# Date 2008-01-16 Time 02:57:24 PST -0800 (1200481044.79 s)
#phil __OFF__

Command line arguments: "../1046.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4908
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1046

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.3993, 84.6622, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96139
Completeness in resolution range: 0.92615
Completeness with d_max=infinity: 0.9234

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0711
                             d_min =   1.9614

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96139
Completeness in resolution range: 0.92615
Completeness with d_max=infinity: 0.9234

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0715 -  4.1981 [2219/2248]  1999   220   9.9%
  bin  2:  4.1981 -  3.3441 [2128/2151]  1915   213  10.0%
  bin  3:  3.3441 -  2.9249 [2097/2122]  1882   215  10.3%
  bin  4:  2.9249 -  2.6591 [2097/2113]  1894   203   9.7%
  bin  5:  2.6591 -  2.4694 [2051/2090]  1844   207  10.1%
  bin  6:  2.4694 -  2.3243 [2078/2110]  1876   202   9.7%
  bin  7:  2.3243 -  2.2083 [2041/2078]  1827   214  10.5%
  bin  8:  2.2083 -  2.1125 [2019/2061]  1821   198   9.8%
  bin  9:  2.1125 -  2.0313 [2062/2100]  1858   204   9.9%
  bin 10:  2.0313 -  1.9614 [ 797/2078]   714    83  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1046/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:
        1.70 -     2.34: 28
        2.34 -     2.98: 1814
        2.98 -     3.62: 4568
        3.62 -     4.26: 9138
        4.26 -     4.90: 12724
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.702 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.746 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.884 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.912 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28267 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1046/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1046/model_refine_001.geo

CPU time processing inputs: 9.49


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.3993 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4780   r_free= 0.4727   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.279319                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6829 0.99   1437  162 0.3912 0.3780        6.59      6.5607|
|  2:  4.6829 -  3.7356 0.99   1385  149 0.3883 0.4104      6.7748      6.8537|
|  3:  3.7356 -  3.2689 0.99   1364  155 0.4393 0.3963      6.6587      6.6347|
|  4:  3.2689 -  2.9725 0.99   1350  148 0.4616 0.4652      6.5006      6.4987|
|  5:  2.9725 -  2.7608 0.98   1331  148 0.5066 0.5330      6.3637      6.3655|
|  6:  2.7608 -  2.5989 0.99   1343  151 0.5036 0.5130      6.2701      6.2257|
|  7:  2.5989 -  2.4694 0.99   1324  145 0.5185 0.4300      6.2492      6.1375|
|  8:  2.4694 -  2.3623 0.99   1331  148 0.5326 0.5366      6.1606      6.2084|
|  9:  2.3623 -  2.2717 0.99   1314  151 0.5298 0.5188      6.1283      6.1104|
| 10:  2.2717 -  2.1935 0.98   1328  146 0.5210 0.5434      6.0839      6.0956|
| 11:  2.1935 -  2.1251 0.98   1311  138 0.5170 0.5267      6.0237      6.0342|
| 12:  2.1251 -  2.0645 1.00   1314  149 0.5474 0.5713       5.952      5.9901|
| 13:  2.0645 -  2.0103 0.88   1170  139 0.5397 0.5106      5.8708      5.8371|
| 14:  2.0103 -  1.9614 0.24    328   30 0.5602 0.5968      5.8226      5.8157|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6829  1437   162  0.71  33.18   0.80     0.74      67031.78|
|  2:  4.6829 -  3.7356  1385   149  0.70  34.89   0.88     0.77     102763.53|
|  3:  3.7356 -  3.2689  1364   155  0.58  45.27   0.83     0.70     116226.46|
|  4:  3.2689 -  2.9725  1350   148  0.47  54.28   0.80     0.58     107760.42|
|  5:  2.9725 -  2.7608  1331   148  0.38  61.04   0.73     0.48      88740.48|
|  6:  2.7608 -  2.5989  1343   151  0.39  60.79   0.74     0.46      71593.46|
|  7:  2.5989 -  2.4694  1324   145  0.41  58.93   0.73     0.47      60333.49|
|  8:  2.4694 -  2.3623  1331   148  0.39  60.93   0.71     0.46      56441.45|
|  9:  2.3623 -  2.2717  1314   151  0.35  64.13   0.74     0.42      53980.24|
| 10:  2.2717 -  2.1935  1328   146  0.30  67.50   0.75     0.36      53589.90|
| 11:  2.1935 -  2.1251  1311   138  0.25  71.33   0.77     0.31      50141.42|
| 12:  2.1251 -  2.0645  1314   149  0.20  75.30   0.72     0.26      48611.94|
| 13:  2.0645 -  2.0103  1170   139  0.19  75.81   0.72     0.25      41765.65|
| 14:  2.0103 -  1.9614   328    30  0.22  73.67   0.68     0.27      33953.80|
|alpha:            min =        0.25 max =            0.77 mean =         0.48|
|beta:             min =    33953.80 max =       116226.46 mean =     70541.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.55|
|phase err.(test): min =        0.00 max =           89.96 mean =        58.62|
|-----------------------------------------------------------------------------|

============================== 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 = 15.291373             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.180   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.313313              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.762   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      703 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1500 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2632 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3923 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5037 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6558 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7747 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.768 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.886 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4829   r_free= 0.4797   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.280778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4694   r_free= 0.4619   ksol= 0.34   Bsol= 20.00   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.85,8.65,8.47,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.279273                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.271510             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.532   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.145121              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.072   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4694      final r-factor (work) = 0.3910          |
| start r-factor (free) = 0.4619      final r-factor (free) = 0.4235          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 92.2844 = 12.27 * 0.50 * 6.2774 + 1.00 * 53.7676                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.1160 = 12.27 * 0.50 * 6.1881 + 1.00 * 0.1476                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3910      final r-factor (work) = 0.3507          |
| start r-factor (free) = 0.4235      final r-factor (free) = 0.4090          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1004 = 1.15 * 1.00 * 6.1881 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0170 = 1.15 * 1.00 * 6.1142 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.66   12.76    None  None   None       |
|    all(noH): 2823   0      0.00    79.66   12.76    None  None   None       |
|    Sol.    : 438    0      0.00    79.66   25.99    None  None   None       |
|    Mac.    : 2385   0      0.00    73.13   10.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.966: 1213   |   5:    39.828 -  47.793:   61        |
|      1:     7.966 -  15.931:  799   |   6:    47.793 -  55.759:   23        |
|      2:    15.931 -  23.897:  398   |   7:    55.759 -  63.724:   17        |
|      3:    23.897 -  31.862:  197   |   8:    63.724 -  71.690:    5        |
