# Date 2008-01-16 Time 03:03:36 PST -0800 (1200481416.14 s)
#phil __OFF__

Command line arguments: "../1089.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21940
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1089

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 45.7567, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95037
Completeness in resolution range: 0.942549
Completeness with d_max=infinity: 0.939836

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1017
                             d_min =   1.9504

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95037
Completeness in resolution range: 0.942549
Completeness with d_max=infinity: 0.939836

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1022 -  4.1751 [2180/2207]  1967   213   9.8%
  bin  2:  4.1751 -  3.3256 [2097/2117]  1884   213  10.2%
  bin  3:  3.3256 -  2.9086 [2061/2080]  1851   210  10.2%
  bin  4:  2.9086 -  2.6442 [2044/2074]  1841   203   9.9%
  bin  5:  2.6442 -  2.4555 [2047/2066]  1846   201   9.8%
  bin  6:  2.4555 -  2.3113 [2021/2046]  1812   209  10.3%
  bin  7:  2.3113 -  2.1959 [2037/2065]  1831   206  10.1%
  bin  8:  2.1959 -  2.1006 [1995/2031]  1805   190   9.5%
  bin  9:  2.1006 -  2.0199 [1967/2051]  1775   192   9.8%
  bin 10:  2.0199 -  1.9504 [1140/2046]  1018   122  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1089/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:
        1.13 -     1.88: 9
        1.88 -     2.64: 140
        2.64 -     3.39: 4403
        3.39 -     4.15: 9540
        4.15 -     4.90: 14756
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.128 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.416 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.704 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  ... (remaining 28843 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_1089/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1089/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 45.75675 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5285   r_free= 0.5323   ksol= 0.00   Bsol= 0.00   scale= 0.761    |
|                                                                             |
| 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:   1.05 A                  |
| x-ray target function (ml) for work reflections: 6.318006                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6576 0.99   1418  161 0.4566 0.5089      6.6871      6.7598|
|  2:  4.6576 -  3.7150 0.99   1363  148 0.4876 0.4703      6.9023      6.9178|
|  3:  3.7150 -  3.2507 0.99   1322  141 0.5233 0.4868      6.7563      6.7715|
|  4:  3.2507 -  2.9559 0.99   1345  163 0.5316 0.5183      6.5858      6.5444|
|  5:  2.9559 -  2.7454 0.99   1320  136 0.5415 0.5569      6.3984      6.3802|
|  6:  2.7454 -  2.5844 0.99   1303  152 0.5611 0.5516      6.3085      6.2996|
|  7:  2.5844 -  2.4555 0.99   1318  139 0.5546 0.4938      6.2678       6.169|
|  8:  2.4555 -  2.3491 0.98   1288  154 0.5611 0.5591      6.1739       6.219|
|  9:  2.3491 -  2.2589 0.98   1290  145 0.5480 0.5441      6.1577      6.1361|
| 10:  2.2589 -  2.1812 1.00   1287  143 0.5486 0.6033      6.0986      6.1048|
| 11:  2.1812 -  2.1132 0.98   1324  135 0.5496 0.5587      6.0522      6.0629|
| 12:  2.1132 -  2.0530 0.98   1266  152 0.5402 0.5967      5.9656      6.0007|
| 13:  2.0530 -  1.9990 0.89   1162  130 0.5591 0.5460      5.8809      5.8349|
| 14:  1.9990 -  1.9504 0.46    624   60 0.5588 0.4917      5.8277      5.8327|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1022 -  4.6576  1418   161  0.53  48.72   0.76     0.59     127617.20|
|  2:  4.6576 -  3.7150  1363   148  0.54  48.48   0.81     0.64     179227.82|
|  3:  3.7150 -  3.2507  1322   141  0.40  59.85   0.79     0.54     182784.26|
|  4:  3.2507 -  2.9559  1345   163  0.29  68.23   0.76     0.39     153870.94|
|  5:  2.9559 -  2.7454  1320   136  0.19  75.75   0.71     0.25     112763.60|
|  6:  2.7454 -  2.5844  1303   152  0.20  74.97   0.70     0.25      91599.58|
|  7:  2.5844 -  2.4555  1318   139  0.21  73.96   0.72     0.25      74744.40|
|  8:  2.4555 -  2.3491  1288   154  0.24  71.88   0.71     0.30      66587.48|
|  9:  2.3491 -  2.2589  1290   145  0.21  74.42   0.73     0.25      62257.72|
| 10:  2.2589 -  2.1812  1287   143  0.17  77.30   0.73     0.21      59170.66|
| 11:  2.1812 -  2.1132  1324   135  0.11  81.80   0.76     0.14      57174.94|
| 12:  2.1132 -  2.0530  1266   152  0.09  83.09   0.75     0.12      51399.43|
| 13:  2.0530 -  1.9990  1162   130  0.06  85.22   0.72     0.09      44879.47|
| 14:  1.9990 -  1.9504   624    60  0.04  87.07   0.74     0.05      37955.40|
|alpha:            min =        0.05 max =            0.64 mean =         0.31|
|beta:             min =    37955.40 max =       182784.26 mean =     96392.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.25|
|phase err.(work): min =        0.00 max =           89.99 mean =        71.25|
|phase err.(test): min =        0.00 max =           89.91 mean =        71.45|
|-----------------------------------------------------------------------------|

============================== 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 = 35.813332             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.783   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.799207              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.692   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       38 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      192 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      724 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1555 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2686 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3994 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5160 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6654 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7862 |
|-----------------------------------------------------------------------------|
|-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 |       52.971 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.196 |       2.656 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.494)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.494)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5318   r_free= 0.5338   ksol= 0.00   Bsol= 0.00   scale= 0.733    |
|                                                                             |
| 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:   1.11 A                  |
| x-ray target function (ml) for work reflections: 6.318296                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5231   r_free= 0.5212   ksol= 0.39   Bsol= 20.00   scale= 0.920   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.00,7.21,6.80,0.00,0.00,0.00); trace/3= 7.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.25 A                  |
| x-ray target function (ml) for work reflections: 6.110458                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 28.324094             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.646   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.031076              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.839   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5231      final r-factor (work) = 0.4857          |
| start r-factor (free) = 0.5212      final r-factor (free) = 0.5153          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 142.4077 = 28.32 * 0.50 * 6.3152 + 1.00 * 52.9713                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.3385 = 28.32 * 0.50 * 6.0855 + 1.00 * 0.1559                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4857      final r-factor (work) = 0.4576          |
| start r-factor (free) = 0.5153      final r-factor (free) = 0.5160          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.4599 = 3.03 * 1.00 * 6.0855 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.0217 = 3.03 * 1.00 * 6.2668 + 1.00 * 0.0265                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.494)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.35  21.38    None  None   None       |
|    all(noH): 2823   0      0.00    114.35  21.38    None  None   None       |
|    Sol.    : 438    0      0.00    97.25   25.20    None  None   None       |
|    Mac.    : 2385   0      0.00    114.35  20.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.436:  802   |   5:    57.177 -  68.613:   52        |
|      1:    11.436 -  22.871:  907   |   6:    68.613 -  80.048:   20        |
|      2:    22.871 -  34.306:  610   |   7:    80.048 -  91.484:    6        |
|      3:    34.306 -  45.742:  294   |   8:    91.484 - 102.919:    5        |
|      4:    45.742 -  57.177:  126   |   9:   102.919 - 114.355:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4576 r_free = 0.5160             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4574 r_free = 0.5152             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4574   r_free= 0.5152   ksol= 0.39   Bsol= 20.00   scale= 1.134   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.00,7.21,6.80,0.00,0.00,0.00); trace/3= 7.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.14 A                  |
