# Date 2008-01-16 Time 01:34:10 PST -0800 (1200476050.76 s)
#phil __OFF__

Command line arguments: "../479.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 = 27232
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 479

-------------------------------------------------------------------------------
  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: (69.5475, 48.1033, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0412 1.98072
Completeness in resolution range: 0.940377
Completeness with d_max=infinity: 0.937497

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0412
                             d_min =   1.9807

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: (69.5475, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0412 1.98072
Completeness in resolution range: 0.940377
Completeness with d_max=infinity: 0.937497

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0416 -  4.2385 [2196/2224]  1973   223  10.2%
  bin  2:  4.2385 -  3.3767 [2093/2116]  1887   206   9.8%
  bin  3:  3.3767 -  2.9536 [2075/2100]  1863   212  10.2%
  bin  4:  2.9536 -  2.6852 [2051/2067]  1850   201   9.8%
  bin  5:  2.6852 -  2.4937 [2023/2067]  1814   209  10.3%
  bin  6:  2.4937 -  2.3472 [2047/2075]  1853   194   9.5%
  bin  7:  2.3472 -  2.2301 [2008/2044]  1806   202  10.1%
  bin  8:  2.2301 -  2.1333 [2013/2055]  1814   199   9.9%
  bin  9:  2.1333 -  2.0513 [2008/2054]  1804   204  10.2%
  bin 10:  2.0513 -  1.9807 [1075/2029]   966   109  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_479/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 24
        2.42 -     3.04: 2186
        3.04 -     3.66: 4651
        3.66 -     4.28: 8937
        4.28 -     4.90: 12249
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.817 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.852 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.914 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.915 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28042 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_479/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_479/model_refine_001.geo