|      4:    31.862 -  39.828:  106   |   9:    71.690 -  79.655:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3507 r_free = 0.4090             target_work(ml) = 6.096         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3504 r_free = 0.4098             target_work(ml) = 6.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3504   r_free= 0.4098   ksol= 0.34   Bsol= 20.00   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.85,8.65,8.47,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.095457                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3481   r_free= 0.4048   ksol= 0.32   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.42,5.22,5.70,0.00,0.00,0.00); trace/3= 5.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.096016                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.300403             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.051   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.645542              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.840  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3481      final r-factor (work) = 0.2433          |
| start r-factor (free) = 0.4048      final r-factor (free) = 0.3128          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.6720 = 11.30 * 0.50 * 6.1103 + 1.00 * 0.1476                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.8559 = 11.30 * 0.50 * 5.9749 + 1.00 * 0.0963                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2433      final r-factor (work) = 0.2157          |
| start r-factor (free) = 0.3128      final r-factor (free) = 0.2786          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8729 = 0.65 * 1.00 * 5.9749 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7360 = 0.65 * 1.00 * 5.7690 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.29   13.18    None  None   None       |
|    all(noH): 2823   0      0.00    78.29   13.18    None  None   None       |
|    Sol.    : 438    0      1.49    78.29   33.87    None  None   None       |
|    Mac.    : 2385   0      0.00    70.64   9.38     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.829: 1307   |   5:    39.145 -  46.974:  103        |
|      1:     7.829 -  15.658:  796   |   6:    46.974 -  54.803:   57        |
|      2:    15.658 -  23.487:  255   |   7:    54.803 -  62.632:   26        |
|      3:    23.487 -  31.316:  138   |   8:    62.632 -  70.460:   14        |
|      4:    31.316 -  39.145:  124   |   9:    70.460 -  78.289:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2157 r_free = 0.2786             target_work(ml) = 5.711         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2155 r_free = 0.2784             target_work(ml) = 5.710         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2155   r_free= 0.2784   ksol= 0.32   Bsol= 50.00   scale= 1.058   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.42,5.22,5.70,0.00,0.00,0.00); trace/3= 5.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.709881                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2121   r_free= 0.2748   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,2.83,3.05,0.00,0.00,0.00); trace/3= 2.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.707670                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.317587              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.529  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.658033              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.832  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2121      final r-factor (work) = 0.1599          |
| start r-factor (free) = 0.2748      final r-factor (free) = 0.2082          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5710 = 4.32 * 0.50 * 5.7785 + 1.00 * 0.0963                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1690 = 4.32 * 0.50 * 5.6058 + 1.00 * 0.0673                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1599      final r-factor (work) = 0.1460          |
| start r-factor (free) = 0.2082      final r-factor (free) = 0.1960          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7007 = 0.66 * 1.00 * 5.6058 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5710 = 0.66 * 1.00 * 5.4073 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.90   13.81    None  None   None       |
|    all(noH): 2823   0      0.00    90.90   13.81    None  None   None       |
|    Sol.    : 438    0      1.21    81.39   38.88    None  None   None       |
|    Mac.    : 2385   0      0.00    90.90   9.21     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.090: 1595   |   5:    45.452 -  54.542:   94        |
|      1:     9.090 -  18.181:  637   |   6:    54.542 -  63.633:   63        |
|      2:    18.181 -  27.271:  171   |   7:    63.633 -  72.723:   27        |
|      3:    27.271 -  36.362:  101   |   8:    72.723 -  81.813:   11        |
|      4:    36.362 -  45.452:  120   |   9:    81.813 -  90.904:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1460 r_free = 0.1960             target_work(ml) = 5.376         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1458 r_free = 0.1958             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.1958   ksol= 0.33   Bsol= 50.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,2.83,3.05,0.00,0.00,0.00); trace/3= 2.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.375384                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1455   r_free= 0.1966   ksol= 0.33   Bsol= 49.17   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,2.17,2.26,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.376916                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.377412              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.945  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.451074              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.793  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1455      final r-factor (work) = 0.1248          |
| start r-factor (free) = 0.1966      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2039 = 3.38 * 0.50 * 5.4104 + 1.00 * 0.0673                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0508 = 3.38 * 0.50 * 5.3168 + 1.00 * 0.0724                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1720      final r-factor (free) = 0.1681          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4109 = 0.45 * 1.00 * 5.3168 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3721 = 0.45 * 1.00 * 5.2327 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.97   13.54    None  None   None       |
|    all(noH): 2823   0      0.00    93.97   13.54    None  None   None       |
|    Sol.    : 438    0      1.76    82.12   38.07    None  None   None       |
|    Mac.    : 2385   0      0.00    93.97   9.03     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.397: 1653   |   5:    46.986 -  56.383:   90        |
|      1:     9.397 -  18.794:  622   |   6:    56.383 -  65.780:   58        |
|      2:    18.794 -  28.191:  162   |   7:    65.780 -  75.177:   15        |
|      3:    28.191 -  37.588:  105   |   8:    75.177 -  84.574:    7        |
|      4:    37.588 -  46.986:  107   |   9:    84.574 -  93.971:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1211 r_free = 0.1681             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1210 r_free = 0.1682             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1210   r_free= 0.1682   ksol= 0.33   Bsol= 49.17   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,2.17,2.26,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.220308                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1685   ksol= 0.33   Bsol= 49.17   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,2.17,2.26,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.223193                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.687129              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.829  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.418938              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.341  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1042 = 2.69 * 0.50 * 5.2337 + 1.00 * 0.0724                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0649 = 2.69 * 0.50 * 5.2078 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1935 = 0.42 * 1.00 * 5.2078 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1922 = 0.42 * 1.00 * 5.1909 + 1.00 * 0.0175                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.37   13.22    None  None   None       |
