# Date 2008-01-16 Time 03:31:38 PST -0800 (1200483098.37 s)
#phil __OFF__

Command line arguments: "../1267.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 = 2530
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1267

-------------------------------------------------------------------------------
  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: (72.0062, 46.93, 85.0941, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (72.0062, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97119
Completeness in resolution range: 0.935616
Completeness with d_max=infinity: 0.932854

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1990
                             d_min =   1.9712

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: (72.0062, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97119
Completeness in resolution range: 0.935616
Completeness with d_max=infinity: 0.932854

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1995 -  4.2194 [2194/2223]  1977   217   9.9%
  bin  2:  4.2194 -  3.3609 [2111/2127]  1898   213  10.1%
  bin  3:  3.3609 -  2.9396 [2076/2095]  1866   210  10.1%
  bin  4:  2.9396 -  2.6724 [2082/2112]  1881   201   9.7%
  bin  5:  2.6724 -  2.4817 [2046/2065]  1843   203   9.9%
  bin  6:  2.4817 -  2.3360 [2050/2086]  1840   210  10.2%
  bin  7:  2.3360 -  2.2194 [2036/2069]  1826   210  10.3%
  bin  8:  2.2194 -  2.1230 [2017/2051]  1822   195   9.7%
  bin  9:  2.1230 -  2.0415 [1995/2037]  1795   200  10.0%
  bin 10:  2.0415 -  1.9712 [ 982/2072]   882   100  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1267/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:
        1.72 -     2.35: 19
        2.35 -     2.99: 1846
        2.99 -     3.63: 4578
        3.63 -     4.26: 9144
        4.26 -     4.90: 12652
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.716 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.865 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  1.958 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.016 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28234 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_1267/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1267/model_refine_001.geo

CPU time processing inputs: 9.21


============================ 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 = 72.00625 46.93 85.09415 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: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4718   r_free= 0.4701   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.272876                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7068 0.99   1422  161 0.3896 0.3934      6.5798      6.5666|
|  2:  4.7068 -  3.7544 0.99   1382  146 0.3848 0.3990      6.7658       6.829|
|  3:  3.7544 -  3.2853 0.99   1339  153 0.4340 0.3933      6.6416      6.6294|
|  4:  3.2853 -  2.9874 0.99   1344  151 0.4486 0.4652      6.5025      6.4846|
|  5:  2.9874 -  2.7747 0.99   1332  145 0.4920 0.5331      6.3567      6.3616|
|  6:  2.7747 -  2.6120 0.99   1318  149 0.5031 0.5072      6.2732       6.272|
|  7:  2.6120 -  2.4817 0.99   1328  139 0.5296 0.4881      6.2512      6.1605|
|  8:  2.4817 -  2.3741 0.98   1295  154 0.5221 0.5028      6.1596      6.1881|
|  9:  2.3741 -  2.2831 0.98   1320  148 0.5135 0.4739      6.1225      6.0648|
| 10:  2.2831 -  2.2045 0.98   1298  142 0.5161 0.5284      6.0753      6.1028|
| 11:  2.2045 -  2.1358 1.00   1320  140 0.5188 0.5350      6.0455       6.041|
| 12:  2.1358 -  2.0749 0.97   1278  148 0.5190 0.5550      5.9376       5.993|
| 13:  2.0749 -  2.0204 0.90   1194  139 0.5402 0.4890      5.8845       5.823|
| 14:  2.0204 -  1.9712 0.34    460   44 0.5318 0.4830       5.818      5.7862|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7068  1422   161  0.70  34.23   0.80     0.74      70916.32|
|  2:  4.7068 -  3.7544  1382   146  0.71  34.26   0.88     0.78     100654.01|
|  3:  3.7544 -  3.2853  1339   153  0.60  43.91   0.84     0.72     110607.90|
|  4:  3.2853 -  2.9874  1344   151  0.50  51.47   0.80     0.62     103761.37|
|  5:  2.9874 -  2.7747  1332   145  0.40  59.91   0.73     0.48      86591.57|
|  6:  2.7747 -  2.6120  1318   149  0.37  61.83   0.74     0.46      74475.53|
|  7:  2.6120 -  2.4817  1328   139  0.39  60.91   0.72     0.43      63065.40|
|  8:  2.4817 -  2.3741  1295   154  0.40  60.07   0.72     0.48      56231.73|
|  9:  2.3741 -  2.2831  1320   148  0.40  59.76   0.74     0.47      49418.16|
| 10:  2.2831 -  2.2045  1298   142  0.38  61.32   0.75     0.45      47051.78|
| 11:  2.2045 -  2.1358  1320   140  0.33  65.60   0.77     0.40      46646.35|
| 12:  2.1358 -  2.0749  1278   148  0.26  70.66   0.73     0.33      45375.01|
| 13:  2.0749 -  2.0204  1194   139  0.25  71.08   0.72     0.33      40079.93|
| 14:  2.0204 -  1.9712   460    44  0.32  65.97   0.70     0.38      31487.73|
|alpha:            min =        0.33 max =            0.78 mean =         0.51|
|beta:             min =    31487.73 max =       110607.90 mean =     68393.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           90.00 mean =        56.41|
|phase err.(test): min =        0.00 max =           89.91 mean =        56.55|
|-----------------------------------------------------------------------------|

