# Date 2008-01-16 Time 06:24:03 PST -0800 (1200493443.38 s)
#phil __OFF__

Command line arguments: "../1131.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1205
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1131

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 46.4607, 88.1178, 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, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 1.98365
Completeness in resolution range: 0.935036
Completeness with d_max=infinity: 0.932366

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2939
                             d_min =   1.9836

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, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 1.98365
Completeness in resolution range: 0.935036
Completeness with d_max=infinity: 0.932366

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2943 -  4.2460 [2202/2229]  1981   221  10.0%
  bin  2:  4.2460 -  3.3822 [2121/2141]  1909   212  10.0%
  bin  3:  3.3822 -  2.9582 [2082/2101]  1876   206   9.9%
  bin  4:  2.9582 -  2.6893 [2070/2100]  1859   211  10.2%
  bin  5:  2.6893 -  2.4974 [2057/2076]  1860   197   9.6%
  bin  6:  2.4974 -  2.3507 [2057/2082]  1844   213  10.4%
  bin  7:  2.3507 -  2.2334 [2030/2058]  1824   206  10.1%
  bin  8:  2.2334 -  2.1364 [2015/2051]  1813   202  10.0%
  bin  9:  2.1364 -  2.0544 [2032/2074]  1835   197   9.7%
  bin 10:  2.0544 -  1.9836 [ 923/2038]   829    94  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1131/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 21
        2.42 -     3.04: 2168
        3.04 -     3.66: 4634
        3.66 -     4.28: 8905
        4.28 -     4.90: 12207
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.219 3.040 -x,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27930 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 =====================


==================== 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/noshake/run_1131/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1131/model_refine_001.geo

CPU time processing inputs: 9.15


============================ 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 46.4607 88.1178 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4389   r_free= 0.4308   ksol= 0.00   Bsol= 0.00   scale= 0.901    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.242480                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.7365 0.99   1426  158 0.3447 0.3180      6.5093      6.4033|
|  2:  4.7365 -  3.7782 0.99   1382  155 0.3615 0.3592      6.7416      6.7082|
|  3:  3.7782 -  3.3061 0.99   1343  144 0.3985 0.3538      6.5911      6.5398|
|  4:  3.3061 -  3.0063 0.99   1344  156 0.4239 0.4550      6.4614      6.4762|
|  5:  3.0063 -  2.7922 0.99   1335  149 0.4759 0.4514      6.3238        6.32|
|  6:  2.7922 -  2.6285 0.99   1331  147 0.4484 0.4653      6.2051       6.172|
|  7:  2.6285 -  2.4974 0.99   1324  138 0.4819 0.4389       6.207      6.1496|
|  8:  2.4974 -  2.3891 0.98   1300  153 0.5057 0.4915      6.1591      6.1706|
|  9:  2.3891 -  2.2975 0.98   1303  144 0.4919 0.4990      6.0927      6.1326|
| 10:  2.2975 -  2.2184 1.00   1323  152 0.5114 0.4881      6.0817      6.0385|
| 11:  2.2184 -  2.1493 0.98   1307  138 0.4917 0.5031      6.0195      6.0228|
| 12:  2.1493 -  2.0880 0.98   1297  145 0.5125 0.4907      5.9263      5.9568|
| 13:  2.0880 -  2.0331 0.96   1258  138 0.4970 0.5046      5.8607      5.7872|
| 14:  2.0331 -  1.9836 0.27    357   42 0.5014 0.5558      5.8327      5.8673|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.7365  1426   158  0.77  28.07   0.83     0.80      50907.43|
|  2:  4.7365 -  3.7782  1382   155  0.78  27.76   0.92     0.87      74135.23|
|  3:  3.7782 -  3.3061  1343   144  0.68  37.32   0.93     0.85      82888.95|
|  4:  3.3061 -  3.0063  1344   156  0.60  43.85   0.91     0.77      79118.93|
|  5:  3.0063 -  2.7922  1335   149  0.50  52.03   0.90     0.68      66747.29|
|  6:  2.7922 -  2.6285  1331   147  0.48  53.95   0.92     0.64      58477.09|
|  7:  2.6285 -  2.4974  1324   138  0.47  54.75   0.91     0.61      54390.21|
|  8:  2.4974 -  2.3891  1300   153  0.44  56.68   0.89     0.61      49888.28|
|  9:  2.3891 -  2.2975  1303   144  0.44  56.97   0.92     0.62      47115.94|
| 10:  2.2975 -  2.2184  1323   152  0.43  58.05   0.94     0.61      42855.62|
| 11:  2.2184 -  2.1493  1307   138  0.40  59.97   0.94     0.59      42911.82|
| 12:  2.1493 -  2.0880  1297   145  0.36  62.83   0.92     0.55      39965.66|
| 13:  2.0880 -  2.0331  1258   138  0.33  65.33   0.92     0.52      36433.11|
| 14:  2.0331 -  1.9836   357    42  0.35  63.87   0.93     0.49      30540.90|
|alpha:            min =        0.49 max =            0.87 mean =         0.67|
|beta:             min =    30540.90 max =        82888.95 mean =     55545.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.52|
|phase err.(test): min =        0.00 max =           90.00 mean =        50.25|
|-----------------------------------------------------------------------------|