|    all(noH): 2823   0      0.00    96.37   13.22    None  None   None       |
|    Sol.    : 438    0      1.73    81.91   36.83    None  None   None       |
|    Mac.    : 2385   0      0.00    96.37   8.88     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.637: 1707   |   5:    48.186 -  57.823:   72        |
|      1:     9.637 -  19.274:  595   |   6:    57.823 -  67.460:   43        |
|      2:    19.274 -  28.912:  153   |   7:    67.460 -  77.097:   15        |
|      3:    28.912 -  38.549:  121   |   8:    77.097 -  86.734:    5        |
|      4:    38.549 -  48.186:  108   |   9:    86.734 -  96.372:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1640             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1639             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1639   ksol= 0.33   Bsol= 49.17   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,2.17,2.26,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.189616                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6829 0.99   1437  162 0.0968 0.1294      5.3629      5.5297|
|  2:  4.6829 -  3.7356 0.99   1385  149 0.0870 0.1132      5.4413      5.6811|
|  3:  3.7356 -  3.2689 0.99   1364  155 0.1078 0.1727      5.4883      5.9111|
|  4:  3.2689 -  2.9725 0.99   1350  148 0.1305 0.1519      5.4943      5.6176|
|  5:  2.9725 -  2.7608 0.98   1331  148 0.1359 0.1826       5.357      5.5468|
|  6:  2.7608 -  2.5989 0.99   1343  151 0.1309 0.1958      5.2673      5.5231|
|  7:  2.5989 -  2.4694 0.99   1324  145 0.1299 0.1746      5.2092      5.4196|
|  8:  2.4694 -  2.3623 0.99   1331  148 0.1208 0.1744      5.0995      5.3276|
|  9:  2.3623 -  2.2717 0.99   1314  151 0.1217 0.2026      5.0655      5.3651|
| 10:  2.2717 -  2.1935 0.98   1328  146 0.1183 0.1732      5.0235      5.2522|
| 11:  2.1935 -  2.1251 0.98   1311  138 0.1179 0.1925      4.9682      5.3243|
| 12:  2.1251 -  2.0645 1.00   1314  149 0.1180 0.1774      4.9142      5.1329|
| 13:  2.0645 -  2.0103 0.88   1170  139 0.1202 0.1848      4.8094      5.0488|
| 14:  2.0103 -  1.9614 0.24    328   30 0.1103 0.1640      4.6758      4.9508|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6829  1437   162  0.94   8.71   0.98     0.95       6924.89|
|  2:  4.6829 -  3.7356  1385   149  0.95   8.16   1.01     0.99       8972.39|
|  3:  3.7356 -  3.2689  1364   155  0.93  11.95   1.03     1.02      11024.92|
|  4:  3.2689 -  2.9725  1350   148  0.91  15.08   1.01     0.98      11276.13|
|  5:  2.9725 -  2.7608  1331   148  0.89  17.30   0.99     0.96       9131.27|
|  6:  2.7608 -  2.5989  1343   151  0.89  17.26   0.99     0.96       8023.09|
|  7:  2.5989 -  2.4694  1324   145  0.90  16.44   0.99     0.96       6868.00|
|  8:  2.4694 -  2.3623  1331   148  0.89  16.87   0.99     0.95       5901.89|
|  9:  2.3623 -  2.2717  1314   151  0.89  17.17   1.00     0.97       5530.71|
| 10:  2.2717 -  2.1935  1328   146  0.90  16.49   1.00     0.96       5145.12|
| 11:  2.1935 -  2.1251  1311   138  0.89  17.19   0.99     0.95       4744.04|
| 12:  2.1251 -  2.0645  1314   149  0.90  16.91   1.00     1.00       4396.93|
| 13:  2.0645 -  2.0103  1170   139  0.89  17.25   0.99     0.97       3543.15|
| 14:  2.0103 -  1.9614   328    30  0.89  16.87   0.99     0.96       2779.80|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2779.80 max =        11276.13 mean =      7014.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.19 mean =        14.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1639   ksol= 0.33   Bsol= 51.23   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,0.05,0.15,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.189578                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1639   ksol= 0.33   Bsol= 51.23   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,0.05,0.15,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.189578                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6829 0.99   1437  162 0.0968 0.1294      5.3627      5.5297|
|  2:  4.6829 -  3.7356 0.99   1385  149 0.0870 0.1133      5.4415      5.6816|
|  3:  3.7356 -  3.2689 0.99   1364  155 0.1078 0.1728      5.4886      5.9115|
|  4:  3.2689 -  2.9725 0.99   1350  148 0.1306 0.1519      5.4942      5.6174|
|  5:  2.9725 -  2.7608 0.98   1331  148 0.1359 0.1825      5.3567      5.5465|
|  6:  2.7608 -  2.5989 0.99   1343  151 0.1308 0.1959      5.2672      5.5234|
|  7:  2.5989 -  2.4694 0.99   1324  145 0.1300 0.1746      5.2094      5.4199|
|  8:  2.4694 -  2.3623 0.99   1331  148 0.1208 0.1744      5.0997      5.3278|
|  9:  2.3623 -  2.2717 0.99   1314  151 0.1217 0.2027      5.0656      5.3653|
| 10:  2.2717 -  2.1935 0.98   1328  146 0.1183 0.1732      5.0234      5.2518|
| 11:  2.1935 -  2.1251 0.98   1311  138 0.1178 0.1923      4.9679      5.3236|
| 12:  2.1251 -  2.0645 1.00   1314  149 0.1179 0.1774      4.9138      5.1327|
| 13:  2.0645 -  2.0103 0.88   1170  139 0.1202 0.1846      4.8092      5.0482|
| 14:  2.0103 -  1.9614 0.24    328   30 0.1103 0.1638      4.6755      4.9513|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6829  1437   162  0.94   8.71   0.98     0.95       6923.64|
|  2:  4.6829 -  3.7356  1385   149  0.95   8.16   1.01     0.99       8975.82|
|  3:  3.7356 -  3.2689  1364   155  0.93  11.95   1.03     1.02      11037.26|
|  4:  3.2689 -  2.9725  1350   148  0.91  15.08   1.00     0.98      11273.90|
|  5:  2.9725 -  2.7608  1331   148  0.89  17.30   0.99     0.96       9130.78|
|  6:  2.7608 -  2.5989  1343   151  0.89  17.26   0.99     0.96       8021.33|
|  7:  2.5989 -  2.4694  1324   145  0.90  16.44   0.99     0.96       6870.66|
|  8:  2.4694 -  2.3623  1331   148  0.89  16.88   0.99     0.95       5906.32|
|  9:  2.3623 -  2.2717  1314   151  0.89  17.18   1.00     0.97       5533.34|
| 10:  2.2717 -  2.1935  1328   146  0.90  16.49   1.00     0.96       5146.09|
| 11:  2.1935 -  2.1251  1311   138  0.89  17.19   0.99     0.95       4741.63|
| 12:  2.1251 -  2.0645  1314   149  0.90  16.90   1.00     1.00       4392.30|
| 13:  2.0645 -  2.0103  1170   139  0.89  17.24   0.99     0.97       3540.63|
| 14:  2.0103 -  1.9614   328    30  0.89  16.87   0.99     0.96       2778.37|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2778.37 max =        11273.90 mean =      7015.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.19 mean =        14.44|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.965)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.05    98.43   15.27    None  None   None       |
|    all(noH): 2823   0      2.05    98.43   15.27    None  None   None       |
|    Sol.    : 438    0      3.78    83.96   38.88    None  None   None       |
|    Mac.    : 2385   0      2.05    98.43   10.94    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:     2.054 -  11.691: 1707   |   5:    50.239 -  59.877:   72        |
|      1:    11.691 -  21.328:  595   |   6:    59.877 -  69.514:   43        |
|      2:    21.328 -  30.965:  153   |   7:    69.514 -  79.151:   15        |
|      3:    30.965 -  40.602:  121   |   8:    79.151 -  88.788:    5        |
|      4:    40.602 -  50.239:  108   |   9:    88.788 -  98.425:    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)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.439 - 5.920
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 338 from: 342
   mapped sites are within: 0.707 - 5.920

peak=    9.942 closest distance to " CG2 VAL A 230 " =    1.442
peak=    8.137 closest distance to " CG2 VAL A 296 " =    1.179
peak=    6.393 closest distance to " NH2 ARG A  56 " =    2.285