| x-ray target function (ml) for work reflections: 5.833567                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4560   r_free= 0.5111   ksol= 0.34   Bsol= 33.58   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,3.40,3.93,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.13 A                  |
| x-ray target function (ml) for work reflections: 5.833437                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.336367             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.783  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.037372              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.368  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4560      final r-factor (work) = 0.4246          |
| start r-factor (free) = 0.5111      final r-factor (free) = 0.4927          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.4598 = 17.34 * 0.50 * 6.2647 + 1.00 * 0.1559                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.4437 = 17.34 * 0.50 * 5.8081 + 1.00 * 0.0979                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4246      final r-factor (work) = 0.4240          |
| start r-factor (free) = 0.4927      final r-factor (free) = 0.4849          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0516 = 1.04 * 1.00 * 5.8081 + 1.00 * 0.0264                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4671 = 1.04 * 1.00 * 6.2251 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.494)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.98  19.84    None  None   None       |
|    all(noH): 2823   0      0.00    115.98  19.84    None  None   None       |
|    Sol.    : 438    0      0.00    93.31   22.79    None  None   None       |
|    Mac.    : 2385   0      0.00    115.98  19.30    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 -  11.598:  730   |   5:    57.988 -  69.585:   11        |
|      1:    11.598 -  23.195: 1171   |   6:    69.585 -  81.183:    5        |
|      2:    23.195 -  34.793:  639   |   7:    81.183 -  92.780:    4        |
|      3:    34.793 -  46.390:  187   |   8:    92.780 - 104.378:    2        |
|      4:    46.390 -  57.988:   73   |   9:   104.378 - 115.975:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4240 r_free = 0.4849             target_work(ml) = 6.221         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4239 r_free = 0.4851             target_work(ml) = 6.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4239   r_free= 0.4851   ksol= 0.34   Bsol= 33.58   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,3.40,3.93,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.220621                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4239   r_free= 0.4844   ksol= 0.34   Bsol= 33.58   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,1.12,1.92,0.00,0.00,0.00); trace/3= 1.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.221985                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.380941             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.844  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.853886              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 162.068  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4239      final r-factor (work) = 0.3834          |
| start r-factor (free) = 0.4844      final r-factor (free) = 0.4618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.9761 = 15.38 * 0.50 * 6.2257 + 1.00 * 0.0979                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.7367 = 15.38 * 0.50 * 6.1936 + 1.00 * 0.1047                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3834      final r-factor (work) = 0.3688          |
| start r-factor (free) = 0.4618      final r-factor (free) = 0.4592          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2981 = 0.85 * 1.00 * 6.1936 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2644 = 0.85 * 1.00 * 6.1534 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 36     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.494)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.02  19.04    None  None   None       |
|    all(noH): 2823   0      0.00    116.02  19.04    None  None   None       |
|    Sol.    : 438    0      0.00    91.04   24.41    None  None   None       |
|    Mac.    : 2385   0      0.00    116.02  18.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.602:  801   |   5:    58.011 -  69.614:    9        |
|      1:    11.602 -  23.205: 1189   |   6:    69.614 -  81.216:    6        |
|      2:    23.205 -  34.807:  583   |   7:    81.216 -  92.818:    3        |
|      3:    34.807 -  46.409:  169   |   8:    92.818 - 104.420:    2        |
|      4:    46.409 -  58.011:   60   |   9:   104.420 - 116.023:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3688 r_free = 0.4592             target_work(ml) = 6.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3686 r_free = 0.4600             target_work(ml) = 6.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3686   r_free= 0.4600   ksol= 0.34   Bsol= 33.58   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,1.12,1.92,0.00,0.00,0.00); trace/3= 1.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.148811                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3684   r_free= 0.4596   ksol= 0.33   Bsol= 33.58   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.92,0.43,1.07,0.00,0.00,0.00); trace/3= 0.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.148225                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.648623              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.004  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 27.961736             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.611  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3684      final r-factor (work) = 0.3293          |
| start r-factor (free) = 0.4596      final r-factor (free) = 0.4124          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.7892 = 9.65 * 0.50 * 6.1530 + 1.00 * 0.1052                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.6084 = 9.65 * 0.50 * 6.1187 + 1.00 * 0.0898                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3293      final r-factor (work) = 0.3019          |
| start r-factor (free) = 0.4124      final r-factor (free) = 0.4087          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 171.1004 = 27.96 * 1.00 * 6.1187 + 1.00 * 0.0101                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 168.5375 = 27.96 * 1.00 * 6.0258 + 1.00 * 0.0461                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.494)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    155.10  23.45    None  None   None       |
|    all(noH): 2823   0      0.00    155.10  23.45    None  None   None       |
|    Sol.    : 438    0      0.91    135.69  38.78    None  None   None       |
|    Mac.    : 2385   0      0.00    155.10  20.64    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 -  15.511: 1344   |   5:    77.553 -  93.063:   65        |
|      1:    15.511 -  31.021:  717   |   6:    93.063 - 108.573:   22        |
|      2:    31.021 -  46.532:  353   |   7:   108.573 - 124.084:    7        |
|      3:    46.532 -  62.042:  199   |   8:   124.084 - 139.594:    6        |
|      4:    62.042 -  77.553:  109   |   9:   139.594 - 155.105:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3019 r_free = 0.4087             target_work(ml) = 6.017         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3018 r_free = 0.4089             target_work(ml) = 6.017         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3018   r_free= 0.4089   ksol= 0.33   Bsol= 33.58   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.92,0.43,1.07,0.00,0.00,0.00); trace/3= 0.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.017094                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3019   r_free= 0.4077   ksol= 0.34   Bsol= 51.36   scale= 1.067   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.73,0.70,1.63,0.00,0.00,0.00); trace/3= 1.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.016444                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.862672             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.465   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.423147              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.787  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3019      final r-factor (work) = 0.2625          |