============================== 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 = 14.504148             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.048   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.222838              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.018   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      695 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1511 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2610 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3932 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5051 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6537 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7700 |
|-----------------------------------------------------------------------------|
|-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 |       53.863 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.729 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.009)------------------------------------------|
|    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 = 12.009)------------------------------------------|
|    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: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4772   r_free= 0.4765   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.275130                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4632   r_free= 0.4574   ksol= 0.32   Bsol= 8.49   scale= 1.000    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.44,7.45,8.22,0.00,0.00,0.00); trace/3= 8.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.269479                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.374040             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.852   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.104548              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.449   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4632      final r-factor (work) = 0.3792          |
| start r-factor (free) = 0.4574      final r-factor (free) = 0.4087          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 92.6689 = 12.37 * 0.50 * 6.2722 + 1.00 * 53.8625                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.3574 = 12.37 * 0.50 * 6.1765 + 1.00 * 0.1434                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3792      final r-factor (work) = 0.3321          |
| start r-factor (free) = 0.4087      final r-factor (free) = 0.3825          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8366 = 1.10 * 1.00 * 6.1765 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7365 = 1.10 * 1.00 * 6.0853 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.009)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.42   12.45    None  None   None       |
|    all(noH): 2823   0      0.00    87.42   12.45    None  None   None       |
|    Sol.    : 438    0      0.00    73.67   26.81    None  None   None       |
|    Mac.    : 2385   0      0.00    87.42   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:     0.000 -   8.742: 1419   |   5:    43.709 -  52.450:   41        |
|      1:     8.742 -  17.484:  706   |   6:    52.450 -  61.192:   24        |
|      2:    17.484 -  26.225:  354   |   7:    61.192 -  69.934:    8        |
|      3:    26.225 -  34.967:  165   |   8:    69.934 -  78.676:    5        |
|      4:    34.967 -  43.709:   99   |   9:    78.676 -  87.417:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3321 r_free = 0.3825             target_work(ml) = 6.058         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3314 r_free = 0.3830             target_work(ml) = 6.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3314   r_free= 0.3830   ksol= 0.32   Bsol= 8.49   scale= 1.093    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.44,7.45,8.22,0.00,0.00,0.00); trace/3= 8.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.057808                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3284   r_free= 0.3802   ksol= 0.33   Bsol= 35.03   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.46,4.05,5.42,0.00,0.00,0.00); trace/3= 5.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.057607                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.487914              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.482   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.519768              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.600  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3284      final r-factor (work) = 0.2350          |
| start r-factor (free) = 0.3802      final r-factor (free) = 0.2960          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9519 = 8.49 * 0.50 * 6.0812 + 1.00 * 0.1434                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2536 = 8.49 * 0.50 * 5.9304 + 1.00 * 0.0851                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2350      final r-factor (work) = 0.2107          |
| start r-factor (free) = 0.2960      final r-factor (free) = 0.2706          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0976 = 0.52 * 1.00 * 5.9304 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9929 = 0.52 * 1.00 * 5.7364 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.009)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.75   12.52    None  None   None       |
|    all(noH): 2823   0      0.00    84.75   12.52    None  None   None       |
|    Sol.    : 438    0      0.95    73.00   32.48    None  None   None       |
|    Mac.    : 2385   0      0.00    84.75   8.85     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 -   8.475: 1495   |   5:    42.375 -  50.850:   87        |
|      1:     8.475 -  16.950:  709   |   6:    50.850 -  59.325:   37        |
|      2:    16.950 -  25.425:  200   |   7:    59.325 -  67.800:    8        |
|      3:    25.425 -  33.900:  159   |   8:    67.800 -  76.275:    3        |
|      4:    33.900 -  42.375:  123   |   9:    76.275 -  84.750:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2107 r_free = 0.2706             target_work(ml) = 5.692         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2105 r_free = 0.2705             target_work(ml) = 5.691         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2105   r_free= 0.2705   ksol= 0.33   Bsol= 35.03   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.46,4.05,5.42,0.00,0.00,0.00); trace/3= 5.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.691218                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2087   r_free= 0.2664   ksol= 0.32   Bsol= 35.03   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.76,2.67,3.53,0.00,0.00,0.00); trace/3= 3.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.688288                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.524204              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.317  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.981232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.312  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2087      final r-factor (work) = 0.1581          |
| start r-factor (free) = 0.2664      final r-factor (free) = 0.2067          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2058 = 3.52 * 0.50 * 5.7435 + 1.00 * 0.0851                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9040 = 3.52 * 0.50 * 5.5828 + 1.00 * 0.0666                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1581      final r-factor (work) = 0.1439          |
| start r-factor (free) = 0.2067      final r-factor (free) = 0.1956          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4892 = 0.98 * 1.00 * 5.5828 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3071 = 0.98 * 1.00 * 5.3942 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.009)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.21   13.41    None  None   None       |
|    all(noH): 2823   0      0.00    93.21   13.41    None  None   None       |
|    Sol.    : 438    0      1.75    84.91   38.23    None  None   None       |
|    Mac.    : 2385   0      0.00    93.21   8.85     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 -   9.321: 1673   |   5:    46.605 -  55.926:   99        |
|      1:     9.321 -  18.642:  580   |   6:    55.926 -  65.247:   52        |
|      2:    18.642 -  27.963:  164   |   7:    65.247 -  74.567:   20        |
|      3:    27.963 -  37.284:  111   |   8:    74.567 -  83.888:    5        |
|      4:    37.284 -  46.605:  115   |   9:    83.888 -  93.209:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1439 r_free = 0.1956             target_work(ml) = 5.368         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1438 r_free = 0.1954             target_work(ml) = 5.368         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1438   r_free= 0.1954   ksol= 0.32   Bsol= 35.03   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.76,2.67,3.53,0.00,0.00,0.00); trace/3= 3.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.367769                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1436   r_free= 0.1955   ksol= 0.32   Bsol= 51.85   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.72,2.05,2.69,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.367025                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.157000              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.532  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.333861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.757  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1436      final r-factor (work) = 0.1258          |
| start r-factor (free) = 0.1955      final r-factor (free) = 0.1784          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5885 = 3.16 * 0.50 * 5.3987 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4585 = 3.16 * 0.50 * 5.3132 + 1.00 * 0.0717                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1258      final r-factor (work) = 0.1234          |