CPU time processing inputs: 9.47


============================ 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 = 69.5475 48.10325 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4992   r_free= 0.4828   ksol= 0.00   Bsol= 0.00   scale= 0.773    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.301175                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0416 -  4.7275 0.99   1420  158 0.4094 0.4332      6.6291        6.67|
|  2:  4.7275 -  3.7718 0.99   1363  153 0.4383 0.4499      6.8542      6.8865|
|  3:  3.7718 -  3.3008 0.99   1353  147 0.4681 0.4255      6.7175      6.6722|
|  4:  3.3008 -  3.0016 0.99   1322  143 0.5023 0.4409      6.5464      6.4739|
|  5:  3.0016 -  2.7879 0.98   1328  150 0.5395 0.5276      6.3842      6.4251|
|  6:  2.7879 -  2.6245 0.99   1315  147 0.5287 0.4848      6.2984      6.1567|
|  7:  2.6245 -  2.4937 0.98   1286  153 0.5090 0.4803       6.247      6.1821|
|  8:  2.4937 -  2.3855 0.99   1328  135 0.5318 0.4798      6.1869      6.1556|
|  9:  2.3855 -  2.2940 0.99   1306  151 0.5375 0.5715      6.1208      6.2048|
| 10:  2.2940 -  2.2151 0.98   1300  140 0.5491 0.5333      6.1189      6.1235|
| 11:  2.2151 -  2.1461 0.97   1288  146 0.5516 0.5391      6.0287       6.039|
| 12:  2.1461 -  2.0849 0.99   1295  150 0.5326 0.4721      5.9582      5.9603|
| 13:  2.0849 -  2.0301 0.94   1233  132 0.5243 0.5458      5.8792      5.8556|
| 14:  2.0301 -  1.9807 0.38    493   54 0.5757 0.5024       5.887      5.7033|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0416 -  4.7275  1420   158  0.63  40.08   0.79     0.65      91907.51|
|  2:  4.7275 -  3.7718  1363   153  0.65  39.62   0.86     0.70     124607.72|
|  3:  3.7718 -  3.3008  1353   147  0.56  47.22   0.81     0.67     126599.79|
|  4:  3.3008 -  3.0016  1322   143  0.49  52.77   0.76     0.58     102690.89|
|  5:  3.0016 -  2.7879  1328   150  0.40  59.46   0.72     0.49      83813.31|
|  6:  2.7879 -  2.6245  1315   147  0.39  60.24   0.70     0.45      70800.36|
|  7:  2.6245 -  2.4937  1286   153  0.36  62.62   0.74     0.42      65708.44|
|  8:  2.4937 -  2.3855  1328   135  0.36  63.39   0.71     0.41      59511.11|
|  9:  2.3855 -  2.2940  1306   151  0.32  66.10   0.70     0.38      57269.52|
| 10:  2.2940 -  2.2151  1300   140  0.31  66.49   0.73     0.38      52430.42|
| 11:  2.2151 -  2.1461  1288   146  0.29  67.99   0.72     0.38      49638.52|
| 12:  2.1461 -  2.0849  1295   150  0.29  68.09   0.74     0.38      45582.84|
| 13:  2.0849 -  2.0301  1233   132  0.28  69.05   0.72     0.36      38845.01|
| 14:  2.0301 -  1.9807   493    54  0.28  69.16   0.71     0.30      29423.40|
|alpha:            min =        0.30 max =            0.70 mean =         0.48|
|beta:             min =    29423.40 max =       126599.79 mean =     73945.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.72|
|phase err.(test): min =        0.00 max =           89.98 mean =        58.81|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.272190             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.301   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.482371              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.178   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      688 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1501 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2621 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3867 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5027 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6506 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7682 |
|-----------------------------------------------------------------------------|
|-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 |       54.092 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.905 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.052)------------------------------------------|
|    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 = 12.052)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5048   r_free= 0.4862   ksol= 0.00   Bsol= 0.00   scale= 0.744    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.302092                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4932   r_free= 0.4773   ksol= 0.33   Bsol= 20.00   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.01,12.30,7.53,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.293865                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.972564             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.573   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.406890              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.480   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4932      final r-factor (work) = 0.4252          |
| start r-factor (free) = 0.4773      final r-factor (free) = 0.4347          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.3975 = 15.97 * 0.50 * 6.2990 + 1.00 * 54.0917                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.9505 = 15.97 * 0.50 * 6.2368 + 1.00 * 0.1420                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4252      final r-factor (work) = 0.3839          |
| start r-factor (free) = 0.4347      final r-factor (free) = 0.4284          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7891 = 1.41 * 1.00 * 6.2368 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7081 = 1.41 * 1.00 * 6.1748 + 1.00 * 0.0208                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.052)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.47  15.57    None  None   None       |
|    all(noH): 2823   0      0.00    107.47  15.57    None  None   None       |
|    Sol.    : 438    0      0.00    107.47  26.45    None  None   None       |
|    Mac.    : 2385   0      0.00    65.35   13.57    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 -  10.747: 1261   |   5:    53.735 -  64.482:   30        |
|      1:    10.747 -  21.494:  829   |   6:    64.482 -  75.229:   12        |
|      2:    21.494 -  32.241:  419   |   7:    75.229 -  85.976:    3        |
|      3:    32.241 -  42.988:  192   |   8:    85.976 -  96.723:    2        |
|      4:    42.988 -  53.735:   74   |   9:    96.723 - 107.470:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3839 r_free = 0.4284             target_work(ml) = 6.163         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3833 r_free = 0.4275             target_work(ml) = 6.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3833   r_free= 0.4275   ksol= 0.33   Bsol= 20.00   scale= 1.102   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.01,12.30,7.53,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.162133                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3799   r_free= 0.4211   ksol= 0.30   Bsol= 27.89   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,7.11,3.71,0.00,0.00,0.00); trace/3= 4.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.163566                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.187067              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.222  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514312              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.421  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3799      final r-factor (work) = 0.3252          |
| start r-factor (free) = 0.4211      final r-factor (free) = 0.3882          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3122 = 7.19 * 0.50 * 6.1696 + 1.00 * 0.1415                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.9780 = 7.19 * 0.50 * 6.0915 + 1.00 * 0.0880                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3252      final r-factor (work) = 0.3181          |
| start r-factor (free) = 0.3882      final r-factor (free) = 0.3806          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1544 = 0.51 * 1.00 * 6.0915 + 1.00 * 0.0215                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1277 = 0.51 * 1.00 * 6.0577 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.052)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.98   14.61    None  None   None       |
|    all(noH): 2823   0      0.00    92.98   14.61    None  None   None       |
|    Sol.    : 438    0      0.00    92.98   26.48    None  None   None       |
|    Mac.    : 2385   0      0.00    62.55   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.298: 1185   |   5:    46.492 -  55.790:   32        |
|      1:     9.298 -  18.597:  845   |   6:    55.790 -  65.088:   21        |
|      2:    18.597 -  27.895:  457   |   7:    65.088 -  74.387:    3        |
|      3:    27.895 -  37.193:  196   |   8:    74.387 -  83.685:    1        |
|      4:    37.193 -  46.492:   80   |   9:    83.685 -  92.983:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3181 r_free = 0.3806             target_work(ml) = 6.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3178 r_free = 0.3803             target_work(ml) = 6.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3178   r_free= 0.3803   ksol= 0.30   Bsol= 27.89   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,7.11,3.71,0.00,0.00,0.00); trace/3= 4.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.050568                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3180   r_free= 0.3810   ksol= 0.28   Bsol= 37.35   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,5.20,2.54,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.051610                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.100261              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.679   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.545323              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.082  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3180      final r-factor (work) = 0.2576          |
| start r-factor (free) = 0.3810      final r-factor (free) = 0.3085          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.6244 = 8.10 * 0.50 * 6.0582 + 1.00 * 0.0880                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2480 = 8.10 * 0.50 * 5.9630 + 1.00 * 0.0970                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2576      final r-factor (work) = 0.2341          |
| start r-factor (free) = 0.3085      final r-factor (free) = 0.2901          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2750 = 0.55 * 1.00 * 5.9630 + 1.00 * 0.0232                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1815 = 0.55 * 1.00 * 5.8131 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.052)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.28   14.54    None  None   None       |
|    all(noH): 2823   0      0.00    88.28   14.54    None  None   None       |
|    Sol.    : 438    0      0.00    88.28   32.46    None  None   None       |
|    Mac.    : 2385   0      0.00    70.55   11.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.828: 1255   |   5:    44.138 -  52.966:   77        |
|      1:     8.828 -  17.655:  799   |   6:    52.966 -  61.794:   26        |
|      2:    17.655 -  26.483:  309   |   7:    61.794 -  70.621:   14        |
|      3:    26.483 -  35.311:  198   |   8:    70.621 -  79.449:    0        |