| start r-factor (free) = 0.4077      final r-factor (free) = 0.3675          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.8376 = 11.86 * 0.50 * 6.0269 + 1.00 * 0.0898                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.5053 = 11.86 * 0.50 * 5.9704 + 1.00 * 0.0929                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2625      final r-factor (work) = 0.2536          |
| start r-factor (free) = 0.3675      final r-factor (free) = 0.3419          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5718 = 0.42 * 1.00 * 5.9704 + 1.00 * 0.0455                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5171 = 0.42 * 1.00 * 5.9130 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.494)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    149.27  20.14    None  None   None       |
|    all(noH): 2823   0      0.00    149.27  20.14    None  None   None       |
|    Sol.    : 438    0      0.00    120.43  37.32    None  None   None       |
|    Mac.    : 2385   0      0.00    149.27  16.98    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 -  14.927: 1431   |   5:    74.637 -  89.565:   27        |
|      1:    14.927 -  29.855:  774   |   6:    89.565 - 104.492:    8        |
|      2:    29.855 -  44.782:  367   |   7:   104.492 - 119.419:    2        |
|      3:    44.782 -  59.710:  150   |   8:   119.419 - 134.347:    3        |
|      4:    59.710 -  74.637:   60   |   9:   134.347 - 149.274:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2536 r_free = 0.3419             target_work(ml) = 5.871         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2532 r_free = 0.3413             target_work(ml) = 5.869         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2532   r_free= 0.3413   ksol= 0.34   Bsol= 51.36   scale= 1.077   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.73,0.70,1.63,0.00,0.00,0.00); trace/3= 1.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.869410                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6576 0.99   1418  161 0.1319 0.2274      5.7264      6.1521|
|  2:  4.6576 -  3.7150 0.99   1363  148 0.1631 0.2579       6.088      6.4487|
|  3:  3.7150 -  3.2507 0.99   1322  141 0.2230 0.3216      6.1853      6.4401|
|  4:  3.2507 -  2.9559 0.99   1345  163 0.2568 0.3300       6.105      6.2782|
|  5:  2.9559 -  2.7454 0.99   1320  136 0.2802 0.3801      6.0073      6.1664|
|  6:  2.7454 -  2.5844 0.99   1303  152 0.2912 0.3683      5.9536      6.0998|
|  7:  2.5844 -  2.4555 0.99   1318  139 0.2861 0.4133      5.9231      6.0689|
|  8:  2.4555 -  2.3491 0.98   1288  154 0.3071 0.3935      5.8485      6.0288|
|  9:  2.3491 -  2.2589 0.98   1290  145 0.2936 0.3564      5.7988      5.8872|
| 10:  2.2589 -  2.1812 1.00   1287  143 0.2974 0.4299      5.7627      5.9461|
| 11:  2.1812 -  2.1132 0.98   1324  135 0.3181 0.3929      5.7509       5.918|
| 12:  2.1132 -  2.0530 0.98   1266  152 0.3038 0.3647       5.648      5.7978|
| 13:  2.0530 -  1.9990 0.89   1162  130 0.3151 0.3820      5.5786      5.6889|
| 14:  1.9990 -  1.9504 0.46    624   60 0.3424 0.4222      5.6105      5.7384|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1022 -  4.6576  1418   161  0.87  17.46   0.99     0.96      18642.36|
|  2:  4.6576 -  3.7150  1363   148  0.86  20.15   1.11     1.09      36869.18|
|  3:  3.7150 -  3.2507  1322   141  0.75  31.05   1.13     1.08      56479.40|
|  4:  3.2507 -  2.9559  1345   163  0.71  34.52   1.10     1.00      47180.18|
|  5:  2.9559 -  2.7454  1320   136  0.67  38.07   1.09     0.99      41402.71|
|  6:  2.7454 -  2.5844  1303   152  0.65  39.83   1.05     0.89      37096.53|
|  7:  2.5844 -  2.4555  1318   139  0.61  42.83   1.06     0.86      37638.74|
|  8:  2.4555 -  2.3491  1288   154  0.63  41.80   1.05     0.87      30295.03|
|  9:  2.3491 -  2.2589  1290   145  0.65  39.44   1.09     0.90      25597.23|
| 10:  2.2589 -  2.1812  1287   143  0.65  39.86   1.11     0.97      25055.13|
| 11:  2.1812 -  2.1132  1324   135  0.63  41.17   1.13     0.96      23935.19|
| 12:  2.1132 -  2.0530  1266   152  0.65  40.14   1.11     0.95      20203.10|
| 13:  2.0530 -  1.9990  1162   130  0.62  42.07   1.11     0.94      18123.74|
| 14:  1.9990 -  1.9504   624    60  0.60  44.62   1.11     0.84      17900.38|
|alpha:            min =        0.84 max =            1.09 mean =         0.95|
|beta:             min =    17900.38 max =        56479.40 mean =     31831.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           89.97 mean =        36.10|
|phase err.(test): min =        0.00 max =           89.96 mean =        35.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2530   r_free= 0.3403   ksol= 0.35   Bsol= 54.04   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.17,-0.56,0.39,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.868466                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2530   r_free= 0.3403   ksol= 0.35   Bsol= 54.04   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.17,-0.56,0.39,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.868466                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6576 0.99   1418  161 0.1370 0.2213      5.7241      6.1258|
|  2:  4.6576 -  3.7150 0.99   1363  148 0.1647 0.2576      6.0871      6.4593|
|  3:  3.7150 -  3.2507 0.99   1322  141 0.2228 0.3194      6.1836      6.4339|
|  4:  3.2507 -  2.9559 0.99   1345  163 0.2571 0.3303      6.1034      6.2776|
|  5:  2.9559 -  2.7454 0.99   1320  136 0.2795 0.3797      6.0053      6.1654|
|  6:  2.7454 -  2.5844 0.99   1303  152 0.2913 0.3676      5.9523      6.0982|
|  7:  2.5844 -  2.4555 0.99   1318  139 0.2860 0.4143      5.9212      6.0689|
|  8:  2.4555 -  2.3491 0.98   1288  154 0.3074 0.3938      5.8489      6.0288|
|  9:  2.3491 -  2.2589 0.98   1290  145 0.2936 0.3555      5.7984      5.8861|
| 10:  2.2589 -  2.1812 1.00   1287  143 0.2973 0.4295      5.7624      5.9462|
| 11:  2.1812 -  2.1132 0.98   1324  135 0.3179 0.3928      5.7505      5.9182|
| 12:  2.1132 -  2.0530 0.98   1266  152 0.3040 0.3653      5.6482      5.7982|
| 13:  2.0530 -  1.9990 0.89   1162  130 0.3148 0.3827      5.5782      5.6901|
| 14:  1.9990 -  1.9504 0.46    624   60 0.3423 0.4223      5.6108      5.7384|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1022 -  4.6576  1418   161  0.88  16.80   0.98     0.96      17580.94|
|  2:  4.6576 -  3.7150  1363   148  0.86  19.65   1.09     1.07      35317.31|
|  3:  3.7150 -  3.2507  1322   141  0.75  30.94   1.10     1.06      56054.03|
|  4:  3.2507 -  2.9559  1345   163  0.71  34.38   1.06     0.97      46874.70|
|  5:  2.9559 -  2.7454  1320   136  0.67  37.88   1.05     0.95      41071.40|
|  6:  2.7454 -  2.5844  1303   152  0.65  39.61   1.00     0.85      36868.62|
|  7:  2.5844 -  2.4555  1318   139  0.61  42.68   1.01     0.82      37404.46|
|  8:  2.4555 -  2.3491  1288   154  0.63  41.80   1.00     0.83      30370.18|
|  9:  2.3491 -  2.2589  1290   145  0.65  39.43   1.03     0.86      25599.81|
| 10:  2.2589 -  2.1812  1287   143  0.65  39.80   1.05     0.92      25027.27|
| 11:  2.1812 -  2.1132  1324   135  0.64  41.10   1.06     0.90      23898.77|
| 12:  2.1132 -  2.0530  1266   152  0.65  40.11   1.04     0.89      20214.82|
| 13:  2.0530 -  1.9990  1162   130  0.62  42.05   1.03     0.87      18126.58|
| 14:  1.9990 -  1.9504   624    60  0.59  44.70   1.03     0.78      17953.74|
|alpha:            min =        0.78 max =            1.07 mean =         0.92|
|beta:             min =    17580.94 max =        56054.03 mean =     31515.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           89.96 mean =        35.93|
|phase err.(test): min =        0.00 max =           89.86 mean =        34.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.494)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.16    149.44  20.30    None  None   None       |
|    all(noH): 2823   0      0.16    149.44  20.30    None  None   None       |
|    Sol.    : 438    0      0.16    120.60  37.49    None  None   None       |
|    Mac.    : 2385   0      0.16    149.44  17.14    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:     0.163 -  15.091: 1431   |   5:    74.800 -  89.728:   27        |
|      1:    15.091 -  30.018:  774   |   6:    89.728 - 104.655:    8        |
|      2:    30.018 -  44.946:  367   |   7:   104.655 - 119.583:    2        |
|      3:    44.946 -  59.873:  150   |   8:   119.583 - 134.510:    3        |
|      4:    59.873 -  74.800:   60   |   9:   134.510 - 149.437:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.545 - 5.817
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 326
   mapped sites are within: 0.706 - 5.817

peak=    7.072 closest distance to " C   GLU A  37 " =    1.811
peak=    7.029 closest distance to " C   LYS A  48 " =    1.217
peak=    5.915 closest distance to " O   HOH Z  72 " =    1.849
peak=    5.706 closest distance to " O   GLY A  35 " =    1.136
peak=    5.687 closest distance to " C   SER A  62 " =    1.101
peak=    5.655 closest distance to " O   TYR A  68 " =    0.938
peak=    5.507 closest distance to " O   VAL A  67 " =    1.126
peak=    5.373 closest distance to " C   ALA A  51 " =    0.898
peak=    5.301 closest distance to " NH1 ARG A  24 " =    1.482
