# Date 2008-01-16 Time 02:09:08 PST -0800 (1200478148.09 s)
#phil __OFF__

Command line arguments: "../714.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12259
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 714

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.8686, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00077
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941869

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   2.0008

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00077
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941869

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2808 [2183/2211]  1962   221  10.1%
  bin  2:  4.2808 -  3.4107 [2078/2097]  1870   208  10.0%
  bin  3:  3.4107 -  2.9834 [2075/2095]  1871   204   9.8%
  bin  4:  2.9834 -  2.7123 [2040/2065]  1833   207  10.1%
  bin  5:  2.7123 -  2.5189 [2022/2041]  1822   200   9.9%
  bin  6:  2.5189 -  2.3709 [2016/2062]  1813   203  10.1%
  bin  7:  2.3709 -  2.2526 [2017/2051]  1819   198   9.8%
  bin  8:  2.2526 -  2.1548 [2005/2040]  1796   209  10.4%
  bin  9:  2.1548 -  2.0721 [2007/2037]  1813   194   9.7%
  bin 10:  2.0721 -  2.0008 [1146/2035]  1031   115  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_714/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:
        1.43 -     2.12: 7
        2.12 -     2.82: 829
        2.82 -     3.51: 4333
        3.51 -     4.21: 9095
        4.21 -     4.90: 13464
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.429 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.691 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.691 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.811 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 27723 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_714/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_714/model_refine_001.geo

CPU time processing inputs: 9.77


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.8686 88.54975 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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5114   r_free= 0.5008   ksol= 0.00   Bsol= 0.00   scale= 0.755    |
|                                                                             |
| 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:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.307275                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7744 0.99   1412  157 0.4189 0.4122       6.646      6.6274|
|  2:  4.7744 -  3.8097 0.99   1364  153 0.4519 0.5079      6.8631      6.9982|
|  3:  3.8097 -  3.3340 0.99   1335  149 0.4902 0.4573      6.7349      6.6851|
|  4:  3.3340 -  3.0319 0.99   1325  139 0.5089 0.4616      6.5599      6.5114|
|  5:  3.0319 -  2.8161 0.99   1312  150 0.5438 0.4828       6.398      6.4303|
|  6:  2.8161 -  2.6510 0.98   1304  147 0.5396 0.5656      6.2921      6.1974|
|  7:  2.6510 -  2.5189 0.99   1306  145 0.5275 0.4596      6.2481      6.1455|
|  8:  2.5189 -  2.4097 0.98   1303  145 0.5459 0.5035      6.2016      6.1923|
|  9:  2.4097 -  2.3172 0.98   1305  144 0.5441 0.6187      6.1203      6.1986|
| 10:  2.3172 -  2.2375 0.98   1275  141 0.5729 0.5157      6.1192      6.1072|
| 11:  2.2375 -  2.1678 0.99   1311  146 0.5383 0.5401      6.0348      6.0564|
| 12:  2.1678 -  2.1060 0.98   1279  144 0.5431 0.5576      5.9666      6.0173|
| 13:  2.1060 -  2.0507 0.97   1280  131 0.5589 0.5085      5.8934       5.816|
| 14:  2.0507 -  2.0008 0.40    519   68 0.5535 0.5893      5.8841      5.7811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7744  1412   157  0.65  38.25   0.78     0.67      84326.69|
|  2:  4.7744 -  3.8097  1364   153  0.63  41.31   0.84     0.68     134850.81|
|  3:  3.8097 -  3.3340  1335   149  0.51  50.94   0.77     0.62     142409.06|
|  4:  3.3340 -  3.0319  1325   139  0.41  58.96   0.76     0.50     122462.03|
|  5:  3.0319 -  2.8161  1312   150  0.34  64.56   0.70     0.40      92779.85|
|  6:  2.8161 -  2.6510  1304   147  0.32  66.13   0.69     0.37      78814.66|
|  7:  2.6510 -  2.5189  1306   145  0.34  64.54   0.71     0.38      68477.22|
|  8:  2.5189 -  2.4097  1303   145  0.33  65.25   0.71     0.39      61413.28|
|  9:  2.4097 -  2.3172  1305   144  0.27  69.88   0.67     0.32      60578.29|
| 10:  2.3172 -  2.2375  1275   141  0.22  73.84   0.70     0.26      57175.36|
| 11:  2.2375 -  2.1678  1311   146  0.18  76.25   0.72     0.23      55104.43|
| 12:  2.1678 -  2.1060  1279   144  0.19  75.85   0.73     0.24      49200.78|
| 13:  2.1060 -  2.0507  1280   131  0.17  77.07   0.69     0.22      42292.92|
| 14:  2.0507 -  2.0008   519    68  0.16  78.36   0.70     0.16      33559.74|
|alpha:            min =        0.16 max =            0.68 mean =         0.40|
|beta:             min =    33559.74 max =       142409.06 mean =     79864.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.98 mean =        63.44|
|phase err.(test): min =        0.00 max =           89.97 mean =        63.67|
|-----------------------------------------------------------------------------|