|      4:    35.311 -  44.138:  141   |   9:    79.449 -  88.277:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2341 r_free = 0.2901             target_work(ml) = 5.792         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2339 r_free = 0.2902             target_work(ml) = 5.792         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2339   r_free= 0.2902   ksol= 0.28   Bsol= 37.35   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,5.20,2.54,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.791809                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2332   r_free= 0.2892   ksol= 0.32   Bsol= 54.40   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.55,3.32,2.15,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.790613                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.569496              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.533   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.805580              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.919  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2332      final r-factor (work) = 0.1891          |
| start r-factor (free) = 0.2892      final r-factor (free) = 0.2343          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4723 = 3.57 * 0.50 * 5.8131 + 1.00 * 0.0974                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2424 = 3.57 * 0.50 * 5.7019 + 1.00 * 0.0659                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1891      final r-factor (work) = 0.1740          |
| start r-factor (free) = 0.2343      final r-factor (free) = 0.2207          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6048 = 0.81 * 1.00 * 5.7019 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5043 = 0.81 * 1.00 * 5.5484 + 1.00 * 0.0346                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.052)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.43   15.37    None  None   None       |
|    all(noH): 2823   0      0.00    89.43   15.37    None  None   None       |
|    Sol.    : 438    0      2.60    89.43   39.69    None  None   None       |
|    Mac.    : 2385   0      0.00    87.86   10.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.943: 1332   |   5:    44.713 -  53.656:   99        |
|      1:     8.943 -  17.885:  778   |   6:    53.656 -  62.598:   73        |
|      2:    17.885 -  26.828:  235   |   7:    62.598 -  71.541:   29        |
|      3:    26.828 -  35.770:  140   |   8:    71.541 -  80.483:   19        |
|      4:    35.770 -  44.713:  107   |   9:    80.483 -  89.426:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1740 r_free = 0.2207             target_work(ml) = 5.525         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1738 r_free = 0.2213             target_work(ml) = 5.525         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1738   r_free= 0.2213   ksol= 0.32   Bsol= 54.40   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.55,3.32,2.15,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.524805                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1743   r_free= 0.2215   ksol= 0.33   Bsol= 66.48   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.18,2.32,1.97,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.526714                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.358545              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.401  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.670668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.971   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1743      final r-factor (work) = 0.1399          |
| start r-factor (free) = 0.2215      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1622 = 4.36 * 0.50 * 5.5506 + 1.00 * 0.0659                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9208 = 4.36 * 0.50 * 5.4304 + 1.00 * 0.0865                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1399      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.1879      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6568 = 0.67 * 1.00 * 5.4304 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5717 = 0.67 * 1.00 * 5.3054 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.052)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.23   15.20    None  None   None       |
|    all(noH): 2823   0      0.00    95.23   15.20    None  None   None       |
|    Sol.    : 438    0      2.65    94.13   41.46    None  None   None       |
|    Mac.    : 2385   0      0.00    95.23   10.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.523: 1495   |   5:    47.617 -  57.141:   93        |
|      1:     9.523 -  19.047:  729   |   6:    57.141 -  66.664:   54        |
|      2:    19.047 -  28.570:  175   |   7:    66.664 -  76.187:   36        |
|      3:    28.570 -  38.094:  108   |   8:    76.187 -  85.711:   18        |
|      4:    38.094 -  47.617:  106   |   9:    85.711 -  95.234:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1307 r_free = 0.1792             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1306 r_free = 0.1792             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1306   r_free= 0.1792   ksol= 0.33   Bsol= 66.48   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.18,2.32,1.97,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.277692                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0416 -  4.7275 0.99   1420  158 0.1019 0.1367      5.4148      5.6056|
|  2:  4.7275 -  3.7718 0.99   1363  153 0.0922 0.1123      5.5016       5.683|
|  3:  3.7718 -  3.3008 0.99   1353  147 0.1214 0.1813      5.5893      5.9943|
|  4:  3.3008 -  3.0016 0.99   1322  143 0.1428 0.1824       5.577      5.7476|
|  5:  3.0016 -  2.7879 0.98   1328  150 0.1577 0.1731      5.4644      5.5685|
|  6:  2.7879 -  2.6245 0.99   1315  147 0.1451 0.2388      5.3513       5.623|
|  7:  2.6245 -  2.4937 0.98   1286  153 0.1484 0.1909      5.3096       5.488|
|  8:  2.4937 -  2.3855 0.99   1328  135 0.1411 0.1943      5.2208      5.4362|
|  9:  2.3855 -  2.2940 0.99   1306  151 0.1443 0.2140      5.1621      5.4666|
| 10:  2.2940 -  2.2151 0.98   1300  140 0.1354 0.1968      5.1129      5.3384|
| 11:  2.2151 -  2.1461 0.97   1288  146 0.1382 0.2207      5.0692      5.3799|
| 12:  2.1461 -  2.0849 0.99   1295  150 0.1369 0.1877      5.0085      5.2306|
| 13:  2.0849 -  2.0301 0.94   1233  132 0.1416 0.1974      4.9366      5.1614|
| 14:  2.0301 -  1.9807 0.38    493   54 0.1292 0.1833      4.8221      4.9359|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0416 -  4.7275  1420   158  0.93   9.95   0.97     0.94       7907.14|
|  2:  4.7275 -  3.7718  1363   153  0.94   9.28   1.02     1.01      10617.18|
|  3:  3.7718 -  3.3008  1353   147  0.92  13.30   1.03     1.01      12968.75|
|  4:  3.3008 -  3.0016  1322   143  0.90  16.35   1.02     1.01      13225.22|
|  5:  3.0016 -  2.7879  1328   150  0.87  19.14   1.01     0.99      11168.65|
|  6:  2.7879 -  2.6245  1315   147  0.87  19.28   0.99     0.95       9416.76|
|  7:  2.6245 -  2.4937  1286   153  0.88  18.56   1.00     0.96       8211.44|
|  8:  2.4937 -  2.3855  1328   135  0.88  18.42   1.00     0.97       7269.69|
|  9:  2.3855 -  2.2940  1306   151  0.87  19.00   1.01     0.96       6489.17|
| 10:  2.2940 -  2.2151  1300   140  0.88  18.84   1.00     0.97       6075.69|
| 11:  2.2151 -  2.1461  1288   146  0.87  19.62   1.00     0.96       5840.64|
| 12:  2.1461 -  2.0849  1295   150  0.88  18.78   1.01     0.99       5140.23|
| 13:  2.0849 -  2.0301  1233   132  0.88  19.20   0.99     0.98       4345.67|
| 14:  2.0301 -  1.9807   493    54  0.89  17.62   0.96     0.92       3415.41|
|alpha:            min =        0.92 max =            1.01 mean =         0.98|
|beta:             min =     3415.41 max =        13225.22 mean =      8267.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.83|
|phase err.(test): min =        0.00 max =           89.86 mean =        16.09|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1308   r_free= 0.1798   ksol= 0.33   Bsol= 64.81   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,0.50,0.66,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.279386                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1308   r_free= 0.1798   ksol= 0.33   Bsol= 64.81   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,0.50,0.66,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.279386                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0416 -  4.7275 0.99   1420  158 0.1032 0.1407      5.4316      5.6162|
|  2:  4.7275 -  3.7718 0.99   1363  153 0.0928 0.1116      5.5097       5.683|
|  3:  3.7718 -  3.3008 0.99   1353  147 0.1217 0.1812      5.5917      5.9932|
|  4:  3.3008 -  3.0016 0.99   1322  143 0.1429 0.1835      5.5769      5.7495|
|  5:  3.0016 -  2.7879 0.98   1328  150 0.1578 0.1730      5.4649      5.5669|
|  6:  2.7879 -  2.6245 0.99   1315  147 0.1451 0.2371       5.349      5.6199|
|  7:  2.6245 -  2.4937 0.98   1286  153 0.1485 0.1912      5.3085      5.4877|
|  8:  2.4937 -  2.3855 0.99   1328  135 0.1407 0.1935      5.2196      5.4354|
|  9:  2.3855 -  2.2940 0.99   1306  151 0.1440 0.2140      5.1606      5.4657|
| 10:  2.2940 -  2.2151 0.98   1300  140 0.1351 0.1978      5.1122      5.3421|
| 11:  2.2151 -  2.1461 0.97   1288  146 0.1378 0.2203       5.069      5.3787|
| 12:  2.1461 -  2.0849 0.99   1295  150 0.1371 0.1883      5.0086      5.2322|
| 13:  2.0849 -  2.0301 0.94   1233  132 0.1421 0.1966      4.9372      5.1585|
| 14:  2.0301 -  1.9807 0.38    493   54 0.1291 0.1824      4.8208      4.9344|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0416 -  4.7275  1420   158  0.93  10.21   0.96     0.94       8142.83|
|  2:  4.7275 -  3.7718  1363   153  0.94   9.33   1.02     1.01      10761.93|
|  3:  3.7718 -  3.3008  1353   147  0.92  13.32   1.02     1.01      13028.91|
|  4:  3.3008 -  3.0016  1322   143  0.90  16.33   1.02     1.01      13198.85|
|  5:  3.0016 -  2.7879  1328   150  0.87  19.11   1.01     0.99      11156.16|
|  6:  2.7879 -  2.6245  1315   147  0.87  19.21   0.98     0.94       9369.07|
|  7:  2.6245 -  2.4937  1286   153  0.88  18.52   0.99     0.95       8193.38|
|  8:  2.4937 -  2.3855  1328   135  0.88  18.39   1.00     0.96       7254.73|
|  9:  2.3855 -  2.2940  1306   151  0.87  19.00   1.00     0.96       6492.11|
| 10:  2.2940 -  2.2151  1300   140  0.88  18.83   0.99     0.96       6074.18|
| 11:  2.2151 -  2.1461  1288   146  0.87  19.64   0.99     0.95       5849.75|
| 12:  2.1461 -  2.0849  1295   150  0.88  18.78   1.00     0.98       5141.33|
| 13:  2.0849 -  2.0301  1233   132  0.88  19.16   0.98     0.97       4331.67|
| 14:  2.0301 -  1.9807   493    54  0.89  17.58   0.95     0.91       3390.29|
|alpha:            min =        0.91 max =            1.01 mean =         0.97|
|beta:             min =     3390.29 max =        13198.85 mean =      8292.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.84|
|phase err.(test): min =        0.00 max =           89.60 mean =        16.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.052)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    96.54   16.50    None  None   None       |
|    all(noH): 2823   0      1.30    96.54   16.50    None  None   None       |
|    Sol.    : 438    0      3.96    95.44   42.76    None  None   None       |
|    Mac.    : 2385   0      1.30    96.54   11.68    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:     1.304 -  10.827: 1495   |   5:    48.921 -  58.444:   93        |
|      1:    10.827 -  20.350:  729   |   6:    58.444 -  67.967:   54        |
|      2:    20.350 -  29.874:  175   |   7:    67.967 -  77.491:   36        |
|      3:    29.874 -  39.397:  108   |   8:    77.491 -  87.014:   18        |
|      4:    39.397 -  48.921:  106   |   9:    87.014 -  96.538:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.667 - 5.330
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 338 from: 341
   mapped sites are within: 0.751 - 5.330