peak=    5.217 closest distance to " O   HOH Z 396 " =    1.336
peak=    5.133 closest distance to " O   HOH Z 401 " =    2.056
peak=    5.132 closest distance to " CG2 VAL A 230 " =    1.391
peak=    5.087 closest distance to " O   HOH Z  15 " =    1.764
peak=    5.026 closest distance to " O   SER A 164 " =    1.173
peak=    4.977 closest distance to " O   ARG A  36 " =    1.045
peak=    4.933 closest distance to " O   HOH Z  82 " =    1.523
peak=    4.913 closest distance to " O   HOH Z 289 " =    1.733
peak=    4.909 closest distance to " ND2 ASN A  74 " =    1.363
peak=    4.851 closest distance to " O   HOH Z 223 " =    1.155
peak=    4.838 closest distance to " O   HOH Z 187 " =    2.358
peak=    4.817 closest distance to " N   ALA A  51 " =    0.838
peak=    4.794 closest distance to " CB  LEU A   5 " =    1.551
peak=    4.789 closest distance to " N   ARG A  56 " =    0.835
peak=    4.744 closest distance to " CA  ARG A  24 " =    1.172
peak=    4.742 closest distance to " OG1 THR A  42 " =    1.088
peak=    4.736 closest distance to " CG2 THR A  52 " =    1.198
peak=    4.712 closest distance to " O   PRO A  54 " =    1.016
peak=    4.706 closest distance to " OG1 THR A 221 " =    1.618
peak=    4.692 closest distance to " O   ILE A  33 " =    1.133
peak=    4.633 closest distance to " O   PRO A 280 " =    1.010
peak=    4.613 closest distance to " CG1 VAL A 296 " =    1.280
peak=    4.546 closest distance to " N   SER A  63 " =    0.706
peak=    4.533 closest distance to " N   ASN A  69 " =    0.828
peak=    4.521 closest distance to " CE3 TRP A  92 " =    1.105
peak=    4.511 closest distance to " N   ARG A  24 " =    0.987
peak=    4.464 closest distance to " N   ASN A  60 " =    0.974
peak=    4.409 closest distance to " N   ASP A  65 " =    0.911
peak=    4.390 closest distance to " N   TYR A  68 " =    0.806
peak=    4.387 closest distance to " CD1 LEU A   5 " =    1.288
peak=    4.373 closest distance to " N   SER A  26 " =    0.910
peak=    4.356 closest distance to " CB  ALA A 256 " =    1.329
peak=    4.339 closest distance to " O   HOH Z  45 " =    1.457
peak=    4.326 closest distance to " CG  LEU A 167 " =    1.533
peak=    4.323 closest distance to " O   HOH Z 167 " =    1.361
peak=    4.314 closest distance to " O   HOH Z  41 " =    1.511
peak=    4.311 closest distance to " N   ASP A  50 " =    0.887
peak=    4.256 closest distance to " CG2 VAL A 112 " =    1.017
peak=    4.252 closest distance to " CB  ASP A 270 " =    0.903
peak=    4.248 closest distance to " O   HOH Z 179 " =    1.302
peak=    4.246 closest distance to " NH2 ARG A 138 " =    2.182
peak=    4.214 closest distance to " N   VAL A  67 " =    0.969
peak=    4.213 closest distance to " OG  SER A 276 " =    1.260
peak=    4.196 closest distance to " CG1 ILE A 106 " =    1.347
peak=    4.164 closest distance to " O   HOH Z 130 " =    2.046
peak=    4.156 closest distance to " OG ASER A 164 " =    1.083
peak=    4.130 closest distance to " O   SER A 212 " =    1.608
peak=    4.105 closest distance to " CG2BVAL A 121 " =    1.010
peak=    4.089 closest distance to " O   GLY A  23 " =    1.198
peak=    4.078 closest distance to " CZ3 TRP A  70 " =    1.028
peak=    4.073 closest distance to " CB  ARG A 139 " =    1.693
peak=    4.073 closest distance to " CB  ALA A 233 " =    1.319
peak=    4.069 closest distance to " CB  ASN A 148 " =    2.008
peak=    4.062 closest distance to " O   SER A  97 " =    1.187
peak=    4.061 closest distance to " CB  ASN A  69 " =    0.996
peak=    4.048 closest distance to " O   HOH Z 321 " =    1.525
peak=    4.031 closest distance to " CB  ARG A 275 " =    1.471
peak=    4.029 closest distance to " CB  ARG A  79 " =    1.343
peak=    4.019 closest distance to " N   ARG A  66 " =    0.842
peak=    4.014 closest distance to " CA  TYR A  30 " =    1.370
peak=    4.001 closest distance to " CB  LYS A  48 " =    1.198
peak=    3.985 closest distance to " N   SER A   3 " =    0.734
peak=    3.979 closest distance to " OG ASER A 134 " =    1.644
peak=    3.979 closest distance to " ND2 ASN A  69 " =    1.063
peak=    3.962 closest distance to " O   HOH Z 222 " =    2.022
peak=    3.948 closest distance to " CB  ALA A  51 " =    1.132
peak=    3.947 closest distance to " O   HOH Z  86 " =    1.080
peak=    3.936 closest distance to " O   HOH Z 189 " =    2.366
peak=    3.936 closest distance to " CB  ASP A  50 " =    1.073
peak=    3.934 closest distance to " O   ASN A  69 " =    1.411
peak=    3.931 closest distance to " OG  SER A  22 " =    1.170
peak=    3.931 closest distance to " CG  ASN A  60 " =    0.784
peak=    3.920 closest distance to " O   HOH Z 316 " =    1.484
peak=    3.916 closest distance to " N   ALA A  64 " =    0.910
peak=    3.904 closest distance to " ND2 ASN A  60 " =    4.261
peak=    3.898 closest distance to " O   HOH Z 366 " =    3.027
peak=    3.894 closest distance to " CA  TRP A  70 " =    1.151
peak=    3.889 closest distance to " O   HOH Z 320 " =    1.703
peak=    3.888 closest distance to " CB  SER A 271 " =    1.192
peak=    3.885 closest distance to " N   ASN A 285 " =    0.868
peak=    3.885 closest distance to " C   PHE A  61 " =    0.936
peak=    3.884 closest distance to " O   HOH Z 177 " =    1.494
peak=    3.883 closest distance to " O   HOH Z 395 " =    1.402
peak=    3.859 closest distance to " O   HOH Z 289 " =    1.560
peak=    3.857 closest distance to " CG  ASP A 270 " =    1.254
peak=    3.855 closest distance to " O   ALA A 165 " =    1.142
peak=    3.835 closest distance to " NH2 ARG A  24 " =    1.380
peak=    3.834 closest distance to " CB  SER A  63 " =    1.658
peak=    3.832 closest distance to " O   HOH Z 362 " =    1.959
peak=    3.805 closest distance to " CE2 PHE A  61 " =    1.106
peak=    3.797 closest distance to " NZ BLYS A 290 " =    1.018
peak=    3.796 closest distance to " O   HOH Z 389 " =    1.778
peak=    3.793 closest distance to " O   HOH Z 224 " =    1.228
peak=    3.792 closest distance to " O   HOH Z 119 " =    1.411
peak=    3.792 closest distance to " O   GLU A  37 " =    1.558
peak=    3.784 closest distance to " N   LYS A 119 " =    1.094
peak=    3.773 closest distance to " CB  ASP A 298 " =    0.938
peak=    3.770 closest distance to " O   GLN A  55 " =    1.413
peak=    3.764 closest distance to " N   ASP A 107 " =    1.161
peak=    3.750 closest distance to " NH1AARG A 145 " =    1.147
peak=    3.745 closest distance to " CG  GLU A 277 " =    1.043
peak=    3.739 closest distance to " CA  PRO A  54 " =    0.923
peak=    3.736 closest distance to " O   ASN A  39 " =    1.248
peak=    3.733 closest distance to " O   HOH Z 331 " =    1.622
peak=    3.726 closest distance to " CA  GLY A 241 " =    3.993
peak=    3.726 closest distance to " O   ASN A  60 " =    1.008
peak=    3.721 closest distance to " CB  SER A  63 " =    1.830
peak=    3.710 closest distance to " CE1 TYR A  68 " =    1.008
peak=    3.710 closest distance to " CG  LEU A   5 " =    1.695
peak=    3.705 closest distance to " CG2 VAL A 232 " =    1.479
peak=    3.698 closest distance to " O   HOH Z 324 " =    1.462
peak=    3.694 closest distance to " O   HOH Z 178 " =    1.784
peak=    3.685 closest distance to " O   HOH Z 215 " =    1.826
peak=    3.670 closest distance to " O   HOH Z  49 " =    2.662
peak=    3.666 closest distance to " O   GLU A   2 " =    1.030
peak=    3.645 closest distance to " N   GLY A 287 " =    0.898
peak=    3.644 closest distance to " O   HOH Z 105 " =    1.436
peak=    3.639 closest distance to " O   HOH Z 333 " =    1.763
peak=    3.637 closest distance to " O   VAL A 296 " =    1.155
peak=    3.625 closest distance to " O   HOH Z 389 " =    2.866
peak=    3.625 closest distance to " ND2 ASN A 176 " =    1.045
peak=    3.616 closest distance to " O   HOH Z 262 " =    1.860
peak=    3.611 closest distance to " O   HOH Z 165 " =    2.443
peak=    3.608 closest distance to " O   HOH Z 251 " =    1.724
peak=    3.603 closest distance to " CB  ASN A  60 " =    1.321
peak=    3.600 closest distance to " O   HOH Z 111 " =    1.490
peak=    3.598 closest distance to " CG  GLU A  37 " =    0.822
peak=    3.588 closest distance to " CB AVAL A  41 " =    1.147
peak=    3.576 closest distance to " C   PHE A  38 " =    0.802
peak=    3.575 closest distance to " OG1 THR A 178 " =    1.696
peak=    3.571 closest distance to " O   SER A  62 " =    1.977
peak=    3.562 closest distance to " CD2 LEU A 228 " =    2.165
peak=    3.560 closest distance to " N   CYS A 260 " =    1.763
peak=    3.560 closest distance to " O   SER A 271 " =    1.077
peak=    3.556 closest distance to " CE3 TRP A 266 " =    1.111
peak=    3.548 closest distance to " CB  ASN A 224 " =    0.947
peak=    3.542 closest distance to " O   ARG A  56 " =    0.924
peak=    3.535 closest distance to " CG2 THR A 246 " =    1.586
peak=    3.533 closest distance to " O   HOH Z 106 " =    2.151
peak=    3.531 closest distance to " O   HOH Z 434 " =    2.624
peak=    3.530 closest distance to " CB  ALA A 291 " =    2.310
peak=    3.530 closest distance to " N   GLY A  75 " =    1.113
