# Date 2008-01-16 Time 02:55:50 PST -0800 (1200480950.24 s)
#phil __OFF__

Command line arguments: "../1029.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8583
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1029

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.93, 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: 3.44, per 1000 atoms: 1.22


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.00158
Completeness in resolution range: 0.968793
Completeness with d_max=infinity: 0.965832

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             d_min =   2.0016

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.00158
Completeness in resolution range: 0.968793
Completeness with d_max=infinity: 0.965832

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.2830 [2115/2140]  1905   210   9.9%
  bin  2:  4.2830 -  3.4122 [2042/2062]  1836   206  10.1%
  bin  3:  3.4122 -  2.9846 [2018/2037]  1815   203  10.1%
  bin  4:  2.9846 -  2.7134 [2001/2031]  1808   193   9.6%
  bin  5:  2.7134 -  2.5199 [1983/2002]  1784   199  10.0%
  bin  6:  2.5199 -  2.3719 [1968/1993]  1764   204  10.4%
  bin  7:  2.3719 -  2.2535 [1949/1977]  1753   196  10.1%
  bin  8:  2.2535 -  2.1557 [1976/2012]  1779   197  10.0%
  bin  9:  2.1557 -  2.0729 [1951/1993]  1760   191   9.8%
  bin 10:  2.0729 -  2.0016 [1586/1973]  1426   160  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1029/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: 0.15 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: 8
        2.42 -     3.04: 2177
        3.04 -     3.66: 4597
        3.66 -     4.28: 8976
        4.28 -     4.90: 12244
  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 207 " - " O   HOH Z 341 "  1.952 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.346 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27997 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_1029/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1029/model_refine_001.geo

CPU time processing inputs: 9.32


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.93 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: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4285   r_free= 0.4157   ksol= 0.00   Bsol= 0.00   scale= 0.817    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.221749                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7771 0.99   1383  154 0.3628 0.3328      6.5316      6.4169|
|  2:  4.7771 -  3.8115 0.99   1327  146 0.3199 0.3271       6.635      6.6578|
|  3:  3.8115 -  3.3355 0.99   1300  143 0.3668 0.3359      6.5404      6.5546|
|  4:  3.3355 -  3.0332 0.99   1285  148 0.4035 0.3548      6.4475      6.3508|
|  5:  3.0332 -  2.8173 0.99   1291  141 0.4488 0.4437        6.31      6.3475|
|  6:  2.8173 -  2.6521 0.99   1279  141 0.4500 0.4798      6.2288      6.1703|
|  7:  2.6521 -  2.5199 0.99   1283  138 0.4924 0.4938      6.2091      6.2407|
|  8:  2.5199 -  2.4107 0.98   1255  147 0.4813 0.4341      6.1487       6.107|
|  9:  2.4107 -  2.3182 0.98   1267  138 0.4606 0.5041      6.0775      6.1009|
| 10:  2.3182 -  2.2385 1.00   1264  141 0.4908 0.4582      6.0876      6.0743|
| 11:  2.2385 -  2.1687 0.97   1251  137 0.4883 0.4396      6.0195       5.993|
| 12:  2.1687 -  2.1068 0.98   1256  142 0.4824 0.4827      5.9621       6.009|
| 13:  2.1068 -  2.0515 0.99   1281  139 0.5047 0.5042      5.8824      5.8345|
| 14:  2.0515 -  2.0016 0.72    908  104 0.4887 0.4328      5.8578      5.6676|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7771  1383   154  0.75  29.77   0.81     0.78      54511.14|
|  2:  4.7771 -  3.8115  1327   146  0.79  26.85   0.91     0.83      68527.98|
|  3:  3.8115 -  3.3355  1300   143  0.72  33.28   0.87     0.80      72164.62|
|  4:  3.3355 -  3.0332  1285   148  0.66  38.85   0.84     0.72      66300.33|
|  5:  3.0332 -  2.8173  1291   141  0.56  47.03   0.76     0.64      60492.19|
|  6:  2.8173 -  2.6521  1279   141  0.52  50.07   0.76     0.58      55995.93|
|  7:  2.6521 -  2.5199  1283   138  0.48  53.79   0.74     0.53      53931.59|
|  8:  2.5199 -  2.4107  1255   147  0.47  54.75   0.76     0.53      49961.71|
|  9:  2.4107 -  2.3182  1267   138  0.49  53.21   0.75     0.54      44488.17|
| 10:  2.3182 -  2.2385  1264   141  0.50  52.37   0.78     0.56      38928.16|
| 11:  2.2385 -  2.1687  1251   137  0.48  53.52   0.77     0.55      36352.06|
| 12:  2.1687 -  2.1068  1256   142  0.47  54.63   0.78     0.55      34839.26|
| 13:  2.1068 -  2.0515  1281   139  0.47  54.48   0.74     0.55      29422.21|
| 14:  2.0515 -  2.0016   908   104  0.59  45.31   0.73     0.61      19410.48|
|alpha:            min =        0.53 max =            0.83 mean =         0.63|
|beta:             min =    19410.48 max =        72164.62 mean =     49748.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.98 mean =        46.09|
|phase err.(test): min =        0.00 max =           89.95 mean =        46.13|
|-----------------------------------------------------------------------------|