| start r-factor (free) = 0.1784      final r-factor (free) = 0.1739          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7878 = 0.33 * 1.00 * 5.3132 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7645 = 0.33 * 1.00 * 5.2508 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.009)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.99   13.07    None  None   None       |
|    all(noH): 2823   0      0.00    93.99   13.07    None  None   None       |
|    Sol.    : 438    0      2.15    84.94   36.78    None  None   None       |
|    Mac.    : 2385   0      0.00    93.99   8.71     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 -   9.399: 1713   |   5:    46.993 -  56.392:   83        |
|      1:     9.399 -  18.797:  573   |   6:    56.392 -  65.791:   48        |
|      2:    18.797 -  28.196:  152   |   7:    65.791 -  75.189:   15        |
|      3:    28.196 -  37.595:  124   |   8:    75.189 -  84.588:    5        |
|      4:    37.595 -  46.993:  107   |   9:    84.588 -  93.987:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1234 r_free = 0.1739             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1232 r_free = 0.1736             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1736   ksol= 0.32   Bsol= 51.85   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.72,2.05,2.69,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.235069                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1734   ksol= 0.33   Bsol= 51.85   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.44,1.96,2.58,0.00,0.00,0.00); trace/3= 2.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.234802                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.940065              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.173  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.224561              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.135  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1232      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1668          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7900 = 2.94 * 0.50 * 5.2505 + 1.00 * 0.0717                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7398 = 2.94 * 0.50 * 5.2144 + 1.00 * 0.0745                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1668      final r-factor (free) = 0.1649          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1823 = 0.22 * 1.00 * 5.2144 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1764 = 0.22 * 1.00 * 5.1937 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.009)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.37   12.81    None  None   None       |
|    all(noH): 2823   0      0.00    93.37   12.81    None  None   None       |
|    Sol.    : 438    0      2.19    84.54   35.61    None  None   None       |
|    Mac.    : 2385   0      0.00    93.37   8.62     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 -   9.337: 1713   |   5:    46.686 -  56.023:   75        |
|      1:     9.337 -  18.674:  593   |   6:    56.023 -  65.360:   43        |
|      2:    18.674 -  28.012:  147   |   7:    65.360 -  74.698:   14        |
|      3:    28.012 -  37.349:  126   |   8:    74.698 -  84.035:    4        |
|      4:    37.349 -  46.686:  105   |   9:    84.035 -  93.372:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1168 r_free = 0.1649             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1167 r_free = 0.1646             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1646   ksol= 0.33   Bsol= 51.85   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.44,1.96,2.58,0.00,0.00,0.00); trace/3= 2.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.186872                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7068 0.99   1422  161 0.1007 0.1377      5.3992      5.5883|
|  2:  4.7068 -  3.7544 0.99   1382  146 0.0890 0.1123       5.462      5.6585|
|  3:  3.7544 -  3.2853 0.99   1339  153 0.1103 0.1704       5.503      5.9071|
|  4:  3.2853 -  2.9874 0.99   1344  151 0.1288 0.1559      5.4997      5.6018|
|  5:  2.9874 -  2.7747 0.99   1332  145 0.1386 0.1885        5.37      5.5795|
|  6:  2.7747 -  2.6120 0.99   1318  149 0.1299 0.1925      5.2562       5.517|
|  7:  2.6120 -  2.4817 0.99   1328  139 0.1311 0.1696      5.2081      5.3573|
|  8:  2.4817 -  2.3741 0.98   1295  154 0.1195 0.1842      5.0755      5.3909|
|  9:  2.3741 -  2.2831 0.98   1320  148 0.1239 0.1926      5.0635      5.3531|
| 10:  2.2831 -  2.2045 0.98   1298  142 0.1173 0.1712      4.9796      5.2133|
| 11:  2.2045 -  2.1358 1.00   1320  140 0.1224 0.1850      4.9878      5.3179|
| 12:  2.1358 -  2.0749 0.97   1278  148 0.1185 0.1774       4.917      5.1421|
| 13:  2.0749 -  2.0204 0.90   1194  139 0.1237 0.1765      4.8204      5.0696|
| 14:  2.0204 -  1.9712 0.34    460   44 0.0995 0.1779      4.6041      4.9714|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7068  1422   161  0.94   9.13   0.98     0.96       7623.99|
|  2:  4.7068 -  3.7544  1382   146  0.95   8.38   1.01     0.99       9478.22|
|  3:  3.7544 -  3.2853  1339   153  0.93  12.04   1.02     1.02      11110.26|
|  4:  3.2853 -  2.9874  1344   151  0.91  14.84   1.00     0.98      11346.31|
|  5:  2.9874 -  2.7747  1332   145  0.89  16.88   0.99     0.97       9182.79|
|  6:  2.7747 -  2.6120  1318   149  0.89  17.21   0.98     0.95       7788.63|
|  7:  2.6120 -  2.4817  1328   139  0.90  16.00   0.99     0.97       6688.72|
|  8:  2.4817 -  2.3741  1295   154  0.90  15.96   0.99     0.96       5452.38|
|  9:  2.3741 -  2.2831  1320   148  0.90  16.58   1.01     0.97       5281.74|
| 10:  2.2831 -  2.2045  1298   142  0.90  15.59   1.00     0.97       4511.59|
| 11:  2.2045 -  2.1358  1320   140  0.89  17.20   0.99     0.95       4714.70|
| 12:  2.1358 -  2.0749  1278   148  0.90  16.50   1.01     1.02       4366.04|
| 13:  2.0749 -  2.0204  1194   139  0.90  16.70   1.00     0.99       3491.63|
| 14:  2.0204 -  1.9712   460    44  0.91  14.51   0.99     0.96       2307.09|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2307.09 max =        11346.31 mean =      6940.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.77 mean =        14.76|
|phase err.(test): min =        0.00 max =           88.21 mean =        14.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1642   ksol= 0.33   Bsol= 54.06   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,-0.34,0.26,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.186662                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1642   ksol= 0.33   Bsol= 54.06   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,-0.34,0.26,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.186662                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7068 0.99   1422  161 0.1002 0.1319       5.388      5.5817|
|  2:  4.7068 -  3.7544 0.99   1382  146 0.0895 0.1126      5.4632      5.6672|
|  3:  3.7544 -  3.2853 0.99   1339  153 0.1106 0.1697      5.5075      5.8992|
|  4:  3.2853 -  2.9874 0.99   1344  151 0.1294 0.1559      5.4999      5.6027|
|  5:  2.9874 -  2.7747 0.99   1332  145 0.1390 0.1884      5.3706      5.5768|
|  6:  2.7747 -  2.6120 0.99   1318  149 0.1300 0.1922      5.2559      5.5188|
|  7:  2.6120 -  2.4817 0.99   1328  139 0.1310 0.1702      5.2084      5.3592|
|  8:  2.4817 -  2.3741 0.98   1295  154 0.1194 0.1848       5.077      5.3943|
|  9:  2.3741 -  2.2831 0.98   1320  148 0.1236 0.1924      5.0635      5.3528|
| 10:  2.2831 -  2.2045 0.98   1298  142 0.1172 0.1710      4.9797      5.2132|
| 11:  2.2045 -  2.1358 1.00   1320  140 0.1223 0.1848      4.9874       5.318|
| 12:  2.1358 -  2.0749 0.97   1278  148 0.1185 0.1772      4.9175      5.1422|
| 13:  2.0749 -  2.0204 0.90   1194  139 0.1236 0.1766      4.8209      5.0701|
| 14:  2.0204 -  1.9712 0.34    460   44 0.0997 0.1787      4.6053       4.976|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7068  1422   161  0.94   8.93   0.97     0.96       7237.53|
|  2:  4.7068 -  3.7544  1382   146  0.95   8.34   1.01     0.99       9380.08|
|  3:  3.7544 -  3.2853  1339   153  0.93  12.08   1.02     1.02      11232.36|
|  4:  3.2853 -  2.9874  1344   151  0.91  14.84   1.00     0.97      11309.34|
|  5:  2.9874 -  2.7747  1332   145  0.89  16.83   0.99     0.97       9148.74|
|  6:  2.7747 -  2.6120  1318   149  0.89  17.23   0.98     0.95       7792.89|
|  7:  2.6120 -  2.4817  1328   139  0.90  16.03   0.99     0.96       6718.51|
|  8:  2.4817 -  2.3741  1295   154  0.90  16.00   0.98     0.95       5485.33|
|  9:  2.3741 -  2.2831  1320   148  0.90  16.60   1.00     0.97       5297.52|
| 10:  2.2831 -  2.2045  1298   142  0.90  15.59   0.99     0.96       4517.82|
| 11:  2.2045 -  2.1358  1320   140  0.89  17.19   0.99     0.94       4712.52|
| 12:  2.1358 -  2.0749  1278   148  0.90  16.51   1.01     1.01       4372.96|
| 13:  2.0749 -  2.0204  1194   139  0.90  16.72   0.99     0.99       3497.75|
| 14:  2.0204 -  1.9712   460    44  0.91  14.53   0.98     0.96       2312.34|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2312.34 max =        11309.34 mean =      6913.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.75|
|phase err.(test): min =        0.00 max =           88.60 mean =        14.09|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.009)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.21    95.58   15.01    None  None   None       |
|    all(noH): 2823   0      2.21    95.58   15.01    None  None   None       |
|    Sol.    : 438    0      4.39    86.75   37.82    None  None   None       |
|    Mac.    : 2385   0      2.21    95.58   10.82    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:     2.205 -  11.542: 1713   |   5:    48.891 -  58.228:   75        |
|      1:    11.542 -  20.880:  593   |   6:    58.228 -  67.565:   43        |
|      2:    20.880 -  30.217:  147   |   7:    67.565 -  76.903:   14        |
|      3:    30.217 -  39.554:  126   |   8:    76.903 -  86.240:    4        |
|      4:    39.554 -  48.891:  105   |   9:    86.240 -  95.577:    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)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.376 - 5.671
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 337 from: 345
   mapped sites are within: 0.729 - 5.671