peak=    3.527 closest distance to " OG  SER A  22 " =    2.823
peak=    3.526 closest distance to " O   HOH Z 232 " =    1.423
peak=    3.518 closest distance to " CB  GLN A 122 " =    1.158
peak=    3.517 closest distance to " O   HOH Z 217 " =    1.883
peak=    3.511 closest distance to " O   HOH Z 197 " =    1.615
peak=    3.501 closest distance to " N   VAL A 121 " =    0.966
peak=    3.500 closest distance to " N   GLY A  57 " =    1.392
peak=    3.496 closest distance to " CD1BILE A 234 " =    1.259
peak=    3.495 closest distance to " OD2 ASP A 140 " =    1.265
peak=    3.493 closest distance to " OD1 ASN A  39 " =    0.927
peak=    3.486 closest distance to " CB  ALA A  21 " =    1.657
peak=    3.481 closest distance to " O   THR A  82 " =    0.829
peak=    3.478 closest distance to " O   HOH Z 184 " =    2.025
peak=    3.473 closest distance to " N   ALA A 158 " =    1.105
peak=    3.473 closest distance to " O   GLY A  57 " =    2.881
peak=    3.460 closest distance to " O   HOH Z 139 " =    2.220
peak=    3.458 closest distance to " O   HOH Z 126 " =    1.719
peak=    3.457 closest distance to " O   HOH Z 153 " =    1.861
peak=    3.455 closest distance to " O   HOH Z 353 " =    1.654
peak=    3.453 closest distance to " O   HOH Z 350 " =    1.498
peak=    3.450 closest distance to " OH  TYR A 169 " =    1.668
peak=    3.446 closest distance to " O   HOH Z 351 " =    1.655
peak=    3.446 closest distance to " CG  GLN A 278 " =    1.351
peak=    3.445 closest distance to " O   HOH Z  84 " =    1.071
peak=    3.444 closest distance to " O   HOH Z 141 " =    1.593
peak=    3.443 closest distance to " O   HOH Z 416 " =    1.602
peak=    3.441 closest distance to " CA  SER A  87 " =    0.917
peak=    3.441 closest distance to " O   HOH Z 138 " =    1.634
peak=    3.431 closest distance to " O   THR A 294 " =    0.746
peak=    3.428 closest distance to " O   HOH Z 269 " =    1.808
peak=    3.424 closest distance to " O   VAL A 268 " =    1.367
peak=    3.422 closest distance to " CA  GLY A 133 " =    1.574
peak=    3.421 closest distance to " O   HOH Z 159 " =    1.665
peak=    3.419 closest distance to " CA  GLU A  44 " =    1.124
peak=    3.418 closest distance to " NE2 GLN A 223 " =    1.682
peak=    3.416 closest distance to " CE2 TYR A  68 " =    2.343
peak=    3.415 closest distance to " CD1 PHE A  16 " =    1.089
peak=    3.408 closest distance to " CB  ASN A 301 " =    0.900
peak=    3.406 closest distance to " CG2 VAL A 268 " =    1.021
peak=    3.404 closest distance to " O   HOH Z 388 " =    1.533
peak=    3.399 closest distance to " OG1 THR A 221 " =    2.284
peak=    3.398 closest distance to " O   HOH Z 423 " =    1.767
peak=    3.396 closest distance to " N   GLU A  37 " =    0.870
peak=    3.393 closest distance to " OD2 ASP A  27 " =    0.852
peak=    3.390 closest distance to " OD1 ASN A 285 " =    1.552
peak=    3.387 closest distance to " OG1 THR A 251 " =    1.001
peak=    3.386 closest distance to " O   HOH Z 330 " =    1.132
peak=    3.385 closest distance to " O   HOH Z 183 " =    1.958
peak=    3.384 closest distance to " OE2 GLU A  53 " =    1.185
peak=    3.383 closest distance to " CB  ARG A  36 " =    1.069
peak=    3.382 closest distance to " NH2BARG A 102 " =    0.861
peak=    3.382 closest distance to " O   THR A 157 " =    1.896
peak=    3.378 closest distance to " O   HOH Z  46 " =    1.901
peak=    3.374 closest distance to " O   HOH Z 434 " =    2.637
peak=    3.374 closest distance to " CA  ARG A  36 " =    0.918
peak=    3.373 closest distance to " O   MET A  47 " =    0.896
peak=    3.367 closest distance to " O   ARG A  14 " =    1.933
peak=    3.363 closest distance to " CG  ASP A  50 " =    1.393
peak=    3.362 closest distance to " O   HOH Z 257 " =    1.855
peak=    3.359 closest distance to " O   HOH Z 260 " =    2.406
peak=    3.357 closest distance to " CD1 TYR A  68 " =    1.000
peak=    3.351 closest distance to " CA  HIS A 108 " =    1.267
peak=    3.347 closest distance to " C   VAL A 296 " =    0.777
peak=    3.345 closest distance to " OE2 GLU A   2 " =    2.319
peak=    3.340 closest distance to " O   HOH Z 192 " =    1.741
peak=    3.340 closest distance to " O   HOH Z 215 " =    1.610
peak=    3.339 closest distance to " CE1 PHE A 208 " =    0.855
peak=    3.338 closest distance to " CB  ARG A 139 " =    2.094
peak=    3.337 closest distance to " NH2AARG A 275 " =    4.024
peak=    3.335 closest distance to " CB  SER A 210 " =    0.981
peak=    3.335 closest distance to " C   SER A  63 " =    1.172
peak=    3.332 closest distance to " N   ASN A 110 " =    0.738
peak=    3.332 closest distance to " N   GLN A 103 " =    1.199
peak=    3.328 closest distance to " O   HOH Z 390 " =    2.077
peak=    3.327 closest distance to " CA  ARG A 219 " =    1.392
peak=    3.326 closest distance to " CA  THR A 220 " =    0.851
peak=    3.324 closest distance to " N   GLY A 111 " =    0.822
peak=    3.323 closest distance to " CA  ARG A 159 " =    1.325
peak=    3.323 closest distance to " NH2 ARG A 138 " =    1.307
peak=    3.322 closest distance to " CG  ARG A 159 " =    1.423
peak=    3.318 closest distance to " N   ASN A 173 " =    1.156
peak=    3.318 closest distance to " OXT GLY A 302 " =    3.171
peak=    3.314 closest distance to " OG BSER A  12 " =    1.144
peak=    3.310 closest distance to " O   GLY A  13 " =    1.320
peak=    3.305 closest distance to " CB  THR A   4 " =    1.164
peak=    3.304 closest distance to " N   GLY A 267 " =    1.332
peak=    3.303 closest distance to " O   GLU A  46 " =    1.300
peak=    3.301 closest distance to " N   ALA A 165 " =    1.121
peak=    3.301 closest distance to " CG  LYS A 119 " =    1.433
peak=    3.300 closest distance to " CG1 VAL A 265 " =    1.281
peak=    3.294 closest distance to " CB  ASN A 284 " =    0.992
peak=    3.293 closest distance to " O   HOH Z 305 " =    1.650
peak=    3.292 closest distance to " NH1 ARG A 269 " =    1.216
peak=    3.289 closest distance to " OE1 GLN A  58 " =    1.872
peak=    3.285 closest distance to " CG  LYS A  76 " =    1.804
peak=    3.283 closest distance to " C   GLN A  73 " =    0.771
peak=    3.283 closest distance to " O   HOH Z 147 " =    1.925
peak=    3.281 closest distance to " O   HOH Z 152 " =    3.278
peak=    3.277 closest distance to " CG  LYS A 119 " =    1.611
peak=    3.276 closest distance to " CG1 ILE A 151 " =    2.194
peak=    3.272 closest distance to " O   HOH Z 403 " =    2.397
peak=    3.271 closest distance to " O   HOH Z 283 " =    3.409
peak=    3.269 closest distance to " CB  ALA A   8 " =    1.265
peak=    3.268 closest distance to " CB  MET A 105 " =    0.730
peak=    3.267 closest distance to " O   GLN A  94 " =    1.456
peak=    3.262 closest distance to " O   LEU A   5 " =    1.090
peak=    3.258 closest distance to " N   THR A  29 " =    0.956
peak=    3.258 closest distance to " CB  LYS A 289 " =    1.115
peak=    3.257 closest distance to " O   HOH Z 117 " =    2.373
peak=    3.256 closest distance to " O   THR A   4 " =    0.747
peak=    3.256 closest distance to " CB  PHE A 283 " =    0.932
peak=    3.254 closest distance to " OD1 ASP A  27 " =    1.829
peak=    3.251 closest distance to " CD2 LEU A  25 " =    1.185
peak=    3.249 closest distance to " O   TYR A 116 " =    0.931
peak=    3.246 closest distance to " N   TYR A 186 " =    1.445
peak=    3.245 closest distance to " O   HOH Z 326 " =    2.216
peak=    3.244 closest distance to " CB  GLU A   2 " =    1.160
peak=    3.237 closest distance to " O   ASP A 272 " =    1.167
peak=    3.236 closest distance to " O   HOH Z 254 " =    2.023
peak=    3.235 closest distance to " O   HOH Z 102 " =    1.475
peak=    3.234 closest distance to " O   HOH Z 398 " =    1.737
peak=    3.231 closest distance to " CA  ALA A 184 " =    1.872
peak=    3.225 closest distance to " N   SER A  32 " =    1.289
peak=    3.222 closest distance to " O   HOH Z 102 " =    1.670
peak=    3.218 closest distance to " O   LEU A 255 " =    0.939
peak=    3.209 closest distance to " O   HOH Z 171 " =    2.208
peak=    3.204 closest distance to " O   HOH Z 169 " =    2.129
peak=    3.204 closest distance to " O   TRP A 123 " =    1.782
peak=    3.202 closest distance to " NH1BARG A 145 " =    1.210
peak=    3.200 closest distance to " O   LYS A  76 " =    2.290
peak=    3.199 closest distance to " O   HOH Z 316 " =    2.511
peak=    3.197 closest distance to " CG1 ILE A  33 " =    1.807
peak=    3.194 closest distance to " O   HOH Z 428 " =    1.673
peak=    3.185 closest distance to " O   HOH Z 161 " =    1.162
peak=    3.180 closest distance to " CG2 THR A 220 " =    0.860
peak=    3.179 closest distance to " ND2 ASN A 301 " =    1.035
peak=    3.174 closest distance to " CB  ASP A 200 " =    1.199
peak=    3.171 closest distance to " O   SER A  26 " =    1.595
peak=    3.169 closest distance to " O   HOH Z  59 " =    4.682
peak=    3.162 closest distance to " CB  VAL A 202 " =    1.307
peak=    3.162 closest distance to " O   TRP A  92 " =    1.286
peak=    3.161 closest distance to " CB  MET A  40 " =    1.566