============================== 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 = 7.640557              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.640   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.613269              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.885   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1484 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2585 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3911 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4992 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6497 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7706 |
|-----------------------------------------------------------------------------|
|-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 |       54.140 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.611 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    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 = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4364   r_free= 0.4223   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.226292                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4217   r_free= 0.4017   ksol= 0.33   Bsol= 27.68   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.49,7.39,8.16,0.00,0.00,0.00); trace/3= 8.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.215936                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.151181              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.301   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.605366              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.445   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4217      final r-factor (work) = 0.3100          |
| start r-factor (free) = 0.4017      final r-factor (free) = 0.3309          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.4322 = 7.15 * 0.50 * 6.2345 + 1.00 * 54.1401                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7678 = 7.15 * 0.50 * 6.0554 + 1.00 * 0.1162                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3100      final r-factor (work) = 0.2432          |
| start r-factor (free) = 0.3309      final r-factor (free) = 0.2781          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6805 = 0.61 * 1.00 * 6.0554 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5650 = 0.61 * 1.00 * 5.8696 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.42   10.50    None  None   None       |
|    all(noH): 2823   0      0.00    69.42   10.50    None  None   None       |
|    Sol.    : 438    0      0.00    69.42   28.14    None  None   None       |
|    Mac.    : 2385   0      0.00    64.86   7.26     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 -   6.942: 1477   |   5:    34.709 -  41.651:   67        |
|      1:     6.942 -  13.884:  688   |   6:    41.651 -  48.593:   52        |
|      2:    13.884 -  20.826:  235   |   7:    48.593 -  55.535:   20        |
|      3:    20.826 -  27.768:  145   |   8:    55.535 -  62.477:   13        |
|      4:    27.768 -  34.709:  122   |   9:    62.477 -  69.419:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2432 r_free = 0.2781             target_work(ml) = 5.795         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2426 r_free = 0.2784             target_work(ml) = 5.794         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2426   r_free= 0.2784   ksol= 0.33   Bsol= 27.68   scale= 1.072   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.49,7.39,8.16,0.00,0.00,0.00); trace/3= 8.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.793991                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2387   r_free= 0.2740   ksol= 0.34   Bsol= 52.72   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.44,4.29,5.46,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.792338                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.309089              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.734   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.341606              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.786  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2387      final r-factor (work) = 0.1644          |
| start r-factor (free) = 0.2740      final r-factor (free) = 0.2066          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8332 = 3.31 * 0.50 * 5.8731 + 1.00 * 0.1159                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3759 = 3.31 * 0.50 * 5.6273 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1644      final r-factor (work) = 0.1506          |
| start r-factor (free) = 0.2066      final r-factor (free) = 0.1950          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9341 = 0.34 * 1.00 * 5.6273 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8599 = 0.34 * 1.00 * 5.4130 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.47   10.93    None  None   None       |
|    all(noH): 2823   0      0.00    69.47   10.93    None  None   None       |
|    Sol.    : 438    0      0.00    69.47   31.26    None  None   None       |
|    Mac.    : 2385   0      0.00    63.55   7.20     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.947: 1539   |   5:    34.735 -  41.682:  122        |
|      1:     6.947 -  13.894:  636   |   6:    41.682 -  48.629:   59        |
|      2:    13.894 -  20.841:  197   |   7:    48.629 -  55.576:   29        |
|      3:    20.841 -  27.788:  113   |   8:    55.576 -  62.523:   15        |
|      4:    27.788 -  34.735:  110   |   9:    62.523 -  69.470:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1506 r_free = 0.1950             target_work(ml) = 5.385         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1505 r_free = 0.1949             target_work(ml) = 5.384         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1505   r_free= 0.1949   ksol= 0.34   Bsol= 52.72   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.44,4.29,5.46,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.384371                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1502   r_free= 0.1940   ksol= 0.33   Bsol= 52.72   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,3.43,4.58,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.384687                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.582579              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.272  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.722239              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.260  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1502      final r-factor (work) = 0.1266          |
| start r-factor (free) = 0.1940      final r-factor (free) = 0.1710          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0650 = 2.58 * 0.50 * 5.4206 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9194 = 2.58 * 0.50 * 5.3059 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1266      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1710      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 25.0662 = 4.72 * 1.00 * 5.3059 + 1.00 * 0.0107                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.6685 = 4.72 * 1.00 * 5.2205 + 1.00 * 0.0159                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.68   11.89    None  None   None       |
|    all(noH): 2823   0      0.00    77.68   11.89    None  None   None       |
|    Sol.    : 438    0      0.00    77.68   35.93    None  None   None       |
|    Mac.    : 2385   0      0.00    75.77   7.47     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.768: 1644   |   5:    38.841 -  46.609:   81        |
|      1:     7.768 -  15.536:  573   |   6:    46.609 -  54.377:   94        |
|      2:    15.536 -  23.305:  164   |   7:    54.377 -  62.145:   43        |
|      3:    23.305 -  31.073:  108   |   8:    62.145 -  69.914:   20        |
|      4:    31.073 -  38.841:   88   |   9:    69.914 -  77.682:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1680             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1680             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1680   ksol= 0.33   Bsol= 52.72   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,3.43,4.58,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.212163                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1679   ksol= 0.33   Bsol= 56.69   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.54,3.36,4.51,0.00,0.00,0.00); trace/3= 3.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211775                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.512147              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.810  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.317765              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.972   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1679      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6245 = 2.51 * 0.50 * 5.2198 + 1.00 * 0.0680                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5934 = 2.51 * 0.50 * 5.1929 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6658 = 0.32 * 1.00 * 5.1929 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6754 = 0.32 * 1.00 * 5.1855 + 1.00 * 0.0276                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.22   11.45    None  None   None       |