peak=    8.422 closest distance to " CB  VAL A 230 " =    1.413
peak=    7.148 closest distance to " O   HOH Z 120 " =    1.442
peak=    6.992 closest distance to " O   HOH Z 400 " =    1.025
peak=    6.628 closest distance to " CG1 ILE A 234 " =    1.400
peak=    6.236 closest distance to " O   GLN A  11 " =    1.030
peak=    5.989 closest distance to " O   HOH Z 210 " =    1.614
peak=    5.604 closest distance to " O   HOH Z 404 " =    1.412
peak=    5.594 closest distance to " CG  LEU A   5 " =    1.302
peak=    5.368 closest distance to " OD1 ASN A 301 " =    1.092
peak=    5.262 closest distance to " NH2 ARG A  56 " =    2.232
peak=    5.158 closest distance to " O   HOH Z 403 " =    2.085
peak=    5.016 closest distance to " O   HOH Z 124 " =    1.503
peak=    4.863 closest distance to " CG1 VAL A 296 " =    1.199
peak=    4.850 closest distance to " O   HOH Z 102 " =    1.560
peak=    4.812 closest distance to " NE2 GLN A  11 " =    1.100
peak=    4.752 closest distance to " O   HOH Z 128 " =    1.821
peak=    4.725 closest distance to " O   HOH Z 422 " =    1.017
peak=    4.718 closest distance to " O   HOH Z 431 " =    1.833
peak=    4.694 closest distance to " CB  VAL A 296 " =    1.382
peak=    4.631 closest distance to " CB  SER A  63 " =    1.231
peak=    4.620 closest distance to " O   HOH Z 209 " =    2.414
peak=    4.610 closest distance to " CA  TYR A  30 " =    0.927
peak=    4.582 closest distance to " O   HOH Z  49 " =    1.454
peak=    4.548 closest distance to " O   HOH Z 248 " =    1.596
peak=    4.545 closest distance to " CD2 LEU A 228 " =    1.264
peak=    4.516 closest distance to " O   HOH Z 146 " =    1.581
peak=    4.511 closest distance to " O   HOH Z 193 " =    1.476
peak=    4.490 closest distance to " CD2 TRP A 179 " =    1.272
peak=    4.485 closest distance to " O   HOH Z 426 " =    1.214
peak=    4.480 closest distance to " CB  ARG A 275 " =    0.917
peak=    4.475 closest distance to " O   HOH Z 247 " =    1.461
peak=    4.442 closest distance to " O   HOH Z 142 " =    2.418
peak=    4.414 closest distance to " CB  GLN A 183 " =    1.238
peak=    4.387 closest distance to " CB  VAL A 230 " =    1.217
peak=    4.386 closest distance to " O   HOH Z 126 " =    1.574
peak=    4.343 closest distance to " O   HOH Z 412 " =    3.322
peak=    4.339 closest distance to " O   HOH Z 425 " =    1.588
peak=    4.339 closest distance to " OE1 GLN A  55 " =    1.540
peak=    4.336 closest distance to " CG  PRO A 280 " =    0.899
peak=    4.316 closest distance to " O   HOH Z 154 " =    1.729
peak=    4.314 closest distance to " O   HOH Z 146 " =    1.688
peak=    4.306 closest distance to " O   HOH Z  40 " =    2.090
peak=    4.301 closest distance to " O   HOH Z  80 " =    2.325
peak=    4.281 closest distance to " CE1 HIS A 108 " =    1.131
peak=    4.271 closest distance to " N   SER A 164 " =    0.971
peak=    4.270 closest distance to " O   HOH Z 130 " =    2.642
peak=    4.265 closest distance to " CG  LEU A 228 " =    1.248
peak=    4.251 closest distance to " CB  ASN A 285 " =    0.955
peak=    4.228 closest distance to " CE  LYS A 119 " =    1.381
peak=    4.228 closest distance to " CB  TRP A 179 " =    1.319
peak=    4.203 closest distance to " NH2 ARG A 156 " =    1.189
peak=    4.200 closest distance to " O   HOH Z 134 " =    2.428
peak=    4.189 closest distance to " O   HOH Z  44 " =    2.045
peak=    4.172 closest distance to " O   HOH Z 389 " =    2.152
peak=    4.167 closest distance to " O   HOH Z 234 " =    3.520
peak=    4.160 closest distance to " O   HOH Z 265 " =    1.966
peak=    4.127 closest distance to " CA  ARG A 195 " =    1.184
peak=    4.124 closest distance to " CD  LYS A 166 " =    1.645
peak=    4.114 closest distance to " CD  ARG A  36 " =    1.114
peak=    4.070 closest distance to " O   HOH Z 126 " =    2.429
peak=    4.063 closest distance to " O   HOH Z  54 " =    1.313
peak=    4.063 closest distance to " O   ALA A 165 " =    1.241
peak=    4.050 closest distance to " O   HOH Z  43 " =    1.724
peak=    4.033 closest distance to " O   HOH Z 433 " =    2.003
peak=    4.009 closest distance to " O   ASP A 200 " =    1.625
peak=    4.000 closest distance to " CA  SER A  12 " =    1.398
peak=    3.998 closest distance to " CB  GLU A 175 " =    1.358
peak=    3.965 closest distance to " OE1 GLN A  11 " =    2.102
peak=    3.955 closest distance to " CG  PRO A  54 " =    1.201
peak=    3.954 closest distance to " N   ASN A  39 " =    1.331
peak=    3.950 closest distance to " CD  ARG A  36 " =    1.163
peak=    3.947 closest distance to " CD  GLN A  73 " =    1.137
peak=    3.936 closest distance to " OE1 GLU A   2 " =    1.430
peak=    3.932 closest distance to " O   HOH Z 394 " =    1.800
peak=    3.927 closest distance to " O   HOH Z 414 " =    2.239
peak=    3.924 closest distance to " CA  VAL A  41 " =    0.924
peak=    3.912 closest distance to " NH1AARG A 145 " =    1.135
peak=    3.912 closest distance to " O   HOH Z  85 " =    1.382
peak=    3.911 closest distance to " O   HOH Z 369 " =    1.590
peak=    3.899 closest distance to " O   HOH Z 142 " =    1.521
peak=    3.896 closest distance to " O   HOH Z 357 " =    2.151
peak=    3.893 closest distance to " CB  ASN A 187 " =    1.229
peak=    3.890 closest distance to " O   HOH Z 144 " =    2.029
peak=    3.886 closest distance to " CG1 ILE A  33 " =    1.234
peak=    3.883 closest distance to " CG  GLN A  77 " =    0.801
peak=    3.883 closest distance to " O   HOH Z   7 " =    1.010
peak=    3.874 closest distance to " CG  PRO A 213 " =    1.293
peak=    3.853 closest distance to " O   HOH Z 418 " =    1.657
peak=    3.845 closest distance to " O   HOH Z 327 " =    1.659
peak=    3.841 closest distance to " CG  PRO A 243 " =    1.193
peak=    3.840 closest distance to " O   HOH Z 370 " =    1.113
peak=    3.840 closest distance to " CB  ALA A 299 " =    1.198
peak=    3.832 closest distance to " CB  PRO A  54 " =    0.888
peak=    3.831 closest distance to " N   ALA A   1 " =    1.311
peak=    3.827 closest distance to " O   HOH Z 402 " =    1.546
peak=    3.824 closest distance to " NZ  LYS A  76 " =    1.088
peak=    3.819 closest distance to " NH1 ARG A  36 " =    1.253
peak=    3.819 closest distance to " O   SER A  87 " =    2.235
peak=    3.815 closest distance to " O   HOH Z 183 " =    1.819
peak=    3.810 closest distance to " O   HOH Z 236 " =    1.533
peak=    3.808 closest distance to " O   GLY A  23 " =    2.433
peak=    3.794 closest distance to " O   ASP A 124 " =    1.610
peak=    3.789 closest distance to " O   HOH Z 435 " =    1.858
peak=    3.787 closest distance to " CG  ARG A  66 " =    1.010
peak=    3.787 closest distance to " OG  SER A  62 " =    2.838
peak=    3.782 closest distance to " CB  GLN A 223 " =    1.483
peak=    3.773 closest distance to " O   HOH Z  48 " =    1.740
peak=    3.772 closest distance to " CB BVAL A  41 " =    1.107
peak=    3.770 closest distance to " O   HOH Z 427 " =    2.875
peak=    3.738 closest distance to " O   HOH Z 401 " =    1.162
peak=    3.734 closest distance to " O   HOH Z 227 " =    1.678
peak=    3.732 closest distance to " CB  SER A  62 " =    0.931
peak=    3.721 closest distance to " NE2 HIS A 115 " =    1.124
peak=    3.716 closest distance to " CG AARG A 275 " =    1.166
peak=    3.712 closest distance to " CA  ARG A  66 " =    0.962
peak=    3.706 closest distance to " O   HOH Z  46 " =    1.242
peak=    3.692 closest distance to " OG  SER A 245 " =    1.454
peak=    3.687 closest distance to " NE  ARG A  14 " =    1.221
peak=    3.676 closest distance to " CA  ALA A  51 " =    1.073
peak=    3.674 closest distance to " NE1 TRP A  92 " =    1.407
peak=    3.662 closest distance to " O   HOH Z  59 " =    1.935
peak=    3.649 closest distance to " O   HOH Z 291 " =    1.469
peak=    3.647 closest distance to " CG2AVAL A  72 " =    1.870
peak=    3.644 closest distance to " O   HOH Z 116 " =    1.168
peak=    3.641 closest distance to " OD2 ASP A 298 " =    0.848
peak=    3.629 closest distance to " CZ  PHE A 218 " =    1.281
peak=    3.623 closest distance to " CB  THR A  31 " =    1.387
peak=    3.619 closest distance to " O   HOH Z  15 " =    2.447
peak=    3.618 closest distance to " OG BSER A 210 " =    1.012
peak=    3.618 closest distance to " O   PRO A 198 " =    1.507
peak=    3.617 closest distance to " CG2 ILE A 234 " =    1.169
peak=    3.617 closest distance to " CG2 ILE A  20 " =    1.452
peak=    3.613 closest distance to " O   HOH Z  88 " =    3.637
peak=    3.610 closest distance to " O   HOH Z 301 " =    1.861
peak=    3.605 closest distance to " O   HOH Z 232 " =    2.321
peak=    3.605 closest distance to " CB  ARG A 275 " =    1.195
peak=    3.598 closest distance to " O   HOH Z 280 " =    3.076
peak=    3.594 closest distance to " O   HOH Z 408 " =    1.891
peak=    3.591 closest distance to " O   HOH Z 155 " =    2.804
peak=    3.584 closest distance to " CB  VAL A 202 " =    1.363
peak=    3.577 closest distance to " CB  ASN A 148 " =    1.282
peak=    3.573 closest distance to " NE2 GLN A 194 " =    1.613
peak=    3.556 closest distance to " CA  TRP A  85 " =    1.172
peak=    3.556 closest distance to " O   HOH Z 273 " =    2.999
peak=    3.553 closest distance to " O   HOH Z  78 " =    1.648
peak=    3.552 closest distance to " O   ARG A  14 " =    1.591
peak=    3.549 closest distance to " O   HOH Z 162 " =    2.447
peak=    3.549 closest distance to " O   HOH Z 156 " =    3.347
peak=    3.542 closest distance to " O   HOH Z  68 " =    2.062
peak=    3.540 closest distance to " O   HOH Z 344 " =    2.982
peak=    3.539 closest distance to " O   HOH Z 417 " =    3.083
peak=    3.539 closest distance to " CB  ALA A 100 " =    1.295
peak=    3.525 closest distance to " CB  LEU A 261 " =    1.100
peak=    3.514 closest distance to " CB  GLU A 152 " =    1.085
peak=    3.510 closest distance to " O   HOH Z 289 " =    1.643
peak=    3.504 closest distance to " NZ  LYS A  48 " =    1.289
peak=    3.502 closest distance to " O   HOH Z 245 " =    1.341
peak=    3.501 closest distance to " O   HOH Z 299 " =    4.126
peak=    3.500 closest distance to " CG2 VAL A 197 " =    1.272
peak=    3.500 closest distance to " CD2 LEU A 297 " =    1.014
peak=    3.498 closest distance to " CG2 ILE A  33 " =    1.283
peak=    3.492 closest distance to " O   HOH Z 279 " =    1.207
peak=    3.488 closest distance to " CA  ALA A 100 " =    1.149
peak=    3.487 closest distance to " O   HOH Z 383 " =    2.213
peak=    3.481 closest distance to " CB  ARG A 190 " =    1.890
peak=    3.480 closest distance to " CB  SER A 141 " =    1.012
peak=    3.480 closest distance to " O   GLU A   2 " =    1.498
peak=    3.478 closest distance to " OG  SER A  97 " =    3.026
peak=    3.477 closest distance to " CB  VAL A 265 " =    1.353