peak=    3.160 closest distance to " CG  LEU A 282 " =    1.956
peak=    3.154 closest distance to " CA  GLY A 118 " =    1.955
peak=    3.146 closest distance to " O   HOH Z 397 " =    1.304
peak=    3.140 closest distance to " NH1 ARG A  66 " =    5.817
peak=    3.138 closest distance to " CB  ALA A  34 " =    1.597
peak=    3.137 closest distance to " CG  GLN A  77 " =    1.798
peak=    3.136 closest distance to " CD2 LEU A 297 " =    0.727
peak=    3.135 closest distance to " O   HOH Z 365 " =    2.618
peak=    3.133 closest distance to " N   SER A  97 " =    0.829
peak=    3.132 closest distance to " O   ALA A 129 " =    1.082
peak=    3.124 closest distance to " CG  ASP A  27 " =    1.109
peak=    3.124 closest distance to " CG  GLU A  46 " =    1.153
peak=    3.121 closest distance to " CA  GLU A  44 " =    0.869
peak=    3.120 closest distance to " O   HOH Z 434 " =    5.007
peak=    3.117 closest distance to " OG BSER A  99 " =    1.246
peak=    3.106 closest distance to " O   HOH Z  15 " =    2.071
peak=    3.095 closest distance to " CA  GLY A 111 " =    1.093
peak=    3.076 closest distance to " O   HOH Z 110 " =    1.199
peak=    3.074 closest distance to " N   SER A  62 " =    0.747
peak=    3.060 closest distance to " C   ALA A 137 " =    1.467
peak=    3.053 closest distance to " O   HOH Z  90 " =    1.854
peak=    3.052 closest distance to " CA  GLN A  55 " =    0.857
peak=    3.030 closest distance to " CA  PHE A  59 " =    0.891
peak=    3.022 closest distance to " O   HOH Z   7 " =    1.952

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 238         
Filter by distance & map next to the model:
   mapped sites are within: 0.205 - 5.501
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 230 from: 238
   mapped sites are within: 0.704 - 5.501

peak=   -4.743 closest distance to " O   HOH Z 265 " =    1.549
peak=   -4.687 closest distance to " C   GLU A  37 " =    0.740
peak=   -4.633 closest distance to " O   LYS A  48 " =    0.866
peak=   -4.505 closest distance to " O   ALA A 226 " =    1.049
peak=   -4.498 closest distance to " O   VAL A  67 " =    0.977
peak=   -4.449 closest distance to " O   TRP A  70 " =    1.143
peak=   -4.421 closest distance to " O   LYS A  76 " =    0.942
peak=   -4.314 closest distance to " O   ASN A  60 " =    0.972
peak=   -4.295 closest distance to " CB  TYR A  68 " =    1.311
peak=   -4.181 closest distance to " CB  TRP A  85 " =    1.282
peak=   -4.170 closest distance to " C   ASP A 124 " =    1.316
peak=   -4.157 closest distance to " CB  PHE A  38 " =    1.243
peak=   -4.108 closest distance to " O   HOH Z 362 " =    4.104
peak=   -4.100 closest distance to " O   MET A  47 " =    0.967
peak=   -4.091 closest distance to " N   SER A 271 " =    1.247
peak=   -4.049 closest distance to " CE3 TRP A 266 " =    1.417
peak=   -4.047 closest distance to " OG  SER A  32 " =    1.662
peak=   -4.041 closest distance to " N   LEU A 255 " =    0.873
peak=   -3.994 closest distance to " O   LEU A 101 " =    1.100
peak=   -3.993 closest distance to " C   ALA A  34 " =    1.443
peak=   -3.989 closest distance to " CA  GLY A  98 " =    1.639
peak=   -3.981 closest distance to " O   SER A  62 " =    1.653
peak=   -3.974 closest distance to " O   HOH Z  80 " =    3.408
peak=   -3.959 closest distance to " O   HOH Z 172 " =    2.148
peak=   -3.947 closest distance to " O   HOH Z 102 " =    1.423
peak=   -3.934 closest distance to " C   LEU A 297 " =    0.741
peak=   -3.903 closest distance to " O   HOH Z 222 " =    2.385
peak=   -3.870 closest distance to " N   SER A  26 " =    1.258
peak=   -3.862 closest distance to " N   LYS A 289 " =    1.116
peak=   -3.851 closest distance to " CB  PRO A  90 " =    2.569
peak=   -3.835 closest distance to " N   PRO A  90 " =    1.024
peak=   -3.801 closest distance to " O   ASN A  39 " =    0.745
peak=   -3.800 closest distance to " O   THR A  52 " =    1.245
peak=   -3.798 closest distance to " N   ASP A  27 " =    1.173
peak=   -3.797 closest distance to " N   ALA A  64 " =    1.157
peak=   -3.792 closest distance to " O   GLY A  57 " =    1.111
peak=   -3.785 closest distance to " NH1BARG A 190 " =    2.266
peak=   -3.774 closest distance to " NH2 ARG A  24 " =    2.243
peak=   -3.773 closest distance to " CB  PHE A  59 " =    1.334
peak=   -3.772 closest distance to " CD1 TYR A 214 " =    1.269
peak=   -3.771 closest distance to " O   HOH Z 380 " =    4.768
peak=   -3.766 closest distance to " CB  SER A 271 " =    1.588
peak=   -3.756 closest distance to " C   ASP A  50 " =    0.974
peak=   -3.755 closest distance to " O   GLY A  98 " =    2.387
peak=   -3.748 closest distance to " N   ASN A 284 " =    0.816
peak=   -3.744 closest distance to " O   ALA A 154 " =    1.109
peak=   -3.737 closest distance to " OD2 ASP A  50 " =    1.120
peak=   -3.734 closest distance to " C   PHE A  61 " =    1.224
peak=   -3.733 closest distance to " O   SER A  97 " =    0.798
peak=   -3.729 closest distance to " N   LYS A 119 " =    0.951
peak=   -3.726 closest distance to " O   HOH Z 423 " =    1.174
peak=   -3.724 closest distance to " CB  ASN A 285 " =    1.937
peak=   -3.711 closest distance to " C   SER A 164 " =    1.040
peak=   -3.701 closest distance to " CB  ALA A  51 " =    1.830
peak=   -3.700 closest distance to " O   ALA A  51 " =    1.556
peak=   -3.696 closest distance to " C   ARG A  36 " =    1.271
peak=   -3.696 closest distance to " C   THR A  18 " =    1.841
peak=   -3.693 closest distance to " CA  VAL A  67 " =    1.068
peak=   -3.671 closest distance to " N   GLN A  55 " =    1.583
peak=   -3.664 closest distance to " O   HOH Z 145 " =    2.424
peak=   -3.660 closest distance to " CD2 LEU A 297 " =    1.174
peak=   -3.653 closest distance to " CZ  PHE A 204 " =    1.554
peak=   -3.650 closest distance to " OG BSER A 164 " =    3.135
peak=   -3.646 closest distance to " O   SER A   3 " =    2.009
peak=   -3.634 closest distance to " O   HOH Z 151 " =    0.842
peak=   -3.631 closest distance to " C   THR A  31 " =    0.894
peak=   -3.623 closest distance to " CD2 TYR A  15 " =    1.894
peak=   -3.623 closest distance to " OE1 GLN A  94 " =    2.587
peak=   -3.614 closest distance to " N   LYS A 290 " =    1.316
peak=   -3.612 closest distance to " O   SER A 271 " =    1.506
peak=   -3.611 closest distance to " N   ASN A  60 " =    1.047
peak=   -3.596 closest distance to " OE1 GLN A 223 " =    2.655
peak=   -3.592 closest distance to " OE1 GLU A 277 " =    1.256
peak=   -3.587 closest distance to " O   HOH Z 132 " =    2.384
peak=   -3.586 closest distance to " CB  ALA A 256 " =    1.144
peak=   -3.573 closest distance to " O   GLN A 183 " =    1.267
peak=   -3.572 closest distance to " CG1 VAL A 296 " =    0.704
peak=   -3.568 closest distance to " OE2 GLU A  44 " =    1.019
peak=   -3.561 closest distance to " N   THR A 220 " =    1.705
peak=   -3.561 closest distance to " CA  THR A  42 " =    1.020
peak=   -3.552 closest distance to " OG1 THR A 251 " =    2.727
peak=   -3.550 closest distance to " N   PHE A 192 " =    1.033
peak=   -3.533 closest distance to " CE2 PHE A  16 " =    3.469
peak=   -3.529 closest distance to " O   HOH Z 336 " =    5.501
peak=   -3.526 closest distance to " CB  LEU A 167 " =    1.477
peak=   -3.525 closest distance to " CD2 LEU A 300 " =    2.479
peak=   -3.519 closest distance to " OG1 THR A 294 " =    1.543
peak=   -3.518 closest distance to " C   LEU A 143 " =    0.944
peak=   -3.516 closest distance to " O   GLY A  91 " =    1.390
peak=   -3.513 closest distance to " OG BSER A 164 " =    2.721
peak=   -3.510 closest distance to " CG1 VAL A 265 " =    0.978
peak=   -3.503 closest distance to " O   ALA A 256 " =    1.795
peak=   -3.494 closest distance to " CD1 LEU A 281 " =    1.948
peak=   -3.487 closest distance to " O   HOH Z 119 " =    2.133
peak=   -3.485 closest distance to " O   GLU A 236 " =    0.938
peak=   -3.484 closest distance to " O   SER A  22 " =    1.806
peak=   -3.473 closest distance to " CE1 TYR A  68 " =    1.858
peak=   -3.468 closest distance to " O   HOH Z 304 " =    1.378
peak=   -3.465 closest distance to " O   HOH Z 395 " =    1.960
peak=   -3.462 closest distance to " O   HOH Z  34 " =    1.219
peak=   -3.459 closest distance to " O   HOH Z 186 " =    1.910
peak=   -3.458 closest distance to " OG1 THR A  29 " =    1.284
peak=   -3.454 closest distance to " CD2 PHE A 283 " =    1.366
peak=   -3.453 closest distance to " O   LEU A  25 " =    0.815
peak=   -3.452 closest distance to " CE3 TRP A  85 " =    2.223
peak=   -3.446 closest distance to " CD1BILE A 234 " =    2.857
peak=   -3.436 closest distance to " CG  ASN A 209 " =    0.738
peak=   -3.431 closest distance to " CB  THR A 251 " =    0.800
peak=   -3.429 closest distance to " N   ASP A  50 " =    1.022
peak=   -3.422 closest distance to " CE2 PHE A 218 " =    2.239
peak=   -3.420 closest distance to " C   GLY A  35 " =    1.130
peak=   -3.416 closest distance to " O   HOH Z  38 " =    1.383
peak=   -3.407 closest distance to " O   ASN A  69 " =    1.449
