.00  11.76  87.53   0.00  32.11
   3_adp:  99.47   0.00  15.87  98.35   0.00  11.29  99.47   0.72  40.82
   3_occ:  99.47   0.00  15.87  98.35   0.00  11.29  99.47   0.72  40.82
   4_bss:  99.47   0.00  15.87  98.35   0.00  11.29  99.47   0.72  40.82
   4_xyz:  99.47   0.00  15.87  98.35   0.00  11.29  99.47   0.72  40.82
   4_adp: 105.96   0.00  15.74 105.96   0.00  10.75 103.96   3.15  42.88
   4_occ: 105.96   0.00  15.74 105.96   0.00  10.75 103.96   3.15  42.88
   5_bss: 105.96   0.00  15.74 105.96   0.00  10.75 103.96   3.15  42.88
   5_xyz: 105.96   0.00  15.74 105.96   0.00  10.75 103.96   3.15  42.88
   5_adp: 114.97   0.00  15.30 114.97   0.00  10.35 106.04   3.74  42.25
   5_occ: 114.97   0.00  15.30 114.97   0.00  10.35 106.04   3.74  42.25
   5_bss: 116.16   1.19  16.49 116.16   1.19  11.54 107.23   4.93  43.44
------------------------------------------------------------------------
 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:    1.231    0.023    0.410
   1_adp:    1.231    0.023    0.410
   1_occ:    1.231    0.023    0.410
   2_bss:    1.231    0.023    0.410
   2_xyz:    1.783    0.052    0.563
   2_adp:    1.783    0.052    0.563
   2_occ:    1.783    0.052    0.563
   3_bss:    1.783    0.052    0.563
   3_xyz:    1.633    0.021    0.651
   3_adp:    1.633    0.021    0.651
   3_occ:    1.633    0.021    0.651
   4_bss:    1.633    0.021    0.651
   4_xyz:    1.865    0.073    0.730
   4_adp:    1.865    0.073    0.730
   4_occ:    1.865    0.073    0.730
   5_bss:    1.865    0.073    0.730
   5_xyz:    1.844    0.057    0.770
   5_adp:    1.844    0.057    0.770
   5_occ:    1.844    0.057    0.770
   5_bss:    1.844    0.057    0.770
------------------------------------------------------------------------

CPU time actual refinement: 351.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1155/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_1155/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1155/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1155/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1155/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.55 
  Macro-tasks:
    bulk solvent and scale       = 40.66  
    individual site refinement   = 146.19 
    weights calculation          = 31.95  
    collect and process          = 6.37   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 225.27 
  Micro-tasks:
    mask                            = 3.08   
    f_calc                          = 113.82 
    alpha_beta                      = 8.39   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 121.68 
    fmodel                         = 7.04   
    r_factors                      = 0.23   
    phase_errors                   = 10.14  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 265.77 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.009 micro seconds
Total CPU time: 6.09 minutes
from_scatterers_fft:    627 calls, 113.51 s
gradients_fft:          571 calls, 109.16 s

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

# Date 2008-01-16 Time 03:20:13 PST -0800 (1200482413.61 s)
Start R-work = 0.4869, R-free = 0.4915 (no bulk solvent and anisotropic scale)
Final R-work = 0.1419, R-free = 0.1956 (no bulk solvent and anisotropic scale)

Start R-work = 0.4803, R-free = 0.4790
Final R-work = 0.1262, R-free = 0.1783