============================== 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 = 10.119498             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.905   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.857879              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.406   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      189 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1979 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1829 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2805 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4575 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4330 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5555 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6652 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.156 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4389   r_free= 0.4308   ksol= 0.00   Bsol= 0.00   scale= 0.901    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.242480                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4303   r_free= 0.4249   ksol= 0.32   Bsol= 68.27   scale= 0.948   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,-1.42,3.37,-0.00,0.00,0.00); trace/3= 0.88                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.234057                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.684930              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.813   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.898157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.996   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4303      final r-factor (work) = 0.2652          |
| start r-factor (free) = 0.4249      final r-factor (free) = 0.2958          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2178 = 8.68 * 0.50 * 6.2304 + 1.00 * 0.1626                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3281 = 8.68 * 0.50 * 6.0389 + 1.00 * 0.1044                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2652      final r-factor (work) = 0.2439          |
| start r-factor (free) = 0.2958      final r-factor (free) = 0.3014          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4315 = 0.90 * 1.00 * 6.0389 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4398 = 0.90 * 1.00 * 5.7993 + 1.00 * 0.2312                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.71  17.06    None  None   None       |
|    all(noH): 2823   0      0.00    114.71  17.06    None  None   None       |
|    Sol.    : 438    0      4.51    65.04   38.93    None  None   None       |
|    Mac.    : 2385   0      0.00    114.71  13.05    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 -  11.471: 1176   |   5:    57.354 -  68.825:   30        |
|      1:    11.471 -  22.942: 1041   |   6:    68.825 -  80.295:    0        |
|      2:    22.942 -  34.412:  267   |   7:    80.295 -  91.766:    0        |
|      3:    34.412 -  45.883:  185   |   8:    91.766 - 103.237:    0        |
|      4:    45.883 -  57.354:  123   |   9:   103.237 - 114.708:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2439 r_free = 0.3014             target_work(ml) = 5.810         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2434 r_free = 0.3011             target_work(ml) = 5.810         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2434   r_free= 0.3011   ksol= 0.32   Bsol= 68.27   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,-1.42,3.37,-0.00,0.00,0.00); trace/3= 0.88                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.809639                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2413   r_free= 0.3003   ksol= 0.35   Bsol= 78.65   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,-2.59,0.57,-0.00,0.00,0.00); trace/3= -1.16                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.811829                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.763800              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.640   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.862732              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.807   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2413      final r-factor (work) = 0.1736          |
| start r-factor (free) = 0.3003      final r-factor (free) = 0.2257          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0467 = 3.76 * 0.50 * 5.8144 + 1.00 * 0.1046                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7625 = 3.76 * 0.50 * 5.6852 + 1.00 * 0.0635                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1736      final r-factor (work) = 0.1560          |
| start r-factor (free) = 0.2257      final r-factor (free) = 0.2131          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6664 = 1.86 * 1.00 * 5.6852 + 1.00 * 0.0764                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2109 = 1.86 * 1.00 * 5.4737 + 1.00 * 0.0148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.49  18.85    None  None   None       |
|    all(noH): 2823   0      0.00    117.49  18.85    None  None   None       |
|    Sol.    : 438    0      4.98    117.49  47.58    None  None   None       |
|    Mac.    : 2385   0      0.00    90.72   13.58    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 -  11.749: 1343   |   5:    58.747 -  70.496:   92        |
|      1:    11.749 -  23.499:  899   |   6:    70.496 -  82.245:   63        |
|      2:    23.499 -  35.248:  179   |   7:    82.245 -  93.994:   15        |
|      3:    35.248 -  46.997:  127   |   8:    93.994 - 105.744:    6        |
|      4:    46.997 -  58.747:   98   |   9:   105.744 - 117.493:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1560 r_free = 0.2131             target_work(ml) = 5.446         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1558 r_free = 0.2130             target_work(ml) = 5.445         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1558   r_free= 0.2130   ksol= 0.35   Bsol= 78.65   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,-2.59,0.57,-0.00,0.00,0.00); trace/3= -1.16                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.445132                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1559   r_free= 0.2132   ksol= 0.34   Bsol= 85.22   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-2.34,-0.01,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.444037                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.067355              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.204  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.351919              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.174  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1559      final r-factor (work) = 0.1324          |
| start r-factor (free) = 0.2132      final r-factor (free) = 0.1845          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4577 = 3.07 * 0.50 * 5.4732 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3123 = 3.07 * 0.50 * 5.3783 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1324      final r-factor (work) = 0.1276          |
| start r-factor (free) = 0.1845      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9074 = 0.35 * 1.00 * 5.3783 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9106 = 0.35 * 1.00 * 5.2848 + 1.00 * 0.0508                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.45  18.32    None  None   None       |
|    all(noH): 2823   0      0.00    114.45  18.32    None  None   None       |
|    Sol.    : 438    0      4.68    114.45  46.06    None  None   None       |
|    Mac.    : 2385   0      0.00    89.55   13.23    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 -  11.445: 1348   |   5:    57.223 -  68.667:   89        |
|      1:    11.445 -  22.889:  905   |   6:    68.667 -  80.112:   54        |
|      2:    22.889 -  34.334:  187   |   7:    80.112 -  91.556:   17        |
|      3:    34.334 -  45.778:  118   |   8:    91.556 - 103.001:    8        |
|      4:    45.778 -  57.223:   96   |   9:   103.001 - 114.446:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1276 r_free = 0.1761             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1274 r_free = 0.1760             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1274   r_free= 0.1760   ksol= 0.34   Bsol= 85.22   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-2.34,-0.01,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.258347                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1275   r_free= 0.1758   ksol= 0.33   Bsol= 77.25   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-2.56,-0.50,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.258062                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.850875              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.795  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.780500              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.031   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1275      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1668          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2412 = 3.85 * 0.50 * 5.2858 + 1.00 * 0.0638                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1388 = 3.85 * 0.50 * 5.2229 + 1.00 * 0.0825                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1668      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0938 = 0.78 * 1.00 * 5.2229 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0585 = 0.78 * 1.00 * 5.1852 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.26  17.91    None  None   None       |