peak=   10.158 closest distance to " CG2 VAL A 230 " =    1.449
peak=    7.901 closest distance to " CG2 VAL A 296 " =    1.133
peak=    6.310 closest distance to " O   HOH Z 111 " =    2.119
peak=    5.901 closest distance to " CG  LEU A   5 " =    1.219
peak=    5.786 closest distance to " O   HOH Z 102 " =    0.952
peak=    5.523 closest distance to " CB  GLN A 223 " =    1.432
peak=    5.433 closest distance to " CG  ARG A 138 " =    1.019
peak=    5.317 closest distance to " CD2 LEU A   5 " =    1.206
peak=    5.107 closest distance to " O   HOH Z 112 " =    1.509
peak=    4.989 closest distance to " CG  PRO A 213 " =    1.263
peak=    4.962 closest distance to " CB  SER A  63 " =    1.321
peak=    4.951 closest distance to " CG  LEU A 228 " =    1.235
peak=    4.846 closest distance to " NE2 GLN A  11 " =    1.134
peak=    4.787 closest distance to " O   HOH Z 368 " =    2.083
peak=    4.780 closest distance to " O   HOH Z 183 " =    1.457
peak=    4.769 closest distance to " O   HOH Z 278 " =    0.920
peak=    4.709 closest distance to " O   HOH Z 193 " =    1.818
peak=    4.675 closest distance to " O   HOH Z  37 " =    1.235
peak=    4.654 closest distance to " CB  GLN A 183 " =    1.203
peak=    4.641 closest distance to " CB  VAL A 230 " =    1.285
peak=    4.638 closest distance to " NH1 ARG A 138 " =    1.053
peak=    4.618 closest distance to " CB  GLU A 152 " =    1.221
peak=    4.580 closest distance to " O   PRO A 198 " =    1.571
peak=    4.512 closest distance to " O   HOH Z 186 " =    1.336
peak=    4.504 closest distance to " NH1 ARG A  56 " =    0.977
peak=    4.496 closest distance to " O   HOH Z 369 " =    1.927
peak=    4.467 closest distance to " O   HOH Z 236 " =    1.925
peak=    4.452 closest distance to " CG  PRO A 243 " =    1.120
peak=    4.439 closest distance to " O   HOH Z 247 " =    1.463
peak=    4.428 closest distance to " O   HOH Z  80 " =    1.799
peak=    4.426 closest distance to " CD1AILE A 234 " =    1.031
peak=    4.420 closest distance to " CD2 LEU A 228 " =    1.232
peak=    4.411 closest distance to " O   HOH Z 272 " =    1.938
peak=    4.398 closest distance to " O   HOH Z 263 " =    1.661
peak=    4.369 closest distance to " O   HOH Z 303 " =    2.121
peak=    4.320 closest distance to " O   HOH Z  15 " =    2.001
peak=    4.271 closest distance to " O   HOH Z 126 " =    1.892
peak=    4.254 closest distance to " O   HOH Z 108 " =    1.515
peak=    4.251 closest distance to " CB  VAL A 265 " =    1.274
peak=    4.249 closest distance to " OD2 ASP A 286 " =    2.970
peak=    4.248 closest distance to " CB  ASN A 148 " =    1.337
peak=    4.243 closest distance to " O   HOH Z 316 " =    3.052
peak=    4.238 closest distance to " CB  GLU A 128 " =    1.059
peak=    4.232 closest distance to " O   HOH Z 427 " =    3.165
peak=    4.225 closest distance to " O   HOH Z 298 " =    1.731
peak=    4.201 closest distance to " CB  SER A   3 " =    1.474
peak=    4.170 closest distance to " O   HOH Z 232 " =    2.262
peak=    4.158 closest distance to " CG  PRO A 198 " =    1.283
peak=    4.088 closest distance to " CB  LEU A 228 " =    1.246
peak=    4.085 closest distance to " CB  TYR A 169 " =    0.783
peak=    4.082 closest distance to " CD  ARG A 138 " =    1.169
peak=    4.065 closest distance to " O   HOH Z 403 " =    1.732
peak=    4.058 closest distance to " OD1 ASN A  69 " =    2.661
peak=    4.056 closest distance to " CG  PRO A 280 " =    0.807
peak=    4.052 closest distance to " CD2 LEU A 255 " =    1.547
peak=    4.045 closest distance to " O   HOH Z 425 " =    1.469
peak=    4.014 closest distance to " O   HOH Z  78 " =    2.265
peak=    4.012 closest distance to " O   HOH Z  58 " =    1.568
peak=    4.008 closest distance to " O   HOH Z 126 " =    1.581
peak=    3.995 closest distance to " CA  ALA A  21 " =    1.203
peak=    3.988 closest distance to " O   ASP A 132 " =    3.783
peak=    3.984 closest distance to " O   HOH Z 132 " =    2.502
peak=    3.979 closest distance to " CD1 LEU A 300 " =    1.254
peak=    3.975 closest distance to " CG2 THR A 221 " =    1.018
peak=    3.963 closest distance to " O   HOH Z 193 " =    2.169
peak=    3.955 closest distance to " O   HOH Z  48 " =    1.595
peak=    3.950 closest distance to " O   HOH Z 135 " =    1.954
peak=    3.949 closest distance to " O   HOH Z  97 " =    1.965
peak=    3.937 closest distance to " CB  TRP A 266 " =    0.958
peak=    3.913 closest distance to " O   HOH Z  44 " =    2.271
peak=    3.910 closest distance to " CB  VAL A 202 " =    1.496
peak=    3.909 closest distance to " CD  ARG A  66 " =    2.544
peak=    3.909 closest distance to " O   HOH Z  88 " =    3.322
peak=    3.904 closest distance to " CB  VAL A 296 " =    1.134
peak=    3.886 closest distance to " O   HOH Z 410 " =    1.436
peak=    3.885 closest distance to " O   HOH Z  68 " =    1.646
peak=    3.877 closest distance to " CG1 ILE A  33 " =    1.306
peak=    3.869 closest distance to " O   HOH Z 371 " =    3.320
peak=    3.864 closest distance to " O   HOH Z 184 " =    1.463
peak=    3.860 closest distance to " O   HOH Z  55 " =    2.454
peak=    3.859 closest distance to " CD ALYS A 290 " =    1.063
peak=    3.856 closest distance to " O   HOH Z 411 " =    3.582
peak=    3.851 closest distance to " CB  GLU A 277 " =    3.641
peak=    3.851 closest distance to " O   HOH Z 295 " =    1.575
peak=    3.850 closest distance to " O   HOH Z 280 " =    3.055
peak=    3.824 closest distance to " O   HOH Z 437 " =    2.049
peak=    3.817 closest distance to " O   HOH Z 281 " =    4.328
peak=    3.813 closest distance to " NH1AARG A 145 " =    1.167
peak=    3.812 closest distance to " O   HOH Z 346 " =    1.582
peak=    3.811 closest distance to " CD  ARG A 159 " =    0.792
peak=    3.806 closest distance to " CA  ALA A  51 " =    1.072
peak=    3.798 closest distance to " CB  ARG A 275 " =    0.830
peak=    3.798 closest distance to " OD1 ASN A 217 " =    1.660
peak=    3.797 closest distance to " CA  THR A 221 " =    0.914
peak=    3.794 closest distance to " CB  ASN A 187 " =    1.040
peak=    3.789 closest distance to " CG  GLN A  88 " =    1.087
peak=    3.766 closest distance to " CA  MET A  40 " =    1.138
peak=    3.763 closest distance to " O   HOH Z  63 " =    2.010
peak=    3.761 closest distance to " NZ  LYS A 117 " =    3.293
peak=    3.741 closest distance to " CB  SER A 216 " =    0.827
peak=    3.736 closest distance to " CZ  PHE A 192 " =    1.033
peak=    3.730 closest distance to " CG BARG A 275 " =    1.549
peak=    3.705 closest distance to " O   HOH Z  21 " =    1.708
peak=    3.705 closest distance to " OE1 GLN A  58 " =    1.189
peak=    3.698 closest distance to " CG1BVAL A  72 " =    1.607
peak=    3.694 closest distance to " O   TRP A 274 " =    1.814
peak=    3.694 closest distance to " CB  ALA A 291 " =    1.355
peak=    3.693 closest distance to " O   HOH Z 423 " =    1.622
peak=    3.677 closest distance to " O   HOH Z  78 " =    1.782
peak=    3.668 closest distance to " CA  LEU A 282 " =    1.020
peak=    3.660 closest distance to " CD1 ILE A  33 " =    1.644
peak=    3.659 closest distance to " O   HOH Z 271 " =    2.117