|    all(noH): 2823   0      0.00    77.22   11.45    None  None   None       |
|    Sol.    : 438    0      0.85    77.22   34.07    None  None   None       |
|    Mac.    : 2385   0      0.00    74.95   7.30     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.722: 1691   |   5:    38.609 -  46.331:   67        |
|      1:     7.722 -  15.444:  547   |   6:    46.331 -  54.052:   89        |
|      2:    15.444 -  23.165:  162   |   7:    54.052 -  61.774:   31        |
|      3:    23.165 -  30.887:  105   |   8:    61.774 -  69.496:   16        |
|      4:    30.887 -  38.609:  107   |   9:    69.496 -  77.218:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1621             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1620             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1620   ksol= 0.33   Bsol= 56.69   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.54,3.36,4.51,0.00,0.00,0.00); trace/3= 3.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175416                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1617   ksol= 0.33   Bsol= 56.69   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,3.31,4.48,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175566                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.207453              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.897  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.537199              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.126   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7937 = 2.21 * 0.50 * 5.1852 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7735 = 2.21 * 0.50 * 5.1704 + 1.00 * 0.0668                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7903 = 0.54 * 1.00 * 5.1704 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7893 = 0.54 * 1.00 * 5.1634 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.50   11.39    None  None   None       |
|    all(noH): 2823   0      0.00    78.50   11.39    None  None   None       |
|    Sol.    : 438    0      0.84    78.17   33.85    None  None   None       |
|    Mac.    : 2385   0      0.00    78.50   7.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.850: 1703   |   5:    39.249 -  47.099:   78        |
|      1:     7.850 -  15.700:  537   |   6:    47.099 -  54.949:   73        |
|      2:    15.700 -  23.549:  153   |   7:    54.949 -  62.798:   26        |
|      3:    23.549 -  31.399:  117   |   8:    62.798 -  70.648:   14        |
|      4:    31.399 -  39.249:  114   |   9:    70.648 -  78.498:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1136 r_free = 0.1608             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1136 r_free = 0.1608             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1608   ksol= 0.33   Bsol= 56.69   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,3.31,4.48,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164603                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7771 0.99   1383  154 0.1003 0.1342      5.3969      5.5413|
|  2:  4.7771 -  3.8115 0.99   1327  146 0.0880 0.1123      5.4575      5.6385|
|  3:  3.8115 -  3.3355 0.99   1300  143 0.1057 0.1506      5.4834      5.8528|
|  4:  3.3355 -  3.0332 0.99   1285  148 0.1203 0.1594      5.4611      5.6113|
|  5:  3.0332 -  2.8173 0.99   1291  141 0.1342 0.1777      5.3419       5.583|
|  6:  2.8173 -  2.6521 0.99   1279  141 0.1217 0.1953      5.2309      5.5026|
|  7:  2.6521 -  2.5199 0.99   1283  138 0.1311 0.1569      5.1993      5.3501|
|  8:  2.5199 -  2.4107 0.98   1255  147 0.1207 0.1796      5.1027      5.3887|
|  9:  2.4107 -  2.3182 0.98   1267  138 0.1201 0.1778      5.0716       5.299|
| 10:  2.3182 -  2.2385 1.00   1264  141 0.1160 0.1774      4.9907      5.2898|
| 11:  2.2385 -  2.1687 0.97   1251  137 0.1169 0.1739      4.9768      5.2374|
| 12:  2.1687 -  2.1068 0.98   1256  142 0.1149 0.1805      4.8966      5.2469|
| 13:  2.1068 -  2.0515 0.99   1281  139 0.1166 0.1766       4.814      5.0974|
| 14:  2.0515 -  2.0016 0.72    908  104 0.1075 0.1733      4.6937       4.924|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7771  1383   154  0.94   9.34   0.97     0.95       7434.11|
|  2:  4.7771 -  3.8115  1327   146  0.95   8.12   1.00     0.99       9324.80|
|  3:  3.8115 -  3.3355  1300   143  0.93  11.40   1.02     1.01      10664.25|
|  4:  3.3355 -  3.0332  1285   148  0.92  13.72   1.00     0.98      10475.59|
|  5:  3.0332 -  2.8173  1291   141  0.90  16.11   0.99     0.96       8517.10|
|  6:  2.8173 -  2.6521  1279   141  0.90  16.13   0.98     0.96       7472.58|
|  7:  2.6521 -  2.5199  1283   138  0.90  16.11   0.98     0.96       6563.02|
|  8:  2.5199 -  2.4107  1255   147  0.91  15.63   0.99     0.96       5637.79|
|  9:  2.4107 -  2.3182  1267   138  0.90  16.00   1.00     0.96       5399.59|
| 10:  2.3182 -  2.2385  1264   141  0.90  15.79   0.99     0.95       4607.43|
| 11:  2.2385 -  2.1687  1251   137  0.89  17.00   0.99     0.96       4709.40|
| 12:  2.1687 -  2.1068  1256   142  0.91  15.22   1.00     0.98       4046.30|
| 13:  2.1068 -  2.0515  1281   139  0.90  16.50   0.99     0.97       3523.80|
| 14:  2.0515 -  2.0016   908   104  0.91  15.15   0.98     0.94       2712.82|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2712.82 max =        10664.25 mean =      6616.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.37|
|phase err.(test): min =        0.00 max =           87.87 mean =        13.82|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1608   ksol= 0.32   Bsol= 54.36   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,-0.42,0.76,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164586                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1608   ksol= 0.32   Bsol= 54.36   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,-0.42,0.76,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164586                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7771 0.99   1383  154 0.0999 0.1340      5.3924       5.537|
|  2:  4.7771 -  3.8115 0.99   1327  146 0.0876 0.1119      5.4537       5.634|
|  3:  3.8115 -  3.3355 0.99   1300  143 0.1056 0.1505      5.4817      5.8518|
|  4:  3.3355 -  3.0332 0.99   1285  148 0.1204 0.1594      5.4622      5.6122|
|  5:  3.0332 -  2.8173 0.99   1291  141 0.1344 0.1782      5.3437      5.5851|
|  6:  2.8173 -  2.6521 0.99   1279  141 0.1220 0.1956      5.2329      5.5044|
|  7:  2.6521 -  2.5199 0.99   1283  138 0.1313 0.1571      5.2007      5.3511|
|  8:  2.5199 -  2.4107 0.98   1255  147 0.1209 0.1799      5.1037        5.39|
|  9:  2.4107 -  2.3182 0.98   1267  138 0.1202 0.1777      5.0722      5.2986|
| 10:  2.3182 -  2.2385 1.00   1264  141 0.1161 0.1777      4.9914      5.2911|
| 11:  2.2385 -  2.1687 0.97   1251  137 0.1169 0.1741      4.9774      5.2382|
| 12:  2.1687 -  2.1068 0.98   1256  142 0.1149 0.1807      4.8971      5.2476|
| 13:  2.1068 -  2.0515 0.99   1281  139 0.1166 0.1768      4.8144       5.098|
| 14:  2.0515 -  2.0016 0.72    908  104 0.1076 0.1734      4.6941      4.9243|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7771  1383   154  0.94   9.28   0.97     0.95       7348.52|
|  2:  4.7771 -  3.8115  1327   146  0.95   8.07   1.00     0.99       9251.55|
|  3:  3.8115 -  3.3355  1300   143  0.93  11.37   1.02     1.01      10623.72|
|  4:  3.3355 -  3.0332  1285   148  0.92  13.73   1.00     0.98      10490.69|
|  5:  3.0332 -  2.8173  1291   141  0.90  16.13   0.99     0.96       8544.95|
|  6:  2.8173 -  2.6521  1279   141  0.90  16.17   0.98     0.96       7503.37|
|  7:  2.6521 -  2.5199  1283   138  0.90  16.13   0.98     0.96       6582.77|
|  8:  2.5199 -  2.4107  1255   147  0.91  15.65   0.99     0.96       5649.73|
|  9:  2.4107 -  2.3182  1267   138  0.90  16.01   1.00     0.96       5405.88|
| 10:  2.3182 -  2.2385  1264   141  0.90  15.81   0.99     0.95       4613.97|
| 11:  2.2385 -  2.1687  1251   137  0.89  17.02   0.99     0.96       4716.99|
| 12:  2.1687 -  2.1068  1256   142  0.91  15.23   1.00     0.98       4052.73|
| 13:  2.1068 -  2.0515  1281   139  0.90  16.51   0.99     0.97       3528.78|
| 14:  2.0515 -  2.0016   908   104  0.91  15.16   0.98     0.94       2715.30|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2715.30 max =        10623.72 mean =      6611.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.37|
|phase err.(test): min =        0.00 max =           88.05 mean =        13.83|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.74    82.24   15.13    None  None   None       |
|    all(noH): 2823   0      3.74    82.24   15.13    None  None   None       |
|    Sol.    : 438    0      4.58    81.91   37.59    None  None   None       |
|    Mac.    : 2385   0      3.74    82.24   11.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.743 -  11.592: 1703   |   5:    42.991 -  50.841:   78        |
|      1:    11.592 -  19.442:  537   |   6:    50.841 -  58.691:   73        |
|      2:    19.442 -  27.292:  153   |   7:    58.691 -  66.541:   26        |
|      3:    27.292 -  35.142:  117   |   8:    66.541 -  74.391:   14        |
|      4:    35.142 -  42.991:  114   |   9:    74.391 -  82.240:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.353 - 4.797
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 316
   mapped sites are within: 0.713 - 4.797