peak=   -3.406 closest distance to " CB  ASN A  60 " =    1.130
peak=   -3.400 closest distance to " CG  TRP A 177 " =    1.639
peak=   -3.390 closest distance to " CD1 LEU A  96 " =    1.794
peak=   -3.390 closest distance to " O   VAL A 265 " =    2.100
peak=   -3.386 closest distance to " O   HOH Z 140 " =    2.607
peak=   -3.381 closest distance to " ND2 ASN A 285 " =    0.929
peak=   -3.378 closest distance to " CE1 PHE A 130 " =    1.132
peak=   -3.377 closest distance to " OG ASER A 210 " =    2.303
peak=   -3.376 closest distance to " O   HOH Z 368 " =    1.610
peak=   -3.375 closest distance to " C   GLY A  13 " =    1.070
peak=   -3.365 closest distance to " N   ALA A 242 " =    1.029
peak=   -3.364 closest distance to " O   HOH Z 193 " =    2.928
peak=   -3.360 closest distance to " CG  GLN A 122 " =    1.557
peak=   -3.358 closest distance to " O   GLN A 223 " =    0.917
peak=   -3.354 closest distance to " CB  SER A 276 " =    1.324
peak=   -3.352 closest distance to " CB  SER A  62 " =    4.373
peak=   -3.350 closest distance to " OG1 THR A  31 " =    1.578
peak=   -3.349 closest distance to " C   ALA A   8 " =    1.042
peak=   -3.344 closest distance to " C   HIS A 108 " =    0.855
peak=   -3.344 closest distance to " CD2 LEU A 282 " =    1.872
peak=   -3.341 closest distance to " SG  CYS A 168 " =    1.194
peak=   -3.333 closest distance to " CA  GLN A  58 " =    1.243
peak=   -3.332 closest distance to " CA  PHE A 225 " =    0.709
peak=   -3.332 closest distance to " OE1 GLN A 194 " =    2.405
peak=   -3.330 closest distance to " O   HOH Z 117 " =    0.743
peak=   -3.330 closest distance to " C   GLU A 152 " =    1.729
peak=   -3.327 closest distance to " CB  GLN A 122 " =    0.890
peak=   -3.320 closest distance to " CG2 VAL A  78 " =    2.799
peak=   -3.314 closest distance to " C   ASP A  65 " =    1.127
peak=   -3.312 closest distance to " N   ARG A 275 " =    1.185
peak=   -3.312 closest distance to " CG2 VAL A 257 " =    2.007
peak=   -3.303 closest distance to " CD  ARG A 195 " =    2.563
peak=   -3.303 closest distance to " CA  ASN A  39 " =    1.521
peak=   -3.302 closest distance to " O   ARG A  56 " =    1.678
peak=   -3.292 closest distance to " CZ2 TRP A  70 " =    1.210
peak=   -3.290 closest distance to " O   SER A  32 " =    0.984
peak=   -3.288 closest distance to " O   HOH Z 386 " =    2.168
peak=   -3.288 closest distance to " O   HOH Z 150 " =    3.014
peak=   -3.287 closest distance to " ND2 ASN A 301 " =    1.896
peak=   -3.285 closest distance to " CB  ALA A  43 " =    0.998
peak=   -3.281 closest distance to " O   HOH Z 396 " =    2.319
peak=   -3.276 closest distance to " N   SER A  95 " =    2.223
peak=   -3.275 closest distance to " CG1 ILE A 151 " =    0.986
peak=   -3.267 closest distance to " O   HOH Z 162 " =    2.874
peak=   -3.267 closest distance to " CA  ASP A 298 " =    1.241
peak=   -3.265 closest distance to " CA  GLY A  57 " =    1.861
peak=   -3.263 closest distance to " O   ALA A  64 " =    0.992
peak=   -3.262 closest distance to " CD2 PHE A 155 " =    1.225
peak=   -3.258 closest distance to " O   HOH Z 343 " =    2.740
peak=   -3.255 closest distance to " O   ALA A  34 " =    0.914
peak=   -3.255 closest distance to " CB  TRP A 123 " =    1.133
peak=   -3.253 closest distance to " O   HOH Z 148 " =    3.445
peak=   -3.251 closest distance to " O   HOH Z 430 " =    3.892
peak=   -3.250 closest distance to " O   HOH Z  75 " =    0.991
peak=   -3.247 closest distance to " N   GLN A  55 " =    1.343
peak=   -3.246 closest distance to " CD1 ILE A  33 " =    1.773
peak=   -3.241 closest distance to " ND2 ASN A  60 " =    1.172
peak=   -3.240 closest distance to " OD2 ASP A 253 " =    1.249
peak=   -3.238 closest distance to " CG  ARG A  66 " =    1.184
peak=   -3.234 closest distance to " O   HOH Z  32 " =    3.754
peak=   -3.230 closest distance to " CG  PRO A 213 " =    1.203
peak=   -3.230 closest distance to " O   LEU A 237 " =    1.724
peak=   -3.229 closest distance to " O   HOH Z 231 " =    0.975
peak=   -3.226 closest distance to " CA  GLN A 103 " =    1.124
peak=   -3.223 closest distance to " CA  ILE A 263 " =    1.001
peak=   -3.223 closest distance to " O   HOH Z 415 " =    1.853
peak=   -3.222 closest distance to " O   HOH Z  82 " =    1.860
peak=   -3.219 closest distance to " O   ALA A  34 " =    1.264
peak=   -3.219 closest distance to " O   HOH Z 218 " =    1.560
peak=   -3.218 closest distance to " C   ARG A  56 " =    0.927
peak=   -3.213 closest distance to " O   SER A 276 " =    1.706
peak=   -3.212 closest distance to " C   ASN A 285 " =    1.642
peak=   -3.211 closest distance to " OG1 THR A  18 " =    1.789
peak=   -3.206 closest distance to " OH  TYR A 247 " =    1.030
peak=   -3.204 closest distance to " O   HOH Z 406 " =    1.054
peak=   -3.203 closest distance to " O   VAL A 125 " =    2.555
peak=   -3.203 closest distance to " CA  VAL A 121 " =    1.071
peak=   -3.202 closest distance to " CZ  ARG A 156 " =    1.125
peak=   -3.196 closest distance to " CZ3 TRP A 177 " =    1.334
peak=   -3.193 closest distance to " CB  GLN A 240 " =    2.358
peak=   -3.189 closest distance to " O   HOH Z  60 " =    1.327
peak=   -3.177 closest distance to " NH1 ARG A  66 " =    1.665
peak=   -3.174 closest distance to " O   HOH Z 102 " =    1.929
peak=   -3.171 closest distance to " C   GLU A  53 " =    1.895
peak=   -3.169 closest distance to " SG ACYS A 201 " =    2.167
peak=   -3.165 closest distance to " CZ2 TRP A 123 " =    1.741
peak=   -3.164 closest distance to " NE2 GLN A 223 " =    1.657
peak=   -3.161 closest distance to " O   HOH Z 282 " =    4.065
peak=   -3.159 closest distance to " OE2 GLU A  53 " =    1.752
peak=   -3.158 closest distance to " O   HOH Z  40 " =    3.844
peak=   -3.154 closest distance to " O   HOH Z 225 " =    1.263
peak=   -3.151 closest distance to " O   HOH Z 404 " =    1.236
peak=   -3.151 closest distance to " O   ILE A  33 " =    0.882
peak=   -3.148 closest distance to " CG2 VAL A 296 " =    2.093
peak=   -3.145 closest distance to " CB  ASP A 270 " =    1.939
peak=   -3.145 closest distance to " C   ARG A  66 " =    1.296
peak=   -3.137 closest distance to " CG  TRP A 266 " =    1.587
peak=   -3.135 closest distance to " O   HOH Z 401 " =    1.038
peak=   -3.133 closest distance to " CB  ASP A 162 " =    1.901
peak=   -3.131 closest distance to " CB  ALA A  19 " =    2.164
peak=   -3.127 closest distance to " NH1 ARG A  79 " =    2.280
peak=   -3.125 closest distance to " CB  ARG A 159 " =    1.647
peak=   -3.118 closest distance to " O   PRO A  54 " =    0.892
peak=   -3.113 closest distance to " CZ  PHE A  38 " =    2.591
peak=   -3.112 closest distance to " CA  PRO A 198 " =    1.304
peak=   -3.106 closest distance to " CE1 HIS A  86 " =    2.161
peak=   -3.103 closest distance to " NE2 HIS A  86 " =    1.543
peak=   -3.101 closest distance to " N   SER A  63 " =    1.436
peak=   -3.098 closest distance to " CG  GLN A  55 " =    1.289
peak=   -3.095 closest distance to " C   ASN A 187 " =    1.246
peak=   -3.095 closest distance to " O   HOH Z 124 " =    3.059
peak=   -3.092 closest distance to " CB  VAL A 230 " =    0.735
peak=   -3.090 closest distance to " CB  GLN A  55 " =    1.726
peak=   -3.083 closest distance to " O   HOH Z 147 " =    1.457
peak=   -3.079 closest distance to " O   HOH Z 426 " =    1.847
peak=   -3.075 closest distance to " O   THR A   4 " =    1.653
peak=   -3.075 closest distance to " N   ASP A 191 " =    1.189

================= 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    :  0.5285 0.5323   6.318006e+00   6.317488e+00
   1_bss:  0.5231 0.5212   6.110458e+00   6.134746e+00
   1_xyz:  0.4857 0.5153   6.286817e+00   6.304070e+00
   1_adp:  0.4576 0.5160   5.833720e+00   5.838267e+00
   1_occ:  0.4574 0.5152   5.833567e+00   5.838295e+00
   2_bss:  0.4560 0.5111   5.833437e+00   5.837070e+00
   2_xyz:  0.4246 0.4927   6.220762e+00   6.289318e+00
   2_adp:  0.4240 0.4849   6.220680e+00   6.286506e+00
   2_occ:  0.4239 0.4851   6.220621e+00   6.286579e+00
   3_bss:  0.4239 0.4844   6.221985e+00   6.286276e+00
   3_xyz:  0.3834 0.4618   6.162325e+00   6.258407e+00
   3_adp:  0.3688 0.4592   6.148548e+00   6.254204e+00
   3_occ:  0.3686 0.4600   6.148811e+00   6.254425e+00
   4_bss:  0.3684 0.4596   6.148225e+00   6.253143e+00
   4_xyz:  0.3293 0.4124   6.060464e+00   6.195266e+00
   4_adp:  0.3019 0.4087   6.017113e+00   6.188607e+00
   4_occ:  0.3018 0.4089   6.017094e+00   6.188552e+00
   5_bss:  0.3019 0.4077   6.016444e+00   6.188217e+00
   5_xyz:  0.2625 0.3675   5.916230e+00   6.123471e+00
   5_adp:  0.2536 0.3419   5.870647e+00   6.066085e+00
   5_occ:  0.2532 0.3413   5.869410e+00   6.065395e+00
   5_bss:  0.2530 0.3403   5.868466e+00   6.063396e+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:  0.386  20.000   7.002   7.215   6.798   0.000   0.000   0.000
   1_xyz:  0.386  20.000   7.002   7.215   6.798   0.000   0.000   0.000
   1_adp:  0.386  20.000   7.002   7.215   6.798   0.000   0.000   0.000
   1_occ:  0.386  20.000   7.002   7.215   6.798   0.000   0.000   0.000