============================== 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 = 21.770447             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.548   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.403157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.901   (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:        7 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      672 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1478 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2566 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3819 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4970 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6451 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7571 |
|-----------------------------------------------------------------------------|
|-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 |       54.653 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.866 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    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 = 12.350)------------------------------------------|
|    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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5160   r_free= 0.5046   ksol= 0.00   Bsol= 0.00   scale= 0.728    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.307963                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5048   r_free= 0.4952   ksol= 0.30   Bsol= 20.00   scale= 0.947   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.42,10.09,10.78,0.00,0.00,0.00); trace/3= 8.77                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.301466                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.799351             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.510   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.012524              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.785   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5048      final r-factor (work) = 0.4452          |
| start r-factor (free) = 0.4952      final r-factor (free) = 0.4641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 113.9215 = 18.80 * 0.50 * 6.3054 + 1.00 * 54.6528                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 58.9395 = 18.80 * 0.50 * 6.2545 + 1.00 * 0.1495                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4452      final r-factor (work) = 0.4017          |
| start r-factor (free) = 0.4641      final r-factor (free) = 0.4568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6017 = 2.01 * 1.00 * 6.2545 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.5034 = 2.01 * 1.00 * 6.1986 + 1.00 * 0.0285                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    120.15  18.39    None  None   None       |
|    all(noH): 2823   0      0.00    120.15  18.39    None  None   None       |
|    Sol.    : 438    0      0.00    120.15  29.67    None  None   None       |
|    Mac.    : 2385   0      0.00    90.20   16.32    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 -  12.015: 1238   |   5:    60.076 -  72.092:   44        |
|      1:    12.015 -  24.031:  800   |   6:    72.092 -  84.107:   26        |
|      2:    24.031 -  36.046:  412   |   7:    84.107 -  96.122:    6        |
|      3:    36.046 -  48.061:  198   |   8:    96.122 - 108.137:    2        |
|      4:    48.061 -  60.076:   95   |   9:   108.137 - 120.153:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4017 r_free = 0.4568             target_work(ml) = 6.188         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4010 r_free = 0.4562             target_work(ml) = 6.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4010   r_free= 0.4562   ksol= 0.30   Bsol= 20.00   scale= 1.109   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.42,10.09,10.78,0.00,0.00,0.00); trace/3= 8.77                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.187944                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3992   r_free= 0.4511   ksol= 0.32   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.45,6.06,6.68,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.190315                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.351985             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.333  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.602814              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.818  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3992      final r-factor (work) = 0.3428          |
| start r-factor (free) = 0.4511      final r-factor (free) = 0.4144          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.2080 = 10.35 * 0.50 * 6.1937 + 1.00 * 0.1495                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.7958 = 10.35 * 0.50 * 6.1240 + 1.00 * 0.0982                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3428      final r-factor (work) = 0.3313          |
| start r-factor (free) = 0.4144      final r-factor (free) = 0.3960          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7216 = 0.60 * 1.00 * 6.1240 + 1.00 * 0.0300                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6746 = 0.60 * 1.00 * 6.0724 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 47     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.07  15.96    None  None   None       |
|    all(noH): 2823   0      0.00    119.07  15.96    None  None   None       |
|    Sol.    : 438    0      0.00    119.07  30.01    None  None   None       |
|    Mac.    : 2385   0      0.00    74.78   13.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.907: 1383   |   5:    59.533 -  71.439:   28        |
|      1:    11.907 -  23.813:  851   |   6:    71.439 -  83.346:    7        |
|      2:    23.813 -  35.720:  372   |   7:    83.346 -  95.252:    1        |
|      3:    35.720 -  47.626:  125   |   8:    95.252 - 107.159:    2        |
|      4:    47.626 -  59.533:   53   |   9:   107.159 - 119.065:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3313 r_free = 0.3960             target_work(ml) = 6.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3311 r_free = 0.3965             target_work(ml) = 6.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3311   r_free= 0.3965   ksol= 0.32   Bsol= 50.00   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.45,6.06,6.68,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.058923                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3299   r_free= 0.3952   ksol= 0.33   Bsol= 66.67   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,3.59,4.14,0.00,0.00,0.00); trace/3= 2.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.060643                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.445000              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.306  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.824386              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.008  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3299      final r-factor (work) = 0.2500          |
| start r-factor (free) = 0.3952      final r-factor (free) = 0.2991          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7388 = 8.44 * 0.50 * 6.0724 + 1.00 * 0.0982                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2717 = 8.44 * 0.50 * 5.9620 + 1.00 * 0.0973                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2500      final r-factor (work) = 0.2199          |
| start r-factor (free) = 0.2991      final r-factor (free) = 0.2749          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9260 = 0.82 * 1.00 * 5.9620 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7634 = 0.82 * 1.00 * 5.7605 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.06  15.86    None  None   None       |
|    all(noH): 2823   0      0.00    115.06  15.86    None  None   None       |
|    Sol.    : 438    0      0.00    115.06  38.23    None  None   None       |
|    Mac.    : 2385   0      0.00    77.40   11.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.506: 1529   |   5:    57.529 -  69.035:   48        |
|      1:    11.506 -  23.012:  684   |   6:    69.035 -  80.541:   12        |
|      2:    23.012 -  34.518:  263   |   7:    80.541 -  92.047:    5        |
|      3:    34.518 -  46.024:  176   |   8:    92.047 - 103.553:    2        |
|      4:    46.024 -  57.529:  103   |   9:   103.553 - 115.059:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2199 r_free = 0.2749             target_work(ml) = 5.724         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2196 r_free = 0.2749             target_work(ml) = 5.724         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2196   r_free= 0.2749   ksol= 0.33   Bsol= 66.67   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,3.59,4.14,0.00,0.00,0.00); trace/3= 2.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.724075                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2186   r_free= 0.2730   ksol= 0.34   Bsol= 79.24   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.09,1.82,2.54,0.00,0.00,0.00); trace/3= 1.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.721270                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.188805              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.678   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.623897              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.875  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2186      final r-factor (work) = 0.1673          |
| start r-factor (free) = 0.2730      final r-factor (free) = 0.2150          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9349 = 6.19 * 0.50 * 5.7645 + 1.00 * 0.0973                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4733 = 6.19 * 0.50 * 5.6183 + 1.00 * 0.0879                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1673      final r-factor (work) = 0.1523          |
| start r-factor (free) = 0.2150      final r-factor (free) = 0.2050          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.7565 = 2.62 * 1.00 * 5.6183 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.2978 = 2.62 * 1.00 * 5.4426 + 1.00 * 0.0169                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.22  16.18    None  None   None       |