peak=   10.602 closest distance to " CG2 VAL A 230 " =    1.420
peak=    7.133 closest distance to " CG2 VAL A 296 " =    1.134
peak=    6.274 closest distance to " O   HOH Z 111 " =    2.246
peak=    6.153 closest distance to " CG  LEU A   5 " =    1.237
peak=    5.682 closest distance to " CB  GLN A 223 " =    1.439
peak=    5.668 closest distance to " CD2 LEU A   5 " =    1.210
peak=    5.626 closest distance to " CG  LEU A 228 " =    1.161
peak=    5.007 closest distance to " NE2 GLN A  11 " =    1.139
peak=    4.893 closest distance to " CB  GLN A 183 " =    1.275
peak=    4.887 closest distance to " O   HOH Z 232 " =    2.329
peak=    4.836 closest distance to " CB  SER A  63 " =    1.306
peak=    4.751 closest distance to " CB  VAL A 230 " =    1.189
peak=    4.636 closest distance to " O   HOH Z 142 " =    1.674
peak=    4.598 closest distance to " CG  PRO A 213 " =    1.212
peak=    4.582 closest distance to " O   HOH Z 369 " =    2.077
peak=    4.572 closest distance to " CB  VAL A 296 " =    1.093
peak=    4.545 closest distance to " CG  PRO A 243 " =    1.130
peak=    4.540 closest distance to " O   HOH Z  78 " =    1.764
peak=    4.514 closest distance to " CZ  PHE A 218 " =    1.069
peak=    4.504 closest distance to " CG  PRO A 198 " =    1.250
peak=    4.498 closest distance to " O   HOH Z 427 " =    3.105
peak=    4.477 closest distance to " O   HOH Z 126 " =    1.957
peak=    4.423 closest distance to " CB  ASN A 148 " =    1.350
peak=    4.375 closest distance to " O   HOH Z 298 " =    1.815
peak=    4.301 closest distance to " CB  TRP A 266 " =    0.960
peak=    4.298 closest distance to " CB  ARG A 275 " =    0.889
peak=    4.284 closest distance to " C   PRO A 198 " =    1.554
peak=    4.272 closest distance to " O   HOH Z 316 " =    3.113
peak=    4.271 closest distance to " O   HOH Z  54 " =    2.404
peak=    4.265 closest distance to " O   HOH Z 236 " =    2.015
peak=    4.249 closest distance to " O   HOH Z 368 " =    2.188
peak=    4.246 closest distance to " O   HOH Z 425 " =    1.423
peak=    4.246 closest distance to " O   HOH Z 261 " =    2.077
peak=    4.244 closest distance to " CB  GLU A 128 " =    1.142
peak=    4.214 closest distance to " O   HOH Z  61 " =    1.688
peak=    4.196 closest distance to " CD2 LEU A 228 " =    1.169
peak=    4.189 closest distance to " ND2 ASN A 187 " =    1.437
peak=    4.175 closest distance to " O   HOH Z 303 " =    2.093
peak=    4.124 closest distance to " CB  ASP A 124 " =    0.713
peak=    4.119 closest distance to " CB  GLU A 152 " =    1.155
peak=    4.111 closest distance to " OD1 ASN A  69 " =    2.640
peak=    4.091 closest distance to " O   HOH Z 158 " =    3.145
peak=    4.090 closest distance to " CB  ASP A 140 " =    0.927
peak=    4.052 closest distance to " CB  ARG A  79 " =    1.469
peak=    4.046 closest distance to " CA  TYR A  30 " =    0.985
peak=    4.039 closest distance to " CD  ARG A 159 " =    0.767
peak=    4.037 closest distance to " O   HOH Z  44 " =    2.244
peak=    4.036 closest distance to " O   HOH Z 346 " =    1.618
peak=    4.018 closest distance to " O   HOH Z 403 " =    1.678
peak=    4.007 closest distance to " CB  SER A   3 " =    1.356
peak=    4.006 closest distance to " O   HOH Z 272 " =    1.867
peak=    3.974 closest distance to " O   HOH Z  43 " =    1.884
peak=    3.967 closest distance to " CB  VAL A 265 " =    1.258
peak=    3.963 closest distance to " CB  LEU A 143 " =    1.191
peak=    3.953 closest distance to " NH1AARG A 145 " =    1.179
peak=    3.952 closest distance to " O   HOH Z 234 " =    3.826
peak=    3.945 closest distance to " O   HOH Z 411 " =    3.731
peak=    3.929 closest distance to " O   HOH Z 423 " =    1.715
peak=    3.924 closest distance to " CB  GLU A 277 " =    3.658
peak=    3.919 closest distance to " CB  ALA A   9 " =    1.615
peak=    3.910 closest distance to " CB  PRO A  54 " =    0.828
peak=    3.903 closest distance to " CB  ARG A 190 " =    1.596
peak=    3.872 closest distance to " CB  ASN A  39 " =    0.911
peak=    3.870 closest distance to " CA  ALA A  51 " =    0.984
peak=    3.865 closest distance to " O   SER A  87 " =    2.297
peak=    3.856 closest distance to " O   HOH Z  15 " =    2.157
peak=    3.842 closest distance to " CZ  PHE A 192 " =    0.941
peak=    3.836 closest distance to " O   HOH Z 214 " =    2.036
peak=    3.829 closest distance to " CD  ARG A  66 " =    2.462
peak=    3.826 closest distance to " CD ALYS A 290 " =    1.018
peak=    3.798 closest distance to " OG  SER A  97 " =    3.016
peak=    3.775 closest distance to " CB  LEU A 228 " =    1.193
peak=    3.767 closest distance to " O   HOH Z 126 " =    1.564
peak=    3.765 closest distance to " CG2 THR A 221 " =    1.100
peak=    3.765 closest distance to " CG  LEU A 167 " =    1.192
peak=    3.764 closest distance to " CB  SER A 216 " =    0.842
peak=    3.756 closest distance to " O   HOH Z 280 " =    3.017
peak=    3.751 closest distance to " CB  ASN A 142 " =    1.090
peak=    3.749 closest distance to " NH2 ARG A 156 " =    1.108
peak=    3.743 closest distance to " CA  SER A  87 " =    0.957
peak=    3.742 closest distance to " CB  VAL A 202 " =    1.628
peak=    3.741 closest distance to " ND2 ASN A 249 " =    1.891
peak=    3.739 closest distance to " CB  ALA A 291 " =    1.336
peak=    3.730 closest distance to " CG1 VAL A 153 " =    0.980
peak=    3.719 closest distance to " CA  ASN A 215 " =    1.188
peak=    3.719 closest distance to " CD  ARG A 269 " =    0.997
peak=    3.710 closest distance to " O   HOH Z  63 " =    1.962
peak=    3.708 closest distance to " O   HOH Z 193 " =    1.860
peak=    3.707 closest distance to " CB  GLU A  46 " =    1.004
peak=    3.701 closest distance to " O   HOH Z 203 " =    1.727
peak=    3.698 closest distance to " CB  MET A  40 " =    0.822
peak=    3.697 closest distance to " CG1 ILE A  49 " =    1.439
peak=    3.693 closest distance to " CB  ASN A 187 " =    1.130
peak=    3.690 closest distance to " CG2 VAL A 257 " =    0.911
peak=    3.688 closest distance to " CD1 LEU A 300 " =    1.190
peak=    3.680 closest distance to " CA  THR A 264 " =    0.766
peak=    3.676 closest distance to " CB AVAL A  41 " =    1.167
peak=    3.675 closest distance to " CG  MET A 185 " =    1.195
peak=    3.671 closest distance to " O   HOH Z 193 " =    1.715
peak=    3.667 closest distance to " O   HOH Z 248 " =    1.709
peak=    3.666 closest distance to " CA  LYS A 117 " =    1.220
peak=    3.661 closest distance to " CB  SER A 212 " =    1.232
peak=    3.650 closest distance to " O   HOH Z 313 " =    1.793
peak=    3.642 closest distance to " O   HOH Z  21 " =    1.722
peak=    3.641 closest distance to " O   HOH Z 285 " =    2.784
peak=    3.641 closest distance to " O   HOH Z  88 " =    3.313
peak=    3.638 closest distance to " O   HOH Z 112 " =    1.686
peak=    3.629 closest distance to " CA  ARG A 195 " =    1.208
peak=    3.616 closest distance to " CB  THR A  82 " =    1.370
peak=    3.616 closest distance to " O   HOH Z 171 " =    3.867
peak=    3.599 closest distance to " N   ASN A  39 " =    1.210
peak=    3.598 closest distance to " CB  TRP A 179 " =    1.523
peak=    3.596 closest distance to " O   HOH Z 193 " =    2.073
peak=    3.592 closest distance to " CG  GLN A  88 " =    1.082
peak=    3.591 closest distance to " O   MET A 105 " =    1.783
peak=    3.589 closest distance to " N   PHE A 130 " =    1.233
peak=    3.571 closest distance to " CB  HIS A 108 " =    0.795
peak=    3.561 closest distance to " CA  ALA A 295 " =    1.103
peak=    3.560 closest distance to " O   HOH Z 147 " =    1.744
peak=    3.558 closest distance to " CA  MET A  40 " =    1.127
peak=    3.554 closest distance to " CG1 ILE A  33 " =    1.314
peak=    3.550 closest distance to " CG1BVAL A  72 " =    1.743
peak=    3.550 closest distance to " OD2 ASP A 286 " =    2.875
peak=    3.549 closest distance to " N   VAL A 126 " =    1.426
peak=    3.543 closest distance to " O   HOH Z  92 " =    2.452
peak=    3.540 closest distance to " O   ALA A 158 " =    1.416
peak=    3.538 closest distance to " CB  ALA A 104 " =    0.798
peak=    3.518 closest distance to " O   HOH Z 273 " =    2.756
peak=    3.518 closest distance to " CA  ALA A  21 " =    1.159
peak=    3.517 closest distance to " O   HOH Z 437 " =    1.734
peak=    3.512 closest distance to " NE2 HIS A 207 " =    1.334
peak=    3.511 closest distance to " CA  ALA A 291 " =    0.920
peak=    3.505 closest distance to " N   SER A 135 " =    1.394
peak=    3.502 closest distance to " CE  LYS A  76 " =    0.865
peak=    3.499 closest distance to " O   HOH Z  10 " =    1.841
peak=    3.493 closest distance to " CA  ARG A  36 " =    1.151
peak=    3.491 closest distance to " NZ  LYS A 117 " =    3.253
peak=    3.487 closest distance to " CD  LYS A 166 " =    1.301
peak=    3.486 closest distance to " CG BARG A 275 " =    1.511
peak=    3.484 closest distance to " CG  ARG A 138 " =    1.150
peak=    3.482 closest distance to " ND1 HIS A  81 " =    1.689
peak=    3.480 closest distance to " O   HOH Z 263 " =    1.656
peak=    3.479 closest distance to " O   HOH Z  68 " =    2.091
peak=    3.478 closest distance to " O   TRP A 274 " =    1.886
peak=    3.474 closest distance to " O   HOH Z 197 " =    3.120
peak=    3.468 closest distance to " O   HOH Z 368 " =    3.557
peak=    3.465 closest distance to " CD1 LEU A   5 " =    1.336
peak=    3.464 closest distance to " O   HOH Z 128 " =    2.180
peak=    3.464 closest distance to " CA  THR A 221 " =    0.916
peak=    3.462 closest distance to " CB  ARG A 138 " =    0.950
peak=    3.461 closest distance to " O   HOH Z 371 " =    3.089
peak=    3.456 closest distance to " O   HOH Z 402 " =    1.459
peak=    3.453 closest distance to " CB  ARG A  79 " =    0.906
peak=    3.453 closest distance to " CG1 VAL A 296 " =    1.239
peak=    3.452 closest distance to " CB  ALA A  34 " =    0.912