peak=    3.472 closest distance to " CB  MET A  40 " =    0.818
peak=    3.470 closest distance to " O   HOH Z 130 " =    1.094
peak=    3.467 closest distance to " CB  TRP A 150 " =    1.489
peak=    3.461 closest distance to " O   HOH Z 132 " =    2.650
peak=    3.455 closest distance to " CB  SER A  26 " =    1.679
peak=    3.454 closest distance to " O   HOH Z 423 " =    1.851
peak=    3.448 closest distance to " NE  ARG A 138 " =    1.184
peak=    3.445 closest distance to " O   HOH Z 109 " =    1.602
peak=    3.442 closest distance to " CA  ASN A 127 " =    1.135
peak=    3.439 closest distance to " CB  GLU A 128 " =    1.355
peak=    3.439 closest distance to " O   HOH Z 150 " =    2.065
peak=    3.435 closest distance to " CD  PRO A  54 " =    1.002
peak=    3.433 closest distance to " O   HOH Z  53 " =    1.222
peak=    3.427 closest distance to " O   HOH Z 368 " =    3.119
peak=    3.426 closest distance to " CG2 THR A 220 " =    0.789
peak=    3.421 closest distance to " O   HOH Z 196 " =    1.313
peak=    3.420 closest distance to " OE1 GLN A 223 " =    2.199
peak=    3.415 closest distance to " CG1BVAL A 121 " =    1.448
peak=    3.414 closest distance to " O  BHOH Z 338 " =    2.289
peak=    3.410 closest distance to " O   HOH Z  61 " =    1.474
peak=    3.408 closest distance to " CG2 THR A 221 " =    1.322
peak=    3.407 closest distance to " O   HOH Z 137 " =    2.365
peak=    3.402 closest distance to " O   HOH Z 139 " =    1.086
peak=    3.400 closest distance to " O   HOH Z 263 " =    1.364
peak=    3.399 closest distance to " N   TYR A 247 " =    1.373
peak=    3.392 closest distance to " O   HOH Z 214 " =    1.324
peak=    3.392 closest distance to " CB  TYR A  30 " =    1.003
peak=    3.391 closest distance to " CA  THR A 294 " =    1.978
peak=    3.386 closest distance to " CB  THR A 235 " =    1.258
peak=    3.385 closest distance to " O   HOH Z  95 " =    1.626
peak=    3.379 closest distance to " CB  ARG A  79 " =    0.891
peak=    3.372 closest distance to " CG2 VAL A 112 " =    1.643
peak=    3.363 closest distance to " CZ3 TRP A  85 " =    0.924
peak=    3.363 closest distance to " NH2 ARG A  36 " =    1.799
peak=    3.360 closest distance to " N   GLU A  44 " =    1.322
peak=    3.360 closest distance to " O   HOH Z 395 " =    1.359
peak=    3.359 closest distance to " O   HOH Z 393 " =    3.520
peak=    3.357 closest distance to " CB  GLU A 277 " =    0.920
peak=    3.352 closest distance to " CD1 LEU A 101 " =    1.275
peak=    3.344 closest distance to " O   PRO A  90 " =    1.462
peak=    3.343 closest distance to " O   HOH Z 215 " =    1.493
peak=    3.342 closest distance to " CG1 ILE A 120 " =    1.141
peak=    3.341 closest distance to " CE1 TYR A 186 " =    1.419
peak=    3.337 closest distance to " O   HOH Z   4 " =    1.525
peak=    3.333 closest distance to " CD1 LEU A 228 " =    1.693
peak=    3.332 closest distance to " CB  GLN A  58 " =    1.179
peak=    3.329 closest distance to " O   HOH Z 277 " =    2.628
peak=    3.329 closest distance to " O   HOH Z  35 " =    1.779
peak=    3.326 closest distance to " ND2 ASN A 301 " =    0.862
peak=    3.325 closest distance to " O   HOH Z 373 " =    1.664
peak=    3.325 closest distance to " OG  SER A  62 " =    3.208
peak=    3.324 closest distance to " O   HOH Z  97 " =    1.903
peak=    3.323 closest distance to " NH1 ARG A  14 " =    1.194
peak=    3.323 closest distance to " N   ASP A 298 " =    1.058
peak=    3.319 closest distance to " C   ALA A 299 " =    0.964
peak=    3.318 closest distance to " CB  ALA A 242 " =    1.052
peak=    3.317 closest distance to " O   HOH Z 298 " =    5.330
peak=    3.315 closest distance to " CB  ALA A  71 " =    1.309
peak=    3.314 closest distance to " O   HOH Z 421 " =    1.865
peak=    3.314 closest distance to " CD  ARG A  24 " =    1.205
peak=    3.311 closest distance to " ND1 HIS A  81 " =    1.465
peak=    3.310 closest distance to " CB  MET A 105 " =    1.205
peak=    3.305 closest distance to " CA  CYS A 260 " =    1.469
peak=    3.303 closest distance to " CB  GLN A  88 " =    1.265
peak=    3.302 closest distance to " OD1 ASN A 217 " =    1.611
peak=    3.299 closest distance to " CD  ARG A 159 " =    0.835
peak=    3.294 closest distance to " NH2BARG A 190 " =    1.785
peak=    3.285 closest distance to " CD1 LEU A 222 " =    0.783
peak=    3.285 closest distance to " CG  MET A  40 " =    2.390
peak=    3.283 closest distance to " CB  TRP A 266 " =    1.090
peak=    3.282 closest distance to " O   HOH Z 217 " =    2.759
peak=    3.278 closest distance to " CA  ASN A 217 " =    1.221
peak=    3.277 closest distance to " O   HOH Z 419 " =    2.313
peak=    3.275 closest distance to " O   HOH Z 361 " =    2.677
peak=    3.270 closest distance to " CA  ASP A 149 " =    1.228
peak=    3.270 closest distance to " O   HOH Z  48 " =    2.795
peak=    3.270 closest distance to " C   VAL A 265 " =    1.106
peak=    3.265 closest distance to " O   HOH Z 136 " =    1.204
peak=    3.264 closest distance to " CB  TRP A 179 " =    1.802
peak=    3.263 closest distance to " CA  ALA A 248 " =    1.197
peak=    3.258 closest distance to " O   HOH Z 339 " =    1.440
peak=    3.250 closest distance to " CG  PRO A 198 " =    1.184
peak=    3.250 closest distance to " O   HOH Z  85 " =    1.604
peak=    3.249 closest distance to " O   HOH Z 132 " =    2.395
peak=    3.247 closest distance to " CA  TYR A 116 " =    1.524
peak=    3.241 closest distance to " O   HOH Z 409 " =    3.569
peak=    3.241 closest distance to " O   HOH Z 422 " =    2.758
peak=    3.241 closest distance to " CG2 VAL A 126 " =    1.029
peak=    3.235 closest distance to " CA  ASP A 191 " =    0.948
peak=    3.233 closest distance to " N   ASP A 162 " =    1.198
peak=    3.233 closest distance to " CA  GLN A  11 " =    1.094
peak=    3.229 closest distance to " CA  THR A 246 " =    0.980
peak=    3.229 closest distance to " C   TYR A 214 " =    1.579
peak=    3.227 closest distance to " O   HOH Z  80 " =    3.198
peak=    3.227 closest distance to " O   HOH Z 155 " =    1.483
peak=    3.226 closest distance to " O   HOH Z 424 " =    2.866
peak=    3.222 closest distance to " CB  ASN A  45 " =    1.107
peak=    3.222 closest distance to " CA  ARG A 139 " =    1.463
peak=    3.222 closest distance to " O   HOH Z 388 " =    1.101
peak=    3.221 closest distance to " CA  ASP A 140 " =    1.273
peak=    3.219 closest distance to " O   HOH Z 366 " =    2.370
peak=    3.217 closest distance to " O   HOH Z 272 " =    2.052
peak=    3.216 closest distance to " CB  ASN A 142 " =    1.282
peak=    3.213 closest distance to " OG ASER A 134 " =    2.878
peak=    3.212 closest distance to " O   HOH Z 131 " =    2.572
peak=    3.212 closest distance to " NE  ARG A  24 " =    1.028
peak=    3.210 closest distance to " O   HOH Z 394 " =    3.907
peak=    3.209 closest distance to " CD  ARG A 195 " =    1.143
peak=    3.206 closest distance to " OH  TYR A 293 " =    0.900
peak=    3.206 closest distance to " O   HOH Z 152 " =    2.096
peak=    3.205 closest distance to " N   VAL A 125 " =    1.407
peak=    3.191 closest distance to " CA  ALA A 295 " =    1.079
peak=    3.191 closest distance to " O   HOH Z 359 " =    1.414
peak=    3.189 closest distance to " NZ  LYS A 117 " =    2.710
peak=    3.185 closest distance to " O   HOH Z  39 " =    1.548
peak=    3.183 closest distance to " OG BSER A 164 " =    2.018
peak=    3.183 closest distance to " CA  ILE A 106 " =    0.751
peak=    3.181 closest distance to " CD  LYS A 119 " =    2.042
peak=    3.179 closest distance to " CE AMET A  47 " =    1.064
peak=    3.178 closest distance to " O   HOH Z 438 " =    1.915
peak=    3.177 closest distance to " CB  PHE A  16 " =    1.179
peak=    3.177 closest distance to " CB  LEU A 237 " =    0.872
peak=    3.176 closest distance to " N   ALA A 256 " =    1.150
peak=    3.175 closest distance to " O   HOH Z 109 " =    2.844
peak=    3.174 closest distance to " O   HOH Z  95 " =    1.522
peak=    3.165 closest distance to " O   HOH Z  32 " =    1.539
peak=    3.164 closest distance to " CZ3 TRP A  92 " =    1.111
peak=    3.157 closest distance to " CG1 VAL A 153 " =    1.031
peak=    3.156 closest distance to " O   HOH Z 316 " =    2.880
peak=    3.153 closest distance to " O   HOH Z 365 " =    2.257
peak=    3.151 closest distance to " CB  ALA A 248 " =    1.349
peak=    3.145 closest distance to " CE1 TYR A  30 " =    0.996
peak=    3.140 closest distance to " O   HOH Z 326 " =    1.616
peak=    3.139 closest distance to " C   ILE A 106 " =    1.720
peak=    3.136 closest distance to " O   HOH Z  57 " =    2.009
peak=    3.134 closest distance to " O   HOH Z 313 " =    1.675
peak=    3.134 closest distance to " CD1 TRP A 274 " =    1.131
peak=    3.131 closest distance to " ND1 HIS A  81 " =    1.289
peak=    3.130 closest distance to " N   CYS A 260 " =    1.235
peak=    3.130 closest distance to " O   HOH Z  48 " =    2.422
peak=    3.129 closest distance to " CB  SER A 210 " =    1.166
peak=    3.128 closest distance to " O   HOH Z  83 " =    1.620
peak=    3.127 closest distance to " O   HOH Z 433 " =    3.549
peak=    3.124 closest distance to " O   HOH Z 345 " =    2.765
peak=    3.122 closest distance to " O   ASN A 284 " =    1.882
peak=    3.122 closest distance to " CE1 PHE A 208 " =    1.100
peak=    3.122 closest distance to " O   HOH Z 193 " =    1.874
peak=    3.122 closest distance to " O   HOH Z 280 " =    3.700
peak=    3.121 closest distance to " O   HOH Z 173 " =    2.494
peak=    3.118 closest distance to " CD ALYS A 290 " =    1.053
peak=    3.116 closest distance to " OH  TYR A 116 " =    1.347
peak=    3.112 closest distance to " O   HOH Z 271 " =    1.832
peak=    3.110 closest distance to " O   HOH Z 152 " =    1.770
peak=    3.109 closest distance to " N   ASP A 162 " =    2.240
peak=    3.108 closest distance to " CB  ARG A  79 " =    0.910
peak=    3.107 closest distance to " O   HOH Z 250 " =    1.430
peak=    3.105 closest distance to " CG2 THR A  29 " =    1.495
peak=    3.104 closest distance to " O   HOH Z 116 " =    2.972
peak=    3.104 closest distance to " O   HOH Z 214 " =    2.422
peak=    3.096 closest distance to " O   HOH Z 141 " =    1.656
peak=    3.091 closest distance to " O   HOH Z 257 " =    2.350
peak=    3.090 closest distance to " N   TYR A  15 " =    0.850
peak=    3.087 closest distance to " O   HOH Z 358 " =    1.243
peak=    3.086 closest distance to " CZ  PHE A  38 " =    1.197
peak=    3.082 closest distance to " O   HOH Z 162 " =    2.160
peak=    3.079 closest distance to " CA  TYR A 214 " =    1.278
peak=    3.077 closest distance to " CB  LYS A 289 " =    1.168
peak=    3.057 closest distance to " O   HOH Z 415 " =    1.155
peak=    3.044 closest distance to " O   HOH Z  63 " =    2.570