peak=    6.256 closest distance to " CG  LEU A   5 " =    1.274
peak=    5.455 closest distance to " O   HOH Z  37 " =    1.262
peak=    5.437 closest distance to " O   HOH Z 278 " =    1.127
peak=    5.331 closest distance to " O   HOH Z 247 " =    1.482
peak=    5.330 closest distance to " CB  GLN A 223 " =    1.437
peak=    5.273 closest distance to " CD2 LEU A   5 " =    1.195
peak=    5.270 closest distance to " CG  PRO A  54 " =    1.243
peak=    5.228 closest distance to " CG  LEU A 228 " =    1.245
peak=    5.208 closest distance to " CB  SER A  63 " =    1.314
peak=    4.909 closest distance to " O   HOH Z 124 " =    1.482
peak=    4.810 closest distance to " CG  PRO A 213 " =    1.243
peak=    4.807 closest distance to " O   HOH Z 126 " =    1.656
peak=    4.789 closest distance to " O   HOH Z 132 " =    1.154
peak=    4.772 closest distance to " CB  PRO A  54 " =    0.814
peak=    4.772 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.672 closest distance to " CB  VAL A 230 " =    1.275
peak=    4.657 closest distance to " CG  PRO A 198 " =    1.378
peak=    4.636 closest distance to " CB  GLU A 152 " =    1.157
peak=    4.621 closest distance to " O   HOH Z  48 " =    1.835
peak=    4.561 closest distance to " NE2 GLN A  11 " =    1.151
peak=    4.556 closest distance to " O   HOH Z  11 " =    1.267
peak=    4.523 closest distance to " O   HOH Z 368 " =    2.210
peak=    4.474 closest distance to " CB  SER A   3 " =    1.389
peak=    4.359 closest distance to " O   HOH Z 371 " =    3.295
peak=    4.335 closest distance to " O   HOH Z 193 " =    1.910
peak=    4.323 closest distance to " O   HOH Z  15 " =    2.153
peak=    4.319 closest distance to " OD1 ASN A  69 " =    2.623
peak=    4.292 closest distance to " O   HOH Z 128 " =    2.095
peak=    4.282 closest distance to " O   HOH Z  80 " =    1.772
peak=    4.277 closest distance to " O   HOH Z 334 " =    3.120
peak=    4.276 closest distance to " O   HOH Z  78 " =    1.793
peak=    4.261 closest distance to " O   HOH Z 423 " =    1.857
peak=    4.245 closest distance to " O   SER A  87 " =    2.297
peak=    4.237 closest distance to " O   HOH Z  97 " =    1.890
peak=    4.231 closest distance to " O   HOH Z 260 " =    1.257
peak=    4.230 closest distance to " CG1BVAL A  72 " =    1.583
peak=    4.225 closest distance to " O   HOH Z 272 " =    1.922
peak=    4.211 closest distance to " CA  ALA A  21 " =    1.229
peak=    4.210 closest distance to " CD1 LEU A 300 " =    1.152
peak=    4.209 closest distance to " CG  ARG A 138 " =    1.123
peak=    4.204 closest distance to " CB  VAL A 296 " =    1.084
peak=    4.193 closest distance to " O   HOH Z 403 " =    1.716
peak=    4.193 closest distance to " O   HOH Z 369 " =    2.088
peak=    4.177 closest distance to " CB  TYR A 169 " =    0.874
peak=    4.176 closest distance to " O   HOH Z  63 " =    1.407
peak=    4.176 closest distance to " O   HOH Z 108 " =    1.441
peak=    4.169 closest distance to " O   HOH Z 389 " =    1.961
peak=    4.168 closest distance to " CD2 LEU A 228 " =    1.191
peak=    4.159 closest distance to " O   PRO A 198 " =    1.549
peak=    4.137 closest distance to " CB  ARG A 275 " =    0.872
peak=    4.134 closest distance to " O   HOH Z 236 " =    1.832
peak=    4.126 closest distance to " O   HOH Z 232 " =    2.300
peak=    4.121 closest distance to " O   HOH Z 316 " =    2.928
peak=    4.110 closest distance to " CG  ARG A  66 " =    2.767
peak=    4.109 closest distance to " O   HOH Z  20 " =    2.177
peak=    4.098 closest distance to " CA  TYR A  30 " =    0.974
peak=    4.095 closest distance to " NH2 ARG A 156 " =    1.201
peak=    4.074 closest distance to " O   HOH Z 411 " =    3.687
peak=    4.073 closest distance to " CB  GLU A 277 " =    3.643
peak=    4.069 closest distance to " OD2 ASP A 286 " =    2.891
peak=    4.065 closest distance to " O   HOH Z 234 " =    3.842
peak=    4.053 closest distance to " CB  GLU A 128 " =    1.147
peak=    4.042 closest distance to " O   HOH Z 163 " =    1.547
peak=    4.040 closest distance to " CD1AILE A 234 " =    0.943
peak=    4.029 closest distance to " CB  ARG A  79 " =    1.408
peak=    4.027 closest distance to " O   HOH Z 386 " =    2.192
peak=    4.024 closest distance to " O   HOH Z 112 " =    1.503
peak=    4.016 closest distance to " CG2 THR A 221 " =    0.973
peak=    4.007 closest distance to " O   HOH Z  68 " =    1.872
peak=    4.000 closest distance to " CB  VAL A 265 " =    1.234
peak=    4.000 closest distance to " O   HOH Z 132 " =    2.143
peak=    3.998 closest distance to " O   HOH Z  88 " =    3.118
peak=    3.995 closest distance to " CB  VAL A 202 " =    1.557
peak=    3.984 closest distance to " O   HOH Z 298 " =    1.796
peak=    3.973 closest distance to " CB  ASN A 148 " =    1.268
peak=    3.964 closest distance to " O   HOH Z 295 " =    1.552
peak=    3.955 closest distance to " CG  PRO A 243 " =    1.161
peak=    3.948 closest distance to " OG BSER A 164 " =    2.175
peak=    3.928 closest distance to " CG  PRO A 280 " =    0.759
peak=    3.915 closest distance to " O   HOH Z 263 " =    1.526
peak=    3.910 closest distance to " CB  TRP A 179 " =    1.385
peak=    3.908 closest distance to " CA  THR A 221 " =    0.882
peak=    3.896 closest distance to " O   HOH Z 303 " =    2.141
peak=    3.888 closest distance to " O   HOH Z 426 " =    1.460
peak=    3.873 closest distance to " O   HOH Z 344 " =    2.900
peak=    3.866 closest distance to " O   HOH Z 427 " =    3.085
peak=    3.825 closest distance to " O   HOH Z  54 " =    1.552
peak=    3.819 closest distance to " N   ASN A  39 " =    1.315
peak=    3.818 closest distance to " O   HOH Z 126 " =    1.801
peak=    3.815 closest distance to " CA  LYS A 117 " =    1.264
peak=    3.801 closest distance to " O   HOH Z 346 " =    1.496
peak=    3.793 closest distance to " O   TRP A 274 " =    1.842
peak=    3.789 closest distance to " NH1 ARG A  56 " =    1.079
peak=    3.786 closest distance to " CA  ALA A  51 " =    1.049
peak=    3.778 closest distance to " O   HOH Z 374 " =    3.112
peak=    3.770 closest distance to " O   HOH Z 145 " =    2.548
peak=    3.759 closest distance to " O   HOH Z 184 " =    1.318
peak=    3.755 closest distance to " CD  ARG A 159 " =    0.830
peak=    3.741 closest distance to " O   HOH Z 134 " =    1.499
peak=    3.736 closest distance to " CG1 ILE A  33 " =    1.300
peak=    3.735 closest distance to " OE1 GLN A  11 " =    1.795
peak=    3.727 closest distance to " NZ  LYS A 117 " =    3.332
peak=    3.723 closest distance to " O   HOH Z  44 " =    2.354
peak=    3.719 closest distance to " O   HOH Z 394 " =    1.693
peak=    3.715 closest distance to " O   HOH Z 345 " =    3.314
peak=    3.712 closest distance to " CA  ASP A 191 " =    0.838
peak=    3.711 closest distance to " CB  LEU A 143 " =    1.190
peak=    3.709 closest distance to " O   HOH Z  61 " =    1.578
peak=    3.703 closest distance to " CB  TRP A 266 " =    0.992
peak=    3.687 closest distance to " CD BLYS A 290 " =    1.071
peak=    3.685 closest distance to " CB  LEU A 228 " =    1.286
peak=    3.683 closest distance to " O   HOH Z 203 " =    1.675
peak=    3.680 closest distance to " O   ALA A 158 " =    1.376
peak=    3.679 closest distance to " O   MET A 105 " =    1.818
peak=    3.678 closest distance to " O   HOH Z 189 " =    2.432
peak=    3.672 closest distance to " O   HOH Z 116 " =    1.776
peak=    3.670 closest distance to " O   HOH Z  30 " =    1.292
peak=    3.659 closest distance to " O   HOH Z 108 " =    2.067
peak=    3.657 closest distance to " CZ  PHE A 192 " =    1.012
peak=    3.652 closest distance to " CG1 VAL A 153 " =    1.020
peak=    3.646 closest distance to " CD  ARG A 269 " =    0.895
peak=    3.640 closest distance to " CA  ASP A 140 " =    1.227
peak=    3.635 closest distance to " OE1 GLN A  58 " =    5.920
peak=    3.624 closest distance to " O   HOH Z 271 " =    1.944
peak=    3.621 closest distance to " O   HOH Z  93 " =    2.678
peak=    3.621 closest distance to " O   HOH Z 180 " =    2.136