peak=    3.443 closest distance to " O   HOH Z 305 " =    3.576
peak=    3.438 closest distance to " CB  TRP A 150 " =    1.395
peak=    3.436 closest distance to " CG2 THR A 220 " =    0.947
peak=    3.435 closest distance to " O   HOH Z 291 " =    1.646
peak=    3.434 closest distance to " O   HOH Z 180 " =    2.168
peak=    3.432 closest distance to " O   HOH Z 128 " =    2.209
peak=    3.429 closest distance to " CD1 LEU A  96 " =    0.720
peak=    3.426 closest distance to " OG BSER A 164 " =    2.253
peak=    3.424 closest distance to " CD1 ILE A  33 " =    1.650
peak=    3.423 closest distance to " CA  VAL A  41 " =    0.811
peak=    3.422 closest distance to " CB  THR A  31 " =    1.667
peak=    3.419 closest distance to " O   ASP A 124 " =    0.970
peak=    3.419 closest distance to " ND1 HIS A  86 " =    1.657
peak=    3.417 closest distance to " CB  ILE A 120 " =    1.327
peak=    3.412 closest distance to " CE1 TYR A 186 " =    1.318
peak=    3.410 closest distance to " CA  LEU A 282 " =    1.042
peak=    3.409 closest distance to " CA  ALA A 158 " =    1.172
peak=    3.407 closest distance to " O   HOH Z 133 " =    1.696
peak=    3.407 closest distance to " O   HOH Z 353 " =    2.615
peak=    3.401 closest distance to " O   HOH Z 290 " =    1.093
peak=    3.401 closest distance to " CB  ALA A 242 " =    0.809
peak=    3.398 closest distance to " O   HOH Z  97 " =    2.555
peak=    3.396 closest distance to " O   HOH Z 250 " =    1.309
peak=    3.393 closest distance to " O   HOH Z 422 " =    2.712
peak=    3.388 closest distance to " O   HOH Z 132 " =    2.778
peak=    3.388 closest distance to " O   HOH Z 329 " =    3.938
peak=    3.387 closest distance to " CB  ALA A 248 " =    1.368
peak=    3.387 closest distance to " CG1 ILE A 151 " =    1.067
peak=    3.386 closest distance to " CB  LYS A 117 " =    1.211
peak=    3.378 closest distance to " O   HOH Z  48 " =    1.680
peak=    3.376 closest distance to " CB  ASN A 110 " =    1.144
peak=    3.375 closest distance to " NE2 GLN A  77 " =    3.435
peak=    3.369 closest distance to " CB  SER A 273 " =    0.885
peak=    3.368 closest distance to " N   ASN A 127 " =    1.235
peak=    3.362 closest distance to " O   HOH Z  59 " =    2.137
peak=    3.359 closest distance to " OG  SER A  22 " =    2.858
peak=    3.357 closest distance to " O   HOH Z  97 " =    2.047
peak=    3.356 closest distance to " CZ  PHE A  38 " =    1.175
peak=    3.355 closest distance to " O   HOH Z 227 " =    1.683
peak=    3.353 closest distance to " CD1 ILE A 106 " =    0.964
peak=    3.344 closest distance to " O  BHOH Z 338 " =    2.422
peak=    3.343 closest distance to " CA  LYS A 181 " =    1.070
peak=    3.343 closest distance to " CG  MET A 185 " =    1.024
peak=    3.342 closest distance to " OG1 THR A 294 " =    2.423
peak=    3.341 closest distance to " CB  THR A 157 " =    1.144
peak=    3.341 closest distance to " O   HOH Z 184 " =    1.426
peak=    3.338 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.338 closest distance to " CD1 LEU A 228 " =    1.958
peak=    3.335 closest distance to " CD2 TRP A 179 " =    1.373
peak=    3.333 closest distance to " O   HOH Z 350 " =    1.682
peak=    3.332 closest distance to " CA  TYR A  30 " =    1.064
peak=    3.327 closest distance to " O   HOH Z 294 " =    1.558
peak=    3.326 closest distance to " O   HOH Z 344 " =    3.065
peak=    3.325 closest distance to " O   HOH Z 409 " =    3.116
peak=    3.323 closest distance to " O   HOH Z  20 " =    1.641
peak=    3.320 closest distance to " CA  TYR A 116 " =    1.470
peak=    3.316 closest distance to " O   HOH Z 141 " =    1.715
peak=    3.313 closest distance to " CG  ARG A 159 " =    1.029
peak=    3.313 closest distance to " NE  ARG A  79 " =    1.212
peak=    3.300 closest distance to " CA  ALA A 154 " =    1.018
peak=    3.299 closest distance to " CB  ALA A 248 " =    1.091
peak=    3.298 closest distance to " N   SER A 146 " =    1.715
peak=    3.294 closest distance to " O   HOH Z 213 " =    1.848
peak=    3.293 closest distance to " O   HOH Z 245 " =    1.392
peak=    3.289 closest distance to " O   HOH Z 135 " =    1.877
peak=    3.283 closest distance to " O   HOH Z  80 " =    1.585
peak=    3.283 closest distance to " O   HOH Z 166 " =    3.680
peak=    3.281 closest distance to " O   HOH Z 133 " =    2.393
peak=    3.281 closest distance to " O   ALA A 165 " =    1.484
peak=    3.279 closest distance to " O   TYR A 116 " =    1.289
peak=    3.278 closest distance to " NZ  LYS A  48 " =    1.398
peak=    3.276 closest distance to " CB  LEU A  83 " =    0.737
peak=    3.271 closest distance to " CB  VAL A 268 " =    0.864
peak=    3.268 closest distance to " CB  MET A  47 " =    1.071
peak=    3.263 closest distance to " CA  VAL A 125 " =    1.184
peak=    3.259 closest distance to " CA  ASP A 191 " =    0.724
peak=    3.258 closest distance to " CD2 LEU A 255 " =    1.729
peak=    3.258 closest distance to " O   HOH Z 313 " =    1.722
peak=    3.255 closest distance to " O   HOH Z 425 " =    2.014
peak=    3.255 closest distance to " CB  ARG A 139 " =    0.882
peak=    3.249 closest distance to " O   HOH Z 156 " =    2.992
peak=    3.247 closest distance to " CB  ASN A 224 " =    0.997
peak=    3.246 closest distance to " C   ALA A 299 " =    0.969
peak=    3.245 closest distance to " OH  TYR A 214 " =    1.239
peak=    3.245 closest distance to " CZ3 TRP A 274 " =    4.684
peak=    3.241 closest distance to " CA  ALA A 233 " =    1.419
peak=    3.241 closest distance to " CB  ALA A 114 " =    1.193
peak=    3.239 closest distance to " CG BARG A 102 " =    1.849
peak=    3.235 closest distance to " O   HOH Z 133 " =    3.282
peak=    3.234 closest distance to " O   HOH Z 172 " =    3.541
peak=    3.227 closest distance to " CA  ASP A 162 " =    1.032
peak=    3.226 closest distance to " OG  SER A  62 " =    2.950
peak=    3.223 closest distance to " OG BSER A 134 " =    2.911
peak=    3.223 closest distance to " O   HOH Z 171 " =    2.296
peak=    3.221 closest distance to " O   HOH Z 260 " =    1.530
peak=    3.220 closest distance to " O   HOH Z 187 " =    2.314
peak=    3.219 closest distance to " O   HOH Z 326 " =    2.295
peak=    3.217 closest distance to " CD2 LEU A   5 " =    0.746
peak=    3.217 closest distance to " O   HOH Z 435 " =    1.992
peak=    3.215 closest distance to " O   GLN A 278 " =    1.541
peak=    3.210 closest distance to " O   HOH Z 383 " =    2.139
peak=    3.203 closest distance to " CG  GLN A 278 " =    1.304
peak=    3.202 closest distance to " CB  GLN A  89 " =    1.202
peak=    3.200 closest distance to " CB  ALA A 137 " =    1.061
peak=    3.199 closest distance to " O   HOH Z 426 " =    1.567
peak=    3.199 closest distance to " O   HOH Z 302 " =    1.929
peak=    3.194 closest distance to " CB  SER A 210 " =    0.842
peak=    3.194 closest distance to " N   ARG A 156 " =    1.370
peak=    3.193 closest distance to " O   HOH Z 148 " =    3.294
peak=    3.192 closest distance to " CA  ASN A 217 " =    1.288
peak=    3.190 closest distance to " OG  SER A 245 " =    1.692
peak=    3.189 closest distance to " CB  ALA A 227 " =    1.031
peak=    3.184 closest distance to " CA  ASP A 140 " =    1.280
peak=    3.180 closest distance to " NH1 ARG A  14 " =    0.909
peak=    3.179 closest distance to " CB  ALA A   1 " =    4.797
peak=    3.178 closest distance to " CZ3 TRP A 266 " =    1.113
peak=    3.172 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.169 closest distance to " O   HOH Z 109 " =    2.635
peak=    3.169 closest distance to " CA  MET A 105 " =    0.981
peak=    3.166 closest distance to " CA  LYS A 290 " =    1.251
peak=    3.164 closest distance to " N   TYR A  15 " =    0.813
peak=    3.164 closest distance to " CD1 ILE A 199 " =    0.811
peak=    3.162 closest distance to " O   HOH Z 102 " =    1.291
peak=    3.150 closest distance to " CB  TYR A 116 " =    0.854
peak=    3.149 closest distance to " O   HOH Z 417 " =    2.053
peak=    3.148 closest distance to " O   HOH Z 116 " =    1.792
peak=    3.146 closest distance to " CB  TYR A 247 " =    0.966
peak=    3.140 closest distance to " O   HOH Z 216 " =    2.889
peak=    3.134 closest distance to " O   HOH Z 403 " =    1.396
peak=    3.132 closest distance to " CB  SER A  62 " =    1.168
peak=    3.131 closest distance to " O   HOH Z  89 " =    1.795
peak=    3.130 closest distance to " CB  GLN A 278 " =    0.868
peak=    3.129 closest distance to " O   HOH Z 329 " =    2.811
peak=    3.119 closest distance to " O   ARG A  56 " =    2.842
peak=    3.117 closest distance to " ND2 ASN A 110 " =    1.613
peak=    3.116 closest distance to " N   GLN A 278 " =    1.102
peak=    3.116 closest distance to " CB  GLN A 103 " =    0.999
peak=    3.104 closest distance to " O   PRO A  90 " =    1.368
peak=    3.102 closest distance to " CD  LYS A 119 " =    1.582
peak=    3.097 closest distance to " O   HOH Z 156 " =    3.471
peak=    3.097 closest distance to " OD1 ASN A 217 " =    1.660
peak=    3.096 closest distance to " O   HOH Z 345 " =    3.491
peak=    3.092 closest distance to " CG2 ILE A  20 " =    1.493
peak=    3.090 closest distance to " OG  SER A 206 " =    1.165
peak=    3.084 closest distance to " CG  ARG A 269 " =    1.800
peak=    3.079 closest distance to " OG  SER A  62 " =    2.991
peak=    3.077 closest distance to " OE2 GLU A  53 " =    2.012
peak=    3.072 closest distance to " O   HOH Z 271 " =    2.014
peak=    3.072 closest distance to " CA  ILE A 234 " =    0.875
peak=    3.070 closest distance to " CG2 ILE A 234 " =    0.828
peak=    3.069 closest distance to " CB  PRO A 243 " =    1.526
peak=    3.054 closest distance to " CZ3 TRP A  85 " =    1.094
peak=    3.037 closest distance to " O   HOH Z 271 " =    2.475
peak=    3.026 closest distance to " O   ALA A 292 " =    1.672
peak=    3.025 closest distance to " C   ASN A  39 " =    1.036