|    all(noH): 2823   0      0.00    111.26  17.91    None  None   None       |
|    Sol.    : 438    0      0.00    111.26  44.34    None  None   None       |
|    Mac.    : 2385   0      0.00    91.17   13.05    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 -  11.126: 1276   |   5:    55.629 -  66.755:   90        |
|      1:    11.126 -  22.252:  966   |   6:    66.755 -  77.881:   37        |
|      2:    22.252 -  33.378:  196   |   7:    77.881 -  89.007:   19        |
|      3:    33.378 -  44.504:  142   |   8:    89.007 - 100.133:   13        |
|      4:    44.504 -  55.629:   82   |   9:   100.133 - 111.259:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1645             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1644             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1644   ksol= 0.33   Bsol= 77.25   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-2.56,-0.50,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.177827                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1644   ksol= 0.32   Bsol= 69.26   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,-2.39,-0.36,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.177867                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.651419              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.321  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.376668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.022  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1644      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5494 = 3.65 * 0.50 * 5.1853 + 1.00 * 0.0825                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5209 = 3.65 * 0.50 * 5.1697 + 1.00 * 0.0826                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9585 = 0.38 * 1.00 * 5.1697 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9568 = 0.38 * 1.00 * 5.1689 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.31    104.76  17.26    None  None   None       |
|    all(noH): 2823   0      0.31    104.76  17.26    None  None   None       |
|    Sol.    : 438    0      1.85    104.76  41.53    None  None   None       |
|    Mac.    : 2385   0      0.31    90.96   12.80    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:     0.309 -  10.755: 1238   |   5:    52.537 -  62.983:   86        |
|      1:    10.755 -  21.200:  985   |   6:    62.983 -  73.428:   31        |
|      2:    21.200 -  31.646:  206   |   7:    73.428 -  83.874:   18        |
|      3:    31.646 -  42.091:  150   |   8:    83.874 -  94.319:   10        |
|      4:    42.091 -  52.537:   95   |   9:    94.319 - 104.765:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1630             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1120 r_free = 0.1629             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1629   ksol= 0.32   Bsol= 69.26   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,-2.39,-0.36,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166003                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.7365 0.99   1426  158 0.0951 0.1354      5.3791      5.5948|
|  2:  4.7365 -  3.7782 0.99   1382  155 0.0840 0.1105      5.4378      5.6261|
|  3:  3.7782 -  3.3061 0.99   1343  144 0.1054 0.1630      5.4708       5.858|
|  4:  3.3061 -  3.0063 0.99   1344  156 0.1227 0.1729      5.4691      5.6445|
|  5:  3.0063 -  2.7922 0.99   1335  149 0.1348 0.1742       5.336      5.5816|
|  6:  2.7922 -  2.6285 0.99   1331  147 0.1252 0.1927      5.2213      5.4713|
|  7:  2.6285 -  2.4974 0.99   1324  138 0.1276 0.1715       5.192      5.3563|
|  8:  2.4974 -  2.3891 0.98   1300  153 0.1175 0.1684      5.0788      5.3495|
|  9:  2.3891 -  2.2975 0.98   1303  144 0.1209 0.1975      5.0611      5.3635|
| 10:  2.2975 -  2.2184 1.00   1323  152 0.1108 0.1663      4.9411      5.1967|
| 11:  2.2184 -  2.1493 0.98   1307  138 0.1119 0.1789      4.9428      5.3312|
| 12:  2.1493 -  2.0880 0.98   1297  145 0.1177 0.1829      4.8896       5.151|
| 13:  2.0880 -  2.0331 0.96   1258  138 0.1130 0.1673      4.8011      5.0371|
| 14:  2.0331 -  1.9836 0.27    357   42 0.1035 0.1690      4.6777      4.9547|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.7365  1426   158  0.94   9.38   0.97     0.94       7574.13|
|  2:  4.7365 -  3.7782  1382   155  0.95   8.15   1.00     0.99       9450.74|
|  3:  3.7782 -  3.3061  1343   144  0.93  11.69   1.02     1.02      10590.72|
|  4:  3.3061 -  3.0063  1344   156  0.91  14.49   1.01     0.98      10959.26|
|  5:  3.0063 -  2.7922  1335   149  0.90  16.44   1.00     0.98       8701.16|
|  6:  2.7922 -  2.6285  1331   147  0.89  16.90   0.99     0.96       7444.72|
|  7:  2.6285 -  2.4974  1324   138  0.90  15.94   0.99     0.96       6656.63|
|  8:  2.4974 -  2.3891  1300   153  0.90  16.04   0.99     0.96       5552.30|
|  9:  2.3891 -  2.2975  1303   144  0.90  16.30   0.99     0.95       5305.72|
| 10:  2.2975 -  2.2184  1323   152  0.90  15.73   1.00     0.97       4368.52|
| 11:  2.2184 -  2.1493  1307   138  0.90  15.99   0.98     0.93       4317.53|
| 12:  2.1493 -  2.0880  1297   145  0.90  16.40   1.00     1.00       4123.03|
| 13:  2.0880 -  2.0331  1258   138  0.89  17.43   0.99     0.97       3621.00|
| 14:  2.0331 -  1.9836   357    42  0.92  14.14   0.96     0.94       2670.98|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2670.98 max =        10959.26 mean =      6781.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.08|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1629   ksol= 0.32   Bsol= 69.25   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-2.38,-0.35,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1629   ksol= 0.32   Bsol= 69.25   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-2.38,-0.35,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166003                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.7365 0.99   1426  158 0.0951 0.1354      5.3791      5.5948|
|  2:  4.7365 -  3.7782 0.99   1382  155 0.0840 0.1105      5.4378      5.6261|
|  3:  3.7782 -  3.3061 0.99   1343  144 0.1054 0.1630      5.4708       5.858|
|  4:  3.3061 -  3.0063 0.99   1344  156 0.1227 0.1729      5.4691      5.6445|
|  5:  3.0063 -  2.7922 0.99   1335  149 0.1348 0.1742       5.336      5.5816|
|  6:  2.7922 -  2.6285 0.99   1331  147 0.1252 0.1927      5.2213      5.4713|
|  7:  2.6285 -  2.4974 0.99   1324  138 0.1276 0.1715       5.192      5.3563|
|  8:  2.4974 -  2.3891 0.98   1300  153 0.1175 0.1684      5.0788      5.3495|
|  9:  2.3891 -  2.2975 0.98   1303  144 0.1209 0.1975      5.0611      5.3635|
| 10:  2.2975 -  2.2184 1.00   1323  152 0.1108 0.1663      4.9411      5.1967|
| 11:  2.2184 -  2.1493 0.98   1307  138 0.1119 0.1789      4.9428      5.3312|
| 12:  2.1493 -  2.0880 0.98   1297  145 0.1177 0.1829      4.8896       5.151|
| 13:  2.0880 -  2.0331 0.96   1258  138 0.1130 0.1673      4.8011      5.0371|
| 14:  2.0331 -  1.9836 0.27    357   42 0.1035 0.1690      4.6777      4.9547|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.7365  1426   158  0.94   9.38   0.97     0.94       7574.13|
|  2:  4.7365 -  3.7782  1382   155  0.95   8.15   1.00     0.99       9450.74|
|  3:  3.7782 -  3.3061  1343   144  0.93  11.69   1.02     1.02      10590.72|
|  4:  3.3061 -  3.0063  1344   156  0.91  14.49   1.01     0.98      10959.26|
|  5:  3.0063 -  2.7922  1335   149  0.90  16.44   1.00     0.98       8701.16|
|  6:  2.7922 -  2.6285  1331   147  0.89  16.90   0.99     0.96       7444.72|
|  7:  2.6285 -  2.4974  1324   138  0.90  15.94   0.99     0.96       6656.63|
|  8:  2.4974 -  2.3891  1300   153  0.90  16.04   0.99     0.96       5552.30|
|  9:  2.3891 -  2.2975  1303   144  0.90  16.30   0.99     0.95       5305.72|
| 10:  2.2975 -  2.2184  1323   152  0.90  15.73   1.00     0.97       4368.52|
| 11:  2.2184 -  2.1493  1307   138  0.90  15.99   0.98     0.93       4317.53|
| 12:  2.1493 -  2.0880  1297   145  0.90  16.40   1.00     1.00       4123.03|
| 13:  2.0880 -  2.0331  1258   138  0.89  17.43   0.99     0.97       3621.00|
| 14:  2.0331 -  1.9836   357    42  0.92  14.14   0.96     0.94       2670.98|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2670.98 max =        10959.26 mean =      6781.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.30    104.76  17.25    None  None   None       |
|    all(noH): 2823   0      0.30    104.76  17.25    None  None   None       |
|    Sol.    : 438    0      1.85    104.76  41.52    None  None   None       |
|    Mac.    : 2385   0      0.30    90.96   12.79    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:     0.300 -  10.746: 1238   |   5:    52.528 -  62.974:   86        |
|      1:    10.746 -  21.192:  985   |   6:    62.974 -  73.420:   31        |
|      2:    21.192 -  31.637:  206   |   7:    73.420 -  83.865:   18        |
|      3:    31.637 -  42.083:  150   |   8:    83.865 -  94.311:   10        |
|      4:    42.083 -  52.528:   95   |   9:    94.311 - 104.756:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.469 - 4.749
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 316
   mapped sites are within: 0.725 - 4.749