peak=    3.614 closest distance to " O   HOH Z 276 " =    1.317
peak=    3.606 closest distance to " O   HOH Z 118 " =    1.647
peak=    3.604 closest distance to " O   HOH Z 313 " =    1.851
peak=    3.599 closest distance to " CB  ASP A 140 " =    0.707
peak=    3.592 closest distance to " O   HOH Z  21 " =    1.799
peak=    3.592 closest distance to " O   HOH Z  54 " =    2.442
peak=    3.591 closest distance to " O   HOH Z 277 " =    1.073
peak=    3.583 closest distance to " CG2 THR A 220 " =    0.972
peak=    3.581 closest distance to " CB  SER A 216 " =    0.787
peak=    3.574 closest distance to " NH2BARG A 145 " =    2.202
peak=    3.574 closest distance to " CG AARG A 275 " =    1.153
peak=    3.556 closest distance to " CA  ALA A 160 " =    0.848
peak=    3.551 closest distance to " O   ALA A   1 " =    1.490
peak=    3.546 closest distance to " OD1 ASN A 217 " =    1.650
peak=    3.544 closest distance to " O   HOH Z  40 " =    1.496
peak=    3.543 closest distance to " O   HOH Z 406 " =    1.623
peak=    3.537 closest distance to " CA  LEU A 282 " =    1.096
peak=    3.537 closest distance to " O   HOH Z 214 " =    2.014
peak=    3.530 closest distance to " O   HOH Z 114 " =    1.354
peak=    3.528 closest distance to " CD  LYS A 119 " =    1.891
peak=    3.527 closest distance to " O   HOH Z 136 " =    1.243
peak=    3.526 closest distance to " O   HOH Z 425 " =    1.369
peak=    3.523 closest distance to " O   HOH Z 329 " =    3.758
peak=    3.513 closest distance to " O   HOH Z 155 " =    1.596
peak=    3.511 closest distance to " CG2 VAL A 174 " =    1.324
peak=    3.506 closest distance to " CB  ASP A 124 " =    0.717
peak=    3.506 closest distance to " O   HOH Z 281 " =    4.195
peak=    3.504 closest distance to " CZ AARG A 102 " =    1.930
peak=    3.497 closest distance to " O   HOH Z 137 " =    1.661
peak=    3.495 closest distance to " O   HOH Z  48 " =    2.142
peak=    3.494 closest distance to " O   HOH Z 374 " =    2.579
peak=    3.492 closest distance to " CA  MET A  40 " =    1.063
peak=    3.491 closest distance to " O   HOH Z 197 " =    2.018
peak=    3.491 closest distance to " O   HOH Z 215 " =    1.591
peak=    3.488 closest distance to " O   HOH Z 133 " =    1.753
peak=    3.481 closest distance to " CB  ASN A  39 " =    0.849
peak=    3.470 closest distance to " CG  GLN A  88 " =    1.045
peak=    3.468 closest distance to " O   HOH Z 227 " =    1.808
peak=    3.465 closest distance to " NH1 ARG A  14 " =    1.060
peak=    3.461 closest distance to " O   HOH Z  58 " =    1.408
peak=    3.458 closest distance to " CB  SER A 141 " =    1.037
peak=    3.457 closest distance to " CB  ASN A 187 " =    1.055
peak=    3.452 closest distance to " CB  ALA A   9 " =    1.524
peak=    3.452 closest distance to " CB  ALA A 248 " =    1.033
peak=    3.451 closest distance to " CD2 HIS A  81 " =    1.142
peak=    3.440 closest distance to " C   SER A  32 " =    1.040
peak=    3.438 closest distance to " O   HOH Z  92 " =    0.935
peak=    3.435 closest distance to " O   HOH Z 261 " =    1.808
peak=    3.434 closest distance to " C   ALA A 299 " =    0.955
peak=    3.434 closest distance to " CD2 LEU A 255 " =    1.323
peak=    3.433 closest distance to " O   HOH Z   4 " =    1.913
peak=    3.433 closest distance to " ND2 ASN A 187 " =    1.573
peak=    3.427 closest distance to " CA  VAL A 126 " =    0.998
peak=    3.425 closest distance to " CB  TYR A  30 " =    1.432
peak=    3.423 closest distance to " NZ  LYS A  76 " =    1.308
peak=    3.422 closest distance to " CA  ALA A 295 " =    1.068
peak=    3.421 closest distance to " O   HOH Z 423 " =    3.270
peak=    3.416 closest distance to " O   HOH Z 245 " =    1.358
peak=    3.413 closest distance to " O   HOH Z 411 " =    1.807
peak=    3.413 closest distance to " CB  PRO A 198 " =    1.025
peak=    3.412 closest distance to " O   HOH Z 135 " =    1.933
peak=    3.412 closest distance to " CA  ASN A  74 " =    1.199
peak=    3.411 closest distance to " OG  SER A  22 " =    2.807
peak=    3.411 closest distance to " NH2BARG A 102 " =    0.939
peak=    3.410 closest distance to " O   HOH Z 175 " =    3.547
peak=    3.410 closest distance to " O   HOH Z 132 " =    2.894
peak=    3.402 closest distance to " O   HOH Z 355 " =    1.865
peak=    3.402 closest distance to " ND1 HIS A  86 " =    1.665
peak=    3.401 closest distance to " O   HOH Z 131 " =    2.491
peak=    3.399 closest distance to " O   HOH Z 327 " =    2.453
peak=    3.397 closest distance to " O   HOH Z 422 " =    2.672
peak=    3.397 closest distance to " O   HOH Z  85 " =    1.313
peak=    3.397 closest distance to " O   HOH Z 357 " =    2.030
peak=    3.396 closest distance to " O   HOH Z 155 " =    2.788
peak=    3.394 closest distance to " CB  ARG A 139 " =    0.864
peak=    3.384 closest distance to " O   HOH Z 383 " =    2.114
peak=    3.378 closest distance to " O   GLN A 278 " =    1.215
peak=    3.375 closest distance to " O   HOH Z 407 " =    3.557
peak=    3.368 closest distance to " OD1 ASP A 231 " =    1.818
peak=    3.364 closest distance to " CA  GLY A 211 " =    1.180
peak=    3.363 closest distance to " CA  ASN A 215 " =    1.169
peak=    3.355 closest distance to " O   HOH Z 120 " =    1.010
peak=    3.354 closest distance to " CA  ALA A 158 " =    1.139
peak=    3.352 closest distance to " CB  ALA A 100 " =    1.342
peak=    3.345 closest distance to " CA  ARG A  36 " =    1.136
peak=    3.341 closest distance to " CA  VAL A  41 " =    0.894
peak=    3.336 closest distance to " O   HOH Z 280 " =    2.057
peak=    3.335 closest distance to " O   HOH Z  43 " =    2.328
peak=    3.332 closest distance to " CG  GLN A  55 " =    2.112
peak=    3.326 closest distance to " O   HOH Z 367 " =    3.506
peak=    3.323 closest distance to " CA  SER A  87 " =    0.864
peak=    3.323 closest distance to " CB  ALA A 256 " =    1.256
peak=    3.320 closest distance to " O   HOH Z 280 " =    1.569
peak=    3.319 closest distance to " CB  ALA A 295 " =    1.323
peak=    3.318 closest distance to " O   HOH Z 183 " =    1.380
peak=    3.317 closest distance to " CB  ALA A 291 " =    1.369
peak=    3.316 closest distance to " O   HOH Z 420 " =    2.235
peak=    3.312 closest distance to " CG1 VAL A 202 " =    2.038
peak=    3.306 closest distance to " O   HOH Z 279 " =    2.243
peak=    3.306 closest distance to " NH1AARG A 145 " =    1.026
peak=    3.305 closest distance to " CA  ASN A 176 " =    1.166
peak=    3.300 closest distance to " CB  THR A  31 " =    1.628
peak=    3.300 closest distance to " CA  GLY A 267 " =    0.972
peak=    3.298 closest distance to " CB  ALA A 248 " =    1.328
peak=    3.298 closest distance to " O   THR A  31 " =    1.501
peak=    3.293 closest distance to " O   HOH Z 128 " =    2.110
peak=    3.290 closest distance to " NH2 ARG A  79 " =    1.419
peak=    3.289 closest distance to " O   HOH Z 227 " =    2.016
peak=    3.286 closest distance to " O   HOH Z 261 " =    2.029
peak=    3.285 closest distance to " O   HOH Z  19 " =    2.186
peak=    3.279 closest distance to " OE1 GLU A   2 " =    2.164
peak=    3.277 closest distance to " CZ  PHE A 218 " =    1.061
peak=    3.274 closest distance to " O   HOH Z 332 " =    1.545
peak=    3.270 closest distance to " CG1 ILE A  49 " =    1.571
peak=    3.269 closest distance to " CD1 ILE A  33 " =    1.617
peak=    3.266 closest distance to " O   HOH Z 221 " =    1.303
peak=    3.265 closest distance to " CA  TYR A 116 " =    1.573
peak=    3.264 closest distance to " O   HOH Z 387 " =    2.805
peak=    3.261 closest distance to " CA  THR A 264 " =    0.817
peak=    3.259 closest distance to " O   HOH Z 128 " =    1.966
peak=    3.257 closest distance to " O   HOH Z  90 " =    3.176
peak=    3.256 closest distance to " O   ALA A 165 " =    1.315
peak=    3.250 closest distance to " CG  MET A 188 " =    1.246
peak=    3.248 closest distance to " CG1 VAL A 296 " =    1.168
peak=    3.246 closest distance to " O   HOH Z  10 " =    1.835
peak=    3.242 closest distance to " CB AVAL A  41 " =    1.057