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.532 - 5.513
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 207
   mapped sites are within: 0.770 - 5.513

peak=   -5.271 closest distance to " CG2 VAL A 230 " =    0.792
peak=   -4.422 closest distance to " CD  ARG A 156 " =    2.029
peak=   -4.333 closest distance to " CG1 VAL A 112 " =    2.617
peak=   -4.286 closest distance to " CB  PRO A 243 " =    2.654
peak=   -4.208 closest distance to " CD  ARG A  14 " =    3.292
peak=   -4.150 closest distance to " CG  GLN A 223 " =    2.141
peak=   -4.074 closest distance to " O   HOH Z 266 " =    5.320
peak=   -3.992 closest distance to " O   ILE A 109 " =    2.566
peak=   -3.958 closest distance to " O   VAL A  67 " =    2.699
peak=   -3.940 closest distance to " CD  GLN A  58 " =    0.997
peak=   -3.914 closest distance to " CZ3 TRP A 179 " =    1.185
peak=   -3.886 closest distance to " O   HOH Z  52 " =    1.527
peak=   -3.885 closest distance to " OG BSER A 134 " =    1.216
peak=   -3.861 closest distance to " CG2 ILE A  49 " =    2.762
peak=   -3.851 closest distance to " CG2 VAL A 296 " =    1.276
peak=   -3.847 closest distance to " NH2AARG A 275 " =    5.369
peak=   -3.786 closest distance to " O   HOH Z 351 " =    1.510
peak=   -3.786 closest distance to " CA  GLY A 241 " =    3.116
peak=   -3.776 closest distance to " O   HOH Z 231 " =    1.774
peak=   -3.776 closest distance to " CG1 VAL A 296 " =    1.423
peak=   -3.774 closest distance to " CG1 VAL A 250 " =    2.754
peak=   -3.774 closest distance to " O   HOH Z 290 " =    1.250
peak=   -3.773 closest distance to " C   HIS A 108 " =    1.172
peak=   -3.770 closest distance to " O   HOH Z 394 " =    1.502
peak=   -3.754 closest distance to " CG  ASP A 231 " =    0.770
peak=   -3.751 closest distance to " O   HOH Z 196 " =    2.252
peak=   -3.749 closest distance to " O   HOH Z 426 " =    1.684
peak=   -3.738 closest distance to " O   HOH Z  73 " =    2.145
peak=   -3.738 closest distance to " O   HOH Z 211 " =    1.464
peak=   -3.721 closest distance to " O   HOH Z 114 " =    3.158
peak=   -3.720 closest distance to " O   HOH Z 389 " =    2.009
peak=   -3.713 closest distance to " CA  GLY A 241 " =    2.322
peak=   -3.702 closest distance to " O   PRO A 163 " =    2.144
peak=   -3.701 closest distance to " O   HOH Z 185 " =    2.337
peak=   -3.700 closest distance to " OG  SER A  97 " =    2.304
peak=   -3.696 closest distance to " O   HOH Z 435 " =    2.797
peak=   -3.690 closest distance to " CE2 TYR A  30 " =    2.783
peak=   -3.686 closest distance to " O   VAL A 189 " =    2.626
peak=   -3.684 closest distance to " CD2 LEU A 300 " =    2.787
peak=   -3.684 closest distance to " C   ALA A 158 " =    1.365
peak=   -3.672 closest distance to " O   HOH Z  11 " =    1.933
peak=   -3.661 closest distance to " OG  SER A  87 " =    1.528
peak=   -3.657 closest distance to " N   ALA A  43 " =    2.489
peak=   -3.656 closest distance to " O   VAL A  67 " =    2.691
peak=   -3.651 closest distance to " CA  ASP A 298 " =    1.032
peak=   -3.644 closest distance to " OD1 ASN A 148 " =    1.469
peak=   -3.626 closest distance to " O   GLY A 203 " =    2.349
peak=   -3.626 closest distance to " OXT GLY A 302 " =    3.024
peak=   -3.624 closest distance to " O   HOH Z  44 " =    2.206
peak=   -3.619 closest distance to " O   HOH Z 166 " =    1.970
peak=   -3.612 closest distance to " CD1 LEU A 228 " =    2.357
peak=   -3.611 closest distance to " ND2 ASN A  45 " =    1.156
peak=   -3.607 closest distance to " CG2 ILE A 263 " =    2.430
peak=   -3.602 closest distance to " CG1 VAL A 197 " =    2.296
peak=   -3.597 closest distance to " CG1 VAL A 112 " =    3.008
peak=   -3.588 closest distance to " CB  ALA A  43 " =    2.570
peak=   -3.582 closest distance to " CB  ALA A 248 " =    2.113
peak=   -3.579 closest distance to " CB  PHE A 192 " =    1.898
peak=   -3.573 closest distance to " CE3 TRP A 150 " =    2.086
peak=   -3.572 closest distance to " N   THR A 157 " =    1.509
peak=   -3.572 closest distance to " N   ALA A 226 " =    2.206
peak=   -3.571 closest distance to " CG  LEU A 101 " =    2.483
peak=   -3.550 closest distance to " O   GLY A  80 " =    2.522
peak=   -3.547 closest distance to " N   THR A  18 " =    1.324
peak=   -3.545 closest distance to " CB  PRO A 163 " =    2.559
peak=   -3.544 closest distance to " O   HOH Z  10 " =    1.513
peak=   -3.536 closest distance to " CG  TRP A 266 " =    1.814
peak=   -3.528 closest distance to " CD2 TYR A 293 " =    2.068
peak=   -3.524 closest distance to " O   HOH Z 241 " =    1.238
peak=   -3.514 closest distance to " O   HOH Z 103 " =    1.844
peak=   -3.491 closest distance to " C   MET A 188 " =    1.346
peak=   -3.479 closest distance to " CD2 LEU A 167 " =    1.843
peak=   -3.478 closest distance to " CE  MET A 105 " =    2.281
peak=   -3.466 closest distance to " O   PRO A 198 " =    1.219
peak=   -3.466 closest distance to " O   HOH Z 377 " =    2.042
peak=   -3.464 closest distance to " CE BMET A  47 " =    1.726
peak=   -3.460 closest distance to " CB  VAL A 230 " =    1.036
peak=   -3.460 closest distance to " CA  GLY A 203 " =    2.433
peak=   -3.456 closest distance to " CA  ASP A  27 " =    2.514
peak=   -3.447 closest distance to " O   HOH Z 407 " =    3.210
peak=   -3.442 closest distance to " CB  ALA A 248 " =    2.443
peak=   -3.438 closest distance to " O   HOH Z 353 " =    2.111
peak=   -3.437 closest distance to " O   HOH Z 231 " =    1.390
peak=   -3.432 closest distance to " NE2 GLN A 194 " =    1.791
peak=   -3.430 closest distance to " CG  ARG A 269 " =    2.517
peak=   -3.413 closest distance to " OD1 ASN A 187 " =    1.577
peak=   -3.404 closest distance to " O   HOH Z 292 " =    4.706
peak=   -3.401 closest distance to " C   LEU A 222 " =    0.871
peak=   -3.400 closest distance to " O   HOH Z 275 " =    1.496
peak=   -3.396 closest distance to " CD1 LEU A 101 " =    2.455
peak=   -3.395 closest distance to " NH2 ARG A  79 " =    2.020
peak=   -3.393 closest distance to " O   GLY A 196 " =    1.240
peak=   -3.393 closest distance to " OD2 ASP A  50 " =    2.305
peak=   -3.392 closest distance to " CB  ALA A 291 " =    2.217
peak=   -3.389 closest distance to " CG  HIS A  86 " =    1.073
peak=   -3.389 closest distance to " NE2 GLN A  88 " =    2.069
peak=   -3.389 closest distance to " O   HOH Z  38 " =    1.492
peak=   -3.385 closest distance to " SD BMET A  47 " =    1.015
peak=   -3.379 closest distance to " CD1 LEU A 101 " =    2.873
peak=   -3.379 closest distance to " OG BSER A 134 " =    1.828
peak=   -3.378 closest distance to " O   HOH Z  43 " =    1.706