peak=    5.675 closest distance to " NE2 GLN A  11 " =    1.210
peak=    5.265 closest distance to " CB  GLN A 223 " =    1.514
peak=    5.160 closest distance to " O   HOH Z 144 " =    1.852
peak=    4.989 closest distance to " O   HOH Z 111 " =    1.857
peak=    4.945 closest distance to " O   HOH Z 232 " =    2.208
peak=    4.945 closest distance to " CG  PRO A  54 " =    1.292
peak=    4.714 closest distance to " CG  PRO A 213 " =    1.238
peak=    4.693 closest distance to " CZ  PHE A 218 " =    1.075
peak=    4.622 closest distance to " O   HOH Z 298 " =    2.210
peak=    4.599 closest distance to " O   HOH Z 126 " =    1.894
peak=    4.597 closest distance to " O   HOH Z 423 " =    1.718
peak=    4.580 closest distance to " CD  ARG A 159 " =    0.781
peak=    4.563 closest distance to " CB  ARG A 190 " =    1.569
peak=    4.544 closest distance to " CB  SER A  63 " =    1.248
peak=    4.533 closest distance to " CB  GLN A 183 " =    1.258
peak=    4.531 closest distance to " O   HOH Z 369 " =    2.068
peak=    4.409 closest distance to " CB  ARG A  79 " =    1.473
peak=    4.361 closest distance to " O   HOH Z  78 " =    1.801
peak=    4.290 closest distance to " CB  ASN A 148 " =    1.416
peak=    4.281 closest distance to " CB  LEU A 228 " =    1.093
peak=    4.261 closest distance to " CB  PRO A  54 " =    0.987
peak=    4.256 closest distance to " O   HOH Z 126 " =    1.479
peak=    4.229 closest distance to " O   HOH Z 427 " =    2.970
peak=    4.214 closest distance to " CG  PRO A 198 " =    1.262
peak=    4.209 closest distance to " CB  ARG A 275 " =    0.943
peak=    4.191 closest distance to " O   HOH Z 287 " =    2.157
peak=    4.169 closest distance to " O   HOH Z  21 " =    1.748
peak=    4.148 closest distance to " CE  LYS A  76 " =    0.894
peak=    4.144 closest distance to " NH1AARG A 145 " =    1.308
peak=    4.129 closest distance to " O   HOH Z 406 " =    1.748
peak=    4.122 closest distance to " O   HOH Z 180 " =    2.090
peak=    4.077 closest distance to " CA  TYR A  30 " =    1.049
peak=    4.075 closest distance to " ND2 ASN A 187 " =    1.444
peak=    4.058 closest distance to " O   HOH Z 272 " =    1.823
peak=    4.052 closest distance to " CD  ARG A  66 " =    2.195
peak=    4.043 closest distance to " CG  PRO A 243 " =    1.091
peak=    4.035 closest distance to " O   HOH Z  88 " =    4.097
peak=    4.031 closest distance to " CB  ASP A 124 " =    0.805
peak=    4.027 closest distance to " O   HOH Z   9 " =    1.968
peak=    4.025 closest distance to " CA  ALA A 158 " =    1.161
peak=    4.008 closest distance to " O   HOH Z 188 " =    2.820
peak=    3.999 closest distance to " CD1 LEU A 300 " =    1.163
peak=    3.988 closest distance to " O   HOH Z 133 " =    2.680
peak=    3.985 closest distance to " CG  TRP A 179 " =    2.230
peak=    3.973 closest distance to " CG  LEU A 167 " =    1.277
peak=    3.962 closest distance to " O   HOH Z   1 " =    1.936
peak=    3.956 closest distance to " CD2 TRP A 179 " =    1.279
peak=    3.944 closest distance to " O   HOH Z  78 " =    2.266
peak=    3.940 closest distance to " O   HOH Z 158 " =    3.142
peak=    3.922 closest distance to " CA  SER A  87 " =    0.994
peak=    3.920 closest distance to " CB  SER A 212 " =    1.161
peak=    3.903 closest distance to " CB  GLU A 152 " =    1.164
peak=    3.884 closest distance to " CB  VAL A 265 " =    1.315
peak=    3.880 closest distance to " CG  PRO A  90 " =    1.292
peak=    3.877 closest distance to " CZ3 TRP A 266 " =    1.145
peak=    3.875 closest distance to " C   PRO A 198 " =    1.590
peak=    3.869 closest distance to " CB  TRP A 266 " =    1.017
peak=    3.864 closest distance to " O   HOH Z   7 " =    1.353
peak=    3.859 closest distance to " O   HOH Z  10 " =    1.854
peak=    3.852 closest distance to " O   HOH Z 346 " =    1.644
peak=    3.828 closest distance to " ND1 HIS A  86 " =    1.759
peak=    3.819 closest distance to " O   TYR A 116 " =    1.361
peak=    3.809 closest distance to " CD BLYS A 290 " =    0.972
peak=    3.802 closest distance to " CB  GLU A 277 " =    3.729
peak=    3.783 closest distance to " CG2 VAL A 257 " =    0.858
peak=    3.775 closest distance to " CA  ARG A 195 " =    1.316
peak=    3.767 closest distance to " CD  LYS A 166 " =    1.336
peak=    3.754 closest distance to " O   HOH Z 353 " =    2.666
peak=    3.750 closest distance to " CB  GLU A 128 " =    0.998
peak=    3.750 closest distance to " O   HOH Z 380 " =    1.715
peak=    3.749 closest distance to " O   HOH Z 294 " =    1.593
peak=    3.743 closest distance to " O   HOH Z 214 " =    2.159
peak=    3.732 closest distance to " CG2 THR A 221 " =    0.945
peak=    3.730 closest distance to " O   HOH Z 265 " =    1.999
peak=    3.728 closest distance to " CA  TYR A 116 " =    1.408
peak=    3.709 closest distance to " OD1 ASN A  69 " =    2.560
peak=    3.707 closest distance to " CB  ASN A 187 " =    1.052
peak=    3.704 closest distance to " CB  ASN A 142 " =    0.903
peak=    3.703 closest distance to " O   HOH Z 332 " =    1.620
peak=    3.699 closest distance to " O   HOH Z 234 " =    3.787
peak=    3.691 closest distance to " CA  ALA A 154 " =    1.053
peak=    3.685 closest distance to " O   HOH Z 313 " =    1.991
peak=    3.663 closest distance to " CB  ASN A  39 " =    0.966
peak=    3.654 closest distance to " CG1 ILE A 151 " =    1.153
peak=    3.652 closest distance to " O   HOH Z 116 " =    1.852
peak=    3.651 closest distance to " O   HOH Z 285 " =    2.181
peak=    3.651 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.645 closest distance to " O   HOH Z 286 " =    2.286
peak=    3.644 closest distance to " O   HOH Z 394 " =    4.019
peak=    3.644 closest distance to " CB  MET A  40 " =    0.815
peak=    3.640 closest distance to " CB  ALA A 104 " =    0.725
peak=    3.639 closest distance to " CD  ARG A 269 " =    0.944
peak=    3.637 closest distance to " CB  GLU A  46 " =    0.957
peak=    3.635 closest distance to " O   HOH Z 425 " =    1.395
peak=    3.635 closest distance to " O   HOH Z 345 " =    1.817
peak=    3.634 closest distance to " CB  ASN A 110 " =    1.119
peak=    3.634 closest distance to " CA  PRO A  54 " =    1.388
peak=    3.633 closest distance to " O   HOH Z 213 " =    2.154
peak=    3.625 closest distance to " CA  THR A 264 " =    0.896
peak=    3.619 closest distance to " O   HOH Z  58 " =    1.727
peak=    3.618 closest distance to " O   HOH Z  53 " =    2.496
peak=    3.611 closest distance to " CB  VAL A 202 " =    1.609
peak=    3.609 closest distance to " N   ASN A 127 " =    1.314
peak=    3.607 closest distance to " O   HOH Z 217 " =    3.153
peak=    3.600 closest distance to " OG  SER A  62 " =    3.030
peak=    3.594 closest distance to " O   HOH Z 316 " =    3.077
peak=    3.590 closest distance to " O   HOH Z 193 " =    2.222
peak=    3.588 closest distance to " CB  ASP A 140 " =    0.923
peak=    3.579 closest distance to " O   HOH Z 273 " =    2.875
peak=    3.577 closest distance to " O   HOH Z 250 " =    1.397
peak=    3.558 closest distance to " O   SER A  87 " =    2.332
peak=    3.551 closest distance to " CB  TYR A 169 " =    0.751
peak=    3.550 closest distance to " O   HOH Z 132 " =    2.460
peak=    3.550 closest distance to " CA  GLU A  46 " =    0.860
peak=    3.548 closest distance to " O   HOH Z 411 " =    3.659
peak=    3.541 closest distance to " O   HOH Z 365 " =    2.861
peak=    3.537 closest distance to " CB  SER A   3 " =    1.492
peak=    3.527 closest distance to " O   HOH Z 359 " =    4.158
peak=    3.519 closest distance to " CA  VAL A 125 " =    1.215
peak=    3.514 closest distance to " CA  MET A  40 " =    1.278
peak=    3.508 closest distance to " CA  ARG A 102 " =    1.150
peak=    3.506 closest distance to " CB  ALA A   9 " =    1.656
peak=    3.506 closest distance to " CG  GLU A  37 " =    0.929
peak=    3.505 closest distance to " O   HOH Z 422 " =    2.787
peak=    3.499 closest distance to " O   ASN A  74 " =    1.443
peak=    3.494 closest distance to " CB  TRP A 150 " =    1.158
peak=    3.488 closest distance to " CA  ALA A  51 " =    0.922
peak=    3.487 closest distance to " O   HOH Z 258 " =    2.102
peak=    3.482 closest distance to " CB  TYR A 169 " =    0.926
peak=    3.482 closest distance to " CB  TYR A 116 " =    0.906
peak=    3.477 closest distance to " O   HOH Z  61 " =    1.537
peak=    3.475 closest distance to " CB  ALA A   1 " =    4.749
peak=    3.475 closest distance to " CB  ARG A 138 " =    0.988
peak=    3.473 closest distance to " O   HOH Z 193 " =    1.684
peak=    3.472 closest distance to " O   HOH Z 211 " =    1.042
peak=    3.470 closest distance to " O   HOH Z 183 " =    1.510
peak=    3.467 closest distance to " N   PHE A 130 " =    1.232
peak=    3.467 closest distance to " ND2 ASN A 249 " =    0.857
peak=    3.466 closest distance to " O   HOH Z 426 " =    1.934
peak=    3.454 closest distance to " O   HOH Z 389 " =    1.901
peak=    3.452 closest distance to " CB  LEU A 237 " =    0.795
peak=    3.450 closest distance to " CA  ALA A 291 " =    0.868
peak=    3.449 closest distance to " CB  ALA A 248 " =    1.022
peak=    3.443 closest distance to " CG1 VAL A 153 " =    0.946
peak=    3.442 closest distance to " O   HOH Z 128 " =    2.359
peak=    3.441 closest distance to " O   HOH Z 290 " =    1.039
peak=    3.436 closest distance to " O   HOH Z 218 " =    4.559
peak=    3.435 closest distance to " CB  SER A 210 " =    0.754
peak=    3.434 closest distance to " CA  ASN A 215 " =    1.231
peak=    3.434 closest distance to " O   HOH Z 329 " =    4.110
peak=    3.430 closest distance to " O   HOH Z 368 " =    2.001
peak=    3.429 closest distance to " O   ASN A 209 " =    1.307
peak=    3.429 closest distance to " O   HOH Z 145 " =    1.870
peak=    3.429 closest distance to " N   ALA A   1 " =    2.144
peak=    3.428 closest distance to " O   HOH Z 368 " =    3.631
peak=    3.427 closest distance to " O   HOH Z  80 " =    1.506