|    all(noH): 2823   0      0.00    110.22  16.18    None  None   None       |
|    Sol.    : 438    0      1.75    110.22  43.95    None  None   None       |
|    Mac.    : 2385   0      0.00    88.99   11.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.022: 1571   |   5:    55.111 -  66.133:   98        |
|      1:    11.022 -  22.044:  675   |   6:    66.133 -  77.155:   50        |
|      2:    22.044 -  33.066:  176   |   7:    77.155 -  88.177:   13        |
|      3:    33.066 -  44.088:  122   |   8:    88.177 -  99.199:    6        |
|      4:    44.088 -  55.111:  111   |   9:    99.199 - 110.221:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1523 r_free = 0.2050             target_work(ml) = 5.419         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1522 r_free = 0.2051             target_work(ml) = 5.418         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1522   r_free= 0.2051   ksol= 0.34   Bsol= 79.24   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.09,1.82,2.54,0.00,0.00,0.00); trace/3= 1.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.418268                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1526   r_free= 0.2052   ksol= 0.34   Bsol= 81.32   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.17,1.39,2.48,0.00,0.00,0.00); trace/3= 1.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.419921                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.384283              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.196  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.230898              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.648  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1526      final r-factor (work) = 0.1366          |
| start r-factor (free) = 0.2052      final r-factor (free) = 0.1885          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2990 = 3.38 * 0.50 * 5.4435 + 1.00 * 0.0879                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1756 = 3.38 * 0.50 * 5.3771 + 1.00 * 0.0767                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.1885      final r-factor (free) = 0.1848          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.1440 = 5.23 * 1.00 * 5.3771 + 1.00 * 0.0168                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.8285 = 5.23 * 1.00 * 5.3165 + 1.00 * 0.0184                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.00  16.20    None  None   None       |
|    all(noH): 2823   0      0.00    109.00  16.20    None  None   None       |
|    Sol.    : 438    0      2.07    109.00  46.01    None  None   None       |
|    Mac.    : 2385   0      0.00    94.33   10.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.900: 1613   |   5:    54.499 -  65.399:   73        |
|      1:    10.900 -  21.800:  656   |   6:    65.399 -  76.299:   60        |
|      2:    21.800 -  32.699:  166   |   7:    76.299 -  87.199:   41        |
|      3:    32.699 -  43.599:  110   |   8:    87.199 -  98.098:   18        |
|      4:    43.599 -  54.499:   83   |   9:    98.098 - 108.998:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1323 r_free = 0.1848             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1323 r_free = 0.1847             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1323   r_free= 0.1847   ksol= 0.34   Bsol= 81.32   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.17,1.39,2.48,0.00,0.00,0.00); trace/3= 1.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.304911                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7744 0.99   1412  157 0.1034 0.1416      5.4514      5.6176|
|  2:  4.7744 -  3.8097 0.99   1364  153 0.0903 0.1107      5.5021      5.7076|
|  3:  3.8097 -  3.3340 0.99   1335  149 0.1213 0.1707      5.5959      5.9651|
|  4:  3.3340 -  3.0319 0.99   1325  139 0.1431 0.1922      5.5936      5.7781|
|  5:  3.0319 -  2.8161 0.99   1312  150 0.1615 0.1843      5.5118      5.6519|
|  6:  2.8161 -  2.6510 0.98   1304  147 0.1501 0.2551      5.3947      5.6911|
|  7:  2.6510 -  2.5189 0.99   1306  145 0.1551 0.1888      5.3601      5.4991|
|  8:  2.5189 -  2.4097 0.98   1303  145 0.1450 0.2049      5.2778      5.5209|
|  9:  2.4097 -  2.3172 0.98   1305  144 0.1482 0.2434      5.2137      5.5539|
| 10:  2.3172 -  2.2375 0.98   1275  141 0.1382 0.1845      5.1426      5.2724|
| 11:  2.2375 -  2.1678 0.99   1311  146 0.1392 0.2146      5.0941      5.4166|
| 12:  2.1678 -  2.1060 0.98   1279  144 0.1338 0.2064      5.0332      5.3264|
| 13:  2.1060 -  2.0507 0.97   1280  131 0.1343 0.1957      4.9361      5.1388|
| 14:  2.0507 -  2.0008 0.40    519   68 0.1226 0.2072      4.8233      5.1091|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7744  1412   157  0.93  10.32   0.96     0.93       8654.52|
|  2:  4.7744 -  3.8097  1364   153  0.94   9.37   1.01     0.99      10743.92|
|  3:  3.8097 -  3.3340  1335   149  0.92  13.21   1.03     1.03      12998.90|
|  4:  3.3340 -  3.0319  1325   139  0.90  16.27   1.01     0.99      13757.63|
|  5:  3.0319 -  2.8161  1312   150  0.87  19.89   1.01     0.99      12335.09|
|  6:  2.8161 -  2.6510  1304   147  0.86  20.87   0.98     0.94      10775.72|
|  7:  2.6510 -  2.5189  1306   145  0.87  19.64   0.99     0.94       9266.87|
|  8:  2.5189 -  2.4097  1303   145  0.87  19.88   0.99     0.94       8434.98|
|  9:  2.4097 -  2.3172  1305   144  0.87  20.03   1.00     0.95       7366.09|
| 10:  2.3172 -  2.2375  1275   141  0.86  20.05   0.99     0.93       6593.55|
| 11:  2.2375 -  2.1678  1311   146  0.86  20.14   0.98     0.92       6052.64|
| 12:  2.1678 -  2.1060  1279   144  0.88  19.33   0.99     0.98       5654.23|
| 13:  2.1060 -  2.0507  1280   131  0.87  19.85   0.97     0.94       4636.60|
| 14:  2.0507 -  2.0008   519    68  0.89  17.53   0.94     0.89       3533.03|
|alpha:            min =        0.89 max =            1.03 mean =         0.96|
|beta:             min =     3533.03 max =        13757.63 mean =      8890.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.92 mean =        17.51|
|phase err.(test): min =        0.00 max =           89.34 mean =        16.76|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1322   r_free= 0.1845   ksol= 0.34   Bsol= 81.47   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.07,-0.08,1.15,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.304913                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1322   r_free= 0.1845   ksol= 0.34   Bsol= 81.47   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.07,-0.08,1.15,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.304913                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7744 0.99   1412  157 0.1033 0.1416      5.4504       5.618|
|  2:  4.7744 -  3.8097 0.99   1364  153 0.0904 0.1108      5.5025      5.7077|
|  3:  3.8097 -  3.3340 0.99   1335  149 0.1213 0.1707      5.5965      5.9657|
|  4:  3.3340 -  3.0319 0.99   1325  139 0.1432 0.1921      5.5938      5.7783|
|  5:  3.0319 -  2.8161 0.99   1312  150 0.1616 0.1843      5.5118      5.6515|
|  6:  2.8161 -  2.6510 0.98   1304  147 0.1499 0.2549      5.3942      5.6906|
|  7:  2.6510 -  2.5189 0.99   1306  145 0.1552 0.1891      5.3599      5.4995|
|  8:  2.5189 -  2.4097 0.98   1303  145 0.1450 0.2047      5.2779      5.5209|
|  9:  2.4097 -  2.3172 0.98   1305  144 0.1482 0.2434      5.2139      5.5547|
| 10:  2.3172 -  2.2375 0.98   1275  141 0.1382 0.1848      5.1429      5.2731|
| 11:  2.2375 -  2.1678 0.99   1311  146 0.1392 0.2144       5.094       5.416|
| 12:  2.1678 -  2.1060 0.98   1279  144 0.1338 0.2065       5.033      5.3267|
| 13:  2.1060 -  2.0507 0.97   1280  131 0.1343 0.1953       4.936      5.1379|
| 14:  2.0507 -  2.0008 0.40    519   68 0.1226 0.2069      4.8235      5.1082|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7744  1412   157  0.93  10.32   0.96     0.93       8644.96|
|  2:  4.7744 -  3.8097  1364   153  0.94   9.37   1.01     0.99      10747.52|
|  3:  3.8097 -  3.3340  1335   149  0.92  13.23   1.03     1.03      13019.27|
|  4:  3.3340 -  3.0319  1325   139  0.90  16.28   1.02     1.00      13767.72|
|  5:  3.0319 -  2.8161  1312   150  0.87  19.88   1.01     0.99      12329.80|
|  6:  2.8161 -  2.6510  1304   147  0.86  20.86   0.98     0.94      10766.28|
|  7:  2.6510 -  2.5189  1306   145  0.87  19.64   0.99     0.95       9262.17|
|  8:  2.5189 -  2.4097  1303   145  0.87  19.89   0.99     0.95       8439.92|
|  9:  2.4097 -  2.3172  1305   144  0.87  20.05   1.01     0.95       7373.89|
| 10:  2.3172 -  2.2375  1275   141  0.86  20.05   0.99     0.94       6597.51|
| 11:  2.2375 -  2.1678  1311   146  0.86  20.15   0.99     0.92       6056.82|
| 12:  2.1678 -  2.1060  1279   144  0.88  19.32   1.00     0.98       5653.81|
| 13:  2.1060 -  2.0507  1280   131  0.87  19.84   0.98     0.95       4630.24|
| 14:  2.0507 -  2.0008   519    68  0.89  17.52   0.95     0.90       3523.59|
|alpha:            min =        0.90 max =            1.03 mean =         0.96|
|beta:             min =     3523.59 max =        13767.72 mean =      8891.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.51|
|phase err.(test): min =        0.00 max =           89.34 mean =        16.76|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    110.47  17.67    None  None   None       |
|    all(noH): 2823   0      1.47    110.47  17.67    None  None   None       |
|    Sol.    : 438    0      3.54    110.47  47.48    None  None   None       |
|    Mac.    : 2385   0      1.47    95.80   12.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.473 -  12.373: 1613   |   5:    55.972 -  66.872:   73        |
|      1:    12.373 -  23.273:  656   |   6:    66.872 -  77.772:   60        |
|      2:    23.273 -  34.172:  166   |   7:    77.772 -  88.671:   41        |
|      3:    34.172 -  45.072:  110   |   8:    88.671 -  99.571:   18        |
|      4:    45.072 -  55.972:   83   |   9:    99.571 - 110.471:    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)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.711 - 5.240
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 330 from: 331
   mapped sites are within: 0.711 - 5.240