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.513 - 5.466
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 223
   mapped sites are within: 0.780 - 5.466

peak=   -5.318 closest distance to " CG2 VAL A 230 " =    0.894
peak=   -4.830 closest distance to " O   HOH Z 400 " =    0.877
peak=   -4.659 closest distance to " NH2 ARG A  36 " =    1.114
peak=   -4.578 closest distance to " CD  ARG A  14 " =    3.146
peak=   -4.578 closest distance to " CA  SER A 276 " =    1.459
peak=   -4.512 closest distance to " CG  PRO A 243 " =    1.761
peak=   -4.496 closest distance to " OD1 ASN A 301 " =    0.783
peak=   -4.435 closest distance to " CD  GLN A  58 " =    1.063
peak=   -4.386 closest distance to " CG2BVAL A  41 " =    2.696
peak=   -4.329 closest distance to " O   GLN A  11 " =    1.031
peak=   -4.318 closest distance to " CG2 ILE A  49 " =    2.637
peak=   -4.312 closest distance to " CD1 PHE A  59 " =    1.910
peak=   -4.253 closest distance to " O   HOH Z  13 " =    1.717
peak=   -4.250 closest distance to " O   HOH Z 411 " =    5.359
peak=   -4.206 closest distance to " CA  ASP A 298 " =    1.104
peak=   -4.144 closest distance to " CD  GLN A 223 " =    1.571
peak=   -4.066 closest distance to " O   HOH Z 384 " =    1.824
peak=   -4.061 closest distance to " CG1 VAL A 112 " =    2.480
peak=   -3.974 closest distance to " CG1 VAL A 296 " =    1.002
peak=   -3.944 closest distance to " O   HOH Z 196 " =    1.893
peak=   -3.937 closest distance to " O   PRO A 198 " =    1.277
peak=   -3.930 closest distance to " O   HOH Z 151 " =    0.994
peak=   -3.926 closest distance to " O   HOH Z 166 " =    1.670
peak=   -3.889 closest distance to " CB  ALA A 248 " =    2.288
peak=   -3.864 closest distance to " ND2 ASN A  39 " =    1.166
peak=   -3.858 closest distance to " CD2 LEU A 237 " =    2.459
peak=   -3.851 closest distance to " O   HOH Z 250 " =    1.656
peak=   -3.844 closest distance to " OXT GLY A 302 " =    2.952
peak=   -3.842 closest distance to " OG  SER A  97 " =    2.368
peak=   -3.806 closest distance to " CB  ALA A 161 " =    2.579
peak=   -3.793 closest distance to " ND2 ASN A  60 " =    1.409
peak=   -3.787 closest distance to " CG2 THR A 182 " =    2.249
peak=   -3.766 closest distance to " CB  LEU A 167 " =    2.147
peak=   -3.765 closest distance to " N   ALA A 226 " =    2.088
peak=   -3.765 closest distance to " O   HOH Z 109 " =    3.338
peak=   -3.762 closest distance to " O   HOH Z   7 " =    1.227
peak=   -3.754 closest distance to " OD1 ASN A 148 " =    1.405
peak=   -3.753 closest distance to " O   HOH Z 401 " =    1.358
peak=   -3.740 closest distance to " C   VAL A 265 " =    1.046
peak=   -3.739 closest distance to " O   HOH Z 109 " =    3.479
peak=   -3.727 closest distance to " O   HOH Z 174 " =    1.562
peak=   -3.712 closest distance to " CA  GLY A 203 " =    2.270
peak=   -3.694 closest distance to " O   HOH Z 252 " =    1.214
peak=   -3.684 closest distance to " OD1 ASP A 298 " =    2.187
peak=   -3.677 closest distance to " CG  GLN A 103 " =    2.346
peak=   -3.676 closest distance to " N   ALA A   1 " =    2.624
peak=   -3.668 closest distance to " O   HOH Z 119 " =    1.868
peak=   -3.658 closest distance to " C   ASN A 285 " =    2.349
peak=   -3.631 closest distance to " O   HOH Z  60 " =    1.971
peak=   -3.625 closest distance to " OG BSER A 134 " =    1.508
peak=   -3.622 closest distance to " O   HOH Z 221 " =    1.178
peak=   -3.613 closest distance to " O   HOH Z 110 " =    1.400
peak=   -3.613 closest distance to " O   HOH Z 234 " =    3.917
peak=   -3.597 closest distance to " O   HOH Z 285 " =    1.277
peak=   -3.587 closest distance to " O   HOH Z  37 " =    1.328
peak=   -3.585 closest distance to " OD2 ASP A 298 " =    0.913
peak=   -3.579 closest distance to " O   ALA A  34 " =    2.364
peak=   -3.576 closest distance to " OG BSER A 210 " =    1.139
peak=   -3.575 closest distance to " O   HOH Z 407 " =    1.557
peak=   -3.572 closest distance to " O   HOH Z 227 " =    0.853
peak=   -3.562 closest distance to " C   GLY A 133 " =    1.194
peak=   -3.553 closest distance to " O   HOH Z   6 " =    2.260
peak=   -3.550 closest distance to " O   HOH Z  35 " =    1.004
peak=   -3.548 closest distance to " C   THR A 279 " =    1.145
peak=   -3.529 closest distance to " O   HOH Z 426 " =    1.951
peak=   -3.526 closest distance to " CA  VAL A 197 " =    0.943
peak=   -3.520 closest distance to " O   HOH Z 196 " =    2.484
peak=   -3.508 closest distance to " O   HOH Z 124 " =    1.381
peak=   -3.502 closest distance to " O   HOH Z 423 " =    2.536
peak=   -3.497 closest distance to " CE3 TRP A  70 " =    1.680
peak=   -3.495 closest distance to " O   HOH Z 422 " =    1.365
peak=   -3.494 closest distance to " O   HOH Z   5 " =    1.754
peak=   -3.486 closest distance to " O   HOH Z 290 " =    1.030
peak=   -3.485 closest distance to " O   HOH Z 131 " =    4.296
peak=   -3.473 closest distance to " O   ASP A 200 " =    1.120
peak=   -3.473 closest distance to " O   HOH Z 418 " =    1.470
peak=   -3.466 closest distance to " CB  HIS A  86 " =    2.569
peak=   -3.465 closest distance to " O   HOH Z 171 " =    2.421
peak=   -3.462 closest distance to " CB  ALA A 100 " =    1.710
peak=   -3.461 closest distance to " O   HOH Z 120 " =    0.814
peak=   -3.452 closest distance to " CG1 VAL A 197 " =    2.375
peak=   -3.451 closest distance to " O   HOH Z 362 " =    4.347
peak=   -3.450 closest distance to " O   SER A 273 " =    1.044
peak=   -3.445 closest distance to " O   HOH Z  52 " =    2.053
peak=   -3.441 closest distance to " CG2 ILE A  20 " =    2.796
peak=   -3.441 closest distance to " NE  ARG A 156 " =    2.037
peak=   -3.436 closest distance to " O   HOH Z  30 " =    1.775
peak=   -3.433 closest distance to " O   HOH Z  29 " =    1.434
peak=   -3.433 closest distance to " O   HOH Z 265 " =    1.416
peak=   -3.431 closest distance to " O   HOH Z 388 " =    1.858
peak=   -3.425 closest distance to " CD2 PHE A  59 " =    2.375
peak=   -3.424 closest distance to " CD  ARG A  36 " =    0.985
peak=   -3.422 closest distance to " CG2 THR A 279 " =    1.774
peak=   -3.413 closest distance to " O   HOH Z  92 " =    1.396
peak=   -3.412 closest distance to " O   LEU A 300 " =    2.460
peak=   -3.404 closest distance to " OG  SER A  87 " =    1.780
peak=   -3.403 closest distance to " O   HOH Z 120 " =    1.537
peak=   -3.397 closest distance to " SG BCYS A 201 " =    0.888
peak=   -3.395 closest distance to " O   ASP A 298 " =    1.635
peak=   -3.394 closest distance to " C   HIS A 108 " =    1.207
peak=   -3.394 closest distance to " CA  SER A 164 " =    2.160
peak=   -3.390 closest distance to " CD2 HIS A 115 " =    1.128
peak=   -3.383 closest distance to " O   HOH Z 231 " =    2.036
peak=   -3.378 closest distance to " O   HOH Z 425 " =    1.016
peak=   -3.373 closest distance to " CG  MET A 105 " =    0.914
peak=   -3.371 closest distance to " O   HOH Z 176 " =    1.782
peak=   -3.365 closest distance to " C   THR A 264 " =    1.379
peak=   -3.364 closest distance to " ND2 ASN A 249 " =    1.973