peak=    3.415 closest distance to " O   HOH Z 240 " =    2.243
peak=    3.409 closest distance to " O   HOH Z 371 " =    2.954
peak=    3.407 closest distance to " NH2 ARG A 156 " =    1.174
peak=    3.401 closest distance to " O   HOH Z 386 " =    2.796
peak=    3.401 closest distance to " CB  SER A 216 " =    0.983
peak=    3.399 closest distance to " O   HOH Z 147 " =    1.870
peak=    3.393 closest distance to " CB  ALA A  34 " =    1.107
peak=    3.392 closest distance to " O   HOH Z 172 " =    3.087
peak=    3.390 closest distance to " CD2 LEU A 255 " =    1.759
peak=    3.388 closest distance to " O   HOH Z 391 " =    2.889
peak=    3.386 closest distance to " O   HOH Z 148 " =    3.362
peak=    3.380 closest distance to " O   HOH Z   9 " =    1.356
peak=    3.380 closest distance to " CD2 LEU A 297 " =    0.890
peak=    3.378 closest distance to " O   HOH Z 415 " =    3.871
peak=    3.374 closest distance to " O   HOH Z 280 " =    3.052
peak=    3.372 closest distance to " O   HOH Z 238 " =    3.744
peak=    3.365 closest distance to " CA  GLY A 241 " =    0.800
peak=    3.364 closest distance to " CA  THR A 221 " =    0.978
peak=    3.360 closest distance to " CA  ALA A 233 " =    1.415
peak=    3.360 closest distance to " O   HOH Z  63 " =    1.275
peak=    3.360 closest distance to " CB  ARG A 139 " =    1.047
peak=    3.352 closest distance to " CB  ASP A 171 " =    1.291
peak=    3.348 closest distance to " OG  SER A 135 " =    1.250
peak=    3.347 closest distance to " CB  LEU A  96 " =    1.498
peak=    3.346 closest distance to " O  BHOH Z 338 " =    2.349
peak=    3.343 closest distance to " O   HOH Z 437 " =    1.293
peak=    3.341 closest distance to " O   HOH Z 185 " =    1.973
peak=    3.338 closest distance to " O   HOH Z 145 " =    1.659
peak=    3.334 closest distance to " O   HOH Z 130 " =    3.736
peak=    3.330 closest distance to " CB  GLN A  88 " =    1.227
peak=    3.329 closest distance to " CA  ALA A 160 " =    0.976
peak=    3.328 closest distance to " O   HOH Z 345 " =    3.481
peak=    3.327 closest distance to " OD2 ASP A 286 " =    3.310
peak=    3.327 closest distance to " CA  ASN A  74 " =    1.349
peak=    3.325 closest distance to " O   MET A 105 " =    1.781
peak=    3.322 closest distance to " CD  LYS A  76 " =    1.956
peak=    3.321 closest distance to " O   HOH Z 409 " =    2.404
peak=    3.314 closest distance to " CZ  PHE A  38 " =    1.260
peak=    3.312 closest distance to " O   HOH Z 272 " =    2.469
peak=    3.311 closest distance to " OD1 ASN A 217 " =    1.481
peak=    3.310 closest distance to " OG  SER A  62 " =    3.039
peak=    3.309 closest distance to " CA  ASP A 124 " =    0.769
peak=    3.307 closest distance to " CA  MET A 105 " =    0.965
peak=    3.306 closest distance to " CB  ILE A 120 " =    1.328
peak=    3.304 closest distance to " N   ARG A 156 " =    1.373
peak=    3.301 closest distance to " O   HOH Z 218 " =    1.504
peak=    3.301 closest distance to " O   HOH Z 124 " =    1.961
peak=    3.297 closest distance to " CG2 ILE A  20 " =    1.320
peak=    3.296 closest distance to " O   HOH Z 325 " =    2.304
peak=    3.295 closest distance to " O   HOH Z 359 " =    1.455
peak=    3.292 closest distance to " O   HOH Z 193 " =    1.873
peak=    3.291 closest distance to " NE2 HIS A 207 " =    1.268
peak=    3.290 closest distance to " CB  GLN A  89 " =    1.375
peak=    3.290 closest distance to " O   HOH Z 291 " =    1.498
peak=    3.284 closest distance to " O   HOH Z 227 " =    1.935
peak=    3.283 closest distance to " O   HOH Z 305 " =    3.716
peak=    3.282 closest distance to " OD2 ASP A 286 " =    2.916
peak=    3.281 closest distance to " O   HOH Z 419 " =    1.937
peak=    3.279 closest distance to " CB  SER A 245 " =    3.170
peak=    3.278 closest distance to " O   ARG A 145 " =    1.679
peak=    3.277 closest distance to " O   HOH Z  40 " =    1.808
peak=    3.273 closest distance to " CB  MET A  47 " =    1.027
peak=    3.270 closest distance to " CB  SER A 276 " =    1.068
peak=    3.269 closest distance to " O   THR A 220 " =    1.290
peak=    3.268 closest distance to " CA  ARG A 159 " =    1.325
peak=    3.267 closest distance to " CB  PRO A  90 " =    1.171
peak=    3.261 closest distance to " CG  GLN A  55 " =    2.299
peak=    3.258 closest distance to " N   SER A 271 " =    0.957
peak=    3.255 closest distance to " O   HOH Z  44 " =    2.800
peak=    3.255 closest distance to " OH  TYR A 186 " =    1.149
peak=    3.253 closest distance to " O   THR A 251 " =    1.177
peak=    3.253 closest distance to " CA  SER A  95 " =    0.956
peak=    3.250 closest distance to " O   HOH Z 274 " =    2.181
peak=    3.249 closest distance to " CG2 ILE A 151 " =    0.876
peak=    3.248 closest distance to " CG1 ILE A  33 " =    1.219
peak=    3.247 closest distance to " CA  ASN A 127 " =    1.128
peak=    3.247 closest distance to " CG BARG A 275 " =    1.478
peak=    3.241 closest distance to " O   HOH Z 116 " =    3.277
peak=    3.235 closest distance to " CD2 TYR A 186 " =    1.048
peak=    3.232 closest distance to " CG2 VAL A 197 " =    1.086
peak=    3.227 closest distance to " O   ALA A 291 " =    1.594
peak=    3.225 closest distance to " ND2 ASN A 110 " =    1.630
peak=    3.225 closest distance to " CB  ALA A  43 " =    0.779
peak=    3.223 closest distance to " O   HOH Z 287 " =    2.263
peak=    3.223 closest distance to " CB  LYS A 117 " =    1.168
peak=    3.220 closest distance to " O   HOH Z 188 " =    2.407
peak=    3.219 closest distance to " O   HOH Z 403 " =    1.651
peak=    3.218 closest distance to " N   TYR A  15 " =    0.872
peak=    3.217 closest distance to " O   HOH Z 135 " =    1.722
peak=    3.217 closest distance to " O   PRO A 213 " =    1.538
peak=    3.216 closest distance to " CG1 VAL A 189 " =    2.007
peak=    3.215 closest distance to " O   HOH Z 285 " =    2.045
peak=    3.214 closest distance to " CA  ARG A  36 " =    1.173
peak=    3.213 closest distance to " O   HOH Z 219 " =    1.767
peak=    3.212 closest distance to " O   HOH Z 166 " =    3.896
peak=    3.212 closest distance to " NE  ARG A  79 " =    1.133
peak=    3.212 closest distance to " NH2 ARG A 219 " =    1.836
peak=    3.208 closest distance to " O   HOH Z 352 " =    1.701
peak=    3.204 closest distance to " O   HOH Z  68 " =    2.089
peak=    3.199 closest distance to " CB  PRO A 243 " =    1.160
peak=    3.198 closest distance to " CA  TYR A  30 " =    1.072
peak=    3.195 closest distance to " O   HOH Z 209 " =    2.257
peak=    3.194 closest distance to " CB  VAL A 257 " =    0.811
peak=    3.192 closest distance to " CE1 PHE A 218 " =    1.208
peak=    3.186 closest distance to " CA  ASN A 217 " =    1.176
peak=    3.185 closest distance to " CA  ILE A 106 " =    0.847
peak=    3.183 closest distance to " O   HOH Z 299 " =    2.611
peak=    3.181 closest distance to " O   HOH Z   1 " =    1.686
peak=    3.178 closest distance to " CA  SER A  26 " =    0.976
peak=    3.173 closest distance to " CB  ALA A 114 " =    1.321
peak=    3.173 closest distance to " O   HOH Z 130 " =    2.263
peak=    3.172 closest distance to " N   GLU A   2 " =    1.483
peak=    3.172 closest distance to " O   HOH Z 356 " =    2.974
peak=    3.171 closest distance to " O   HOH Z 271 " =    2.865
peak=    3.170 closest distance to " N   VAL A 296 " =    1.744
peak=    3.167 closest distance to " O   HOH Z 302 " =    1.910
peak=    3.167 closest distance to " O   HOH Z  94 " =    2.405
peak=    3.165 closest distance to " OG BSER A 164 " =    2.460
peak=    3.164 closest distance to " CG  ARG A 159 " =    0.919
peak=    3.163 closest distance to " CG  GLN A 144 " =    0.876
peak=    3.155 closest distance to " CB  SER A 212 " =    1.199
peak=    3.155 closest distance to " CG  GLN A 278 " =    1.442
peak=    3.154 closest distance to " CB  ALA A 160 " =    1.393
peak=    3.146 closest distance to " CE2 PHE A  16 " =    1.019
peak=    3.145 closest distance to " O   HOH Z  22 " =    2.693
peak=    3.144 closest distance to " CA  ASP A 162 " =    0.994
peak=    3.143 closest distance to " O   HOH Z 340 " =    2.199
peak=    3.138 closest distance to " CE2 TYR A 186 " =    0.889
peak=    3.137 closest distance to " O   HOH Z 368 " =    4.249
peak=    3.134 closest distance to " CB  SER A  62 " =    1.119
peak=    3.130 closest distance to " CG  ARG A 138 " =    1.148
peak=    3.127 closest distance to " O   HOH Z 175 " =    3.706
peak=    3.124 closest distance to " NH2 ARG A  14 " =    2.166
peak=    3.124 closest distance to " CA  LEU A  83 " =    1.563
peak=    3.122 closest distance to " CG BARG A 102 " =    1.891
peak=    3.120 closest distance to " CA  TYR A 186 " =    1.646
peak=    3.115 closest distance to " O   HOH Z  57 " =    1.231
peak=    3.114 closest distance to " CB  ASN A 285 " =    0.916
peak=    3.112 closest distance to " O   HOH Z 358 " =    3.805
peak=    3.106 closest distance to " O   THR A 182 " =    1.506
peak=    3.101 closest distance to " CB  ALA A 114 " =    0.961
peak=    3.100 closest distance to " CB  GLN A 103 " =    0.866
peak=    3.095 closest distance to " CB  ASN A 215 " =    1.154
peak=    3.092 closest distance to " O   HOH Z 128 " =    1.807
peak=    3.089 closest distance to " O   HOH Z 301 " =    1.701
peak=    3.089 closest distance to " CD1 ILE A 106 " =    0.839
peak=    3.088 closest distance to " CA  ALA A 299 " =    0.890
peak=    3.078 closest distance to " O   HOH Z 407 " =    2.234
peak=    3.068 closest distance to " CB  ASP A 171 " =    0.807
peak=    3.057 closest distance to " O   HOH Z 132 " =    3.911
peak=    3.046 closest distance to " CB  VAL A 265 " =    2.134
peak=    3.041 closest distance to " O   HOH Z 327 " =    2.330
peak=    3.034 closest distance to " CA  ALA A 100 " =    1.094
peak=    3.032 closest distance to " NE2 GLN A  73 " =    1.603
peak=    3.022 closest distance to " OE2 GLU A  53 " =    2.266
peak=    3.008 closest distance to " CA  ARG A 156 " =    1.165