peak=    3.659 closest distance to " O   HOH Z 227 " =    1.783
peak=    3.652 closest distance to " O   HOH Z   9 " =    2.040
peak=    3.651 closest distance to " CB  ASP A 140 " =    0.800
peak=    3.651 closest distance to " O   HOH Z  15 " =    1.583
peak=    3.648 closest distance to " O   HOH Z 392 " =    1.975
peak=    3.638 closest distance to " CB  LEU A 143 " =    1.186
peak=    3.634 closest distance to " O   HOH Z 128 " =    2.047
peak=    3.628 closest distance to " CA  GLY A 267 " =    0.972
peak=    3.624 closest distance to " O   HOH Z 126 " =    1.589
peak=    3.622 closest distance to " CB  ASN A  39 " =    0.851
peak=    3.611 closest distance to " O   HOH Z 116 " =    1.691
peak=    3.588 closest distance to " O   HOH Z 313 " =    1.849
peak=    3.583 closest distance to " ND2 ASN A 187 " =    1.532
peak=    3.580 closest distance to " O   ALA A 291 " =    1.641
peak=    3.579 closest distance to " NE AARG A 275 " =    1.427
peak=    3.568 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.563 closest distance to " CA  TYR A  30 " =    0.981
peak=    3.563 closest distance to " CA  ALA A 154 " =    1.062
peak=    3.559 closest distance to " O   HOH Z 344 " =    2.990
peak=    3.555 closest distance to " CA  ALA A 295 " =    1.068
peak=    3.554 closest distance to " O   HOH Z 171 " =    3.872
peak=    3.553 closest distance to " O   HOH Z 144 " =    1.422
peak=    3.541 closest distance to " CA  ALA A 158 " =    1.158
peak=    3.537 closest distance to " O   HOH Z 260 " =    1.169
peak=    3.534 closest distance to " O   SER A  87 " =    2.207
peak=    3.531 closest distance to " CB  MET A  47 " =    1.016
peak=    3.528 closest distance to " CG BARG A 102 " =    1.862
peak=    3.525 closest distance to " CB  ARG A  79 " =    1.556
peak=    3.523 closest distance to " O   HOH Z 156 " =    2.719
peak=    3.522 closest distance to " NH2 ARG A 156 " =    1.177
peak=    3.521 closest distance to " CB  ILE A 234 " =    0.935
peak=    3.515 closest distance to " NH2BARG A 102 " =    0.949
peak=    3.514 closest distance to " CB  MET A  40 " =    0.815
peak=    3.513 closest distance to " N   ARG A 156 " =    1.407
peak=    3.513 closest distance to " CB  LEU A 237 " =    0.883
peak=    3.505 closest distance to " NE2 GLN A  58 " =    5.671
peak=    3.499 closest distance to " O   HOH Z 189 " =    2.896
peak=    3.499 closest distance to " O   HOH Z  61 " =    1.576
peak=    3.498 closest distance to " O   HOH Z 426 " =    1.472
peak=    3.497 closest distance to " CB  ALA A 104 " =    0.830
peak=    3.494 closest distance to " CA  ASN A 215 " =    1.221
peak=    3.489 closest distance to " O   HOH Z 345 " =    3.456
peak=    3.488 closest distance to " CA  TYR A 186 " =    1.475
peak=    3.487 closest distance to " O   HOH Z 133 " =    2.526
peak=    3.484 closest distance to " CD  LYS A 166 " =    1.309
peak=    3.483 closest distance to " OG1 THR A 246 " =    3.261
peak=    3.483 closest distance to " O   HOH Z 180 " =    2.100
peak=    3.482 closest distance to " ND1 HIS A  81 " =    1.599
peak=    3.481 closest distance to " CZ  PHE A 218 " =    1.043
peak=    3.477 closest distance to " O   HOH Z 108 " =    2.299
peak=    3.471 closest distance to " CB  ALA A 161 " =    0.922
peak=    3.462 closest distance to " N   PHE A 130 " =    1.307
peak=    3.460 closest distance to " NH2BARG A 145 " =    2.049
peak=    3.459 closest distance to " CD1 LEU A 101 " =    1.146
peak=    3.456 closest distance to " O   HOH Z 158 " =    2.907
peak=    3.454 closest distance to " CD  ARG A 269 " =    0.889
peak=    3.454 closest distance to " CA  THR A 264 " =    0.775
peak=    3.451 closest distance to " O   HOH Z 163 " =    1.560
peak=    3.449 closest distance to " CG  MET A 185 " =    1.146
peak=    3.446 closest distance to " O   HOH Z 128 " =    2.335
peak=    3.444 closest distance to " O   MET A 105 " =    1.770
peak=    3.444 closest distance to " CG  LEU A 167 " =    1.195
peak=    3.442 closest distance to " CG2AVAL A 121 " =    2.376
peak=    3.440 closest distance to " CA  SER A  87 " =    0.882
peak=    3.438 closest distance to " O   HOH Z  93 " =    2.825
peak=    3.433 closest distance to " CD  LYS A 119 " =    1.875
peak=    3.430 closest distance to " O   HOH Z 134 " =    1.481
peak=    3.427 closest distance to " CB  GLU A 236 " =    1.219
peak=    3.427 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.426 closest distance to " O   HOH Z 197 " =    2.813
peak=    3.425 closest distance to " ND1 HIS A  86 " =    1.634
peak=    3.424 closest distance to " NH2 ARG A 219 " =    1.827
peak=    3.418 closest distance to " O   HOH Z  20 " =    2.214
peak=    3.418 closest distance to " O   HOH Z 128 " =    1.751
peak=    3.415 closest distance to " N   ASN A  39 " =    1.232
peak=    3.415 closest distance to " O   ALA A 158 " =    1.365
peak=    3.415 closest distance to " CB  ASN A 148 " =    1.918
peak=    3.408 closest distance to " CB  ALA A 248 " =    1.020
peak=    3.401 closest distance to " O   HOH Z 124 " =    1.235
peak=    3.400 closest distance to " CA  ASP A 140 " =    1.257
peak=    3.396 closest distance to " OG BSER A 164 " =    2.204
peak=    3.395 closest distance to " O   HOH Z 255 " =    1.707
peak=    3.393 closest distance to " O   HOH Z  92 " =    0.813
peak=    3.392 closest distance to " CE  LYS A  76 " =    0.882
peak=    3.392 closest distance to " CB  GLU A  46 " =    1.030
peak=    3.383 closest distance to " O   HOH Z 227 " =    2.059
peak=    3.381 closest distance to " O   HOH Z 248 " =    1.973
peak=    3.379 closest distance to " O   HOH Z 407 " =    2.115
peak=    3.377 closest distance to " O   HOH Z  66 " =    2.276
peak=    3.375 closest distance to " CA  GLY A 211 " =    1.174
peak=    3.371 closest distance to " O   HOH Z 327 " =    2.248
peak=    3.370 closest distance to " CB  TRP A 150 " =    1.507
peak=    3.370 closest distance to " CB  TRP A 179 " =    1.437
peak=    3.367 closest distance to " CB  THR A 157 " =    1.111
peak=    3.367 closest distance to " CD1 TRP A 266 " =    1.127
peak=    3.366 closest distance to " CA  ALA A 160 " =    0.937
peak=    3.365 closest distance to " CB  ILE A 120 " =    1.387
peak=    3.362 closest distance to " O   HOH Z  61 " =    1.626
peak=    3.353 closest distance to " O   HOH Z 244 " =    1.624
peak=    3.353 closest distance to " O   HOH Z 153 " =    1.865
peak=    3.350 closest distance to " O   HOH Z  43 " =    1.956
peak=    3.344 closest distance to " OE1 GLN A  11 " =    1.956
peak=    3.344 closest distance to " O   HOH Z 276 " =    1.256
peak=    3.342 closest distance to " O   HOH Z 166 " =    3.327
peak=    3.340 closest distance to " C   ALA A 299 " =    0.964
peak=    3.337 closest distance to " CG1 ILE A  49 " =    1.535
peak=    3.337 closest distance to " CG1 VAL A 153 " =    0.991
peak=    3.336 closest distance to " CB  ARG A 139 " =    0.853
peak=    3.335 closest distance to " O   HOH Z 209 " =    2.562
peak=    3.333 closest distance to " CD1 LEU A   5 " =    1.298
peak=    3.319 closest distance to " O   HOH Z 175 " =    2.229
peak=    3.317 closest distance to " CB  THR A  82 " =    1.313
peak=    3.317 closest distance to " OD1 ASP A 231 " =    1.873