peak=   -3.377 closest distance to " CD2 PHE A  61 " =    2.511
peak=   -3.373 closest distance to " O   HOH Z 417 " =    2.863
peak=   -3.361 closest distance to " O   HOH Z 176 " =    0.862
peak=   -3.360 closest distance to " O   SER A 271 " =    2.270
peak=   -3.355 closest distance to " O   HOH Z 359 " =    3.186
peak=   -3.352 closest distance to " CD  ARG A 139 " =    1.622
peak=   -3.344 closest distance to " CB  ASN A  69 " =    1.230
peak=   -3.343 closest distance to " O   GLY A 211 " =    1.395
peak=   -3.337 closest distance to " CB  ALA A 291 " =    2.264
peak=   -3.323 closest distance to " ND2 ASN A  60 " =    1.391
peak=   -3.314 closest distance to " O   HOH Z 198 " =    1.502
peak=   -3.310 closest distance to " O   HOH Z  60 " =    2.270
peak=   -3.308 closest distance to " CD1 ILE A 239 " =    2.105
peak=   -3.303 closest distance to " N   SER A 212 " =    1.856
peak=   -3.295 closest distance to " CA  ASN A 127 " =    1.125
peak=   -3.294 closest distance to " O   HOH Z 191 " =    5.513
peak=   -3.291 closest distance to " ND2 ASN A 187 " =    1.678
peak=   -3.291 closest distance to " OG  SER A 206 " =    1.750
peak=   -3.289 closest distance to " O   HOH Z 166 " =    1.621
peak=   -3.287 closest distance to " O   HOH Z 372 " =    2.437
peak=   -3.287 closest distance to " O   HOH Z 140 " =    1.733
peak=   -3.282 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.279 closest distance to " CD1 PHE A  59 " =    1.908
peak=   -3.278 closest distance to " O   MET A  40 " =    2.797
peak=   -3.274 closest distance to " O   HOH Z 102 " =    1.712
peak=   -3.273 closest distance to " CD1 TYR A 247 " =    2.856
peak=   -3.272 closest distance to " CG  MET A 105 " =    0.939
peak=   -3.269 closest distance to " OE1 GLN A  88 " =    0.985
peak=   -3.265 closest distance to " CA  ALA A 248 " =    2.568
peak=   -3.259 closest distance to " O   HOH Z 350 " =    1.787
peak=   -3.257 closest distance to " CD1 ILE A 151 " =    2.401
peak=   -3.256 closest distance to " CG  GLU A 277 " =    1.189
peak=   -3.251 closest distance to " CG  PRO A 163 " =    2.470
peak=   -3.246 closest distance to " ND2 ASN A 249 " =    2.432
peak=   -3.244 closest distance to " N   ALA A 248 " =    1.780
peak=   -3.244 closest distance to " O   HOH Z  51 " =    1.290
peak=   -3.242 closest distance to " C   LEU A 143 " =    1.122
peak=   -3.239 closest distance to " CE1 TYR A 169 " =    2.460
peak=   -3.232 closest distance to " NH2 ARG A 159 " =    2.375
peak=   -3.231 closest distance to " OG  SER A  62 " =    1.764
peak=   -3.229 closest distance to " OH  TYR A 214 " =    1.201
peak=   -3.227 closest distance to " N   SER A   3 " =    2.018
peak=   -3.226 closest distance to " O   HOH Z 281 " =    2.547
peak=   -3.225 closest distance to " CD1 TYR A 247 " =    2.324
peak=   -3.222 closest distance to " O   LEU A 167 " =    1.505
peak=   -3.216 closest distance to " CE2 PHE A 218 " =    2.537
peak=   -3.215 closest distance to " O   HOH Z 174 " =    2.591
peak=   -3.214 closest distance to " O   HOH Z 222 " =    1.566
peak=   -3.209 closest distance to " O   HOH Z 295 " =    1.590
peak=   -3.208 closest distance to " CG1 VAL A 125 " =    1.984
peak=   -3.208 closest distance to " O   ARG A  24 " =    2.110
peak=   -3.204 closest distance to " O   HOH Z 262 " =    2.871
peak=   -3.202 closest distance to " O   HOH Z 396 " =    1.951
peak=   -3.198 closest distance to " N   GLN A  58 " =    1.828
peak=   -3.197 closest distance to " C   ASN A 187 " =    1.830
peak=   -3.190 closest distance to " O   HOH Z 390 " =    2.313
peak=   -3.188 closest distance to " O   PRO A 198 " =    1.367
peak=   -3.186 closest distance to " O   HOH Z 111 " =    2.203
peak=   -3.180 closest distance to " C   ASN A 285 " =    2.446
peak=   -3.180 closest distance to " CB  ASN A  39 " =    2.259
peak=   -3.178 closest distance to " CD2 LEU A   5 " =    1.289
peak=   -3.177 closest distance to " O   SER A  22 " =    2.222
peak=   -3.174 closest distance to " CE3 TRP A  70 " =    1.829
peak=   -3.168 closest distance to " CH2 TRP A 177 " =    2.181
peak=   -3.165 closest distance to " N   ASN A  60 " =    1.254
peak=   -3.163 closest distance to " CA  SER A 135 " =    1.326
peak=   -3.162 closest distance to " O   HOH Z 310 " =    1.983
peak=   -3.161 closest distance to " CG2 VAL A 112 " =    2.521
peak=   -3.159 closest distance to " O   HOH Z  47 " =    1.709
peak=   -3.157 closest distance to " O   HOH Z 326 " =    5.082
peak=   -3.157 closest distance to " CG  PHE A 283 " =    2.776
peak=   -3.157 closest distance to " NH2 ARG A  66 " =    2.124
peak=   -3.155 closest distance to " O   ASP A 272 " =    2.335
peak=   -3.154 closest distance to " OG  SER A  63 " =    1.193
peak=   -3.150 closest distance to " O   HOH Z 139 " =    3.008
peak=   -3.150 closest distance to " CB  TRP A  85 " =    2.502
peak=   -3.148 closest distance to " NE2 GLN A 103 " =    1.775
peak=   -3.145 closest distance to " CG  GLN A  88 " =    0.838
peak=   -3.142 closest distance to " O   HOH Z 184 " =    1.617
peak=   -3.132 closest distance to " O   HOH Z  13 " =    1.453
peak=   -3.126 closest distance to " CA  GLY A 133 " =    2.323
peak=   -3.122 closest distance to " O   HOH Z 123 " =    2.471
peak=   -3.120 closest distance to " CG1 VAL A  67 " =    2.950
peak=   -3.118 closest distance to " O   HOH Z 313 " =    1.119
peak=   -3.116 closest distance to " CB  ASP A 132 " =    2.339
peak=   -3.110 closest distance to " O   HOH Z 357 " =    2.229
peak=   -3.105 closest distance to " CG2 VAL A 230 " =    2.693
peak=   -3.102 closest distance to " CB  ASN A 252 " =    1.681
peak=   -3.101 closest distance to " OD1 ASP A 171 " =    1.630
peak=   -3.099 closest distance to " O   LYS A 289 " =    3.066
peak=   -3.098 closest distance to " O   HOH Z 128 " =    2.582
peak=   -3.098 closest distance to " O   HOH Z 369 " =    2.281
peak=   -3.096 closest distance to " O   THR A  18 " =    1.591
peak=   -3.095 closest distance to " O   HOH Z  17 " =    1.616
peak=   -3.092 closest distance to " NH2BARG A 275 " =    1.781
peak=   -3.084 closest distance to " CD2 TYR A 247 " =    2.309
peak=   -3.073 closest distance to " OG ASER A 134 " =    1.470
peak=   -3.063 closest distance to " OXT GLY A 302 " =    3.521
peak=   -3.052 closest distance to " O   VAL A 125 " =    2.340
peak=   -3.046 closest distance to " CB  TYR A  15 " =    2.230
peak=   -3.038 closest distance to " NE2 GLN A  88 " =    1.059
peak=   -3.033 closest distance to " O   HOH Z 106 " =    1.959
peak=   -3.031 closest distance to " CD1 ILE A 239 " =    2.369