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.554 - 5.660
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 213
   mapped sites are within: 0.740 - 5.660

peak=   -4.659 closest distance to " CB  PRO A 243 " =    2.591
peak=   -4.479 closest distance to " O   HOH Z 377 " =    2.042
peak=   -4.307 closest distance to " CD  ARG A  14 " =    3.499
peak=   -4.185 closest distance to " O   PRO A 198 " =    1.295
peak=   -4.163 closest distance to " CD  ARG A 156 " =    2.150
peak=   -4.158 closest distance to " CB  ALA A  43 " =    2.617
peak=   -4.151 closest distance to " O   HOH Z 231 " =    2.180
peak=   -4.133 closest distance to " CG1 VAL A 250 " =    2.642
peak=   -4.126 closest distance to " N   ALA A  43 " =    2.607
peak=   -4.062 closest distance to " O   HOH Z 211 " =    0.751
peak=   -4.053 closest distance to " O   HOH Z  38 " =    1.356
peak=   -4.032 closest distance to " O   HOH Z  73 " =    2.073
peak=   -3.998 closest distance to " O   HOH Z 290 " =    1.324
peak=   -3.966 closest distance to " CG2 ILE A  49 " =    2.744
peak=   -3.919 closest distance to " CG1 VAL A 112 " =    2.604
peak=   -3.907 closest distance to " O   HOH Z 407 " =    3.322
peak=   -3.897 closest distance to " CZ3 TRP A 179 " =    1.177
peak=   -3.834 closest distance to " O   HOH Z 394 " =    1.503
peak=   -3.822 closest distance to " CD2 TYR A 293 " =    1.900
peak=   -3.810 closest distance to " O   HOH Z 389 " =    2.057
peak=   -3.798 closest distance to " O   VAL A  67 " =    2.733
peak=   -3.788 closest distance to " OG BSER A 134 " =    1.380
peak=   -3.786 closest distance to " CG  GLN A 223 " =    2.318
peak=   -3.763 closest distance to " ND2 ASN A 249 " =    2.132
peak=   -3.763 closest distance to " O   ALA A  10 " =    1.748
peak=   -3.761 closest distance to " CG1 VAL A 112 " =    3.021
peak=   -3.743 closest distance to " O   HOH Z 351 " =    1.518
peak=   -3.741 closest distance to " CA  GLY A 241 " =    2.349
peak=   -3.739 closest distance to " CD1 TYR A 247 " =    2.918
peak=   -3.739 closest distance to " CE2 TYR A  30 " =    2.690
peak=   -3.733 closest distance to " OD1 ASP A 171 " =    1.648
peak=   -3.729 closest distance to " OD1 ASP A 191 " =    1.829
peak=   -3.728 closest distance to " CD  GLN A  58 " =    0.859
peak=   -3.714 closest distance to " CB  ALA A 158 " =    1.697
peak=   -3.713 closest distance to " CB  ASP A 286 " =    2.003
peak=   -3.692 closest distance to " CG2 THR A 178 " =    2.228
peak=   -3.689 closest distance to " CD2 LEU A 143 " =    2.640
peak=   -3.673 closest distance to " O   HOH Z 411 " =    5.461
peak=   -3.663 closest distance to " NH2AARG A 275 " =    5.567
peak=   -3.659 closest distance to " O   HOH Z 198 " =    2.038
peak=   -3.655 closest distance to " O   HOH Z  52 " =    1.322
peak=   -3.646 closest distance to " OXT GLY A 302 " =    3.215
peak=   -3.642 closest distance to " O   HOH Z 326 " =    5.116
peak=   -3.628 closest distance to " O   HOH Z 111 " =    1.737
peak=   -3.625 closest distance to " O   HOH Z 359 " =    3.193
peak=   -3.621 closest distance to " CA  GLY A 241 " =    3.157
peak=   -3.617 closest distance to " CD1 PHE A  59 " =    1.993
peak=   -3.617 closest distance to " O   HOH Z 185 " =    2.312
peak=   -3.614 closest distance to " CB  PRO A  54 " =    2.506
peak=   -3.606 closest distance to " CD1 LEU A 101 " =    2.291
peak=   -3.601 closest distance to " CB  TRP A  85 " =    2.474
peak=   -3.589 closest distance to " CE BMET A  47 " =    1.590
peak=   -3.585 closest distance to " O   HOH Z 118 " =    1.445
peak=   -3.581 closest distance to " O   PHE A 218 " =    1.467
peak=   -3.578 closest distance to " CG  MET A 105 " =    0.972
peak=   -3.574 closest distance to " O   PRO A 163 " =    2.008
peak=   -3.553 closest distance to " N   THR A 157 " =    1.602
peak=   -3.546 closest distance to " CA  GLY A  98 " =    1.900
peak=   -3.538 closest distance to " O   HOH Z 232 " =    1.903
peak=   -3.534 closest distance to " C   LEU A 143 " =    1.355
peak=   -3.532 closest distance to " O   HOH Z 216 " =    1.260
peak=   -3.532 closest distance to " O   HOH Z 368 " =    1.750
peak=   -3.523 closest distance to " C   HIS A 108 " =    1.173
peak=   -3.522 closest distance to " CB  ASP A  27 " =    2.520
peak=   -3.520 closest distance to " O   HOH Z 435 " =    2.857
peak=   -3.507 closest distance to " O   HOH Z 174 " =    2.583
peak=   -3.506 closest distance to " CD2 PHE A  61 " =    2.020
peak=   -3.500 closest distance to " O   HOH Z 231 " =    1.090
peak=   -3.496 closest distance to " OG  SER A  97 " =    2.213
peak=   -3.484 closest distance to " O   PRO A 243 " =    2.509
peak=   -3.480 closest distance to " N   ALA A 248 " =    1.692
peak=   -3.474 closest distance to " O   GLY A  17 " =    1.241
peak=   -3.467 closest distance to " CG  GLN A  88 " =    0.897
peak=   -3.466 closest distance to " CB  ALA A 129 " =    2.445
peak=   -3.461 closest distance to " ND2 ASN A  45 " =    1.282
peak=   -3.453 closest distance to " O   VAL A 189 " =    2.583
peak=   -3.449 closest distance to " O   PRO A 198 " =    1.375
peak=   -3.441 closest distance to " CB  ALA A 291 " =    2.299
peak=   -3.440 closest distance to " ND2 ASN A 187 " =    1.530
peak=   -3.439 closest distance to " CD  LYS A 289 " =    2.324
peak=   -3.435 closest distance to " O   HOH Z   9 " =    1.805
peak=   -3.427 closest distance to " CA  SER A  62 " =    2.722
peak=   -3.426 closest distance to " O   HOH Z 426 " =    1.617
peak=   -3.425 closest distance to " O   HOH Z 275 " =    1.764
peak=   -3.424 closest distance to " OH  TYR A 172 " =    1.761
peak=   -3.420 closest distance to " O   SER A 210 " =    1.869
peak=   -3.407 closest distance to " CE  MET A 105 " =    2.453
peak=   -3.401 closest distance to " CB  ALA A 248 " =    2.436
peak=   -3.399 closest distance to " O   HOH Z 252 " =    4.024
peak=   -3.395 closest distance to " N   ASP A 171 " =    2.400
peak=   -3.394 closest distance to " NZ  LYS A 166 " =    1.188
peak=   -3.393 closest distance to " CG1BVAL A  41 " =    2.811
peak=   -3.392 closest distance to " CE2 PHE A  61 " =    2.726
peak=   -3.391 closest distance to " O   HOH Z 191 " =    5.660
peak=   -3.386 closest distance to " ND2 ASN A  45 " =    2.113
peak=   -3.385 closest distance to " O   HOH Z 313 " =    1.795
peak=   -3.381 closest distance to " CE3 TRP A 150 " =    2.289
peak=   -3.380 closest distance to " O   HOH Z  10 " =    1.476
peak=   -3.379 closest distance to " O   HOH Z  60 " =    1.563
peak=   -3.378 closest distance to " O   HOH Z 100 " =    1.297
peak=   -3.371 closest distance to " O   HOH Z 337 " =    1.473
peak=   -3.370 closest distance to " OD1 ASN A 148 " =    1.555
peak=   -3.369 closest distance to " O   HOH Z 196 " =    2.234
peak=   -3.367 closest distance to " O   GLY A 211 " =    1.316