peak=    3.242 closest distance to " CB  LEU A 255 " =    0.848
peak=    3.236 closest distance to " O   HOH Z 434 " =    2.961
peak=    3.234 closest distance to " CD  LYS A 166 " =    1.371
peak=    3.229 closest distance to " CD  LYS A 119 " =    1.285
peak=    3.229 closest distance to " CD1 TRP A 266 " =    1.183
peak=    3.228 closest distance to " CA  ALA A 154 " =    1.208
peak=    3.227 closest distance to " O   HOH Z 139 " =    5.215
peak=    3.224 closest distance to " CB  MET A  47 " =    1.129
peak=    3.220 closest distance to " O   HOH Z 156 " =    2.908
peak=    3.220 closest distance to " OD2 ASP A 298 " =    4.100
peak=    3.220 closest distance to " CB  LYS A 193 " =    1.188
peak=    3.218 closest distance to " O   HOH Z 197 " =    2.668
peak=    3.218 closest distance to " CB  LYS A 117 " =    1.134
peak=    3.218 closest distance to " O   ASP A 124 " =    1.279
peak=    3.215 closest distance to " O   HOH Z 395 " =    1.379
peak=    3.214 closest distance to " O   HOH Z 147 " =    1.726
peak=    3.212 closest distance to " CB  SER A 273 " =    0.803
peak=    3.209 closest distance to " O   HOH Z 388 " =    1.931
peak=    3.208 closest distance to " O   HOH Z 144 " =    1.538
peak=    3.207 closest distance to " CB  GLU A 152 " =    1.437
peak=    3.206 closest distance to " CD  ARG A  14 " =    1.253
peak=    3.205 closest distance to " CB  ARG A 190 " =    1.703
peak=    3.204 closest distance to " O   ASN A 217 " =    1.297
peak=    3.203 closest distance to " CG BARG A 275 " =    1.517
peak=    3.202 closest distance to " O   HOH Z 236 " =    1.725
peak=    3.199 closest distance to " CA  LEU A 101 " =    1.586
peak=    3.195 closest distance to " O   HOH Z  44 " =    1.729
peak=    3.192 closest distance to " CA  THR A 246 " =    1.143
peak=    3.188 closest distance to " O   HOH Z 403 " =    1.391
peak=    3.187 closest distance to " O   HOH Z  50 " =    1.990
peak=    3.185 closest distance to " NE2 GLN A  58 " =    4.191
peak=    3.184 closest distance to " O   HOH Z 282 " =    2.027
peak=    3.184 closest distance to " CG2 VAL A 257 " =    0.841
peak=    3.180 closest distance to " O   HOH Z 217 " =    1.294
peak=    3.179 closest distance to " O   HOH Z 368 " =    3.492
peak=    3.178 closest distance to " ND1 HIS A  81 " =    1.547
peak=    3.178 closest distance to " O   HOH Z 207 " =    2.292
peak=    3.175 closest distance to " CA  ILE A 106 " =    0.825
peak=    3.175 closest distance to " O   HOH Z 273 " =    2.536
peak=    3.173 closest distance to " CG  LEU A 167 " =    1.154
peak=    3.169 closest distance to " CB  SER A  62 " =    1.216
peak=    3.165 closest distance to " O   HOH Z 328 " =    1.815
peak=    3.165 closest distance to " CD  ARG A 195 " =    3.425
peak=    3.157 closest distance to " NH1 ARG A 269 " =    0.805
peak=    3.157 closest distance to " O   HOH Z 437 " =    2.277
peak=    3.151 closest distance to " CG2 ILE A 120 " =    1.375
peak=    3.150 closest distance to " CA  GLU A 152 " =    0.853
peak=    3.147 closest distance to " CB  ALA A  71 " =    1.304
peak=    3.147 closest distance to " O   HOH Z 438 " =    2.323
peak=    3.147 closest distance to " CG1 VAL A 174 " =    1.235
peak=    3.141 closest distance to " O   HOH Z 345 " =    1.632
peak=    3.139 closest distance to " O   HOH Z 171 " =    3.833
peak=    3.137 closest distance to " O   HOH Z 158 " =    3.002
peak=    3.136 closest distance to " CG  ARG A 219 " =    1.157
peak=    3.135 closest distance to " CA  GLY A  75 " =    1.221
peak=    3.132 closest distance to " NH2 ARG A 219 " =    1.825
peak=    3.130 closest distance to " CG2AVAL A 121 " =    2.214
peak=    3.128 closest distance to " CG2 VAL A 197 " =    1.151
peak=    3.127 closest distance to " NZ  LYS A  48 " =    1.306
peak=    3.121 closest distance to " O   HOH Z 420 " =    5.531
peak=    3.117 closest distance to " CB  THR A 157 " =    1.038
peak=    3.115 closest distance to " CB  LEU A 261 " =    1.329
peak=    3.115 closest distance to " O   HOH Z 187 " =    2.304
peak=    3.112 closest distance to " O   HOH Z 244 " =    1.639
peak=    3.110 closest distance to " O   HOH Z 150 " =    3.385
peak=    3.100 closest distance to " CB  GLN A  89 " =    1.072
peak=    3.097 closest distance to " O   HOH Z  87 " =    2.557
peak=    3.096 closest distance to " OE1 GLU A 152 " =    0.879
peak=    3.085 closest distance to " CG1 ILE A 120 " =    1.073
peak=    3.082 closest distance to " CA  ILE A  33 " =    1.532
peak=    3.081 closest distance to " CD  ARG A 219 " =    1.005
peak=    3.078 closest distance to " O   HOH Z 366 " =    2.826
peak=    3.078 closest distance to " O   HOH Z 109 " =    2.572
peak=    3.075 closest distance to " OD1 ASP A 286 " =    1.664
peak=    3.071 closest distance to " CG1 ILE A 151 " =    1.150
peak=    3.063 closest distance to " O   HOH Z 327 " =    1.918
peak=    3.056 closest distance to " CD  LYS A 119 " =    2.326
peak=    3.047 closest distance to " CA  ASP A 162 " =    1.205
peak=    3.043 closest distance to " O   HOH Z 213 " =    1.695
peak=    3.036 closest distance to " CB  LEU A 237 " =    0.896
peak=    3.035 closest distance to " C   GLY A  80 " =    1.165
peak=    3.032 closest distance to " CD1 LEU A 101 " =    1.173
peak=    3.026 closest distance to " CG2 VAL A 202 " =    1.175

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.700 - 5.605
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 191
   mapped sites are within: 0.813 - 5.605

peak=   -5.255 closest distance to " CG2 VAL A 230 " =    0.897
peak=   -4.413 closest distance to " O   ILE A 109 " =    2.669
peak=   -4.407 closest distance to " O   HOH Z 266 " =    4.390
peak=   -4.242 closest distance to " CG  LEU A 101 " =    2.599
peak=   -4.226 closest distance to " OG ASER A 134 " =    1.239
peak=   -4.209 closest distance to " O   HOH Z 231 " =    1.901
peak=   -4.162 closest distance to " O   HOH Z 290 " =    1.095
peak=   -4.113 closest distance to " CD  ARG A 156 " =    1.952
peak=   -4.087 closest distance to " OG1 THR A   4 " =    1.949
peak=   -4.027 closest distance to " CD  GLN A  88 " =    2.238
peak=   -4.019 closest distance to " CD2 LEU A 237 " =    2.638
peak=   -4.004 closest distance to " O   HOH Z  19 " =    2.139
peak=   -3.981 closest distance to " O   HOH Z  17 " =    1.400
peak=   -3.976 closest distance to " OXT GLY A 302 " =    2.908
peak=   -3.932 closest distance to " O   HOH Z  13 " =    1.299
peak=   -3.929 closest distance to " O   HOH Z 184 " =    1.301
peak=   -3.917 closest distance to " O   HOH Z 407 " =    3.364
peak=   -3.900 closest distance to " C   ALA A 158 " =    1.239
peak=   -3.894 closest distance to " CE2 TYR A  30 " =    2.759
peak=   -3.848 closest distance to " OE2 GLU A   2 " =    1.720
peak=   -3.845 closest distance to " O   HOH Z 166 " =    1.844
peak=   -3.840 closest distance to " CD2 LEU A 300 " =    2.864
peak=   -3.826 closest distance to " NH2 ARG A  66 " =    1.637
peak=   -3.819 closest distance to " CD  LYS A 289 " =    2.490
peak=   -3.795 closest distance to " O   HOH Z  52 " =    1.632
peak=   -3.783 closest distance to " O   HOH Z 221 " =    1.211
peak=   -3.779 closest distance to " O   HOH Z  43 " =    1.540
peak=   -3.770 closest distance to " CH2 TRP A 179 " =    1.213
peak=   -3.764 closest distance to " CG1 VAL A 112 " =    2.622
peak=   -3.763 closest distance to " O   HOH Z  15 " =    1.636
peak=   -3.763 closest distance to " O   HOH Z  92 " =    1.310
peak=   -3.756 closest distance to " O   HOH Z 151 " =    1.457
peak=   -3.753 closest distance to " O   HOH Z 241 " =    1.211
peak=   -3.751 closest distance to " CG  GLN A 223 " =    2.221
peak=   -3.747 closest distance to " CG2 VAL A 112 " =    2.607
peak=   -3.744 closest distance to " N   ALA A 226 " =    2.053
peak=   -3.740 closest distance to " CG  ASP A 231 " =    0.813
peak=   -3.730 closest distance to " O   HOH Z 266 " =    4.649
peak=   -3.720 closest distance to " O   HOH Z  11 " =    1.718
peak=   -3.715 closest distance to " CA  SER A 164 " =    2.065
peak=   -3.702 closest distance to " CD2 TYR A 293 " =    2.116