peak=    3.316 closest distance to " OE1 GLU A   2 " =    2.230
peak=    3.313 closest distance to " CA  GLY A 196 " =    0.767
peak=    3.311 closest distance to " O   HOH Z 214 " =    1.896
peak=    3.307 closest distance to " N   TYR A  15 " =    0.836
peak=    3.303 closest distance to " O   HOH Z 118 " =    1.782
peak=    3.302 closest distance to " CA  ASP A 191 " =    0.729
peak=    3.301 closest distance to " O   HOH Z 273 " =    2.509
peak=    3.299 closest distance to " CA  LYS A  48 " =    1.376
peak=    3.297 closest distance to " O   HOH Z 332 " =    1.557
peak=    3.295 closest distance to " O   HOH Z 409 " =    3.036
peak=    3.295 closest distance to " CD  ARG A  14 " =    1.258
peak=    3.294 closest distance to " CB  SER A 212 " =    1.200
peak=    3.289 closest distance to " O   HOH Z 203 " =    1.808
peak=    3.285 closest distance to " O   HOH Z 185 " =    2.118
peak=    3.285 closest distance to " O   HOH Z 147 " =    1.650
peak=    3.285 closest distance to " CG AARG A 275 " =    1.223
peak=    3.283 closest distance to " O   HOH Z  54 " =    1.488
peak=    3.282 closest distance to " CA  ILE A  33 " =    1.597
peak=    3.281 closest distance to " O   HOH Z  57 " =    1.282
peak=    3.277 closest distance to " O   HOH Z 145 " =    1.644
peak=    3.276 closest distance to " O   HOH Z 290 " =    1.149
peak=    3.275 closest distance to " CA  ASN A  74 " =    1.165
peak=    3.273 closest distance to " CA  VAL A  41 " =    0.915
peak=    3.272 closest distance to " NH2BARG A 190 " =    1.702
peak=    3.270 closest distance to " CG  MET A 188 " =    1.506
peak=    3.268 closest distance to " CA  LYS A 181 " =    1.040
peak=    3.267 closest distance to " O   HOH Z 173 " =    2.082
peak=    3.267 closest distance to " CG1 VAL A 174 " =    1.085
peak=    3.263 closest distance to " O   HOH Z 133 " =    1.758
peak=    3.263 closest distance to " ND2 ASN A 249 " =    1.811
peak=    3.260 closest distance to " O   HOH Z  68 " =    2.024
peak=    3.259 closest distance to " O   HOH Z 298 " =    2.512
peak=    3.259 closest distance to " CB  LYS A 117 " =    1.179
peak=    3.256 closest distance to " CA  ASP A 162 " =    1.021
peak=    3.252 closest distance to " CA  ASN A 127 " =    0.983
peak=    3.250 closest distance to " O   HOH Z 163 " =    1.839
peak=    3.240 closest distance to " CB  ALA A  34 " =    0.857
peak=    3.239 closest distance to " O   HOH Z   4 " =    1.875
peak=    3.236 closest distance to " NH2AARG A 190 " =    1.108
peak=    3.236 closest distance to " CG2 VAL A 257 " =    0.928
peak=    3.228 closest distance to " O   HOH Z 374 " =    2.664
peak=    3.225 closest distance to " O   GLN A  58 " =    1.670
peak=    3.223 closest distance to " CB  TYR A  30 " =    1.428
peak=    3.222 closest distance to " O   HOH Z 148 " =    2.053
peak=    3.222 closest distance to " O   HOH Z 175 " =    3.564
peak=    3.221 closest distance to " NH2AARG A 190 " =    1.445
peak=    3.221 closest distance to " O   HOH Z 261 " =    1.724
peak=    3.220 closest distance to " O   HOH Z 419 " =    1.718
peak=    3.218 closest distance to " CG2 THR A 220 " =    1.058
peak=    3.216 closest distance to " O   HOH Z 328 " =    1.665
peak=    3.211 closest distance to " O   HOH Z 151 " =    1.659
peak=    3.209 closest distance to " CA  GLN A 194 " =    1.218
peak=    3.209 closest distance to " CG1 ILE A 151 " =    1.155
peak=    3.205 closest distance to " CB  ARG A 190 " =    1.724
peak=    3.205 closest distance to " O   GLN A 278 " =    1.199
peak=    3.203 closest distance to " CG2 VAL A 174 " =    1.349
peak=    3.202 closest distance to " CB  SER A 141 " =    0.946
peak=    3.199 closest distance to " CB  PHE A  16 " =    1.167
peak=    3.197 closest distance to " CB  ALA A   9 " =    1.578
peak=    3.192 closest distance to " O   HOH Z 174 " =    1.151
peak=    3.190 closest distance to " O   HOH Z 303 " =    1.780
peak=    3.190 closest distance to " O   HOH Z 353 " =    2.757
peak=    3.189 closest distance to " CD2 LEU A 167 " =    0.755
peak=    3.189 closest distance to " O   ALA A   1 " =    1.533
peak=    3.189 closest distance to " CB  ALA A 137 " =    1.025
peak=    3.187 closest distance to " CA  VAL A 126 " =    0.969
peak=    3.186 closest distance to " OG  SER A  22 " =    2.876
peak=    3.185 closest distance to " O   HOH Z 215 " =    1.600
peak=    3.184 closest distance to " O   HOH Z 216 " =    2.571
peak=    3.179 closest distance to " NE2 GLN A  58 " =    4.067
peak=    3.174 closest distance to " N   ASN A 127 " =    1.258
peak=    3.173 closest distance to " O   HOH Z 334 " =    1.490
peak=    3.168 closest distance to " O   HOH Z 172 " =    3.836
peak=    3.166 closest distance to " CB  ALA A 248 " =    1.314
peak=    3.164 closest distance to " O   HOH Z 151 " =    1.650
peak=    3.160 closest distance to " O   HOH Z 383 " =    2.231
peak=    3.157 closest distance to " CE  MET A  93 " =    1.429
peak=    3.156 closest distance to " CB  SER A  28 " =    0.937
peak=    3.154 closest distance to " O   HOH Z 213 " =    1.871
peak=    3.154 closest distance to " O   HOH Z 302 " =    1.939
peak=    3.151 closest distance to " CB  SER A 271 " =    1.001
peak=    3.148 closest distance to " O   HOH Z  53 " =    2.671
peak=    3.147 closest distance to " CB  ASN A 142 " =    0.941
peak=    3.146 closest distance to " O   HOH Z 355 " =    1.770
peak=    3.142 closest distance to " NZ  LYS A 166 " =    3.107
peak=    3.139 closest distance to " OH  TYR A 214 " =    1.236
peak=    3.138 closest distance to " O   HOH Z 189 " =    3.490
peak=    3.136 closest distance to " CD  ARG A 219 " =    1.099
peak=    3.134 closest distance to " O   HOH Z 301 " =    1.837
peak=    3.133 closest distance to " CB  LEU A 255 " =    0.912
peak=    3.133 closest distance to " CB  ALA A 100 " =    1.357
peak=    3.125 closest distance to " CA  GLN A 223 " =    0.877
peak=    3.125 closest distance to " O   HOH Z  10 " =    1.893
peak=    3.118 closest distance to " OG  SER A  62 " =    2.985
peak=    3.116 closest distance to " O   ALA A   1 " =    1.768
peak=    3.107 closest distance to " N   SER A 135 " =    1.346
peak=    3.107 closest distance to " CA  ILE A 234 " =    0.901
peak=    3.100 closest distance to " O   HOH Z 162 " =    2.040
peak=    3.100 closest distance to " O   HOH Z 193 " =    1.911
peak=    3.099 closest distance to " NZ ALYS A 290 " =    1.175
peak=    3.089 closest distance to " O   HOH Z 329 " =    3.869
peak=    3.075 closest distance to " CD1 ILE A 106 " =    0.838
peak=    3.074 closest distance to " O   HOH Z 109 " =    2.713
peak=    3.070 closest distance to " O   HOH Z  49 " =    2.680
peak=    3.068 closest distance to " O   HOH Z 284 " =    1.763
peak=    3.064 closest distance to " O   HOH Z  22 " =    2.609
peak=    3.058 closest distance to " CE1 PHE A 208 " =    1.054
peak=    3.054 closest distance to " O   HOH Z  85 " =    2.062
peak=    3.053 closest distance to " CA  ARG A  36 " =    1.233
peak=    3.051 closest distance to " O   HOH Z 252 " =    1.796
peak=    3.036 closest distance to " CA  ALA A 291 " =    1.034
peak=    3.028 closest distance to " O   HOH Z 286 " =    2.348