================= 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    :  0.4285 0.4157   6.221749e+00   6.194259e+00
   1_bss:  0.4217 0.4017   6.215936e+00   6.181364e+00
   1_xyz:  0.3100 0.3309   5.996348e+00   6.048325e+00
   1_adp:  0.2432 0.2781   5.795244e+00   5.916700e+00
   1_occ:  0.2426 0.2784   5.793991e+00   5.917647e+00
   2_bss:  0.2387 0.2740   5.792338e+00   5.913414e+00
   2_xyz:  0.1644 0.2066   5.458655e+00   5.635504e+00
   2_adp:  0.1506 0.1950   5.385006e+00   5.579678e+00
   2_occ:  0.1505 0.1949   5.384371e+00   5.579056e+00
   3_bss:  0.1502 0.1940   5.384687e+00   5.578511e+00
   3_xyz:  0.1266 0.1710   5.241810e+00   5.466667e+00
   3_adp:  0.1209 0.1680   5.212215e+00   5.450192e+00
   3_occ:  0.1208 0.1680   5.212163e+00   5.450484e+00
   4_bss:  0.1208 0.1679   5.211775e+00   5.450295e+00
   4_xyz:  0.1153 0.1648   5.182814e+00   5.432410e+00
   4_adp:  0.1156 0.1621   5.175827e+00   5.418278e+00
   4_occ:  0.1154 0.1620   5.175416e+00   5.418144e+00
   5_bss:  0.1157 0.1617   5.175566e+00   5.416611e+00
   5_xyz:  0.1141 0.1606   5.165918e+00   5.408728e+00
   5_adp:  0.1136 0.1608   5.164663e+00   5.409736e+00
   5_occ:  0.1136 0.1608   5.164603e+00   5.409835e+00
   5_bss:  0.1135 0.1608   5.164586e+00   5.409835e+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:  0.332  27.680   8.488   7.394   8.162   0.000   0.000   0.000
   1_xyz:  0.332  27.680   8.488   7.394   8.162   0.000   0.000   0.000
   1_adp:  0.332  27.680   8.488   7.394   8.162   0.000   0.000   0.000
   1_occ:  0.332  27.680   8.488   7.394   8.162   0.000   0.000   0.000
   2_bss:  0.339  52.718   5.436   4.294   5.459   0.000   0.000   0.000
   2_xyz:  0.339  52.718   5.436   4.294   5.459   0.000   0.000   0.000
   2_adp:  0.339  52.718   5.436   4.294   5.459   0.000   0.000   0.000
   2_occ:  0.339  52.718   5.436   4.294   5.459   0.000   0.000   0.000
   3_bss:  0.332  52.718   3.786   3.428   4.583   0.000   0.000   0.000
   3_xyz:  0.332  52.718   3.786   3.428   4.583   0.000   0.000   0.000
   3_adp:  0.332  52.718   3.786   3.428   4.583   0.000   0.000   0.000
   3_occ:  0.332  52.718   3.786   3.428   4.583   0.000   0.000   0.000
   4_bss:  0.327  56.690   3.535   3.355   4.505   0.000   0.000   0.000
   4_xyz:  0.327  56.690   3.535   3.355   4.505   0.000   0.000   0.000
   4_adp:  0.327  56.690   3.535   3.355   4.505   0.000   0.000   0.000
   4_occ:  0.327  56.690   3.535   3.355   4.505   0.000   0.000   0.000
   5_bss:  0.330  56.690   3.408   3.313   4.480   0.000   0.000   0.000
   5_xyz:  0.330  56.690   3.408   3.313   4.480   0.000   0.000   0.000
   5_adp:  0.330  56.690   3.408   3.313   4.480   0.000   0.000   0.000
   5_occ:  0.330  56.690   3.408   3.313   4.480   0.000   0.000   0.000
   5_bss:  0.321  54.364  -0.338  -0.425   0.763  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.096 0.5703  0.6293    49745.991
   1_bss:  45.992 0.5700  0.8004    47771.642
   1_xyz:  36.165 0.6871  0.9343    30810.910
   1_adp:  28.513 0.7749  1.0197    20951.846
   1_occ:  28.549 0.7744  1.0189    20977.760
   2_bss:  28.332 0.7766  0.9189    20679.346
   2_xyz:  19.526 0.8663  0.9942    10602.788
   2_adp:  17.966 0.8814  1.0071     9427.689
   2_occ:  17.949 0.8815  1.0070     9410.757
   3_bss:  17.954 0.8815  0.9659     9420.054
   3_xyz:  15.551 0.9023  0.9766     7465.390
   3_adp:  15.199 0.9054  0.9761     7201.115
   3_occ:  15.204 0.9054  0.9760     7204.571
   4_bss:  15.196 0.9054  0.9712     7199.885
   4_xyz:  14.792 0.9089  0.9721     6930.797
   4_adp:  14.445 0.9118  0.9723     6756.051
   4_occ:  14.452 0.9118  0.9721     6751.628
   5_bss:  14.447 0.9117  0.9690     6713.079
   5_xyz:  14.290 0.9130  0.9695     6608.856
   5_adp:  14.314 0.9129  0.9672     6616.070
   5_occ:  14.317 0.9129  0.9671     6616.054
   5_bss:  14.320 0.9128  0.9673     6610.911
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4140e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4140e+01
   1_xyz:   1.494  0.011  0.100 17.990  0.006  4.125   1.1615e-01
   1_adp:   1.494  0.011  0.100 17.990  0.006  4.125   1.1615e-01
   1_occ:   1.494  0.011  0.100 17.990  0.006  4.125   1.1615e-01
   2_bss:   1.494  0.011  0.100 17.990  0.006  4.125   1.1615e-01
   2_xyz:   1.010  0.008  0.074 16.435  0.004  4.129   6.5375e-02
   2_adp:   1.010  0.008  0.074 16.435  0.004  4.129   6.5375e-02
   2_occ:   1.010  0.008  0.074 16.435  0.004  4.129   6.5375e-02
   3_bss:   1.010  0.008  0.074 16.435  0.004  4.129   6.5375e-02
   3_xyz:   1.050  0.008  0.084 16.233  0.004  4.140   6.8028e-02
   3_adp:   1.050  0.008  0.084 16.233  0.004  4.140   6.8028e-02
   3_occ:   1.050  0.008  0.084 16.233  0.004  4.140   6.8028e-02
   4_bss:   1.050  0.008  0.084 16.233  0.004  4.140   6.8028e-02
   4_xyz:   1.067  0.009  0.086 15.951  0.004  4.113   7.0750e-02
   4_adp:   1.067  0.009  0.086 15.951  0.004  4.113   7.0750e-02
   4_occ:   1.067  0.009  0.086 15.951  0.004  4.113   7.0750e-02
   5_bss:   1.067  0.009  0.086 15.951  0.004  4.113   7.0750e-02
   5_xyz:   1.031  0.009  0.084 15.693  0.004  4.115   6.6837e-02
   5_adp:   1.031  0.009  0.084 15.693  0.004  4.115   6.6837e-02
   5_occ:   1.031  0.009  0.084 15.693  0.004  4.115   6.6837e-02
   5_bss:   1.031  0.009  0.084 15.693  0.004  4.115   6.6837e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0203e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0203e+00
   1_xyz:  12.368  0.135  0.381 86.623  0.038  2.286   8.7215e-02
   1_adp:  12.368  0.135  0.381 86.623  0.038  2.286   8.7215e-02
   1_occ:  12.368  0.135  0.381 86.623  0.038  2.286   8.7215e-02
   2_bss:  12.368  0.135  0.381 86.623  0.038  2.286   8.7215e-02
   2_xyz:   7.291  0.076  0.286 85.995  0.041  2.389   5.5282e-02
   2_adp:   7.291  0.076  0.286 85.995  0.041  2.389   5.5282e-02
   2_occ:   7.291  0.076  0.286 85.995  0.041  2.389   5.5282e-02
   3_bss:   7.291  0.076  0.286 85.995  0.041  2.389   5.5282e-02
   3_xyz:   8.997  0.057  0.508 82.822  0.039  2.348   4.1134e-02
   3_adp:   8.997  0.057  0.508 82.822  0.039  2.348   4.1134e-02
   3_occ:   8.997  0.057  0.508 82.822  0.039  2.348   4.1134e-02
   4_bss:   8.997  0.057  0.508 82.822  0.039  2.348   4.1134e-02
   4_xyz:   7.783  0.040  0.567 83.389  0.038  2.330   4.7643e-02
   4_adp:   7.783  0.040  0.567 83.389  0.038  2.330   4.7643e-02
   4_occ:   7.783  0.040  0.567 83.389  0.038  2.330   4.7643e-02
   5_bss:   7.783  0.040  0.567 83.389  0.038  2.330   4.7643e-02
   5_xyz:   7.660  0.044  0.542 83.186  0.038  2.355   4.3585e-02
   5_adp:   7.660  0.044  0.542 83.186  0.038  2.355   4.3585e-02
   5_occ:   7.660  0.044  0.542 83.186  0.038  2.355   4.3585e-02
   5_bss:   7.660  0.044  0.542 83.186  0.038  2.355   4.3585e-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:  69.42   0.00  10.50  64.86   0.00   7.26  69.42   0.00  28.14
   1_occ:  69.42   0.00  10.50  64.86   0.00   7.26  69.42   0.00  28.14
   2_bss:  69.42   0.00  10.50  64.86   0.00   7.26  69.42   0.00  28.14
   2_xyz:  69.42   0.00  10.50  64.86   0.00   7.26  69.42   0.00  28.14
   2_adp:  69.47   0.00  10.93  63.55   0.00   7.20  69.47   0.00  31.26
   2_occ:  69.47   0.00  10.93  63.55   0.00   7.20  69.47   0.00  31.26
   3_bss:  69.47   0.00  10.93  63.55   0.00   7.20  69.47   0.00  31.26
   3_xyz:  69.47   0.00  10.93  63.55   0.00   7.20  69.47   0.00  31.26
   3_adp:  77.68   0.00  11.89  75.77   0.00   7.47  77.68   0.00  35.93
   3_occ:  77.68   0.00  11.89  75.77   0.00   7.47  77.68   0.00  35.93
   4_bss:  77.68   0.00  11.89  75.77   0.00   7.47  77.68   0.00  35.93
   4_xyz:  77.68   0.00  11.89  75.77   0.00   7.47  77.68   0.00  35.93
   4_adp:  77.22   0.00  11.45  74.95   0.00   7.30  77.22   0.85  34.07
   4_occ:  77.22   0.00  11.45  74.95   0.00   7.30  77.22   0.85  34.07
   5_bss:  77.22   0.00  11.45  74.95   0.00   7.30  77.22   0.85  34.07
   5_xyz:  77.22   0.00  11.45  74.95   0.00   7.30  77.22   0.85  34.07
   5_adp:  78.50   0.00  11.39  78.50   0.00   7.27  78.17   0.84  33.85
   5_occ:  78.50   0.00  11.39  78.50   0.00   7.27  78.17   0.84  33.85
   5_bss:  82.24   3.74  15.13  82.24   3.74  11.01  81.91   4.58  37.59
------------------------------------------------------------------------
 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:    1.187    0.016    0.401
   1_adp:    1.187    0.016    0.401
   1_occ:    1.187    0.016    0.401
   2_bss:    1.187    0.016    0.401
   2_xyz:    1.465    0.015    0.497
   2_adp:    1.465    0.015    0.497
   2_occ:    1.465    0.015    0.497
   3_bss:    1.465    0.015    0.497
   3_xyz:    1.440    0.028    0.526
   3_adp:    1.440    0.028    0.526
   3_occ:    1.440    0.028    0.526
   4_bss:    1.440    0.028    0.526
   4_xyz:    1.501    0.041    0.542
   4_adp:    1.501    0.041    0.542
   4_occ:    1.501    0.041    0.542
   5_bss:    1.501    0.041    0.542
   5_xyz:    1.541    0.043    0.552
   5_adp:    1.541    0.043    0.552
   5_occ:    1.541    0.043    0.552
   5_bss:    1.541    0.043    0.552
------------------------------------------------------------------------

CPU time actual refinement: 316.72


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1029/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_1029/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1029/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1029/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1029/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.56 
  Macro-tasks:
    bulk solvent and scale       = 37.14  
    individual site refinement   = 126.59 
    weights calculation          = 33.02  
    collect and process          = 6.73   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 203.61 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 96.37  
    alpha_beta                      = 8.28   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 105.57 
    fmodel                         = 6.82   
    r_factors                      = 0.24   
    phase_errors                   = 11.03  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 231.45 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.550 micro seconds
Total CPU time: 5.50 minutes
from_scatterers_fft:    621 calls, 96.05 s
gradients_fft:          566 calls, 92.86 s

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

# Date 2008-01-16 Time 03:01:19 PST -0800 (1200481279.66 s)
Start R-work = 0.4285, R-free = 0.4157 (no bulk solvent and anisotropic scale)
Final R-work = 0.1304, R-free = 0.1767 (no bulk solvent and anisotropic scale)

Start R-work = 0.4217, R-free = 0.4017
Final R-work = 0.1135, R-free = 0.1608