peak=   -3.364 closest distance to " O   HOH Z 351 " =    1.811
peak=   -3.361 closest distance to " CG  ARG A 269 " =    2.408
peak=   -3.360 closest distance to " CG2 VAL A 189 " =    2.012
peak=   -3.352 closest distance to " O   SER A  95 " =    1.815
peak=   -3.352 closest distance to " O   HOH Z 411 " =    1.748
peak=   -3.351 closest distance to " CG  PRO A 163 " =    2.148
peak=   -3.350 closest distance to " O   HOH Z 151 " =    1.361
peak=   -3.345 closest distance to " O   HOH Z 378 " =    1.677
peak=   -3.336 closest distance to " O   HOH Z 435 " =    1.475
peak=   -3.334 closest distance to " CD  LYS A 289 " =    2.387
peak=   -3.328 closest distance to " CB  SER A 210 " =    1.269
peak=   -3.325 closest distance to " O   GLY A 241 " =    2.362
peak=   -3.325 closest distance to " O   HOH Z 424 " =    2.955
peak=   -3.321 closest distance to " OE2 GLU A 128 " =    1.784
peak=   -3.318 closest distance to " O   HOH Z 369 " =    2.435
peak=   -3.316 closest distance to " O   HOH Z  15 " =    1.502
peak=   -3.316 closest distance to " O   HOH Z  71 " =    2.164
peak=   -3.316 closest distance to " O   HOH Z 368 " =    1.971
peak=   -3.312 closest distance to " CD2 TYR A  30 " =    2.650
peak=   -3.307 closest distance to " CD2 LEU A 237 " =    2.635
peak=   -3.304 closest distance to " CE3 TRP A 150 " =    2.303
peak=   -3.290 closest distance to " CA  ASN A 127 " =    1.010
peak=   -3.277 closest distance to " N   ALA A  43 " =    2.832
peak=   -3.275 closest distance to " O   HOH Z  19 " =    2.270
peak=   -3.271 closest distance to " O   HOH Z 275 " =    1.792
peak=   -3.270 closest distance to " O   HOH Z 394 " =    5.466
peak=   -3.269 closest distance to " O   HOH Z 200 " =    1.374
peak=   -3.269 closest distance to " C   GLN A 144 " =    0.967
peak=   -3.269 closest distance to " OE2 GLU A 152 " =    1.615
peak=   -3.263 closest distance to " CB  MET A 188 " =    1.700
peak=   -3.261 closest distance to " OD1 ASN A 301 " =    1.926
peak=   -3.260 closest distance to " CD1 TYR A 247 " =    2.367
peak=   -3.259 closest distance to " CB  ALA A  43 " =    2.746
peak=   -3.256 closest distance to " O   HOH Z 236 " =    1.154
peak=   -3.255 closest distance to " O   SER A 271 " =    2.228
peak=   -3.254 closest distance to " O   HOH Z  65 " =    1.278
peak=   -3.254 closest distance to " O   HOH Z 353 " =    1.558
peak=   -3.248 closest distance to " CD1 LEU A  25 " =    2.599
peak=   -3.246 closest distance to " CD1 ILE A 106 " =    2.125
peak=   -3.245 closest distance to " O   HOH Z  39 " =    2.084
peak=   -3.243 closest distance to " NH2 ARG A  66 " =    1.510
peak=   -3.241 closest distance to " O   HOH Z 205 " =    0.928
peak=   -3.233 closest distance to " O   HOH Z 137 " =    1.299
peak=   -3.231 closest distance to " OE2 GLU A 277 " =    2.794
peak=   -3.229 closest distance to " O   TYR A  15 " =    1.815
peak=   -3.225 closest distance to " O   HOH Z 244 " =    1.892
peak=   -3.220 closest distance to " CG  LEU A  83 " =    2.068
peak=   -3.219 closest distance to " CG1 ILE A 263 " =    2.208
peak=   -3.213 closest distance to " N   THR A 235 " =    1.310
peak=   -3.209 closest distance to " O   HOH Z 126 " =    1.841
peak=   -3.207 closest distance to " O   HOH Z 208 " =    1.755
peak=   -3.207 closest distance to " CD1 TRP A 179 " =    1.276
peak=   -3.205 closest distance to " CG  LEU A   5 " =    1.253
peak=   -3.205 closest distance to " O   PHE A  59 " =    2.268
peak=   -3.203 closest distance to " NE2 GLN A 278 " =    1.871
peak=   -3.196 closest distance to " OH  TYR A 169 " =    0.872
peak=   -3.191 closest distance to " CZ  TYR A 169 " =    1.640
peak=   -3.191 closest distance to " O   HOH Z 198 " =    1.262
peak=   -3.191 closest distance to " CD1 ILE A 109 " =    2.211
peak=   -3.191 closest distance to " O   HOH Z  38 " =    1.441
peak=   -3.189 closest distance to " O   HOH Z 166 " =    1.233
peak=   -3.186 closest distance to " O   HOH Z 135 " =    2.131
peak=   -3.185 closest distance to " CG  ASP A 231 " =    0.835
peak=   -3.175 closest distance to " N   ALA A 295 " =    0.955
peak=   -3.172 closest distance to " O   HOH Z 392 " =    1.527
peak=   -3.171 closest distance to " N   SER A   3 " =    2.556
peak=   -3.168 closest distance to " O   VAL A 125 " =    2.242
peak=   -3.164 closest distance to " CZ  TYR A 172 " =    1.900
peak=   -3.164 closest distance to " O   HOH Z 103 " =    1.984
peak=   -3.162 closest distance to " NZ  LYS A  76 " =    1.934
peak=   -3.160 closest distance to " CB  SER A 146 " =    2.054
peak=   -3.160 closest distance to " CD2 TYR A 293 " =    1.895
peak=   -3.154 closest distance to " CG  ARG A 259 " =    2.522
peak=   -3.151 closest distance to " CG2BVAL A  72 " =    1.522
peak=   -3.150 closest distance to " O   HOH Z 165 " =    1.826
peak=   -3.145 closest distance to " O   ILE A 234 " =    1.211
peak=   -3.139 closest distance to " O   HOH Z 387 " =    2.828
peak=   -3.137 closest distance to " CA  TRP A 274 " =    1.206
peak=   -3.133 closest distance to " CG  GLN A  73 " =    0.907
peak=   -3.132 closest distance to " O   TRP A  92 " =    2.095
peak=   -3.130 closest distance to " O   HOH Z 263 " =    0.780
peak=   -3.129 closest distance to " CD  GLN A 223 " =    0.912
peak=   -3.126 closest distance to " C   SER A 206 " =    1.331
peak=   -3.125 closest distance to " CZ  ARG A 259 " =    0.909
peak=   -3.120 closest distance to " CZ  ARG A 156 " =    1.465
peak=   -3.119 closest distance to " CE  MET A 105 " =    2.253
peak=   -3.118 closest distance to " O   THR A  52 " =    1.853
peak=   -3.118 closest distance to " SG ACYS A 201 " =    2.371
peak=   -3.115 closest distance to " O   HOH Z 108 " =    2.143
peak=   -3.114 closest distance to " O   HOH Z 331 " =    1.447
peak=   -3.112 closest distance to " NE2 GLN A  11 " =    1.515
peak=   -3.111 closest distance to " O   HOH Z 310 " =    3.887
peak=   -3.110 closest distance to " CG  ASN A 110 " =    0.950
peak=   -3.105 closest distance to " O   HOH Z 222 " =    1.334
peak=   -3.104 closest distance to " CG2 THR A 235 " =    2.443
peak=   -3.101 closest distance to " O   HOH Z 340 " =    1.511
peak=   -3.099 closest distance to " O   HOH Z 210 " =    1.356
peak=   -3.097 closest distance to " CD1 LEU A 101 " =    2.460
peak=   -3.090 closest distance to " O   HOH Z 184 " =    1.268
peak=   -3.085 closest distance to " CA  GLU A 277 " =    1.291
peak=   -3.073 closest distance to " CG  ARG A 219 " =    2.325
peak=   -3.065 closest distance to " O   HOH Z 127 " =    1.478
peak=   -3.059 closest distance to " O   HOH Z 145 " =    2.478
peak=   -3.058 closest distance to " SG  CYS A 260 " =    1.822
peak=   -3.051 closest distance to " OD1 ASN A 187 " =    1.722
peak=   -3.050 closest distance to " O   HOH Z 422 " =    0.878
peak=   -3.047 closest distance to " O   HOH Z 126 " =    1.654
peak=   -3.045 closest distance to " ND2 ASN A  45 " =    0.983
peak=   -3.036 closest distance to " O   HOH Z 109 " =    1.091
peak=   -3.034 closest distance to " O   HOH Z 340 " =    1.285