peak=   -3.701 closest distance to " O   HOH Z 377 " =    1.148
peak=   -3.687 closest distance to " O   VAL A  67 " =    2.775
peak=   -3.683 closest distance to " O   HOH Z  38 " =    1.541
peak=   -3.682 closest distance to " O   HOH Z 275 " =    1.490
peak=   -3.677 closest distance to " CB  TYR A  15 " =    2.273
peak=   -3.675 closest distance to " CD  ARG A 139 " =    1.564
peak=   -3.666 closest distance to " CG  ASP A  50 " =    2.322
peak=   -3.657 closest distance to " C   ASN A 187 " =    1.776
peak=   -3.654 closest distance to " OG BSER A 134 " =    1.819
peak=   -3.639 closest distance to " OG  SER A  26 " =    1.322
peak=   -3.637 closest distance to " O   HOH Z 292 " =    4.428
peak=   -3.636 closest distance to " CD1 PHE A  59 " =    1.866
peak=   -3.635 closest distance to " O   HOH Z  71 " =    0.992
peak=   -3.632 closest distance to " NH2AARG A 275 " =    5.198
peak=   -3.612 closest distance to " CG1 VAL A 296 " =    1.321
peak=   -3.611 closest distance to " O   HOH Z 234 " =    4.390
peak=   -3.603 closest distance to " O   HOH Z 377 " =    1.911
peak=   -3.596 closest distance to " N   ALA A  43 " =    2.560
peak=   -3.592 closest distance to " CD1 LEU A 228 " =    2.443
peak=   -3.591 closest distance to " CG  GLU A  53 " =    1.654
peak=   -3.588 closest distance to " CD2 LEU A 167 " =    1.744
peak=   -3.578 closest distance to " O   HOH Z 243 " =    1.530
peak=   -3.559 closest distance to " CA  ASN A 127 " =    1.024
peak=   -3.555 closest distance to " CB  CYS A 254 " =    2.366
peak=   -3.551 closest distance to " ND2 ASN A  60 " =    1.506
peak=   -3.549 closest distance to " O   HOH Z 252 " =    4.027
peak=   -3.535 closest distance to " SG  CYS A 254 " =    3.049
peak=   -3.530 closest distance to " C   HIS A 108 " =    1.187
peak=   -3.529 closest distance to " N   SER A 276 " =    1.360
peak=   -3.526 closest distance to " CG  TRP A 266 " =    1.574
peak=   -3.524 closest distance to " O   HOH Z 353 " =    2.336
peak=   -3.521 closest distance to " N   GLN A  58 " =    1.710
peak=   -3.505 closest distance to " O   SER A 271 " =    2.241
peak=   -3.498 closest distance to " ND2 ASN A 187 " =    1.760
peak=   -3.497 closest distance to " CB  PRO A 163 " =    2.750
peak=   -3.493 closest distance to " OG  SER A  87 " =    1.532
peak=   -3.487 closest distance to " O   HOH Z 350 " =    1.810
peak=   -3.481 closest distance to " CG  MET A 105 " =    0.858
peak=   -3.479 closest distance to " CB  ALA A 248 " =    1.899
peak=   -3.471 closest distance to " O   HOH Z 103 " =    1.824
peak=   -3.462 closest distance to " CD1 LEU A 101 " =    2.702
peak=   -3.457 closest distance to " N   THR A 157 " =    1.613
peak=   -3.453 closest distance to " OD1 ASN A 148 " =    1.604
peak=   -3.442 closest distance to " O   HOH Z 389 " =    1.760
peak=   -3.435 closest distance to " CB  ALA A  43 " =    2.482
peak=   -3.432 closest distance to " O   GLY A 196 " =    1.134
peak=   -3.431 closest distance to " O   HOH Z  10 " =    1.578
peak=   -3.430 closest distance to " CZ  TYR A 169 " =    1.825
peak=   -3.427 closest distance to " O   HOH Z 388 " =    1.968
peak=   -3.426 closest distance to " O   HOH Z 426 " =    1.796
peak=   -3.426 closest distance to " OG BSER A 134 " =    1.269
peak=   -3.420 closest distance to " O   VAL A  67 " =    2.604
peak=   -3.419 closest distance to " O   HOH Z 423 " =    2.294
peak=   -3.415 closest distance to " ND2 ASN A  45 " =    0.956
peak=   -3.414 closest distance to " CA  GLY A 203 " =    2.196
peak=   -3.410 closest distance to " CG  PRO A 163 " =    2.511
peak=   -3.409 closest distance to " CG2 VAL A 296 " =    1.516
peak=   -3.408 closest distance to " O   HOH Z 128 " =    2.415
peak=   -3.406 closest distance to " O   HOH Z 351 " =    1.389
peak=   -3.402 closest distance to " OG  SER A  97 " =    2.263
peak=   -3.402 closest distance to " OD1 ASP A 191 " =    1.644
peak=   -3.391 closest distance to " C   LEU A 143 " =    1.267
peak=   -3.387 closest distance to " O   HOH Z 166 " =    1.621
peak=   -3.382 closest distance to " O   HOH Z 165 " =    2.038
peak=   -3.377 closest distance to " O   HOH Z 385 " =    3.854
peak=   -3.376 closest distance to " O   HOH Z 189 " =    2.033
peak=   -3.373 closest distance to " CA  ASN A 142 " =    1.331
peak=   -3.367 closest distance to " O   VAL A 125 " =    2.200
peak=   -3.367 closest distance to " CE3 TRP A  70 " =    1.722
peak=   -3.365 closest distance to " O   GLY A 211 " =    1.487
peak=   -3.364 closest distance to " O   HOH Z  60 " =    2.221
peak=   -3.361 closest distance to " O   HOH Z  98 " =    1.983
peak=   -3.340 closest distance to " O   HOH Z 295 " =    1.318
peak=   -3.339 closest distance to " CA  ASP A 298 " =    1.094
peak=   -3.339 closest distance to " O   HOH Z 283 " =    1.948
peak=   -3.330 closest distance to " O   HOH Z 177 " =    1.507
peak=   -3.330 closest distance to " O   HOH Z 196 " =    2.366
peak=   -3.322 closest distance to " O   ALA A 256 " =    1.631
peak=   -3.320 closest distance to " CE  MET A 105 " =    2.045
peak=   -3.316 closest distance to " N   ALA A 248 " =    2.523
peak=   -3.312 closest distance to " CD  ARG A  14 " =    3.178
peak=   -3.297 closest distance to " CD  GLN A  88 " =    0.842
peak=   -3.294 closest distance to " CB  PRO A 243 " =    2.620
peak=   -3.283 closest distance to " O   HOH Z 385 " =    2.170
peak=   -3.278 closest distance to " CG1 VAL A 197 " =    2.313
peak=   -3.269 closest distance to " O   SER A 210 " =    1.873
peak=   -3.263 closest distance to " NE2 GLN A  88 " =    0.913
peak=   -3.261 closest distance to " CG  GLU A   2 " =    1.658
peak=   -3.258 closest distance to " CZ  TYR A 172 " =    1.672
peak=   -3.257 closest distance to " C   GLN A 240 " =    2.190
peak=   -3.256 closest distance to " CE1 TYR A 169 " =    2.508
peak=   -3.255 closest distance to " O   HOH Z 396 " =    1.663
peak=   -3.253 closest distance to " O   HOH Z 431 " =    1.755
peak=   -3.252 closest distance to " NH2 ARG A  79 " =    1.868
peak=   -3.249 closest distance to " CG  GLU A 277 " =    1.144
peak=   -3.245 closest distance to " CA  GLY A 133 " =    2.273
peak=   -3.244 closest distance to " OH  TYR A 169 " =    0.987
peak=   -3.241 closest distance to " O   HOH Z 185 " =    2.371
peak=   -3.236 closest distance to " O   HOH Z 265 " =    1.768
peak=   -3.233 closest distance to " O   HOH Z 191 " =    5.605
peak=   -3.233 closest distance to " O   HOH Z 211 " =    1.528
peak=   -3.231 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.229 closest distance to " CD1 LEU A   5 " =    2.526
peak=   -3.221 closest distance to " O   HOH Z 411 " =    3.542
peak=   -3.221 closest distance to " CB  GLN A  55 " =    1.517
peak=   -3.217 closest distance to " N   GLY A 133 " =    1.887
peak=   -3.214 closest distance to " O   VAL A 197 " =    1.350
peak=   -3.214 closest distance to " CB  SER A 245 " =    2.356
peak=   -3.209 closest distance to " O   HOH Z  22 " =    2.540
peak=   -3.206 closest distance to " O   HOH Z 222 " =    1.460
peak=   -3.205 closest distance to " N   PHE A  59 " =    2.216
peak=   -3.201 closest distance to " C   ASN A 285 " =    2.405
peak=   -3.199 closest distance to " O   HOH Z 292 " =    2.944
peak=   -3.197 closest distance to " CG  PHE A 283 " =    2.814
peak=   -3.195 closest distance to " SG ACYS A 201 " =    1.153
peak=   -3.193 closest distance to " O   HOH Z 402 " =    1.482
peak=   -3.186 closest distance to " O   ALA A 161 " =    1.700
peak=   -3.186 closest distance to " OG1 THR A  82 " =    1.511
peak=   -3.170 closest distance to " O   ALA A 100 " =    2.389
peak=   -3.167 closest distance to " ND2 ASN A  60 " =    1.651
peak=   -3.167 closest distance to " CD1 LEU A 255 " =    2.793
peak=   -3.166 closest distance to " O   ASP A 191 " =    1.418
peak=   -3.160 closest distance to " O   ALA A   8 " =    1.990
peak=   -3.158 closest distance to " O   PRO A 198 " =    1.262
peak=   -3.148 closest distance to " NH1 ARG A 195 " =    2.215
peak=   -3.147 closest distance to " NH1 ARG A  56 " =    2.555