peak=   -3.365 closest distance to " O   HOH Z  53 " =    1.670
peak=   -3.357 closest distance to " CB  ALA A   9 " =    2.463
peak=   -3.349 closest distance to " NH2BARG A 275 " =    1.844
peak=   -3.349 closest distance to " O   HOH Z 372 " =    2.473
peak=   -3.348 closest distance to " C   ASN A 285 " =    2.419
peak=   -3.347 closest distance to " C   LEU A 222 " =    0.740
peak=   -3.340 closest distance to " NH2 ARG A  79 " =    1.560
peak=   -3.339 closest distance to " CG  TRP A 266 " =    1.811
peak=   -3.335 closest distance to " CG2 ILE A 263 " =    2.343
peak=   -3.333 closest distance to " CG1 VAL A 197 " =    2.293
peak=   -3.326 closest distance to " O   HOH Z 281 " =    2.660
peak=   -3.325 closest distance to " OE1 GLN A  88 " =    1.162
peak=   -3.324 closest distance to " O   SER A 135 " =    1.477
peak=   -3.323 closest distance to " CA  ASP A 298 " =    1.077
peak=   -3.317 closest distance to " CG2 VAL A 189 " =    1.988
peak=   -3.317 closest distance to " O   ILE A 106 " =    2.217
peak=   -3.310 closest distance to " SG BCYS A 201 " =    2.119
peak=   -3.309 closest distance to " O   HOH Z 345 " =    2.261
peak=   -3.308 closest distance to " O   HOH Z  65 " =    1.382
peak=   -3.304 closest distance to " O   HOH Z  43 " =    1.592
peak=   -3.300 closest distance to " OG BSER A 134 " =    1.797
peak=   -3.296 closest distance to " NE2 GLN A 278 " =    1.799
peak=   -3.295 closest distance to " SD  MET A 188 " =    2.461
peak=   -3.292 closest distance to " O   HOH Z 295 " =    1.661
peak=   -3.290 closest distance to " O   HOH Z 275 " =    1.564
peak=   -3.287 closest distance to " O   HOH Z 241 " =    1.381
peak=   -3.286 closest distance to " ND2 ASN A  60 " =    4.076
peak=   -3.282 closest distance to " CA  GLY A 241 " =    2.910
peak=   -3.281 closest distance to " CG  PRO A 163 " =    2.461
peak=   -3.279 closest distance to " CB  ASP A 132 " =    2.383
peak=   -3.279 closest distance to " OG  SER A  87 " =    1.287
peak=   -3.278 closest distance to " O   HOH Z 145 " =    1.184
peak=   -3.273 closest distance to " O   HOH Z 131 " =    4.118
peak=   -3.272 closest distance to " CB  PRO A 163 " =    2.566
peak=   -3.270 closest distance to " CB  PHE A 192 " =    1.959
peak=   -3.260 closest distance to " O   VAL A  67 " =    2.914
peak=   -3.259 closest distance to " CD1 LEU A 228 " =    2.425
peak=   -3.256 closest distance to " NE  ARG A  36 " =    2.044
peak=   -3.247 closest distance to " CB  ASN A  39 " =    2.268
peak=   -3.246 closest distance to " O   HOH Z 357 " =    2.188
peak=   -3.245 closest distance to " CE2 PHE A 218 " =    2.402
peak=   -3.245 closest distance to " CG  HIS A  86 " =    1.106
peak=   -3.245 closest distance to " CD  ARG A  79 " =    1.074
peak=   -3.245 closest distance to " O   HOH Z 102 " =    1.619
peak=   -3.241 closest distance to " O   HOH Z 243 " =    1.908
peak=   -3.239 closest distance to " O   GLN A 240 " =    2.462
peak=   -3.234 closest distance to " CB  CYS A 254 " =    2.207
peak=   -3.234 closest distance to " CE3 TRP A 274 " =    2.421
peak=   -3.227 closest distance to " O   HOH Z 103 " =    1.832
peak=   -3.227 closest distance to " CD2 PHE A 192 " =    2.373
peak=   -3.223 closest distance to " O   VAL A 125 " =    2.286
peak=   -3.221 closest distance to " O   HOH Z 353 " =    2.216
peak=   -3.216 closest distance to " O   HOH Z 409 " =    4.660
peak=   -3.216 closest distance to " O   HOH Z 198 " =    1.752
peak=   -3.208 closest distance to " O   HOH Z 298 " =    2.405
peak=   -3.207 closest distance to " CG  LEU A  83 " =    1.960
peak=   -3.204 closest distance to " N   THR A  52 " =    1.726
peak=   -3.195 closest distance to " O   ARG A 145 " =    1.534
peak=   -3.188 closest distance to " CA  GLY A 203 " =    2.451
peak=   -3.187 closest distance to " O   SER A  22 " =    2.575
peak=   -3.176 closest distance to " CB  GLN A  11 " =    1.769
peak=   -3.174 closest distance to " NH1AARG A 275 " =    1.955
peak=   -3.173 closest distance to " CD2 HIS A 207 " =    2.360
peak=   -3.171 closest distance to " O   HOH Z 348 " =    2.231
peak=   -3.170 closest distance to " ND2 ASN A 285 " =    2.134
peak=   -3.169 closest distance to " O   HOH Z 266 " =    5.170
peak=   -3.162 closest distance to " CB  ALA A 100 " =    2.224
peak=   -3.162 closest distance to " CG  PHE A 283 " =    2.734
peak=   -3.160 closest distance to " O   HOH Z  71 " =    2.133
peak=   -3.160 closest distance to " CG2 ILE A 151 " =    2.640
peak=   -3.158 closest distance to " OH  TYR A 247 " =    1.843
peak=   -3.158 closest distance to " CD1 TRP A  70 " =    1.098
peak=   -3.152 closest distance to " CA  GLY A 133 " =    2.058
peak=   -3.146 closest distance to " C   MET A 188 " =    1.538
peak=   -3.144 closest distance to " CD1 LEU A 297 " =    2.643
peak=   -3.144 closest distance to " OD2 ASP A 140 " =    1.842
peak=   -3.144 closest distance to " O   HOH Z 377 " =    0.903
peak=   -3.141 closest distance to " O   VAL A 189 " =    1.709
peak=   -3.138 closest distance to " CG  GLU A  53 " =    1.473
peak=   -3.134 closest distance to " N   ALA A 226 " =    2.172
peak=   -3.132 closest distance to " O   HOH Z  51 " =    1.756
peak=   -3.126 closest distance to " CG2 ILE A  20 " =    2.939
peak=   -3.120 closest distance to " CG  ARG A 269 " =    2.556
peak=   -3.112 closest distance to " CG  GLU A 277 " =    1.229
peak=   -3.105 closest distance to " O   HOH Z 218 " =    3.879
peak=   -3.105 closest distance to " O   HOH Z 128 " =    2.687
peak=   -3.104 closest distance to " CD2 TYR A 293 " =    2.139
peak=   -3.100 closest distance to " CB  TYR A  15 " =    2.372
peak=   -3.099 closest distance to " O   HOH Z 114 " =    0.862
peak=   -3.098 closest distance to " O   HOH Z 177 " =    1.854
peak=   -3.096 closest distance to " O   ASP A  27 " =    1.916
peak=   -3.094 closest distance to " CB  ALA A 291 " =    2.232
peak=   -3.092 closest distance to " OD2 ASP A 171 " =    1.845
peak=   -3.091 closest distance to " O   ARG A  56 " =    1.990
peak=   -3.091 closest distance to " O   HOH Z 417 " =    2.974
peak=   -3.086 closest distance to " CG2BVAL A  41 " =    1.150
peak=   -3.086 closest distance to " O   HOH Z 193 " =    1.544
peak=   -3.085 closest distance to " OD1AASN A 224 " =    1.784
peak=   -3.079 closest distance to " O   HOH Z 166 " =    1.851
peak=   -3.072 closest distance to " O   HOH Z  90 " =    1.703
peak=   -3.062 closest distance to " O   GLY A  80 " =    2.493
peak=   -3.062 closest distance to " OG  SER A 245 " =    1.413
peak=   -3.047 closest distance to " O   HOH Z 323 " =    1.517
peak=   -3.040 closest distance to " O   HOH Z  85 " =    2.348
peak=   -3.028 closest distance to " O   MET A  47 " =    2.777
peak=   -3.028 closest distance to " CA  SER A 135 " =    1.266
peak=   -3.009 closest distance to " CB  ALA A  10 " =    2.260