peak=    9.068 closest distance to " CB  VAL A 230 " =    1.374
peak=    7.134 closest distance to " CG1 VAL A 296 " =    1.246
peak=    6.480 closest distance to " CD1AILE A 234 " =    1.310
peak=    5.909 closest distance to " O   HOH Z 210 " =    1.581
peak=    5.772 closest distance to " O   HOH Z 120 " =    1.221
peak=    5.369 closest distance to " O   HOH Z 248 " =    1.540
peak=    5.224 closest distance to " O   HOH Z 431 " =    1.560
peak=    4.872 closest distance to " O   HOH Z 128 " =    1.857
peak=    4.817 closest distance to " CG  LEU A   5 " =    1.100
peak=    4.754 closest distance to " O   HOH Z 425 " =    1.682
peak=    4.676 closest distance to " CA  TYR A  30 " =    0.962
peak=    4.666 closest distance to " CB  GLN A 223 " =    1.552
peak=    4.644 closest distance to " OE1 GLN A  88 " =    0.968
peak=    4.570 closest distance to " NE2 GLN A  11 " =    1.196
peak=    4.557 closest distance to " CB  TRP A 179 " =    1.366
peak=    4.552 closest distance to " O   HOH Z 117 " =    1.358
peak=    4.545 closest distance to " CB  GLN A 183 " =    1.256
peak=    4.499 closest distance to " O   HOH Z 130 " =    2.575
peak=    4.499 closest distance to " CG  LEU A 228 " =    1.294
peak=    4.485 closest distance to " NH2 ARG A  56 " =    2.092
peak=    4.478 closest distance to " CD2 TRP A 179 " =    1.283
peak=    4.429 closest distance to " CG  PRO A 280 " =    0.996
peak=    4.428 closest distance to " CB  SER A  63 " =    1.304
peak=    4.402 closest distance to " O   HOH Z 412 " =    3.681
peak=    4.399 closest distance to " NH2AARG A 145 " =    1.142
peak=    4.384 closest distance to " CG  PRO A  54 " =    1.337
peak=    4.365 closest distance to " O   PRO A 198 " =    1.588
peak=    4.347 closest distance to " O   HOH Z 394 " =    1.688
peak=    4.335 closest distance to " O   HOH Z 126 " =    1.636
peak=    4.320 closest distance to " CZ3 TRP A 266 " =    1.109
peak=    4.312 closest distance to " O   HOH Z 142 " =    1.714
peak=    4.266 closest distance to " CZ  PHE A 218 " =    1.163
peak=    4.262 closest distance to " CD2 LEU A 228 " =    1.315
peak=    4.186 closest distance to " CA  ASP A 191 " =    1.267
peak=    4.180 closest distance to " O   HOH Z  54 " =    1.170
peak=    4.158 closest distance to " O   HOH Z 403 " =    2.069
peak=    4.147 closest distance to " O   HOH Z 232 " =    2.365
peak=    4.116 closest distance to " O   HOH Z 154 " =    1.636
peak=    4.113 closest distance to " CG  PRO A 243 " =    1.153
peak=    4.113 closest distance to " O   HOH Z 142 " =    2.439
peak=    4.109 closest distance to " CG AARG A 275 " =    1.274
peak=    4.099 closest distance to " CD2 LEU A   5 " =    1.230
peak=    4.096 closest distance to " O   HOH Z 251 " =    1.845
peak=    4.081 closest distance to " O   HOH Z 130 " =    1.114
peak=    4.061 closest distance to " O   HOH Z 214 " =    1.558
peak=    4.055 closest distance to " O   HOH Z 247 " =    1.434
peak=    4.052 closest distance to " O   HOH Z 426 " =    1.256
peak=    4.028 closest distance to " NE2 GLN A  77 " =    3.171
peak=    4.025 closest distance to " O   SER A  87 " =    2.362
peak=    4.016 closest distance to " O   HOH Z 359 " =    1.915
peak=    4.010 closest distance to " O   HOH Z 406 " =    1.692
peak=    3.995 closest distance to " O   HOH Z 146 " =    1.819
peak=    3.988 closest distance to " CG  GLN A  77 " =    0.862
peak=    3.978 closest distance to " CG1 ILE A 120 " =    1.066
peak=    3.974 closest distance to " O   HOH Z 280 " =    2.927
peak=    3.966 closest distance to " CD  PRO A  54 " =    1.141
peak=    3.959 closest distance to " CG  GLN A  58 " =    1.046
peak=    3.952 closest distance to " CB  ASN A 148 " =    1.526
peak=    3.949 closest distance to " O   HOH Z 199 " =    1.552
peak=    3.945 closest distance to " CA  ARG A 195 " =    1.180
peak=    3.944 closest distance to " O   HOH Z  49 " =    1.697
peak=    3.940 closest distance to " CG2 ILE A 234 " =    1.085
peak=    3.938 closest distance to " CA  TYR A 116 " =    1.372
peak=    3.932 closest distance to " CB  ARG A 275 " =    0.975
peak=    3.931 closest distance to " O   HOH Z 402 " =    1.526
peak=    3.922 closest distance to " CA  ALA A 100 " =    1.076
peak=    3.918 closest distance to " CB  ASN A 142 " =    1.232
peak=    3.918 closest distance to " O   ASP A 124 " =    1.366
peak=    3.915 closest distance to " CG2 VAL A 197 " =    1.271
peak=    3.908 closest distance to " CE  LYS A  76 " =    0.841
peak=    3.893 closest distance to " CB  GLU A 128 " =    1.138
peak=    3.888 closest distance to " CA  VAL A 230 " =    1.271
peak=    3.887 closest distance to " O   HOH Z 316 " =    3.177
peak=    3.882 closest distance to " O   HOH Z 124 " =    1.197
peak=    3.880 closest distance to " CB  PRO A 280 " =    1.223
peak=    3.876 closest distance to " CA  ALA A 295 " =    0.959
peak=    3.867 closest distance to " N   SER A 164 " =    1.008
peak=    3.862 closest distance to " CA  ALA A 160 " =    0.908
peak=    3.860 closest distance to " O   HOH Z 357 " =    2.206
peak=    3.859 closest distance to " O   HOH Z  40 " =    1.946
peak=    3.859 closest distance to " O   HOH Z 234 " =    3.578
peak=    3.856 closest distance to " O   HOH Z 144 " =    1.896
peak=    3.852 closest distance to " CB  VAL A 265 " =    1.217
peak=    3.849 closest distance to " O   HOH Z 174 " =    2.063
peak=    3.848 closest distance to " O   HOH Z 279 " =    1.041
peak=    3.842 closest distance to " O   ASN A  74 " =    2.096
peak=    3.822 closest distance to " CA  ALA A  51 " =    1.064
peak=    3.820 closest distance to " CG2AVAL A 121 " =    1.909
peak=    3.820 closest distance to " CB  PRO A  54 " =    0.902
peak=    3.817 closest distance to " CD  ARG A 159 " =    0.792
peak=    3.797 closest distance to " O   HOH Z 393 " =    3.432
peak=    3.791 closest distance to " O   HOH Z 427 " =    2.999
peak=    3.774 closest distance to " O   HOH Z 422 " =    2.453
peak=    3.774 closest distance to " CB  GLU A 152 " =    1.205
peak=    3.763 closest distance to " OD1 ASN A 301 " =    1.172
peak=    3.752 closest distance to " O   HOH Z 403 " =    1.484
peak=    3.744 closest distance to " CB  SER A  26 " =    1.814
peak=    3.743 closest distance to " CB BVAL A  41 " =    1.347
peak=    3.741 closest distance to " O   HOH Z 437 " =    1.881
peak=    3.740 closest distance to " CG  PRO A 198 " =    1.374
peak=    3.739 closest distance to " OE2 GLU A   2 " =    2.102
peak=    3.735 closest distance to " O   HOH Z 146 " =    1.433
peak=    3.730 closest distance to " O   HOH Z  82 " =    0.978
peak=    3.720 closest distance to " O   HOH Z 111 " =    1.717
peak=    3.693 closest distance to " O   HOH Z 417 " =    3.225
peak=    3.692 closest distance to " CB  GLU A 277 " =    3.823
peak=    3.687 closest distance to " O   HOH Z 134 " =    1.692
peak=    3.684 closest distance to " O   HOH Z 133 " =    1.477
peak=    3.674 closest distance to " CB  VAL A 296 " =    1.106
peak=    3.674 closest distance to " O  BHOH Z  74 " =    1.227
peak=    3.672 closest distance to " O   HOH Z 107 " =    1.420
peak=    3.670 closest distance to " O   HOH Z 433 " =    1.567
peak=    3.667 closest distance to " CA  GLY A 267 " =    0.971
peak=    3.659 closest distance to " O   HOH Z 365 " =    2.334
peak=    3.655 closest distance to " NE2 HIS A 115 " =    1.074
peak=    3.653 closest distance to " O   HOH Z  19 " =    1.892
peak=    3.650 closest distance to " NH2 ARG A 156 " =    1.110
peak=    3.648 closest distance to " C   VAL A 265 " =    1.078
peak=    3.648 closest distance to " N   SER A 271 " =    1.120
peak=    3.647 closest distance to " O   HOH Z 343 " =    2.697
peak=    3.645 closest distance to " CA  VAL A 125 " =    1.181
peak=    3.637 closest distance to " NH1AARG A 145 " =    1.298
peak=    3.635 closest distance to " O   HOH Z 346 " =    1.608
peak=    3.632 closest distance to " O   HOH Z   9 " =    1.131
peak=    3.628 closest distance to " CA  ASN A 217 " =    1.213
peak=    3.627 closest distance to " CA  ALA A 291 " =    0.928
peak=    3.622 closest distance to " O   HOH Z 176 " =    1.532
peak=    3.619 closest distance to " O   HOH Z 193 " =    1.619
peak=    3.618 closest distance to " CB  GLN A  89 " =    1.183
peak=    3.616 closest distance to " CB  ARG A  79 " =    1.311
peak=    3.609 closest distance to " O   HOH Z 113 " =    2.243
peak=    3.608 closest distance to " O   HOH Z 277 " =    1.249
peak=    3.607 closest distance to " O   ALA A 165 " =    1.307
peak=    3.600 closest distance to " CE3 TRP A  85 " =    1.056
peak=    3.600 closest distance to " N   TYR A  15 " =    0.969
peak=    3.599 closest distance to " O   HOH Z 393 " =    3.611
peak=    3.595 closest distance to " O   HOH Z 435 " =    3.008
peak=    3.591 closest distance to " O   HOH Z 102 " =    1.362
peak=    3.589 closest distance to " CG2 VAL A 296 " =    1.044
peak=    3.588 closest distance to " O   PRO A  90 " =    1.567
peak=    3.581 closest distance to " CE1 TYR A 186 " =    1.289
peak=    3.577 closest distance to " CB  ARG A 190 " =    1.723
peak=    3.577 closest distance to " CB  SER A 288 " =    1.696
peak=    3.567 closest distance to " CB  TYR A  30 " =    1.118
peak=    3.566 closest distance to " O   HOH Z  38 " =    1.452
peak=    3.565 closest distance to " O   HOH Z   4 " =    1.703
peak=    3.564 closest distance to " CA  ILE A 106 " =    0.798
peak=    3.557 closest distance to " CB  VAL A 202 " =    1.457
peak=    3.546 closest distance to " CA  CYS A 260 " =    1.476
peak=    3.544 closest distance to " O   HOH Z  63 " =    2.151
peak=    3.542 closest distance to " O  BHOH Z 338 " =    2.361
peak=    3.538 closest distance to " O   ASP A 200 " =    1.589
peak=    3.538 closest distance to " CB  ASN A 285 " =    0.926
peak=    3.533 closest distance to " CA  ALA A 154 " =    1.090
peak=    3.532 closest distance to " OE1 GLU A   2 " =    1.382
peak=    3.528 closest distance to " CD1 LEU A  96 " =    0.802
peak=    3.524 closest distance to " CD  LYS A 119 " =    1.774
peak=    3.524 closest distance to " O   HOH Z  80 " =    2.185
peak=    3.520 closest distance to " O   HOH Z 207 " =    1.289
peak=    3.511 closest distance to " CG  PRO A 213 " =    1.187
peak=    3.511 closest distance to " O   HOH Z 420 " =    5.240
peak=    3.511 closest distance to " CG2 THR A 221 " =    1.116
peak=    3.507 closest distance to " O   GLY A  91 " =    1.116
peak=    3.506 closest distance to " CA  ASP A 162 " =    1.103
peak=    3.502 closest distance to " O   HOH Z 213 " =    1.521