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.753 - 5.445
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.753 - 5.445

peak=   -5.587 closest distance to " CG2 VAL A 230 " =    0.878
peak=   -4.509 closest distance to " O   HOH Z 231 " =    1.438
peak=   -4.297 closest distance to " O   HOH Z 102 " =    1.470
peak=   -4.284 closest distance to " O   HOH Z 290 " =    1.230
peak=   -4.189 closest distance to " O   HOH Z 377 " =    1.503
peak=   -4.177 closest distance to " CA  ASP A  27 " =    2.463
peak=   -4.124 closest distance to " CG1 VAL A 296 " =    1.386
peak=   -4.108 closest distance to " O   HOH Z  13 " =    1.333
peak=   -4.053 closest distance to " CG  ASP A 231 " =    0.768
peak=   -4.052 closest distance to " CG  LEU A 101 " =    2.598
peak=   -4.050 closest distance to " CD  ARG A 156 " =    1.983
peak=   -4.005 closest distance to " O   ILE A 109 " =    2.671
peak=   -3.999 closest distance to " CD  ARG A  14 " =    3.219
peak=   -3.979 closest distance to " O   HOH Z 231 " =    0.965
peak=   -3.964 closest distance to " CG1 VAL A 250 " =    2.726
peak=   -3.928 closest distance to " C   ALA A 158 " =    1.285
peak=   -3.892 closest distance to " O   HOH Z  43 " =    1.601
peak=   -3.860 closest distance to " CD1 LEU A 228 " =    2.427
peak=   -3.855 closest distance to " OG  SER A  87 " =    1.473
peak=   -3.850 closest distance to " N   ALA A  43 " =    2.353
peak=   -3.827 closest distance to " CZ3 TRP A 179 " =    1.163
peak=   -3.808 closest distance to " CD1 LEU A 101 " =    2.823
peak=   -3.802 closest distance to " O   HOH Z 266 " =    4.589
peak=   -3.796 closest distance to " O   HOH Z 275 " =    1.595
peak=   -3.779 closest distance to " CD  GLN A  88 " =    0.753
peak=   -3.761 closest distance to " CG2BVAL A  41 " =    2.660
peak=   -3.759 closest distance to " O   HOH Z 436 " =    1.520
peak=   -3.755 closest distance to " C   ASN A 285 " =    2.506
peak=   -3.752 closest distance to " CD1 PHE A  59 " =    1.874
peak=   -3.743 closest distance to " CD  LYS A 289 " =    2.570
peak=   -3.742 closest distance to " O   PRO A 163 " =    1.912
peak=   -3.740 closest distance to " O   GLY A 211 " =    1.476
peak=   -3.718 closest distance to " OE1 GLN A  88 " =    1.072
peak=   -3.715 closest distance to " N   THR A 157 " =    1.512
peak=   -3.707 closest distance to " OG ASER A 134 " =    1.443
peak=   -3.707 closest distance to " CG  MET A 105 " =    0.971
peak=   -3.699 closest distance to " CG  GLN A 223 " =    2.085
peak=   -3.693 closest distance to " CD  ARG A 138 " =    1.183
peak=   -3.680 closest distance to " O   PRO A 198 " =    1.345
peak=   -3.668 closest distance to " O   HOH Z 166 " =    1.909
peak=   -3.662 closest distance to " CG  ASP A  50 " =    2.253
peak=   -3.657 closest distance to " SG  CYS A 254 " =    3.161
peak=   -3.657 closest distance to " O   HOH Z  71 " =    1.055
peak=   -3.654 closest distance to " O   HOH Z 389 " =    1.868
peak=   -3.649 closest distance to " OG  SER A  26 " =    1.232
peak=   -3.645 closest distance to " CG2 VAL A 296 " =    1.321
peak=   -3.643 closest distance to " CD  GLN A  88 " =    2.327
peak=   -3.643 closest distance to " O   HOH Z  38 " =    1.551
peak=   -3.635 closest distance to " OG BSER A 134 " =    1.773
peak=   -3.621 closest distance to " O   HOH Z 274 " =    2.945
peak=   -3.618 closest distance to " O   HOH Z 388 " =    2.010
peak=   -3.617 closest distance to " O   HOH Z 407 " =    3.486
peak=   -3.613 closest distance to " CD2 LEU A 300 " =    2.893
peak=   -3.609 closest distance to " N   ALA A 226 " =    2.066
peak=   -3.589 closest distance to " CG  ARG A 138 " =    1.069
peak=   -3.567 closest distance to " CG  TRP A 266 " =    1.752
peak=   -3.562 closest distance to " CE1 TYR A 169 " =    2.518
peak=   -3.558 closest distance to " NH2 ARG A  66 " =    1.933
peak=   -3.547 closest distance to " O   HOH Z  98 " =    1.579
peak=   -3.547 closest distance to " NH2 ARG A  79 " =    1.900
peak=   -3.539 closest distance to " OG  SER A  97 " =    2.268
peak=   -3.538 closest distance to " C   ASN A 187 " =    1.711
peak=   -3.533 closest distance to " O   HOH Z 283 " =    1.880
peak=   -3.531 closest distance to " O   HOH Z 166 " =    1.468
peak=   -3.521 closest distance to " O   HOH Z 184 " =    1.622
peak=   -3.517 closest distance to " CB  ASN A  39 " =    2.080
peak=   -3.516 closest distance to " O   HOH Z 128 " =    4.043
peak=   -3.516 closest distance to " CD2 LEU A 167 " =    1.815
peak=   -3.510 closest distance to " CB  ALA A  43 " =    2.474
peak=   -3.505 closest distance to " CA  GLY A  98 " =    2.066
peak=   -3.504 closest distance to " CB  PRO A 243 " =    2.620
peak=   -3.503 closest distance to " O   HOH Z 211 " =    1.560
peak=   -3.503 closest distance to " C   HIS A 108 " =    1.172
peak=   -3.501 closest distance to " O   HOH Z 394 " =    1.515
peak=   -3.499 closest distance to " NH2AARG A 275 " =    5.445
peak=   -3.497 closest distance to " O   GLY A  80 " =    2.509
peak=   -3.494 closest distance to " CB  PRO A 163 " =    2.565
peak=   -3.491 closest distance to " OG BSER A 134 " =    1.289
peak=   -3.485 closest distance to " CG2 THR A   4 " =    2.028
peak=   -3.480 closest distance to " CA  SER A 271 " =    2.328
peak=   -3.478 closest distance to " CG  GLU A  53 " =    1.545
peak=   -3.473 closest distance to " CG  PRO A 163 " =    2.451
peak=   -3.471 closest distance to " CD1 ILE A 199 " =    2.567
peak=   -3.471 closest distance to " O   HOH Z 353 " =    2.292
peak=   -3.467 closest distance to " CA  GLY A 241 " =    2.274
peak=   -3.452 closest distance to " OD1 ASN A 148 " =    1.603
peak=   -3.449 closest distance to " CG1 VAL A 296 " =    1.270
peak=   -3.446 closest distance to " O   GLY A 196 " =    1.242
peak=   -3.445 closest distance to " O   HOH Z 435 " =    2.794
peak=   -3.439 closest distance to " CB  TRP A  85 " =    2.494
peak=   -3.436 closest distance to " CD2 TYR A 293 " =    2.071
peak=   -3.433 closest distance to " CZ  TYR A 172 " =    1.613
peak=   -3.418 closest distance to " OG1 THR A 178 " =    1.279
peak=   -3.414 closest distance to " O   HOH Z  63 " =    1.147
peak=   -3.413 closest distance to " CB  CYS A 254 " =    2.110
peak=   -3.412 closest distance to " CE2 TYR A  30 " =    2.935
peak=   -3.411 closest distance to " CG2 VAL A 112 " =    2.582
peak=   -3.404 closest distance to " ND2 ASN A  45 " =    1.016
peak=   -3.403 closest distance to " O   HOH Z  52 " =    1.563
peak=   -3.387 closest distance to " N   GLY A  23 " =    2.159
peak=   -3.378 closest distance to " C   ALA A   8 " =    1.498
peak=   -3.369 closest distance to " O   HOH Z 177 " =    1.624
peak=   -3.364 closest distance to " ND2 ASN A  60 " =    1.827
peak=   -3.360 closest distance to " OG1 THR A 246 " =    1.512
peak=   -3.350 closest distance to " O   HOH Z 241 " =    1.238
peak=   -3.348 closest distance to " O   HOH Z 426 " =    1.717
peak=   -3.348 closest distance to " CB  TYR A 172 " =    2.326
peak=   -3.345 closest distance to " N   GLN A  58 " =    1.700
peak=   -3.342 closest distance to " CB  GLN A  55 " =    1.333
peak=   -3.335 closest distance to " O   HOH Z 350 " =    1.719
peak=   -3.333 closest distance to " CG  ASN A  45 " =    1.736
peak=   -3.332 closest distance to " CG  LEU A 228 " =    0.906
peak=   -3.330 closest distance to " CB  VAL A 230 " =    0.977
peak=   -3.326 closest distance to " O   HOH Z 243 " =    1.584
peak=   -3.325 closest distance to " O   ASN A 301 " =    1.993
peak=   -3.312 closest distance to " O   HOH Z 396 " =    1.790
peak=   -3.298 closest distance to " CA  GLY A 241 " =    2.974
peak=   -3.291 closest distance to " ND2 ASN A  60 " =    1.457
peak=   -3.288 closest distance to " O   HOH Z 377 " =    1.192
peak=   -3.285 closest distance to " NH1 ARG A  56 " =    2.429
peak=   -3.273 closest distance to " CD2 LEU A 237 " =    2.576
peak=   -3.272 closest distance to " C   GLN A 240 " =    2.315
peak=   -3.272 closest distance to " OG1 THR A  82 " =    2.058
peak=   -3.268 closest distance to " O   HOH Z 119 " =    2.576
peak=   -3.266 closest distance to " O   HOH Z  98 " =    1.936
peak=   -3.262 closest distance to " CG  PHE A 283 " =    2.677
peak=   -3.261 closest distance to " CB  ILE A 239 " =    2.090
peak=   -3.260 closest distance to " OXT GLY A 302 " =    3.566
peak=   -3.259 closest distance to " SG ACYS A 201 " =    1.081
peak=   -3.251 closest distance to " O   HOH Z 234 " =    4.425
peak=   -3.244 closest distance to " CG1 VAL A 112 " =    2.927
peak=   -3.241 closest distance to " CE2 PHE A 283 " =    2.506
peak=   -3.238 closest distance to " CE BMET A  47 " =    1.600
peak=   -3.233 closest distance to " CB  TYR A  15 " =    2.209
peak=   -3.232 closest distance to " CD  GLU A 236 " =    0.987
peak=   -3.230 closest distance to " O   HOH Z 250 " =    1.427
peak=   -3.225 closest distance to " CD  ARG A 139 " =    1.638
peak=   -3.222 closest distance to " CB  ALA A 291 " =    2.302
peak=   -3.221 closest distance to " CD1 LEU A   5 " =    2.546
peak=   -3.220 closest distance to " O   HOH Z 317 " =    2.346
peak=   -3.218 closest distance to " N   SER A 212 " =    1.861
peak=   -3.209 closest distance to " C   LEU A 222 " =    0.757
peak=   -3.202 closest distance to " ND2 ASN A 215 " =    2.199
peak=   -3.202 closest distance to " CE  MET A 105 " =    2.034
peak=   -3.202 closest distance to " O   SER A 135 " =    1.405
peak=   -3.199 closest distance to " CB  SER A  63 " =    3.323
peak=   -3.191 closest distance to " O   PRO A 198 " =    1.288
peak=   -3.190 closest distance to " CH2 TRP A 177 " =    2.258
peak=   -3.186 closest distance to " CD  ARG A 195 " =    5.155
peak=   -3.183 closest distance to " CD1 LEU A 297 " =    2.513
peak=   -3.181 closest distance to " CA  ASP A 298 " =    1.099
peak=   -3.181 closest distance to " O   SER A  22 " =    2.183
peak=   -3.180 closest distance to " O   VAL A 197 " =    1.418
peak=   -3.180 closest distance to " N   ALA A 248 " =    1.829
peak=   -3.177 closest distance to " CE  MET A 105 " =    2.074
peak=   -3.176 closest distance to " CE  MET A  93 " =    1.203
peak=   -3.175 closest distance to " O   GLY A 203 " =    2.492
peak=   -3.172 closest distance to " CG2 THR A 178 " =    2.224
peak=   -3.169 closest distance to " O   ASP A 270 " =    1.718
peak=   -3.169 closest distance to " O   HOH Z 411 " =    3.672
peak=   -3.163 closest distance to " O   HOH Z 185 " =    2.361
peak=   -3.161 closest distance to " CA  VAL A 232 " =    2.465
peak=   -3.150 closest distance to " CE3 TRP A 150 " =    2.056
peak=   -3.148 closest distance to " O   HOH Z  10 " =    1.659
peak=   -3.147 closest distance to " OG  SER A 206 " =    1.853
peak=   -3.147 closest distance to " O   TYR A  30 " =    2.709
peak=   -3.146 closest distance to " CA  GLY A  35 " =    2.010
peak=   -3.145 closest distance to " O   VAL A  67 " =    2.579
peak=   -3.144 closest distance to " O   HOH Z 310 " =    3.296
peak=   -3.141 closest distance to " O   HOH Z  22 " =    2.378
peak=   -3.138 closest distance to " SG ACYS A 201 " =    2.141
peak=   -3.137 closest distance to " O   GLN A 194 " =    1.256
peak=   -3.132 closest distance to " ND2 ASN A 249 " =    2.049
peak=   -3.127 closest distance to " CA  ARG A 139 " =    0.966
peak=   -3.125 closest distance to " O   HOH Z 266 " =    4.780
peak=   -3.124 closest distance to " CB  ALA A 248 " =    1.980
peak=   -3.121 closest distance to " CD  PRO A 213 " =    2.167
peak=   -3.109 closest distance to " C   LEU A 143 " =    1.415
peak=   -3.109 closest distance to " CE2 PHE A 218 " =    2.532
peak=   -3.100 closest distance to " SG BCYS A 201 " =    2.240
peak=   -3.095 closest distance to " OD1 ASN A 249 " =    1.298
peak=   -3.094 closest distance to " O   HOH Z 389 " =    4.369
peak=   -3.086 closest distance to " O   HOH Z 205 " =    2.134
peak=   -3.081 closest distance to " NH1 ARG A 195 " =    2.260
peak=   -3.080 closest distance to " N   GLN A 122 " =    1.559
peak=   -3.073 closest distance to " O   HOH Z 252 " =    4.062
peak=   -3.072 closest distance to " N   ALA A 248 " =    2.310
peak=   -3.067 closest distance to " O   THR A  18 " =    1.544
peak=   -3.063 closest distance to " N   PHE A  59 " =    2.153
peak=   -3.046 closest distance to " NE2 GLN A 278 " =    1.179
peak=   -3.037 closest distance to " CA  GLY A 133 " =    2.182
peak=   -3.033 closest distance to " NH2 ARG A 156 " =    1.148
peak=   -3.033 closest distance to " OD1 ASN A 301 " =    1.847