================= 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    :  0.4389 0.4308   6.242480e+00   6.220584e+00
   1_bss:  0.4303 0.4249   6.234057e+00   6.211055e+00
   1_xyz:  0.2652 0.2958   5.855734e+00   5.933861e+00
   1_adp:  0.2439 0.3014   5.810367e+00   5.956918e+00
   1_occ:  0.2434 0.3011   5.809639e+00   5.956987e+00
   2_bss:  0.2413 0.3003   5.811829e+00   5.958683e+00
   2_xyz:  0.1736 0.2257   5.522664e+00   5.712457e+00
   2_adp:  0.1560 0.2131   5.445682e+00   5.661833e+00
   2_occ:  0.1558 0.2130   5.445132e+00   5.661746e+00
   3_bss:  0.1559 0.2132   5.444037e+00   5.660917e+00
   3_xyz:  0.1324 0.1845   5.298732e+00   5.533042e+00
   3_adp:  0.1276 0.1761   5.258837e+00   5.486924e+00
   3_occ:  0.1274 0.1760   5.258347e+00   5.486552e+00
   4_bss:  0.1275 0.1758   5.258062e+00   5.485096e+00
   4_xyz:  0.1172 0.1668   5.192691e+00   5.437302e+00
   4_adp:  0.1148 0.1645   5.177856e+00   5.425806e+00
   4_occ:  0.1147 0.1644   5.177827e+00   5.426285e+00
   5_bss:  0.1147 0.1644   5.177867e+00   5.426318e+00
   5_xyz:  0.1122 0.1641   5.168596e+00   5.425895e+00
   5_adp:  0.1120 0.1630   5.166131e+00   5.422031e+00
   5_occ:  0.1120 0.1629   5.166003e+00   5.422027e+00
   5_bss:  0.1120 0.1629   5.166003e+00   5.422027e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.322  68.274   0.700  -1.417   3.369  -0.000   0.000   0.000
   1_xyz:  0.322  68.274   0.700  -1.417   3.369  -0.000   0.000   0.000
   1_adp:  0.322  68.274   0.700  -1.417   3.369  -0.000   0.000   0.000
   1_occ:  0.322  68.274   0.700  -1.417   3.369  -0.000   0.000   0.000
   2_bss:  0.345  78.646  -1.461  -2.594   0.567  -0.000   0.000   0.000
   2_xyz:  0.345  78.646  -1.461  -2.594   0.567  -0.000   0.000   0.000
   2_adp:  0.345  78.646  -1.461  -2.594   0.567  -0.000   0.000   0.000
   2_occ:  0.345  78.646  -1.461  -2.594   0.567  -0.000   0.000   0.000
   3_bss:  0.342  85.222  -1.630  -2.343  -0.008  -0.000  -0.000  -0.000
   3_xyz:  0.342  85.222  -1.630  -2.343  -0.008  -0.000  -0.000  -0.000
   3_adp:  0.342  85.222  -1.630  -2.343  -0.008  -0.000  -0.000  -0.000
   3_occ:  0.342  85.222  -1.630  -2.343  -0.008  -0.000  -0.000  -0.000
   4_bss:  0.332  77.252  -1.969  -2.555  -0.505  -0.000  -0.000  -0.000
   4_xyz:  0.332  77.252  -1.969  -2.555  -0.505  -0.000  -0.000  -0.000
   4_adp:  0.332  77.252  -1.969  -2.555  -0.505  -0.000  -0.000  -0.000
   4_occ:  0.332  77.252  -1.969  -2.555  -0.505  -0.000  -0.000  -0.000
   5_bss:  0.325  69.257  -1.786  -2.388  -0.364  -0.000  -0.000  -0.000
   5_xyz:  0.325  69.257  -1.786  -2.388  -0.364  -0.000  -0.000  -0.000
   5_adp:  0.325  69.257  -1.786  -2.388  -0.364  -0.000  -0.000  -0.000
   5_occ:  0.325  69.257  -1.786  -2.388  -0.364  -0.000  -0.000  -0.000
   5_bss:  0.325  69.248  -1.777  -2.380  -0.355  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.497 0.5142  0.6695    55545.412
   1_bss:  49.689 0.5234  0.7103    53854.185
   1_xyz:  29.414 0.7655  0.9707    22324.404
   1_adp:  30.718 0.7499  0.9554    23627.916
   1_occ:  30.744 0.7495  0.9546    23609.757
   2_bss:  30.715 0.7500  0.8908    23724.429
   2_xyz:  22.060 0.8406  0.9650    12812.499
   2_adp:  20.473 0.8569  0.9688    11557.833
   2_occ:  20.470 0.8568  0.9685    11547.241
   3_bss:  20.432 0.8571  0.9626    11506.143
   3_xyz:  17.300 0.8862  0.9788     8551.562
   3_adp:  16.170 0.8967  0.9796     7847.663
   3_occ:  16.165 0.8967  0.9795     7837.433
   4_bss:  16.142 0.8969  0.9676     7806.346
   4_xyz:  15.036 0.9064  0.9736     7000.294
   4_adp:  14.730 0.9091  0.9698     6809.194
   4_occ:  14.737 0.9091  0.9697     6808.648
   5_bss:  14.745 0.9090  0.9751     6807.934
   5_xyz:  14.651 0.9099  0.9752     6822.155
   5_adp:  14.547 0.9109  0.9708     6785.490
   5_occ:  14.548 0.9109  0.9707     6781.950
   5_bss:  14.548 0.9109  0.9707     6781.950
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6259e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6259e-01
   1_xyz:   1.320  0.011  0.092 16.056  0.006  4.114   1.0441e-01
   1_adp:   1.320  0.011  0.092 16.056  0.006  4.114   1.0441e-01
   1_occ:   1.320  0.011  0.092 16.056  0.006  4.114   1.0441e-01
   2_bss:   1.320  0.011  0.092 16.056  0.006  4.114   1.0441e-01
   2_xyz:   1.068  0.008  0.078 14.592  0.004  4.130   6.3523e-02
   2_adp:   1.068  0.008  0.078 14.592  0.004  4.130   6.3523e-02
   2_occ:   1.068  0.008  0.078 14.592  0.004  4.130   6.3523e-02
   3_bss:   1.068  0.008  0.078 14.592  0.004  4.130   6.3523e-02
   3_xyz:   1.042  0.009  0.077 14.627  0.004  4.130   6.3752e-02
   3_adp:   1.042  0.009  0.077 14.627  0.004  4.130   6.3752e-02
   3_occ:   1.042  0.009  0.077 14.627  0.004  4.130   6.3752e-02
   4_bss:   1.042  0.009  0.077 14.627  0.004  4.130   6.3752e-02
   4_xyz:   1.162  0.012  0.085 14.738  0.004  4.116   8.2480e-02
   4_adp:   1.162  0.012  0.085 14.738  0.004  4.116   8.2480e-02
   4_occ:   1.162  0.012  0.085 14.738  0.004  4.116   8.2480e-02
   5_bss:   1.162  0.012  0.085 14.738  0.004  4.116   8.2480e-02
   5_xyz:   1.163  0.012  0.086 14.746  0.004  4.119   8.2593e-02
   5_adp:   1.163  0.012  0.086 14.746  0.004  4.119   8.2593e-02
   5_occ:   1.163  0.012  0.086 14.746  0.004  4.119   8.2593e-02
   5_bss:   1.163  0.012  0.086 14.746  0.004  4.119   8.2593e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4333e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4333e-01
   1_xyz:  10.049  0.071  0.289 82.469  0.049  2.077   1.0071e-01
   1_adp:  10.049  0.071  0.289 82.469  0.049  2.077   1.0071e-01
   1_occ:  10.049  0.071  0.289 82.469  0.049  2.077   1.0071e-01
   2_bss:  10.049  0.071  0.289 82.469  0.049  2.077   1.0071e-01
   2_xyz:   7.577  0.044  0.254 81.902  0.044  2.300   4.6238e-02
   2_adp:   7.577  0.044  0.254 81.902  0.044  2.300   4.6238e-02
   2_occ:   7.577  0.044  0.254 81.902  0.044  2.300   4.6238e-02
   3_bss:   7.577  0.044  0.254 81.902  0.044  2.300   4.6238e-02
   3_xyz:   8.310  0.041  0.231 82.235  0.037  2.355   5.5921e-02
   3_adp:   8.310  0.041  0.231 82.235  0.037  2.355   5.5921e-02
   3_occ:   8.310  0.041  0.231 82.235  0.037  2.355   5.5921e-02
   4_bss:   8.310  0.041  0.231 82.235  0.037  2.355   5.5921e-02
   4_xyz:   8.195  0.058  0.280 82.635  0.039  2.295   6.2760e-02
   4_adp:   8.195  0.058  0.280 82.635  0.039  2.295   6.2760e-02
   4_occ:   8.195  0.058  0.280 82.635  0.039  2.295   6.2760e-02
   5_bss:   8.195  0.058  0.280 82.635  0.039  2.295   6.2760e-02
   5_xyz:   8.017  0.058  0.270 83.045  0.040  2.312   6.2607e-02
   5_adp:   8.017  0.058  0.270 83.045  0.040  2.312   6.2607e-02
   5_occ:   8.017  0.058  0.270 83.045  0.040  2.312   6.2607e-02
   5_bss:   8.017  0.058  0.270 83.045  0.040  2.312   6.2607e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 114.71   0.00  17.06 114.71   0.00  13.05  65.04   4.51  38.93
   1_occ: 114.71   0.00  17.06 114.71   0.00  13.05  65.04   4.51  38.93
   2_bss: 114.71   0.00  17.06 114.71   0.00  13.05  65.04   4.51  38.93
   2_xyz: 114.71   0.00  17.06 114.71   0.00  13.05  65.04   4.51  38.93
   2_adp: 117.49   0.00  18.85  90.72   0.00  13.58 117.49   4.98  47.58
   2_occ: 117.49   0.00  18.85  90.72   0.00  13.58 117.49   4.98  47.58
   3_bss: 117.49   0.00  18.85  90.72   0.00  13.58 117.49   4.98  47.58
   3_xyz: 117.49   0.00  18.85  90.72   0.00  13.58 117.49   4.98  47.58
   3_adp: 114.45   0.00  18.32  89.55   0.00  13.23 114.45   4.68  46.06
   3_occ: 114.45   0.00  18.32  89.55   0.00  13.23 114.45   4.68  46.06
   4_bss: 114.45   0.00  18.32  89.55   0.00  13.23 114.45   4.68  46.06
   4_xyz: 114.45   0.00  18.32  89.55   0.00  13.23 114.45   4.68  46.06
   4_adp: 111.26   0.00  17.91  91.17   0.00  13.05 111.26   0.00  44.34
   4_occ: 111.26   0.00  17.91  91.17   0.00  13.05 111.26   0.00  44.34
   5_bss: 111.26   0.00  17.91  91.17   0.00  13.05 111.26   0.00  44.34
   5_xyz: 111.26   0.00  17.91  91.17   0.00  13.05 111.26   0.00  44.34
   5_adp: 104.76   0.31  17.26  90.96   0.31  12.80 104.76   1.85  41.53
   5_occ: 104.76   0.31  17.26  90.96   0.31  12.80 104.76   1.85  41.53
   5_bss: 104.76   0.30  17.25  90.96   0.30  12.79 104.76   1.85  41.52
------------------------------------------------------------------------
 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:    1.433    0.015    0.439
   1_adp:    1.433    0.015    0.439
   1_occ:    1.433    0.015    0.439
   2_bss:    1.433    0.015    0.439
   2_xyz:    1.342    0.026    0.535
   2_adp:    1.342    0.026    0.535
   2_occ:    1.342    0.026    0.535
   3_bss:    1.342    0.026    0.535
   3_xyz:    1.286    0.053    0.603
   3_adp:    1.286    0.053    0.603
   3_occ:    1.286    0.053    0.603
   4_bss:    1.286    0.053    0.603
   4_xyz:    1.408    0.080    0.625
   4_adp:    1.408    0.080    0.625
   4_occ:    1.408    0.080    0.625
   5_bss:    1.408    0.080    0.625
   5_xyz:    1.507    0.097    0.639
   5_adp:    1.507    0.097    0.639
   5_occ:    1.507    0.097    0.639
   5_bss:    1.507    0.097    0.639
------------------------------------------------------------------------

CPU time actual refinement: 354.07


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1131/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/noshake/run_1131/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1131/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1131/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1131/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.93 
  Macro-tasks:
    bulk solvent and scale       = 55.13  
    individual site refinement   = 134.44 
    weights calculation          = 31.29  
    collect and process          = 6.63   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 227.63 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 109.31 
    alpha_beta                      = 8.23   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 115.65 
    fmodel                         = 8.90   
    r_factors                      = 0.38   
    phase_errors                   = 10.99  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 256.78 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.076 micro seconds
Total CPU time: 6.13 minutes
from_scatterers_fft:    623 calls, 108.95 s
gradients_fft:          568 calls, 103.11 s

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

# Date 2008-01-16 Time 06:30:09 PST -0800 (1200493809.98 s)
Start R-work = 0.4389, R-free = 0.4308 (no bulk solvent and anisotropic scale)
Final R-work = 0.1343, R-free = 0.1811 (no bulk solvent and anisotropic scale)

Start R-work = 0.4303, R-free = 0.4249
Final R-work = 0.1120, R-free = 0.1629