peak=    3.500 closest distance to " CG  MET A 185 " =    1.262
peak=    3.498 closest distance to " CB  GLU A  37 " =    0.890
peak=    3.497 closest distance to " CE1 PHE A 218 " =    1.028
peak=    3.494 closest distance to " O   THR A 220 " =    1.247
peak=    3.491 closest distance to " CG  ARG A 138 " =    1.308
peak=    3.491 closest distance to " CA  ARG A  36 " =    0.966
peak=    3.485 closest distance to " O   THR A 251 " =    1.207
peak=    3.483 closest distance to " OG  SER A 245 " =    1.586
peak=    3.481 closest distance to " CZ3 TRP A  85 " =    0.815
peak=    3.481 closest distance to " CG1 ILE A  20 " =    1.276
peak=    3.478 closest distance to " O   HOH Z 203 " =    1.784
peak=    3.476 closest distance to " O   HOH Z  54 " =    1.249
peak=    3.474 closest distance to " O   HOH Z 303 " =    2.416
peak=    3.466 closest distance to " O   HOH Z  30 " =    1.020
peak=    3.463 closest distance to " O   HOH Z 422 " =    0.927
peak=    3.461 closest distance to " O   HOH Z 345 " =    1.829
peak=    3.460 closest distance to " CB  SER A  62 " =    1.039
peak=    3.459 closest distance to " CB  MET A  40 " =    0.893
peak=    3.456 closest distance to " O   GLN A  11 " =    0.906
peak=    3.437 closest distance to " CA  SER A  12 " =    1.368
peak=    3.436 closest distance to " O   HOH Z  56 " =    1.819
peak=    3.435 closest distance to " CA  ARG A 139 " =    1.408
peak=    3.431 closest distance to " CB  THR A  52 " =    0.870
peak=    3.429 closest distance to " CB  LEU A  83 " =    0.711
peak=    3.428 closest distance to " CB  ASP A 124 " =    0.843
peak=    3.427 closest distance to " O   HOH Z 369 " =    2.207
peak=    3.426 closest distance to " O   HOH Z 151 " =    1.944
peak=    3.425 closest distance to " O   HOH Z 404 " =    1.687
peak=    3.424 closest distance to " O   HOH Z 265 " =    2.045
peak=    3.424 closest distance to " O   HOH Z 368 " =    4.037
peak=    3.423 closest distance to " CD1 ILE A 199 " =    1.207
peak=    3.420 closest distance to " OG BSER A 164 " =    2.092
peak=    3.413 closest distance to " O   HOH Z  47 " =    2.764
peak=    3.413 closest distance to " CB  ASN A  39 " =    0.819
peak=    3.409 closest distance to " O   HOH Z 132 " =    3.030
peak=    3.406 closest distance to " CB  GLN A  88 " =    1.334
peak=    3.398 closest distance to " N   TYR A 247 " =    1.298
peak=    3.395 closest distance to " CD1 ILE A  33 " =    1.658
peak=    3.393 closest distance to " O   HOH Z 295 " =    1.006
peak=    3.389 closest distance to " NZ  LYS A  48 " =    1.311
peak=    3.388 closest distance to " CB  ARG A 156 " =    1.121
peak=    3.386 closest distance to " CD  LYS A 166 " =    1.596
peak=    3.385 closest distance to " CA  ALA A  21 " =    1.260
peak=    3.382 closest distance to " NH2 ARG A  56 " =    1.168
peak=    3.381 closest distance to " CB  ASP A 140 " =    1.014
peak=    3.379 closest distance to " CA  GLU A 152 " =    0.898
peak=    3.368 closest distance to " O   HOH Z 147 " =    1.557
peak=    3.366 closest distance to " O   HOH Z  43 " =    2.074
peak=    3.365 closest distance to " O   HOH Z 188 " =    3.086
peak=    3.364 closest distance to " O   HOH Z 361 " =    3.250
peak=    3.360 closest distance to " NH1AARG A 102 " =    1.069
peak=    3.359 closest distance to " CA  ARG A 156 " =    1.086
peak=    3.354 closest distance to " O   HOH Z 331 " =    1.026
peak=    3.354 closest distance to " CB  SER A  95 " =    1.086
peak=    3.352 closest distance to " O   HOH Z  44 " =    2.050
peak=    3.351 closest distance to " CA  MET A 105 " =    1.156
peak=    3.349 closest distance to " O   HOH Z 339 " =    1.142
peak=    3.347 closest distance to " O   ASN A  74 " =    1.680
peak=    3.343 closest distance to " CG2 THR A  31 " =    0.962
peak=    3.342 closest distance to " OG  SER A 135 " =    1.321
peak=    3.340 closest distance to " CB  ASN A 110 " =    1.146
peak=    3.340 closest distance to " CB  SER A  28 " =    1.059
peak=    3.339 closest distance to " O   HOH Z 365 " =    2.654
peak=    3.337 closest distance to " CA  LEU A 101 " =    1.450
peak=    3.333 closest distance to " O   HOH Z 358 " =    1.165
peak=    3.332 closest distance to " CB  SER A   3 " =    1.552
peak=    3.326 closest distance to " CB  ALA A 100 " =    1.404
peak=    3.325 closest distance to " CA  GLN A  94 " =    0.769
peak=    3.325 closest distance to " CA  LYS A 117 " =    1.392
peak=    3.325 closest distance to " CZ  PHE A  38 " =    1.126
peak=    3.323 closest distance to " CB  LEU A 255 " =    2.035
peak=    3.318 closest distance to " O   HOH Z 238 " =    1.243
peak=    3.318 closest distance to " CA  THR A 246 " =    0.997
peak=    3.317 closest distance to " O   HOH Z 357 " =    2.536
peak=    3.304 closest distance to " CB  ALA A 299 " =    0.775
peak=    3.297 closest distance to " ND2 ASN A 249 " =    2.044
peak=    3.297 closest distance to " O   PRO A 213 " =    1.498
peak=    3.293 closest distance to " CA  SER A  87 " =    0.972
peak=    3.289 closest distance to " O   HOH Z 291 " =    1.335
peak=    3.289 closest distance to " O   HOH Z 126 " =    1.646
peak=    3.289 closest distance to " OG BSER A 134 " =    2.822
peak=    3.284 closest distance to " O   HOH Z 336 " =    1.771
peak=    3.283 closest distance to " CB  THR A 235 " =    1.364
peak=    3.282 closest distance to " CA  VAL A  41 " =    0.908
peak=    3.281 closest distance to " CD  ARG A 195 " =    1.171
peak=    3.277 closest distance to " CG1 ILE A  49 " =    1.694
peak=    3.276 closest distance to " O   HOH Z  76 " =    1.112
peak=    3.276 closest distance to " CB  GLU A 236 " =    1.191
peak=    3.275 closest distance to " O   THR A 182 " =    1.537
peak=    3.275 closest distance to " CB  ASP A 107 " =    1.227
peak=    3.274 closest distance to " CG2 VAL A 126 " =    0.895
peak=    3.273 closest distance to " OH  TYR A 293 " =    1.388
peak=    3.267 closest distance to " O   GLU A   2 " =    1.546
peak=    3.261 closest distance to " CB  ALA A  43 " =    1.022
peak=    3.260 closest distance to " NH2AARG A 275 " =    3.196
peak=    3.259 closest distance to " CG1 ILE A  33 " =    1.226
peak=    3.258 closest distance to " O   HOH Z   1 " =    2.488
peak=    3.253 closest distance to " O   HOH Z 281 " =    2.477
peak=    3.253 closest distance to " O   HOH Z 189 " =    3.036
peak=    3.250 closest distance to " OD2 ASP A 298 " =    3.608
peak=    3.249 closest distance to " CG1 VAL A 257 " =    1.338
peak=    3.245 closest distance to " O   HOH Z 438 " =    2.917
peak=    3.236 closest distance to " CD2 LEU A 297 " =    0.830
peak=    3.235 closest distance to " CE  LYS A  76 " =    1.112
peak=    3.234 closest distance to " O   HOH Z  27 " =    1.048
peak=    3.233 closest distance to " O   HOH Z 272 " =    1.847
peak=    3.233 closest distance to " CA  ASP A 140 " =    1.428
peak=    3.224 closest distance to " N   THR A  52 " =    1.181
peak=    3.220 closest distance to " CG1 VAL A 153 " =    1.056
peak=    3.217 closest distance to " O   HOH Z  67 " =    1.486
peak=    3.214 closest distance to " CB  LYS A 117 " =    1.249
peak=    3.213 closest distance to " CB  ARG A 219 " =    1.546
peak=    3.210 closest distance to " CG  LYS A  76 " =    1.134
peak=    3.210 closest distance to " CG  LEU A 167 " =    1.092
peak=    3.209 closest distance to " O   HOH Z 133 " =    2.494
peak=    3.208 closest distance to " O   HOH Z  85 " =    2.163
peak=    3.206 closest distance to " O   LYS A 290 " =    1.724
peak=    3.203 closest distance to " O   HOH Z 419 " =    1.592
peak=    3.195 closest distance to " CB  MET A 105 " =    0.976
peak=    3.193 closest distance to " CB  ALA A  10 " =    1.323
peak=    3.188 closest distance to " CA  GLY A  35 " =    0.900
peak=    3.186 closest distance to " O   HOH Z 116 " =    1.907
peak=    3.181 closest distance to " O   HOH Z 373 " =    1.531
peak=    3.180 closest distance to " CG1 VAL A 174 " =    1.682
peak=    3.179 closest distance to " NE1 TRP A  92 " =    1.708
peak=    3.179 closest distance to " O   HOH Z 377 " =    1.181
peak=    3.178 closest distance to " CG  GLU A  37 " =    0.923
peak=    3.177 closest distance to " O   HOH Z 368 " =    1.900
peak=    3.176 closest distance to " CA  GLN A  11 " =    1.314
peak=    3.167 closest distance to " N   VAL A 126 " =    1.615
peak=    3.167 closest distance to " O   HOH Z  88 " =    3.160
peak=    3.166 closest distance to " O   HOH Z 183 " =    1.900
peak=    3.160 closest distance to " ND1 HIS A  81 " =    1.740
peak=    3.160 closest distance to " CA  ASN A 127 " =    1.334
peak=    3.152 closest distance to " OG1 THR A 221 " =    1.255
peak=    3.152 closest distance to " O   HOH Z 221 " =    1.235
peak=    3.151 closest distance to " O   HOH Z 394 " =    3.951
peak=    3.150 closest distance to " CB  TYR A 169 " =    0.720
peak=    3.148 closest distance to " O   HOH Z 368 " =    4.386
peak=    3.146 closest distance to " O   HOH Z  73 " =    2.412
peak=    3.146 closest distance to " CG  ARG A 219 " =    1.386
peak=    3.143 closest distance to " CD ALYS A 290 " =    0.975
peak=    3.140 closest distance to " OG  SER A  62 " =    2.905
peak=    3.136 closest distance to " CB  PHE A 204 " =    1.127
peak=    3.132 closest distance to " CD2 LEU A 143 " =    1.533
peak=    3.132 closest distance to " CZ3 TRP A 274 " =    4.412
peak=    3.132 closest distance to " CZ3 TRP A  92 " =    1.274
peak=    3.123 closest distance to " N   ALA A 292 " =    1.015
peak=    3.118 closest distance to " CB  GLU A  46 " =    1.016
peak=    3.115 closest distance to " O  BHOH Z 338 " =    0.884
peak=    3.114 closest distance to " O   HOH Z   5 " =    2.029
peak=    3.114 closest distance to " O   HOH Z 285 " =    2.259
peak=    3.111 closest distance to " C   ASN A  39 " =    1.181
peak=    3.107 closest distance to " CB  SER A 210 " =    1.037
peak=    3.106 closest distance to " O   HOH Z 366 " =    2.436
peak=    3.097 closest distance to " O   HOH Z  83 " =    1.554
peak=    3.096 closest distance to " CG2 THR A  42 " =    0.804
peak=    3.094 closest distance to " O   THR A 157 " =    1.214
peak=    3.086 closest distance to " CG ALYS A 290 " =    1.061
peak=    3.085 closest distance to " O   HOH Z 421 " =    1.979
peak=    3.069 closest distance to " CE1 TYR A  30 " =    1.085
peak=    3.065 closest distance to " CB  TYR A 247 " =    1.090
peak=    3.055 closest distance to " CB  ARG A  79 " =    0.881
peak=    3.054 closest distance to " CA  ALA A 158 " =    1.635
peak=    3.033 closest distance to " O   HOH Z 106 " =    3.903