================= 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    :  0.4718 0.4701   6.272876e+00   6.265886e+00
   1_bss:  0.4632 0.4574   6.269479e+00   6.260643e+00
   1_xyz:  0.3792 0.4087   6.146168e+00   6.197645e+00
   1_adp:  0.3321 0.3825   6.058411e+00   6.161191e+00
   1_occ:  0.3314 0.3830   6.057808e+00   6.161199e+00
   2_bss:  0.3284 0.3802   6.057607e+00   6.159056e+00
   2_xyz:  0.2350 0.2960   5.782428e+00   5.959801e+00
   2_adp:  0.2107 0.2706   5.691561e+00   5.880589e+00
   2_occ:  0.2105 0.2705   5.691218e+00   5.880668e+00
   3_bss:  0.2087 0.2664   5.688288e+00   5.875665e+00
   3_xyz:  0.1581 0.2067   5.436626e+00   5.650053e+00
   3_adp:  0.1439 0.1956   5.368383e+00   5.599317e+00
   3_occ:  0.1438 0.1954   5.367769e+00   5.598800e+00
   4_bss:  0.1436 0.1955   5.367025e+00   5.598015e+00
   4_xyz:  0.1258 0.1784   5.256515e+00   5.504785e+00
   4_adp:  0.1234 0.1739   5.236000e+00   5.481599e+00
   4_occ:  0.1232 0.1736   5.235069e+00   5.480525e+00
   5_bss:  0.1232 0.1734   5.234802e+00   5.479997e+00
   5_xyz:  0.1168 0.1668   5.193123e+00   5.442700e+00
   5_adp:  0.1168 0.1649   5.187686e+00   5.433762e+00
   5_occ:  0.1167 0.1646   5.186872e+00   5.432841e+00
   5_bss:  0.1169 0.1642   5.186662e+00   5.432849e+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:  0.322   8.494  10.444   7.448   8.219   0.000   0.000   0.000
   1_xyz:  0.322   8.494  10.444   7.448   8.219   0.000   0.000   0.000
   1_adp:  0.322   8.494  10.444   7.448   8.219   0.000   0.000   0.000
   1_occ:  0.322   8.494  10.444   7.448   8.219   0.000   0.000   0.000
   2_bss:  0.327  35.033   6.458   4.053   5.417   0.000   0.000   0.000
   2_xyz:  0.327  35.033   6.458   4.053   5.417   0.000   0.000   0.000
   2_adp:  0.327  35.033   6.458   4.053   5.417   0.000   0.000   0.000
   2_occ:  0.327  35.033   6.458   4.053   5.417   0.000   0.000   0.000
   3_bss:  0.319  35.033   3.763   2.669   3.529   0.000   0.000   0.000
   3_xyz:  0.319  35.033   3.763   2.669   3.529   0.000   0.000   0.000
   3_adp:  0.319  35.033   3.763   2.669   3.529   0.000   0.000   0.000
   3_occ:  0.319  35.033   3.763   2.669   3.529   0.000   0.000   0.000
   4_bss:  0.319  51.850   2.725   2.050   2.695   0.000   0.000   0.000
   4_xyz:  0.319  51.850   2.725   2.050   2.695   0.000   0.000   0.000
   4_adp:  0.319  51.850   2.725   2.050   2.695   0.000   0.000   0.000
   4_occ:  0.319  51.850   2.725   2.050   2.695   0.000   0.000   0.000
   5_bss:  0.329  51.850   2.438   1.957   2.576   0.000   0.000   0.000
   5_xyz:  0.329  51.850   2.438   1.957   2.576   0.000   0.000   0.000
   5_adp:  0.329  51.850   2.438   1.957   2.576   0.000   0.000   0.000
   5_occ:  0.329  51.850   2.438   1.957   2.576   0.000   0.000   0.000
   5_bss:  0.329  54.055   0.079  -0.338   0.258   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.427 0.4396  0.5144    68393.659
   1_bss:  57.036 0.4293  0.6378    65659.308
   1_xyz:  48.111 0.5418  0.7953    49935.113
   1_adp:  43.357 0.6011  0.9092    43117.560
   1_occ:  43.473 0.5995  0.9061    43257.236
   2_bss:  43.223 0.6026  0.8122    42954.298
   2_xyz:  31.162 0.7433  0.9713    23794.169
   2_adp:  27.448 0.7851  1.0082    19534.601
   2_occ:  27.446 0.7851  1.0083    19530.535
   3_bss:  27.225 0.7872  0.9406    19255.217
   3_xyz:  19.980 0.8613  0.9890    11056.461
   3_adp:  18.639 0.8744  0.9934     9899.114
   3_occ:  18.624 0.8746  0.9934     9876.511
   4_bss:  18.568 0.8752  0.9648     9860.187
   4_xyz:  16.395 0.8948  0.9763     8081.604
   4_adp:  15.753 0.9008  0.9789     7732.684
   4_occ:  15.728 0.9010  0.9789     7706.812
   5_bss:  15.718 0.9011  0.9732     7692.463
   5_xyz:  14.956 0.9074  0.9753     7079.595
   5_adp:  14.716 0.9096  0.9760     6957.879
   5_occ:  14.695 0.9097  0.9761     6941.106
   5_bss:  14.686 0.9098  0.9720     6913.652
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3863e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3863e+01
   1_xyz:   1.702  0.013  0.109 18.287  0.007  4.111   1.4335e-01
   1_adp:   1.702  0.013  0.109 18.287  0.007  4.111   1.4335e-01
   1_occ:   1.702  0.013  0.109 18.287  0.007  4.111   1.4335e-01
   2_bss:   1.702  0.013  0.109 18.287  0.007  4.111   1.4335e-01
   2_xyz:   1.172  0.009  0.081 16.759  0.005  4.113   8.5059e-02
   2_adp:   1.172  0.009  0.081 16.759  0.005  4.113   8.5059e-02
   2_occ:   1.172  0.009  0.081 16.759  0.005  4.113   8.5059e-02
   3_bss:   1.172  0.009  0.081 16.759  0.005  4.113   8.5059e-02
   3_xyz:   1.060  0.007  0.078 15.766  0.004  4.132   6.6630e-02
   3_adp:   1.060  0.007  0.078 15.766  0.004  4.132   6.6630e-02
   3_occ:   1.060  0.007  0.078 15.766  0.004  4.132   6.6630e-02
   4_bss:   1.060  0.007  0.078 15.766  0.004  4.132   6.6630e-02
   4_xyz:   1.096  0.008  0.083 15.897  0.004  4.112   7.1668e-02
   4_adp:   1.096  0.008  0.083 15.897  0.004  4.112   7.1668e-02
   4_occ:   1.096  0.008  0.083 15.897  0.004  4.112   7.1668e-02
   5_bss:   1.096  0.008  0.083 15.897  0.004  4.112   7.1668e-02
   5_xyz:   1.115  0.009  0.086 15.861  0.004  4.116   7.4506e-02
   5_adp:   1.115  0.009  0.086 15.861  0.004  4.116   7.4506e-02
   5_occ:   1.115  0.009  0.086 15.861  0.004  4.116   7.4506e-02
   5_bss:   1.115  0.009  0.086 15.861  0.004  4.116   7.4506e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9834e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9834e+00
   1_xyz:  14.112  0.169  0.466 84.522  0.044  2.164   1.0298e-01
   1_adp:  14.112  0.169  0.466 84.522  0.044  2.164   1.0298e-01
   1_occ:  14.112  0.169  0.466 84.522  0.044  2.164   1.0298e-01
   2_bss:  14.112  0.169  0.466 84.522  0.044  2.164   1.0298e-01
   2_xyz:   7.800  0.071  0.270 82.457  0.044  2.191   5.5772e-02
   2_adp:   7.800  0.071  0.270 82.457  0.044  2.191   5.5772e-02
   2_occ:   7.800  0.071  0.270 82.457  0.044  2.191   5.5772e-02
   3_bss:   7.800  0.071  0.270 82.457  0.044  2.191   5.5772e-02
   3_xyz:   8.688  0.057  0.332 87.509  0.041  2.359   4.7918e-02
   3_adp:   8.688  0.057  0.332 87.509  0.041  2.359   4.7918e-02
   3_occ:   8.688  0.057  0.332 87.509  0.041  2.359   4.7918e-02
   4_bss:   8.688  0.057  0.332 87.509  0.041  2.359   4.7918e-02
   4_xyz:   8.269  0.065  0.452 83.376  0.033  2.312   4.8767e-02
   4_adp:   8.269  0.065  0.452 83.376  0.033  2.312   4.8767e-02
   4_occ:   8.269  0.065  0.452 83.376  0.033  2.312   4.8767e-02
   5_bss:   8.269  0.065  0.452 83.376  0.033  2.312   4.8767e-02
   5_xyz:   8.393  0.072  0.550 83.642  0.030  2.317   6.1555e-02
   5_adp:   8.393  0.072  0.550 83.642  0.030  2.317   6.1555e-02
   5_occ:   8.393  0.072  0.550 83.642  0.030  2.317   6.1555e-02
   5_bss:   8.393  0.072  0.550 83.642  0.030  2.317   6.1555e-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:  87.42   0.00  12.45  87.42   0.00   9.82  73.67   0.00  26.81
   1_occ:  87.42   0.00  12.45  87.42   0.00   9.82  73.67   0.00  26.81
   2_bss:  87.42   0.00  12.45  87.42   0.00   9.82  73.67   0.00  26.81
   2_xyz:  87.42   0.00  12.45  87.42   0.00   9.82  73.67   0.00  26.81
   2_adp:  84.75   0.00  12.52  84.75   0.00   8.85  73.00   0.95  32.48
   2_occ:  84.75   0.00  12.52  84.75   0.00   8.85  73.00   0.95  32.48
   3_bss:  84.75   0.00  12.52  84.75   0.00   8.85  73.00   0.95  32.48
   3_xyz:  84.75   0.00  12.52  84.75   0.00   8.85  73.00   0.95  32.48
   3_adp:  93.21   0.00  13.41  93.21   0.00   8.85  84.91   1.75  38.23
   3_occ:  93.21   0.00  13.41  93.21   0.00   8.85  84.91   1.75  38.23
   4_bss:  93.21   0.00  13.41  93.21   0.00   8.85  84.91   1.75  38.23
   4_xyz:  93.21   0.00  13.41  93.21   0.00   8.85  84.91   1.75  38.23
   4_adp:  93.99   0.00  13.07  93.99   0.00   8.71  84.94   2.15  36.78
   4_occ:  93.99   0.00  13.07  93.99   0.00   8.71  84.94   2.15  36.78
   5_bss:  93.99   0.00  13.07  93.99   0.00   8.71  84.94   2.15  36.78
   5_xyz:  93.99   0.00  13.07  93.99   0.00   8.71  84.94   2.15  36.78
   5_adp:  93.37   0.00  12.81  93.37   0.00   8.62  84.54   2.19  35.61
   5_occ:  93.37   0.00  12.81  93.37   0.00   8.62  84.54   2.19  35.61
   5_bss:  95.58   2.21  15.01  95.58   2.21  10.82  86.75   4.39  37.82
------------------------------------------------------------------------
 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:    1.221    0.039    0.414
   1_adp:    1.221    0.039    0.414
   1_occ:    1.221    0.039    0.414
   2_bss:    1.221    0.039    0.414
   2_xyz:    1.452    0.030    0.587
   2_adp:    1.452    0.030    0.587
   2_occ:    1.452    0.030    0.587
   3_bss:    1.452    0.030    0.587
   3_xyz:    1.619    0.041    0.657
   3_adp:    1.619    0.041    0.657
   3_occ:    1.619    0.041    0.657
   4_bss:    1.619    0.041    0.657
   4_xyz:    1.732    0.049    0.691
   4_adp:    1.732    0.049    0.691
   4_occ:    1.732    0.049    0.691
   5_bss:    1.732    0.049    0.691
   5_xyz:    1.917    0.019    0.709
   5_adp:    1.917    0.019    0.709
   5_occ:    1.917    0.019    0.709
   5_bss:    1.917    0.019    0.709
------------------------------------------------------------------------

CPU time actual refinement: 338.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1267/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_1267/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1267/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1267/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1267/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.77 
  Macro-tasks:
    bulk solvent and scale       = 42.69  
    individual site refinement   = 135.30 
    weights calculation          = 32.28  
    collect and process          = 6.55   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 216.97 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 104.97 
    alpha_beta                      = 8.07   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 114.26 
    fmodel                         = 7.09   
    r_factors                      = 0.19   
    phase_errors                   = 10.67  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 249.13 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.848 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    623 calls, 104.70 s
gradients_fft:          569 calls, 101.58 s

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

# Date 2008-01-16 Time 03:37:30 PST -0800 (1200483450.87 s)
Start R-work = 0.4718, R-free = 0.4701 (no bulk solvent and anisotropic scale)
Final R-work = 0.1330, R-free = 0.1806 (no bulk solvent and anisotropic scale)

Start R-work = 0.4632, R-free = 0.4574
Final R-work = 0.1169, R-free = 0.1642