   2_bss:  0.343  33.584   3.447   3.399   3.933   0.000   0.000   0.000
   2_xyz:  0.343  33.584   3.447   3.399   3.933   0.000   0.000   0.000
   2_adp:  0.343  33.584   3.447   3.399   3.933   0.000   0.000   0.000
   2_occ:  0.343  33.584   3.447   3.399   3.933   0.000   0.000   0.000
   3_bss:  0.335  33.584   1.251   1.119   1.920   0.000   0.000   0.000
   3_xyz:  0.335  33.584   1.251   1.119   1.920   0.000   0.000   0.000
   3_adp:  0.335  33.584   1.251   1.119   1.920   0.000   0.000   0.000
   3_occ:  0.335  33.584   1.251   1.119   1.920   0.000   0.000   0.000
   4_bss:  0.328  33.585   0.915   0.431   1.073   0.000   0.000   0.000
   4_xyz:  0.328  33.585   0.915   0.431   1.073   0.000   0.000   0.000
   4_adp:  0.328  33.585   0.915   0.431   1.073   0.000   0.000   0.000
   4_occ:  0.328  33.585   0.915   0.431   1.073   0.000   0.000   0.000
   5_bss:  0.336  51.363   1.727   0.698   1.626   0.000   0.000   0.000
   5_xyz:  0.336  51.363   1.727   0.698   1.626   0.000   0.000   0.000
   5_adp:  0.336  51.363   1.727   0.698   1.626   0.000   0.000   0.000
   5_occ:  0.336  51.363   1.727   0.698   1.626   0.000   0.000   0.000
   5_bss:  0.347  54.038   0.174  -0.562   0.388  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  71.270 0.2471  0.3063    96398.834
   1_bss:  71.327 0.2455  0.3679    94922.466
   1_xyz:  69.232 0.2718  0.3987    87475.080
   1_adp:  69.160 0.2725  0.4769    87645.707
   1_occ:  69.240 0.2716  0.4750    87880.155
   2_bss:  68.831 0.2768  0.4397    87141.112
   2_xyz:  65.331 0.3219  0.5146    79637.582
   2_adp:  63.225 0.3498  0.5759    77564.064
   2_occ:  63.276 0.3491  0.5740    77619.575
   3_bss:  63.352 0.3480  0.5347    77587.381
   3_xyz:  56.813 0.4321  0.6644    65722.965
   3_adp:  55.523 0.4487  0.6779    64087.022
   3_occ:  55.578 0.4480  0.6765    64206.926
   4_bss:  55.474 0.4492  0.6645    63871.967
   4_xyz:  46.655 0.5604  0.8182    49679.161
   4_adp:  45.098 0.5793  0.8093    47000.527
   4_occ:  45.126 0.5790  0.8085    47007.409
   5_bss:  45.078 0.5794  0.8247    46862.423
   5_xyz:  40.321 0.6368  0.8986    37759.954
   5_adp:  36.028 0.6885  0.9542    31929.572
   5_occ:  35.998 0.6887  0.9540    31828.862
   5_bss:  35.835 0.6904  0.9163    31513.210
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2971e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2971e+01
   1_xyz:   1.723  0.013  0.108 18.757  0.007  4.104   1.5592e-01
   1_adp:   1.723  0.013  0.108 18.757  0.007  4.104   1.5592e-01
   1_occ:   1.723  0.013  0.108 18.757  0.007  4.104   1.5592e-01
   2_bss:   1.723  0.013  0.108 18.757  0.007  4.104   1.5592e-01
   2_xyz:   1.143  0.008  0.077 17.243  0.004  4.101   9.7864e-02
   2_adp:   1.143  0.008  0.077 17.243  0.004  4.101   9.7864e-02
   2_occ:   1.143  0.008  0.077 17.243  0.004  4.101   9.7864e-02
   3_bss:   1.143  0.008  0.077 17.243  0.004  4.101   9.7864e-02
   3_xyz:   1.228  0.009  0.088 17.146  0.005  4.115   1.0467e-01
   3_adp:   1.228  0.009  0.088 17.146  0.005  4.115   1.0467e-01
   3_occ:   1.228  0.009  0.088 17.146  0.005  4.115   1.0467e-01
   4_bss:   1.228  0.009  0.088 17.146  0.005  4.115   1.0467e-01
   4_xyz:   1.163  0.008  0.079 16.671  0.004  4.111   8.9783e-02
   4_adp:   1.163  0.008  0.079 16.671  0.004  4.111   8.9783e-02
   4_occ:   1.163  0.008  0.079 16.671  0.004  4.111   8.9783e-02
   5_bss:   1.163  0.008  0.079 16.671  0.004  4.111   8.9783e-02
   5_xyz:   1.210  0.009  0.085 16.658  0.005  4.102   9.2896e-02
   5_adp:   1.210  0.009  0.085 16.658  0.005  4.102   9.2896e-02
   5_occ:   1.210  0.009  0.085 16.658  0.005  4.102   9.2896e-02
   5_bss:   1.210  0.009  0.085 16.658  0.005  4.102   9.2896e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8609e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8609e+00
   1_xyz:  13.757  0.169  0.449 85.588  0.056  1.996   9.7860e-02
   1_adp:  13.757  0.169  0.449 85.588  0.056  1.996   9.7860e-02
   1_occ:  13.757  0.169  0.449 85.588  0.056  1.996   9.7860e-02
   2_bss:  13.757  0.169  0.449 85.588  0.056  1.996   9.7860e-02
   2_xyz:   9.064  0.087  0.235 73.152  0.040  1.986   6.1653e-02
   2_adp:   9.064  0.087  0.235 73.152  0.040  1.986   6.1653e-02
   2_occ:   9.064  0.087  0.235 73.152  0.040  1.986   6.1653e-02
   3_bss:   9.064  0.087  0.235 73.152  0.040  1.986   6.1653e-02
   3_xyz:   8.659  0.085  0.361 69.627  0.037  2.076   1.2378e-01
   3_adp:   8.659  0.085  0.361 69.627  0.037  2.076   1.2378e-01
   3_occ:   8.659  0.085  0.361 69.627  0.037  2.076   1.2378e-01
   4_bss:   8.659  0.085  0.361 69.627  0.037  2.076   1.2378e-01
   4_xyz:  10.839  0.081  0.330 76.098  0.025  2.204   1.0641e-01
   4_adp:  10.839  0.081  0.330 76.098  0.025  2.204   1.0641e-01
   4_occ:  10.839  0.081  0.330 76.098  0.025  2.204   1.0641e-01
   5_bss:  10.839  0.081  0.330 76.098  0.025  2.204   1.0641e-01
   5_xyz:   9.636  0.069  0.339 70.034  0.038  2.092   7.0972e-02
   5_adp:   9.636  0.069  0.339 70.034  0.038  2.092   7.0972e-02
   5_occ:   9.636  0.069  0.339 70.034  0.038  2.092   7.0972e-02
   5_bss:   9.636  0.069  0.339 70.034  0.038  2.092   7.0972e-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: 114.35   0.00  21.38 114.35   0.00  20.68  97.25   0.00  25.20
   1_occ: 114.35   0.00  21.38 114.35   0.00  20.68  97.25   0.00  25.20
   2_bss: 114.35   0.00  21.38 114.35   0.00  20.68  97.25   0.00  25.20
   2_xyz: 114.35   0.00  21.38 114.35   0.00  20.68  97.25   0.00  25.20
   2_adp: 115.98   0.00  19.84 115.98   0.00  19.30  93.31   0.00  22.79
   2_occ: 115.98   0.00  19.84 115.98   0.00  19.30  93.31   0.00  22.79
   3_bss: 115.98   0.00  19.84 115.98   0.00  19.30  93.31   0.00  22.79
   3_xyz: 115.98   0.00  19.84 115.98   0.00  19.30  93.31   0.00  22.79
   3_adp: 116.02   0.00  19.04 116.02   0.00  18.05  91.04   0.00  24.41
   3_occ: 116.02   0.00  19.04 116.02   0.00  18.05  91.04   0.00  24.41
   4_bss: 116.02   0.00  19.04 116.02   0.00  18.05  91.04   0.00  24.41
   4_xyz: 116.02   0.00  19.04 116.02   0.00  18.05  91.04   0.00  24.41
   4_adp: 155.10   0.00  23.45 155.10   0.00  20.64 135.69   0.91  38.78
   4_occ: 155.10   0.00  23.45 155.10   0.00  20.64 135.69   0.91  38.78
   5_bss: 155.10   0.00  23.45 155.10   0.00  20.64 135.69   0.91  38.78
   5_xyz: 155.10   0.00  23.45 155.10   0.00  20.64 135.69   0.91  38.78
   5_adp: 149.27   0.00  20.14 149.27   0.00  16.98 120.43   0.00  37.32
   5_occ: 149.27   0.00  20.14 149.27   0.00  16.98 120.43   0.00  37.32
   5_bss: 149.44   0.16  20.30 149.44   0.16  17.14 120.60   0.16  37.49
------------------------------------------------------------------------
 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:    1.272    0.027    0.409
   1_adp:    1.272    0.027    0.409
   1_occ:    1.272    0.027    0.409
   2_bss:    1.272    0.027    0.409
   2_xyz:    1.735    0.018    0.537
   2_adp:    1.735    0.018    0.537
   2_occ:    1.735    0.018    0.537
   3_bss:    1.735    0.018    0.537
   3_xyz:    1.645    0.017    0.661
   3_adp:    1.645    0.017    0.661
   3_occ:    1.645    0.017    0.661
   4_bss:    1.645    0.017    0.661
   4_xyz:    2.064    0.049    0.803
   4_adp:    2.064    0.049    0.803
   4_occ:    2.064    0.049    0.803
   5_bss:    2.064    0.049    0.803
   5_xyz:    2.164    0.037    0.912
   5_adp:    2.164    0.037    0.912
   5_occ:    2.164    0.037    0.912
   5_bss:    2.164    0.037    0.912
------------------------------------------------------------------------

CPU time actual refinement: 350.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1089/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_1089/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1089/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1089/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1089/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.21 
  Macro-tasks:
    bulk solvent and scale       = 40.11  
    individual site refinement   = 168.41 
    weights calculation          = 33.44  
    collect and process          = 5.88   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 247.95 
  Micro-tasks:
    mask                            = 3.04   
    f_calc                          = 112.50 
    alpha_beta                      = 7.90   
    target                          = 1.10   
    gradients_wrt_atomic_parameters = 123.74 
    fmodel                         = 6.79   
    r_factors                      = 0.25   
    phase_errors                   = 8.25   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 263.84 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.960 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    561 calls, 112.17 s
gradients_fft:          505 calls, 110.84 s

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

# Date 2008-01-16 Time 03:09:39 PST -0800 (1200481779.67 s)
Start R-work = 0.5285, R-free = 0.5323 (no bulk solvent and anisotropic scale)
Final R-work = 0.2663, R-free = 0.3559 (no bulk solvent and anisotropic scale)

Start R-work = 0.5231, R-free = 0.5212
Final R-work = 0.2530, R-free = 0.3403