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.840 - 5.453
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 225 from: 225
   mapped sites are within: 0.840 - 5.453

peak=   -4.890 closest distance to " CG1 VAL A 296 " =    0.993
peak=   -4.706 closest distance to " CG2 VAL A 230 " =    0.861
peak=   -4.588 closest distance to " CA  ASP A 298 " =    1.101
peak=   -4.518 closest distance to " CG  PRO A 243 " =    1.675
peak=   -4.494 closest distance to " CG1 VAL A 250 " =    2.707
peak=   -4.302 closest distance to " O   PRO A 198 " =    1.354
peak=   -4.274 closest distance to " O   HOH Z 411 " =    5.453
peak=   -4.263 closest distance to " CE3 TRP A 150 " =    2.272
peak=   -4.254 closest distance to " O   VAL A  67 " =    2.865
peak=   -4.230 closest distance to " CG  GLN A  58 " =    0.969
peak=   -4.137 closest distance to " CG2 ILE A  49 " =    2.838
peak=   -4.106 closest distance to " CE2 PHE A  61 " =    2.655
peak=   -4.103 closest distance to " CG2 VAL A 189 " =    2.163
peak=   -4.068 closest distance to " O   HOH Z 340 " =    1.591
peak=   -4.061 closest distance to " CD  ARG A  14 " =    3.308
peak=   -4.047 closest distance to " O   HOH Z 107 " =    0.840
peak=   -4.010 closest distance to " OG BSER A 134 " =    1.504
peak=   -3.999 closest distance to " O   HOH Z 166 " =    1.383
peak=   -3.956 closest distance to " CD1 PHE A  59 " =    2.012
peak=   -3.948 closest distance to " NH1 ARG A 195 " =    1.057
peak=   -3.923 closest distance to " O   HOH Z 103 " =    2.008
peak=   -3.921 closest distance to " OXT GLY A 302 " =    3.072
peak=   -3.903 closest distance to " CD2 TYR A 293 " =    1.980
peak=   -3.880 closest distance to " CG1 VAL A 112 " =    2.590
peak=   -3.870 closest distance to " CG  ARG A 269 " =    2.327
peak=   -3.863 closest distance to " CG  GLN A 103 " =    2.436
peak=   -3.848 closest distance to " O   HOH Z  10 " =    1.576
peak=   -3.844 closest distance to " CG2BVAL A  41 " =    2.199
peak=   -3.843 closest distance to " O   HOH Z 231 " =    1.976
peak=   -3.819 closest distance to " O   HOH Z 196 " =    1.578
peak=   -3.817 closest distance to " OD2 ASP A 298 " =    0.925
peak=   -3.806 closest distance to " O   HOH Z  73 " =    2.576
peak=   -3.805 closest distance to " CA  VAL A  67 " =    2.838
peak=   -3.797 closest distance to " O   SER A 271 " =    2.044
peak=   -3.791 closest distance to " CD2 PHE A  61 " =    2.129
peak=   -3.787 closest distance to " O   HOH Z 196 " =    2.446
peak=   -3.784 closest distance to " CD  ARG A 156 " =    2.049
peak=   -3.774 closest distance to " CZ  TYR A 169 " =    1.893
peak=   -3.739 closest distance to " CB  PRO A 243 " =    2.860
peak=   -3.736 closest distance to " CG  ARG A 259 " =    2.529
peak=   -3.719 closest distance to " O   HOH Z 216 " =    0.983
peak=   -3.715 closest distance to " CG  GLN A  58 " =    1.271
peak=   -3.701 closest distance to " O   HOH Z 193 " =    1.023
peak=   -3.686 closest distance to " CD  GLN A 223 " =    1.333
peak=   -3.677 closest distance to " SG  CYS A 260 " =    2.440
peak=   -3.672 closest distance to " ND2BASN A 224 " =    2.105
peak=   -3.670 closest distance to " O   TYR A 186 " =    1.903
peak=   -3.666 closest distance to " CA  SER A 164 " =    2.113
peak=   -3.664 closest distance to " NZ  LYS A 166 " =    1.954
peak=   -3.664 closest distance to " C   VAL A 265 " =    0.905
peak=   -3.659 closest distance to " O   HOH Z 250 " =    1.715
peak=   -3.652 closest distance to " O   HOH Z  68 " =    1.665
peak=   -3.649 closest distance to " CG2 THR A 182 " =    2.310
peak=   -3.648 closest distance to " CE2 TYR A  30 " =    2.633
peak=   -3.643 closest distance to " O   HOH Z 174 " =    1.626
peak=   -3.635 closest distance to " CE3 TRP A  70 " =    1.962
peak=   -3.633 closest distance to " CZ  TYR A 172 " =    1.857
peak=   -3.624 closest distance to " CH2 TRP A 179 " =    1.240
peak=   -3.623 closest distance to " O   HOH Z  19 " =    2.328
peak=   -3.613 closest distance to " O   HOH Z  52 " =    1.894
peak=   -3.610 closest distance to " O   HOH Z 407 " =    2.963
peak=   -3.609 closest distance to " N   ALA A  43 " =    2.673
peak=   -3.604 closest distance to " N   ILE A 120 " =    1.028
peak=   -3.602 closest distance to " CZ  PHE A  38 " =    2.417
peak=   -3.598 closest distance to " OD1 ASN A 148 " =    1.389
peak=   -3.588 closest distance to " O   HOH Z 431 " =    2.508
peak=   -3.570 closest distance to " CE1 PHE A  59 " =    2.064
peak=   -3.568 closest distance to " O   GLN A  77 " =    1.749
peak=   -3.555 closest distance to " CD  GLN A  88 " =    0.972
peak=   -3.555 closest distance to " NH2 ARG A  79 " =    2.317
peak=   -3.554 closest distance to " O   HOH Z 370 " =    2.455
peak=   -3.553 closest distance to " O   HOH Z 221 " =    1.046
peak=   -3.548 closest distance to " O   HOH Z 388 " =    2.023
peak=   -3.547 closest distance to " CG2 THR A  18 " =    2.813
peak=   -3.534 closest distance to " CD1 LEU A 101 " =    2.371
peak=   -3.525 closest distance to " O   HOH Z 231 " =    2.351
peak=   -3.524 closest distance to " C   HIS A 108 " =    1.193
peak=   -3.519 closest distance to " O   HOH Z  92 " =    1.698
peak=   -3.516 closest distance to " O   HOH Z 407 " =    1.874
peak=   -3.511 closest distance to " N   ALA A 226 " =    2.078
peak=   -3.499 closest distance to " NE  ARG A  79 " =    1.183
peak=   -3.495 closest distance to " O   HOH Z  40 " =    2.710
peak=   -3.492 closest distance to " O   HOH Z  12 " =    2.414
peak=   -3.488 closest distance to " NE2 GLN A 194 " =    2.129
peak=   -3.487 closest distance to " O   HOH Z 251 " =    4.462
peak=   -3.481 closest distance to " CD1 ILE A 263 " =    2.297
peak=   -3.477 closest distance to " O   PHE A 218 " =    1.439
peak=   -3.473 closest distance to " O   HOH Z 215 " =    1.134
peak=   -3.468 closest distance to " O   ASP A 253 " =    2.079
peak=   -3.466 closest distance to " O   HOH Z 150 " =    2.276
peak=   -3.463 closest distance to " CB  ASN A  45 " =    2.199
peak=   -3.463 closest distance to " O   HOH Z 345 " =    3.086
peak=   -3.462 closest distance to " O   HOH Z 155 " =    1.971
peak=   -3.454 closest distance to " O   HOH Z  30 " =    1.679
peak=   -3.453 closest distance to " O   HOH Z 348 " =    2.205
peak=   -3.449 closest distance to " CE2 TRP A  70 " =    2.448
peak=   -3.442 closest distance to " OG  SER A  97 " =    2.398
peak=   -3.438 closest distance to " CG  GLN A  11 " =    1.579
peak=   -3.436 closest distance to " O   SER A 276 " =    1.548
peak=   -3.430 closest distance to " O   GLY A  17 " =    1.113
peak=   -3.425 closest distance to " O   HOH Z 110 " =    1.520
peak=   -3.424 closest distance to " O   HOH Z 329 " =    1.259
peak=   -3.421 closest distance to " O   ALA A  21 " =    2.259
peak=   -3.419 closest distance to " CB  VAL A 230 " =    1.121
peak=   -3.413 closest distance to " O   HOH Z 120 " =    0.907
peak=   -3.409 closest distance to " O   HOH Z  54 " =    1.678
peak=   -3.404 closest distance to " O   HOH Z 359 " =    2.773
peak=   -3.396 closest distance to " O   HOH Z 189 " =    2.384
peak=   -3.388 closest distance to " O   HOH Z  99 " =    4.352
peak=   -3.388 closest distance to " O   HOH Z 211 " =    1.086
peak=   -3.381 closest distance to " N   SER A 134 " =    1.223