================= 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    :  0.4992 0.4828   6.301175e+00   6.284140e+00
   1_bss:  0.4932 0.4773   6.293865e+00   6.281972e+00
   1_xyz:  0.4252 0.4347   6.225606e+00   6.235259e+00
   1_adp:  0.3839 0.4284   6.162935e+00   6.223813e+00
   1_occ:  0.3833 0.4275   6.162133e+00   6.223827e+00
   2_bss:  0.3799 0.4211   6.163566e+00   6.224049e+00
   2_xyz:  0.3252 0.3882   6.062541e+00   6.170209e+00
   2_adp:  0.3181 0.3806   6.051050e+00   6.156182e+00
   2_occ:  0.3178 0.3803   6.050568e+00   6.155837e+00
   3_bss:  0.3180 0.3810   6.051610e+00   6.156426e+00
   3_xyz:  0.2576 0.3085   5.854821e+00   6.000649e+00
   3_adp:  0.2341 0.2901   5.792113e+00   5.954452e+00
   3_occ:  0.2339 0.2902   5.791809e+00   5.955065e+00
   4_bss:  0.2332 0.2892   5.790613e+00   5.953124e+00
   4_xyz:  0.1891 0.2343   5.588645e+00   5.768621e+00
   4_adp:  0.1740 0.2207   5.524523e+00   5.714801e+00
   4_occ:  0.1738 0.2213   5.524805e+00   5.715797e+00
   5_bss:  0.1743 0.2215   5.526714e+00   5.715953e+00
   5_xyz:  0.1399 0.1879   5.334076e+00   5.555666e+00
   5_adp:  0.1307 0.1792   5.277654e+00   5.504649e+00
   5_occ:  0.1306 0.1792   5.277692e+00   5.505074e+00
   5_bss:  0.1308 0.1798   5.279386e+00   5.505515e+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:  0.329  20.001   6.008  12.304   7.531   0.000   0.000   0.000
   1_xyz:  0.329  20.001   6.008  12.304   7.531   0.000   0.000   0.000
   1_adp:  0.329  20.001   6.008  12.304   7.531   0.000   0.000   0.000
   1_occ:  0.329  20.001   6.008  12.304   7.531   0.000   0.000   0.000
   2_bss:  0.304  27.893   2.129   7.115   3.708   0.000   0.000   0.000
   2_xyz:  0.304  27.893   2.129   7.115   3.708   0.000   0.000   0.000
   2_adp:  0.304  27.893   2.129   7.115   3.708   0.000   0.000   0.000
   2_occ:  0.304  27.893   2.129   7.115   3.708   0.000   0.000   0.000
   3_bss:  0.282  37.347   1.123   5.195   2.537   0.000   0.000   0.000
   3_xyz:  0.282  37.347   1.123   5.195   2.537   0.000   0.000   0.000
   3_adp:  0.282  37.347   1.123   5.195   2.537   0.000   0.000   0.000
   3_occ:  0.282  37.347   1.123   5.195   2.537   0.000   0.000   0.000
   4_bss:  0.320  54.404   0.555   3.317   2.155   0.000   0.000   0.000
   4_xyz:  0.320  54.404   0.555   3.317   2.155   0.000   0.000   0.000
   4_adp:  0.320  54.404   0.555   3.317   2.155   0.000   0.000   0.000
   4_occ:  0.320  54.404   0.555   3.317   2.155   0.000   0.000   0.000
   5_bss:  0.327  66.475   0.182   2.317   1.972   0.000   0.000   0.000
   5_xyz:  0.327  66.475   0.182   2.317   1.972   0.000   0.000   0.000
   5_adp:  0.327  66.475   0.182   2.317   1.972   0.000   0.000   0.000
   5_occ:  0.327  66.475   0.182   2.317   1.972   0.000   0.000   0.000
   5_bss:  0.328  64.812  -1.163   0.505   0.659   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.728 0.4113  0.4784    73938.995
   1_bss:  59.346 0.4020  0.6001    73407.546
   1_xyz:  51.062 0.5068  0.7397    57476.818
   1_adp:  48.859 0.5343  0.8568    54057.229
   1_occ:  48.840 0.5345  0.8552    53956.216
   2_bss:  48.535 0.5383  0.7461    53603.049
   2_xyz:  44.208 0.5914  0.8162    45352.298
   2_adp:  43.117 0.6050  0.8305    43576.962
   2_occ:  43.060 0.6057  0.8310    43522.460
   3_bss:  42.892 0.6079  0.7957    43359.228
   3_xyz:  33.155 0.7218  0.9196    26756.469
   3_adp:  30.773 0.7493  0.9330    23741.654
   3_occ:  30.783 0.7492  0.9326    23760.286
   4_bss:  30.649 0.7506  0.9052    23563.507
   4_xyz:  23.451 0.8276  0.9655    14589.831
   4_adp:  21.794 0.8445  0.9709    12941.333
   4_occ:  21.820 0.8443  0.9709    12985.789
   5_bss:  21.810 0.8445  0.9538    13003.813
   5_xyz:  17.974 0.8801  0.9762     9019.239
   5_adp:  16.751 0.8915  0.9760     8252.327
   5_occ:  16.758 0.8915  0.9759     8266.602
   5_bss:  16.766 0.8914  0.9698     8291.658
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4092e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4092e+01
   1_xyz:   1.673  0.013  0.107 18.232  0.007  4.121   1.4204e-01
   1_adp:   1.673  0.013  0.107 18.232  0.007  4.121   1.4204e-01
   1_occ:   1.673  0.013  0.107 18.232  0.007  4.121   1.4204e-01
   2_bss:   1.673  0.013  0.107 18.232  0.007  4.121   1.4204e-01
   2_xyz:   1.201  0.009  0.077 16.608  0.005  4.106   8.8035e-02
   2_adp:   1.201  0.009  0.077 16.608  0.005  4.106   8.8035e-02
   2_occ:   1.201  0.009  0.077 16.608  0.005  4.106   8.8035e-02
   3_bss:   1.201  0.009  0.077 16.608  0.005  4.106   8.8035e-02
   3_xyz:   1.309  0.010  0.090 15.781  0.005  4.132   9.7028e-02
   3_adp:   1.309  0.010  0.090 15.781  0.005  4.132   9.7028e-02
   3_occ:   1.309  0.010  0.090 15.781  0.005  4.132   9.7028e-02
   4_bss:   1.309  0.010  0.090 15.781  0.005  4.132   9.7028e-02
   4_xyz:   1.029  0.008  0.069 15.155  0.004  4.124   6.5938e-02
   4_adp:   1.029  0.008  0.069 15.155  0.004  4.124   6.5938e-02
   4_occ:   1.029  0.008  0.069 15.155  0.004  4.124   6.5938e-02
   5_bss:   1.029  0.008  0.069 15.155  0.004  4.124   6.5938e-02
   5_xyz:   1.198  0.011  0.091 15.433  0.004  4.113   8.6502e-02
   5_adp:   1.198  0.011  0.091 15.433  0.004  4.113   8.6502e-02
   5_occ:   1.198  0.011  0.091 15.433  0.004  4.113   8.6502e-02
   5_bss:   1.198  0.011  0.091 15.433  0.004  4.113   8.6502e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0117e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0117e+00
   1_xyz:  15.134  0.118  0.502 87.751  0.039  2.236   1.0127e-01
   1_adp:  15.134  0.118  0.502 87.751  0.039  2.236   1.0127e-01
   1_occ:  15.134  0.118  0.502 87.751  0.039  2.236   1.0127e-01
   2_bss:  15.134  0.118  0.502 87.751  0.039  2.236   1.0127e-01
   2_xyz:   7.188  0.086  0.291 83.358  0.039  2.156   1.0290e-01
   2_adp:   7.188  0.086  0.291 83.358  0.039  2.156   1.0290e-01
   2_occ:   7.188  0.086  0.291 83.358  0.039  2.156   1.0290e-01
   3_bss:   7.188  0.086  0.291 83.358  0.039  2.156   1.0290e-01
   3_xyz:   8.895  0.082  0.343 86.832  0.043  2.254   1.2414e-01
   3_adp:   8.895  0.082  0.343 86.832  0.043  2.254   1.2414e-01
   3_occ:   8.895  0.082  0.343 86.832  0.043  2.254   1.2414e-01
   4_bss:   8.895  0.082  0.343 86.832  0.043  2.254   1.2414e-01
   4_xyz:   6.764  0.070  0.196 88.297  0.055  2.199   7.6252e-02
   4_adp:   6.764  0.070  0.196 88.297  0.055  2.199   7.6252e-02
   4_occ:   6.764  0.070  0.196 88.297  0.055  2.199   7.6252e-02
   5_bss:   6.764  0.070  0.196 88.297  0.055  2.199   7.6252e-02
   5_xyz:   8.678  0.059  0.465 81.809  0.033  2.207   7.7875e-02
   5_adp:   8.678  0.059  0.465 81.809  0.033  2.207   7.7875e-02
   5_occ:   8.678  0.059  0.465 81.809  0.033  2.207   7.7875e-02
   5_bss:   8.678  0.059  0.465 81.809  0.033  2.207   7.7875e-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: 107.47   0.00  15.57  65.35   0.00  13.57 107.47   0.00  26.45
   1_occ: 107.47   0.00  15.57  65.35   0.00  13.57 107.47   0.00  26.45
   2_bss: 107.47   0.00  15.57  65.35   0.00  13.57 107.47   0.00  26.45
   2_xyz: 107.47   0.00  15.57  65.35   0.00  13.57 107.47   0.00  26.45
   2_adp:  92.98   0.00  14.61  62.55   0.00  12.43  92.98   0.00  26.48
   2_occ:  92.98   0.00  14.61  62.55   0.00  12.43  92.98   0.00  26.48
   3_bss:  92.98   0.00  14.61  62.55   0.00  12.43  92.98   0.00  26.48
   3_xyz:  92.98   0.00  14.61  62.55   0.00  12.43  92.98   0.00  26.48
   3_adp:  88.28   0.00  14.54  70.55   0.00  11.25  88.28   0.00  32.46
   3_occ:  88.28   0.00  14.54  70.55   0.00  11.25  88.28   0.00  32.46
   4_bss:  88.28   0.00  14.54  70.55   0.00  11.25  88.28   0.00  32.46
   4_xyz:  88.28   0.00  14.54  70.55   0.00  11.25  88.28   0.00  32.46
   4_adp:  89.43   0.00  15.37  87.86   0.00  10.90  89.43   2.60  39.69
   4_occ:  89.43   0.00  15.37  87.86   0.00  10.90  89.43   2.60  39.69
   5_bss:  89.43   0.00  15.37  87.86   0.00  10.90  89.43   2.60  39.69
   5_xyz:  89.43   0.00  15.37  87.86   0.00  10.90  89.43   2.60  39.69
   5_adp:  95.23   0.00  15.20  95.23   0.00  10.37  94.13   2.65  41.46
   5_occ:  95.23   0.00  15.20  95.23   0.00  10.37  94.13   2.65  41.46
   5_bss:  96.54   1.30  16.50  96.54   1.30  11.68  95.44   3.96  42.76
------------------------------------------------------------------------
 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:    1.118    0.015    0.407
   1_adp:    1.118    0.015    0.407
   1_occ:    1.118    0.015    0.407
   2_bss:    1.118    0.015    0.407
   2_xyz:    1.556    0.048    0.545
   2_adp:    1.556    0.048    0.545
   2_occ:    1.556    0.048    0.545
   3_bss:    1.556    0.048    0.545
   3_xyz:    1.693    0.025    0.713
   3_adp:    1.693    0.025    0.713
   3_occ:    1.693    0.025    0.713
   4_bss:    1.693    0.025    0.713
   4_xyz:    2.045    0.032    0.801
   4_adp:    2.045    0.032    0.801
   4_occ:    2.045    0.032    0.801
   5_bss:    2.045    0.032    0.801
   5_xyz:    2.022    0.120    0.877
   5_adp:    2.022    0.120    0.877
   5_occ:    2.022    0.120    0.877
   5_bss:    2.022    0.120    0.877
------------------------------------------------------------------------

CPU time actual refinement: 349.21


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_479/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_479/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_479/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_479/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_479/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.06 
  Macro-tasks:
    bulk solvent and scale       = 42.21  
    individual site refinement   = 142.78 
    weights calculation          = 32.70  
    collect and process          = 6.35   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 224.15 
  Micro-tasks:
    mask                            = 3.14   
    f_calc                          = 109.80 
    alpha_beta                      = 8.31   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 119.77 
    fmodel                         = 7.35   
    r_factors                      = 0.25   
    phase_errors                   = 9.93   
    foms                           = 0.28   
    TOTAL for micro-tasks          = 259.97 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.910 micro seconds
Total CPU time: 6.05 minutes
from_scatterers_fft:    660 calls, 109.43 s
gradients_fft:          604 calls, 106.57 s

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

# Date 2008-01-16 Time 01:40:12 PST -0800 (1200476412.05 s)
Start R-work = 0.4992, R-free = 0.4828 (no bulk solvent and anisotropic scale)
Final R-work = 0.1474, R-free = 0.1949 (no bulk solvent and anisotropic scale)

Start R-work = 0.4932, R-free = 0.4773
Final R-work = 0.1308, R-free = 0.1798