peak=   -3.376 closest distance to " O   HOH Z 136 " =    1.479
peak=   -3.375 closest distance to " CA  GLY A 241 " =    2.300
peak=   -3.372 closest distance to " CE  MET A  93 " =    1.669
peak=   -3.365 closest distance to " OD1 ASN A 173 " =    1.331
peak=   -3.354 closest distance to " CA  SER A 276 " =    1.537
peak=   -3.354 closest distance to " O   ALA A 160 " =    1.472
peak=   -3.354 closest distance to " O   HOH Z 351 " =    1.728
peak=   -3.353 closest distance to " O   HOH Z 118 " =    4.933
peak=   -3.353 closest distance to " CG  LEU A 281 " =    2.060
peak=   -3.351 closest distance to " O   HOH Z 128 " =    2.491
peak=   -3.350 closest distance to " O   HOH Z 165 " =    1.748
peak=   -3.345 closest distance to " ND2 ASN A  60 " =    1.470
peak=   -3.340 closest distance to " CZ  ARG A 259 " =    0.996
peak=   -3.338 closest distance to " O   HOH Z 275 " =    1.582
peak=   -3.338 closest distance to " NE2 GLN A 103 " =    1.775
peak=   -3.337 closest distance to " OD2 ASP A 171 " =    1.886
peak=   -3.337 closest distance to " CB  ALA A  10 " =    2.187
peak=   -3.334 closest distance to " CA  ASN A 110 " =    1.044
peak=   -3.327 closest distance to " C   LEU A 143 " =    1.165
peak=   -3.327 closest distance to " OG1 THR A  82 " =    1.365
peak=   -3.326 closest distance to " CA  GLY A 203 " =    2.453
peak=   -3.325 closest distance to " CD  GLN A  77 " =    1.016
peak=   -3.324 closest distance to " O   HOH Z   6 " =    1.700
peak=   -3.319 closest distance to " O   HOH Z 166 " =    1.524
peak=   -3.316 closest distance to " O   HOH Z 124 " =    1.872
peak=   -3.316 closest distance to " CG1BVAL A  72 " =    1.880
peak=   -3.311 closest distance to " CD1 TYR A 247 " =    2.511
peak=   -3.310 closest distance to " O   HOH Z 418 " =    1.573
peak=   -3.306 closest distance to " CB  HIS A  86 " =    1.209
peak=   -3.306 closest distance to " CA  PRO A 243 " =    2.868
peak=   -3.303 closest distance to " CG  GLU A  53 " =    1.640
peak=   -3.302 closest distance to " CE1 PHE A 218 " =    1.470
peak=   -3.294 closest distance to " O   TYR A  15 " =    1.852
peak=   -3.293 closest distance to " SD  MET A 105 " =    2.331
peak=   -3.286 closest distance to " OG  SER A  62 " =    4.354
peak=   -3.282 closest distance to " O   HOH Z 149 " =    1.815
peak=   -3.282 closest distance to " OE1 GLN A 223 " =    2.558
peak=   -3.279 closest distance to " O   HOH Z  64 " =    2.515
peak=   -3.277 closest distance to " O   HOH Z  30 " =    1.042
peak=   -3.273 closest distance to " CB  GLU A 277 " =    1.365
peak=   -3.273 closest distance to " O   HOH Z 147 " =    2.251
peak=   -3.272 closest distance to " CA  VAL A 121 " =    1.524
peak=   -3.272 closest distance to " O   SER A   3 " =    1.054
peak=   -3.271 closest distance to " O   HOH Z 378 " =    1.286
peak=   -3.271 closest distance to " OE1 GLN A  88 " =    1.127
peak=   -3.269 closest distance to " O   HOH Z  60 " =    2.091
peak=   -3.269 closest distance to " OD1 ASP A 298 " =    2.135
peak=   -3.266 closest distance to " CD2 TYR A  15 " =    2.231
peak=   -3.266 closest distance to " O   ARG A  56 " =    3.937
peak=   -3.265 closest distance to " O   HOH Z 255 " =    1.715
peak=   -3.264 closest distance to " O   HOH Z 137 " =    1.849
peak=   -3.256 closest distance to " O   HOH Z  11 " =    1.756
peak=   -3.253 closest distance to " O   HOH Z 198 " =    1.883
peak=   -3.244 closest distance to " O   HOH Z 428 " =    1.333
peak=   -3.233 closest distance to " O   HOH Z 140 " =    1.600
peak=   -3.232 closest distance to " CA  ASN A 127 " =    1.083
peak=   -3.225 closest distance to " O   HOH Z 171 " =    2.558
peak=   -3.225 closest distance to " CE1 HIS A  81 " =    1.582
peak=   -3.221 closest distance to " O   HOH Z 423 " =    2.623
peak=   -3.220 closest distance to " CD1 ILE A 151 " =    2.554
peak=   -3.218 closest distance to " O   HOH Z 396 " =    1.693
peak=   -3.212 closest distance to " ND2 ASN A  39 " =    1.463
peak=   -3.210 closest distance to " CG  TRP A 266 " =    1.599
peak=   -3.210 closest distance to " CZ2 TRP A 179 " =    2.221
peak=   -3.204 closest distance to " CE  LYS A  76 " =    2.633
peak=   -3.203 closest distance to " O   HOH Z 111 " =    1.556
peak=   -3.198 closest distance to " O   HOH Z 384 " =    2.030
peak=   -3.197 closest distance to " O   HOH Z 135 " =    2.204
peak=   -3.195 closest distance to " O   HOH Z 137 " =    1.469
peak=   -3.193 closest distance to " O   HOH Z 192 " =    1.876
peak=   -3.186 closest distance to " SD  MET A  40 " =    1.871
peak=   -3.185 closest distance to " CG1 VAL A 189 " =    2.485
peak=   -3.184 closest distance to " O   HOH Z 105 " =    2.175
peak=   -3.181 closest distance to " CB  ALA A   9 " =    2.326
peak=   -3.181 closest distance to " O   HOH Z 257 " =    1.340
peak=   -3.177 closest distance to " CD1 LEU A   5 " =    2.396
peak=   -3.175 closest distance to " O   HOH Z 252 " =    3.676
peak=   -3.172 closest distance to " O   ASN A 187 " =    1.701
peak=   -3.171 closest distance to " CG2 THR A 251 " =    1.708
peak=   -3.169 closest distance to " CB  ALA A 161 " =    2.574
peak=   -3.164 closest distance to " CD  PRO A 243 " =    1.853
peak=   -3.160 closest distance to " O   HOH Z  43 " =    1.533
peak=   -3.160 closest distance to " O   SER A 210 " =    1.748
peak=   -3.157 closest distance to " O   HOH Z 189 " =    4.745
peak=   -3.157 closest distance to " O   HOH Z 185 " =    2.479
peak=   -3.151 closest distance to " CB  TRP A 177 " =    2.256
peak=   -3.151 closest distance to " O   HOH Z 162 " =    2.973
peak=   -3.150 closest distance to " O   HOH Z  53 " =    1.499
peak=   -3.150 closest distance to " O   HOH Z 352 " =    1.723
peak=   -3.148 closest distance to " O   HOH Z 154 " =    1.381
peak=   -3.140 closest distance to " O   HOH Z 146 " =    1.541
peak=   -3.140 closest distance to " C   ASN A 285 " =    2.334
peak=   -3.139 closest distance to " O   HOH Z 127 " =    1.636
peak=   -3.133 closest distance to " OG  SER A  28 " =    2.102
peak=   -3.126 closest distance to " CG  LEU A  83 " =    2.144
peak=   -3.124 closest distance to " OD2 ASP A 270 " =    1.458
peak=   -3.122 closest distance to " CG2BVAL A  41 " =    1.125
peak=   -3.114 closest distance to " C   ALA A 158 " =    1.307
peak=   -3.105 closest distance to " CG  GLN A  55 " =    1.257
peak=   -3.104 closest distance to " O   HOH Z 411 " =    1.110
peak=   -3.099 closest distance to " OH  TYR A 169 " =    0.983
peak=   -3.097 closest distance to " O   HOH Z 150 " =    1.696
peak=   -3.084 closest distance to " O   HOH Z  78 " =    1.945
peak=   -3.075 closest distance to " O   HOH Z  83 " =    1.388
peak=   -3.073 closest distance to " CD2 HIS A 207 " =    2.309
peak=   -3.072 closest distance to " O   HOH Z 361 " =    4.524
peak=   -3.070 closest distance to " NH2 ARG A  66 " =    2.031
peak=   -3.068 closest distance to " CD1 LEU A  25 " =    2.392
peak=   -3.063 closest distance to " ND2 ASN A  45 " =    2.317
peak=   -3.063 closest distance to " CG1 VAL A 197 " =    2.358
peak=   -3.061 closest distance to " O   ASN A  45 " =    1.990
peak=   -3.059 closest distance to " O   HOH Z 120 " =    1.401
peak=   -3.041 closest distance to " CG  ARG A 259 " =    1.477
peak=   -3.025 closest distance to " CZ  ARG A 156 " =    1.675

================= 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    :  0.5114 0.5008   6.307275e+00   6.297282e+00
   1_bss:  0.5048 0.4952   6.301466e+00   6.294175e+00
   1_xyz:  0.4452 0.4641   6.242894e+00   6.258488e+00
   1_adp:  0.4017 0.4568   6.188482e+00   6.251108e+00
   1_occ:  0.4010 0.4562   6.187944e+00   6.251541e+00
   2_bss:  0.3992 0.4511   6.190315e+00   6.252349e+00
   2_xyz:  0.3428 0.4144   6.078360e+00   6.193089e+00
   2_adp:  0.3313 0.3960   6.059554e+00   6.168966e+00
   2_occ:  0.3311 0.3965   6.058923e+00   6.168873e+00
   3_bss:  0.3299 0.3952   6.060643e+00   6.169588e+00
   3_xyz:  0.2500 0.2991   5.819905e+00   5.968487e+00
   3_adp:  0.2199 0.2749   5.724397e+00   5.900139e+00
   3_occ:  0.2196 0.2749   5.724075e+00   5.900496e+00
   4_bss:  0.2186 0.2730   5.721270e+00   5.897938e+00
   4_xyz:  0.1673 0.2150   5.484588e+00   5.689652e+00
   4_adp:  0.1523 0.2050   5.418530e+00   5.641210e+00
   4_occ:  0.1522 0.2051   5.418268e+00   5.641099e+00
   5_bss:  0.1526 0.2052   5.419921e+00   5.642312e+00
   5_xyz:  0.1366 0.1885   5.330964e+00   5.563161e+00
   5_adp:  0.1323 0.1848   5.305415e+00   5.539471e+00
   5_occ:  0.1323 0.1847   5.304911e+00   5.539086e+00
   5_bss:  0.1322 0.1845   5.304913e+00   5.539131e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   5.420  10.095  10.785   0.000   0.000   0.000
   1_xyz:  0.300  20.000   5.420  10.095  10.785   0.000   0.000   0.000
   1_adp:  0.300  20.000   5.420  10.095  10.785   0.000   0.000   0.000
   1_occ:  0.300  20.000   5.420  10.095  10.785   0.000   0.000   0.000
   2_bss:  0.316  50.000   2.446   6.058   6.683   0.000   0.000   0.000
   2_xyz:  0.316  50.000   2.446   6.058   6.683   0.000   0.000   0.000
   2_adp:  0.316  50.000   2.446   6.058   6.683   0.000   0.000   0.000
   2_occ:  0.316  50.000   2.446   6.058   6.683   0.000   0.000   0.000
   3_bss:  0.327  66.667   1.066   3.594   4.137   0.000   0.000   0.000
   3_xyz:  0.327  66.667   1.066   3.594   4.137   0.000   0.000   0.000
   3_adp:  0.327  66.667   1.066   3.594   4.137   0.000   0.000   0.000
   3_occ:  0.327  66.667   1.066   3.594   4.137   0.000   0.000   0.000
   4_bss:  0.337  79.244   0.090   1.821   2.542   0.000   0.000   0.000
   4_xyz:  0.337  79.244   0.090   1.821   2.542   0.000   0.000   0.000
   4_adp:  0.337  79.244   0.090   1.821   2.542   0.000   0.000   0.000
   4_occ:  0.337  79.244   0.090   1.821   2.542   0.000   0.000   0.000
   5_bss:  0.342  81.321   0.169   1.392   2.476   0.000   0.000   0.000
   5_xyz:  0.342  81.321   0.169   1.392   2.476   0.000   0.000   0.000
   5_adp:  0.342  81.321   0.169   1.392   2.476   0.000   0.000   0.000
   5_occ:  0.342  81.321   0.169   1.392   2.476   0.000   0.000   0.000
   5_bss:  0.338  81.473  -1.072  -0.076   1.148   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.459 0.3489  0.4028    79850.978
   1_bss:  63.329 0.3498  0.5184    79815.536
   1_xyz:  55.262 0.4529  0.6599    64146.868
   1_adp:  53.704 0.4730  0.7735    62301.836
   1_occ:  53.719 0.4728  0.7721    62392.802
   2_bss:  53.531 0.4753  0.6891    62353.230
   2_xyz:  46.835 0.5589  0.8120    49480.108
   2_adp:  44.359 0.5899  0.8459    45692.114
   2_occ:  44.338 0.5901  0.8457    45586.458
   3_bss:  44.250 0.5912  0.7887    45626.852
   3_xyz:  31.664 0.7392  0.9469    24827.916
   3_adp:  28.456 0.7749  0.9620    20689.663
   3_occ:  28.465 0.7748  0.9616    20689.767
   4_bss:  28.284 0.7765  0.9163    20405.434
   4_xyz:  21.448 0.8472  0.9658    12342.733
   4_adp:  19.972 0.8619  0.9616    11142.423
   4_occ:  19.969 0.8619  0.9617    11140.594
   5_bss:  19.975 0.8619  0.9571    11169.614
   5_xyz:  18.025 0.8802  0.9663     9301.462
   5_adp:  17.450 0.8857  0.9562     8897.994
   5_occ:  17.437 0.8858  0.9561     8889.136
   5_bss:  17.437 0.8858  0.9605     8890.272
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4653e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4653e+01
   1_xyz:   1.739  0.014  0.108 18.408  0.007  4.110   1.4948e-01
   1_adp:   1.739  0.014  0.108 18.408  0.007  4.110   1.4948e-01
   1_occ:   1.739  0.014  0.108 18.408  0.007  4.110   1.4948e-01
   2_bss:   1.739  0.014  0.108 18.408  0.007  4.110   1.4948e-01
   2_xyz:   1.347  0.009  0.086 16.650  0.005  4.108   9.8152e-02
   2_adp:   1.347  0.009  0.086 16.650  0.005  4.108   9.8152e-02
   2_occ:   1.347  0.009  0.086 16.650  0.005  4.108   9.8152e-02
   3_bss:   1.347  0.009  0.086 16.650  0.005  4.108   9.8152e-02
   3_xyz:   1.274  0.010  0.086 16.175  0.005  4.116   9.7317e-02
   3_adp:   1.274  0.010  0.086 16.175  0.005  4.116   9.7317e-02
   3_occ:   1.274  0.010  0.086 16.175  0.005  4.116   9.7317e-02
   4_bss:   1.274  0.010  0.086 16.175  0.005  4.116   9.7317e-02
   4_xyz:   1.190  0.011  0.085 15.599  0.004  4.114   8.7894e-02
   4_adp:   1.190  0.011  0.085 15.599  0.004  4.114   8.7894e-02
   4_occ:   1.190  0.011  0.085 15.599  0.004  4.114   8.7894e-02
   5_bss:   1.190  0.011  0.085 15.599  0.004  4.114   8.7894e-02
   5_xyz:   1.147  0.010  0.086 15.373  0.004  4.124   7.6726e-02
   5_adp:   1.147  0.010  0.086 15.373  0.004  4.124   7.6726e-02
   5_occ:   1.147  0.010  0.086 15.373  0.004  4.124   7.6726e-02
   5_bss:   1.147  0.010  0.086 15.373  0.004  4.124   7.6726e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0846e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0846e+00
   1_xyz:  14.598  0.165  0.454 89.935  0.052  2.204   1.0536e-01
   1_adp:  14.598  0.165  0.454 89.935  0.052  2.204   1.0536e-01
   1_occ:  14.598  0.165  0.454 89.935  0.052  2.204   1.0536e-01
   2_bss:  14.598  0.165  0.454 89.935  0.052  2.204   1.0536e-01
   2_xyz:   9.887  0.075  0.274 83.164  0.029  2.102   5.5961e-02
   2_adp:   9.887  0.075  0.274 83.164  0.029  2.102   5.5961e-02
   2_occ:   9.887  0.075  0.274 83.164  0.029  2.102   5.5961e-02
   3_bss:   9.887  0.075  0.274 83.164  0.029  2.102   5.5961e-02
   3_xyz:   8.662  0.073  0.299 85.005  0.049  2.218   1.0416e-01
   3_adp:   8.662  0.073  0.299 85.005  0.049  2.218   1.0416e-01
   3_occ:   8.662  0.073  0.299 85.005  0.049  2.218   1.0416e-01
   4_bss:   8.662  0.073  0.299 85.005  0.049  2.218   1.0416e-01
   4_xyz:   7.893  0.056  0.316 81.295  0.039  2.180   7.3225e-02
   4_adp:   7.893  0.056  0.316 81.295  0.039  2.180   7.3225e-02
   4_occ:   7.893  0.056  0.316 81.295  0.039  2.180   7.3225e-02
   5_bss:   7.893  0.056  0.316 81.295  0.039  2.180   7.3225e-02
   5_xyz:   8.115  0.046  0.373 82.810  0.041  2.296   4.6430e-02
   5_adp:   8.115  0.046  0.373 82.810  0.041  2.296   4.6430e-02
   5_occ:   8.115  0.046  0.373 82.810  0.041  2.296   4.6430e-02
   5_bss:   8.115  0.046  0.373 82.810  0.041  2.296   4.6430e-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: 120.15   0.00  18.39  90.20   0.00  16.32 120.15   0.00  29.67
   1_occ: 120.15   0.00  18.39  90.20   0.00  16.32 120.15   0.00  29.67
   2_bss: 120.15   0.00  18.39  90.20   0.00  16.32 120.15   0.00  29.67
   2_xyz: 120.15   0.00  18.39  90.20   0.00  16.32 120.15   0.00  29.67
   2_adp: 119.07   0.00  15.96  74.78   0.00  13.38 119.07   0.00  30.01
   2_occ: 119.07   0.00  15.96  74.78   0.00  13.38 119.07   0.00  30.01
   3_bss: 119.07   0.00  15.96  74.78   0.00  13.38 119.07   0.00  30.01
   3_xyz: 119.07   0.00  15.96  74.78   0.00  13.38 119.07   0.00  30.01
   3_adp: 115.06   0.00  15.86  77.40   0.00  11.75 115.06   0.00  38.23
   3_occ: 115.06   0.00  15.86  77.40   0.00  11.75 115.06   0.00  38.23
   4_bss: 115.06   0.00  15.86  77.40   0.00  11.75 115.06   0.00  38.23
   4_xyz: 115.06   0.00  15.86  77.40   0.00  11.75 115.06   0.00  38.23
   4_adp: 110.22   0.00  16.18  88.99   0.00  11.08 110.22   1.75  43.95
   4_occ: 110.22   0.00  16.18  88.99   0.00  11.08 110.22   1.75  43.95
   5_bss: 110.22   0.00  16.18  88.99   0.00  11.08 110.22   1.75  43.95
   5_xyz: 110.22   0.00  16.18  88.99   0.00  11.08 110.22   1.75  43.95
   5_adp: 109.00   0.00  16.20  94.33   0.00  10.72 109.00   2.07  46.01
   5_occ: 109.00   0.00  16.20  94.33   0.00  10.72 109.00   2.07  46.01
   5_bss: 110.47   1.47  17.67  95.80   1.47  12.20 110.47   3.54  47.48
------------------------------------------------------------------------
 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:    1.263    0.012    0.409
   1_adp:    1.263    0.012    0.409
   1_occ:    1.263    0.012    0.409
   2_bss:    1.263    0.012    0.409
   2_xyz:    1.885    0.035    0.569
   2_adp:    1.885    0.035    0.569
   2_occ:    1.885    0.035    0.569
   3_bss:    1.885    0.035    0.569
   3_xyz:    1.757    0.087    0.774
   3_adp:    1.757    0.087    0.774
   3_occ:    1.757    0.087    0.774
   4_bss:    1.757    0.087    0.774
   4_xyz:    1.961    0.034    0.850
   4_adp:    1.961    0.034    0.850
   4_occ:    1.961    0.034    0.850
   5_bss:    1.961    0.034    0.850
   5_xyz:    2.234    0.042    0.893
   5_adp:    2.234    0.042    0.893
   5_occ:    2.234    0.042    0.893
   5_bss:    2.234    0.042    0.893
------------------------------------------------------------------------

CPU time actual refinement: 364.42


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_714/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_714/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_714/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_714/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_714/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 364.26 
  Macro-tasks:
    bulk solvent and scale       = 52.89  
    individual site refinement   = 151.59 
    weights calculation          = 31.46  
    collect and process          = 6.43   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 242.51 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 111.92 
    alpha_beta                      = 8.30   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 122.92 
    fmodel                         = 9.06   
    r_factors                      = 0.32   
    phase_errors                   = 9.74   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 265.99 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.063 micro seconds
Total CPU time: 6.31 minutes
from_scatterers_fft:    660 calls, 111.64 s
gradients_fft:          604 calls, 109.51 s

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

# Date 2008-01-16 Time 02:15:26 PST -0800 (1200478526.27 s)
Start R-work = 0.5114, R-free = 0.5008 (no bulk solvent and anisotropic scale)
Final R-work = 0.1486, R-free = 0.1994 (no bulk solvent and anisotropic scale)

Start R-work = 0.5048, R-free = 0.4952
Final R-work = 0.1322, R-free = 0.1845