peak=   -3.146 closest distance to " CG  LEU A 228 " =    0.981
peak=   -3.143 closest distance to " CD1 LEU A 297 " =    1.967
peak=   -3.142 closest distance to " N   GLY A  23 " =    2.083
peak=   -3.140 closest distance to " O   HOH Z 147 " =    2.077
peak=   -3.140 closest distance to " O   HOH Z 264 " =    1.832
peak=   -3.136 closest distance to " CA  PRO A 243 " =    2.670
peak=   -3.128 closest distance to " OD1 ASN A 249 " =    1.142
peak=   -3.128 closest distance to " OD2 ASP A 171 " =    1.817
peak=   -3.122 closest distance to " CG  GLN A  58 " =    1.197
peak=   -3.120 closest distance to " NE2 GLN A  58 " =    1.297
peak=   -3.113 closest distance to " O   ASN A 301 " =    1.422
peak=   -3.106 closest distance to " CG  ARG A 269 " =    2.263
peak=   -3.103 closest distance to " O   HOH Z  97 " =    1.715
peak=   -3.103 closest distance to " CB  ALA A 291 " =    2.331
peak=   -3.103 closest distance to " CG  LYS A 166 " =    2.177
peak=   -3.100 closest distance to " OD2 ASP A 171 " =    2.270
peak=   -3.093 closest distance to " O   HOH Z 352 " =    0.920
peak=   -3.079 closest distance to " O   HOH Z 359 " =    2.943
peak=   -3.056 closest distance to " CB  ALA A 227 " =    2.316
peak=   -3.051 closest distance to " N   ALA A 248 " =    1.676
peak=   -3.050 closest distance to " CG1 VAL A 112 " =    2.858
peak=   -3.041 closest distance to " CD  ARG A 259 " =    2.531

================= 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    :  0.4780 0.4727   6.279319e+00   6.273052e+00
   1_bss:  0.4694 0.4619   6.279273e+00   6.267629e+00
   1_xyz:  0.3910 0.4235   6.164645e+00   6.213381e+00
   1_adp:  0.3507 0.4090   6.095797e+00   6.188956e+00
   1_occ:  0.3504 0.4098   6.095457e+00   6.189376e+00
   2_bss:  0.3481 0.4048   6.096016e+00   6.187660e+00
   2_xyz:  0.2433 0.3128   5.821742e+00   5.996321e+00
   2_adp:  0.2157 0.2786   5.710624e+00   5.904314e+00
   2_occ:  0.2155 0.2784   5.709881e+00   5.903811e+00
   3_bss:  0.2121 0.2748   5.707670e+00   5.899743e+00
   3_xyz:  0.1599 0.2082   5.445553e+00   5.661977e+00
   3_adp:  0.1460 0.1960   5.375737e+00   5.600493e+00
   3_occ:  0.1458 0.1958   5.375384e+00   5.600408e+00
   4_bss:  0.1455 0.1966   5.376916e+00   5.602575e+00
   4_xyz:  0.1248 0.1720   5.243941e+00   5.479321e+00
   4_adp:  0.1211 0.1681   5.220389e+00   5.457946e+00
   4_occ:  0.1210 0.1682   5.220308e+00   5.458206e+00
   5_bss:  0.1215 0.1685   5.223193e+00   5.460407e+00
   5_xyz:  0.1163 0.1643   5.193537e+00   5.436756e+00
   5_adp:  0.1156 0.1640   5.189902e+00   5.434633e+00
   5_occ:  0.1155 0.1639   5.189616e+00   5.434391e+00
   5_bss:  0.1155 0.1639   5.189578e+00   5.434378e+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:  0.337  20.001   7.851   8.648   8.474   0.000   0.000   0.000
   1_xyz:  0.337  20.001   7.851   8.648   8.474   0.000   0.000   0.000
   1_adp:  0.337  20.001   7.851   8.648   8.474   0.000   0.000   0.000
   1_occ:  0.337  20.001   7.851   8.648   8.474   0.000   0.000   0.000
   2_bss:  0.325  50.001   4.425   5.223   5.701   0.000   0.000   0.000
   2_xyz:  0.325  50.001   4.425   5.223   5.701   0.000   0.000   0.000
   2_adp:  0.325  50.001   4.425   5.223   5.701   0.000   0.000   0.000
   2_occ:  0.325  50.001   4.425   5.223   5.701   0.000   0.000   0.000
   3_bss:  0.327  50.001   2.480   2.831   3.048   0.000   0.000   0.000
   3_xyz:  0.327  50.001   2.480   2.831   3.048   0.000   0.000   0.000
   3_adp:  0.327  50.001   2.480   2.831   3.048   0.000   0.000   0.000
   3_occ:  0.327  50.001   2.480   2.831   3.048   0.000   0.000   0.000
   4_bss:  0.326  49.173   1.827   2.171   2.263   0.000   0.000   0.000
   4_xyz:  0.326  49.173   1.827   2.171   2.263   0.000   0.000   0.000
   4_adp:  0.326  49.173   1.827   2.171   2.263   0.000   0.000   0.000
   4_occ:  0.326  49.173   1.827   2.171   2.263   0.000   0.000   0.000
   5_bss:  0.326  49.173   1.827   2.171   2.263   0.000   0.000   0.000
   5_xyz:  0.326  49.173   1.827   2.171   2.263   0.000   0.000   0.000
   5_adp:  0.326  49.173   1.827   2.171   2.263   0.000   0.000   0.000
   5_occ:  0.326  49.173   1.827   2.171   2.263   0.000   0.000   0.000
   5_bss:  0.326  51.226  -0.200   0.053   0.147   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.559 0.4116  0.4826    70538.785
   1_bss:  59.107 0.4017  0.5893    68056.009
   1_xyz:  51.096 0.5031  0.7301    53613.117
   1_adp:  47.382 0.5503  0.8385    48386.475
   1_occ:  47.465 0.5493  0.8369    48571.799
   2_bss:  47.190 0.5527  0.7565    48214.693
   2_xyz:  33.049 0.7225  0.9664    26627.355
   2_adp:  28.426 0.7747  1.0136    20722.637
   2_occ:  28.404 0.7750  1.0135    20687.929
   3_bss:  28.208 0.7769  0.9344    20431.801
   3_xyz:  20.428 0.8567  0.9838    11328.268
   3_adp:  18.770 0.8732  0.9880     9990.870
   3_occ:  18.768 0.8732  0.9879     9989.761
   4_bss:  18.807 0.8730  0.9632    10075.656
   4_xyz:  16.126 0.8969  0.9758     7740.972
   4_adp:  15.602 0.9017  0.9753     7429.893
   4_occ:  15.602 0.9017  0.9752     7436.301
   5_bss:  15.659 0.9013  0.9747     7500.077
   5_xyz:  15.094 0.9061  0.9760     7045.298
   5_adp:  15.020 0.9068  0.9720     7013.583
   5_occ:  15.015 0.9069  0.9719     7014.705
   5_bss:  15.015 0.9069  0.9708     7015.570
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3768e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3768e+01
   1_xyz:   1.747  0.014  0.110 18.145  0.007  4.110   1.4756e-01
   1_adp:   1.747  0.014  0.110 18.145  0.007  4.110   1.4756e-01
   1_occ:   1.747  0.014  0.110 18.145  0.007  4.110   1.4756e-01
   2_bss:   1.747  0.014  0.110 18.145  0.007  4.110   1.4756e-01
   2_xyz:   1.280  0.010  0.086 16.259  0.006  4.118   9.6323e-02
   2_adp:   1.280  0.010  0.086 16.259  0.006  4.118   9.6323e-02
   2_occ:   1.280  0.010  0.086 16.259  0.006  4.118   9.6323e-02
   3_bss:   1.280  0.010  0.086 16.259  0.006  4.118   9.6323e-02
   3_xyz:   1.078  0.007  0.078 15.605  0.004  4.134   6.7318e-02
   3_adp:   1.078  0.007  0.078 15.605  0.004  4.134   6.7318e-02
   3_occ:   1.078  0.007  0.078 15.605  0.004  4.134   6.7318e-02
   4_bss:   1.078  0.007  0.078 15.605  0.004  4.134   6.7318e-02
   4_xyz:   1.110  0.008  0.085 15.722  0.004  4.114   7.2365e-02
   4_adp:   1.110  0.008  0.085 15.722  0.004  4.114   7.2365e-02
   4_occ:   1.110  0.008  0.085 15.722  0.004  4.114   7.2365e-02
   5_bss:   1.110  0.008  0.085 15.722  0.004  4.114   7.2365e-02
   5_xyz:   1.081  0.008  0.083 15.444  0.004  4.113   6.7956e-02
   5_adp:   1.081  0.008  0.083 15.444  0.004  4.113   6.7956e-02
   5_occ:   1.081  0.008  0.083 15.444  0.004  4.113   6.7956e-02
   5_bss:   1.081  0.008  0.083 15.444  0.004  4.113   6.7956e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9699e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9699e+00
   1_xyz:  15.378  0.174  0.500 85.418  0.056  2.196   1.0381e-01
   1_adp:  15.378  0.174  0.500 85.418  0.056  2.196   1.0381e-01
   1_occ:  15.378  0.174  0.500 85.418  0.056  2.196   1.0381e-01
   2_bss:  15.378  0.174  0.500 85.418  0.056  2.196   1.0381e-01
   2_xyz:   7.731  0.119  0.320 79.948  0.043  2.220   7.8240e-02
   2_adp:   7.731  0.119  0.320 79.948  0.043  2.220   7.8240e-02
   2_occ:   7.731  0.119  0.320 79.948  0.043  2.220   7.8240e-02
   3_bss:   7.731  0.119  0.320 79.948  0.043  2.220   7.8240e-02
   3_xyz:   7.665  0.052  0.366 88.842  0.037  2.384   5.3797e-02
   3_adp:   7.665  0.052  0.366 88.842  0.037  2.384   5.3797e-02
   3_occ:   7.665  0.052  0.366 88.842  0.037  2.384   5.3797e-02
   4_bss:   7.665  0.052  0.366 88.842  0.037  2.384   5.3797e-02
   4_xyz:   7.890  0.055  0.538 81.914  0.029  2.302   5.5765e-02
   4_adp:   7.890  0.055  0.538 81.914  0.029  2.302   5.5765e-02
   4_occ:   7.890  0.055  0.538 81.914  0.029  2.302   5.5765e-02
   5_bss:   7.890  0.055  0.538 81.914  0.029  2.302   5.5765e-02
   5_xyz:   7.663  0.041  0.560 83.376  0.031  2.338   4.6087e-02
   5_adp:   7.663  0.041  0.560 83.376  0.031  2.338   4.6087e-02
   5_occ:   7.663  0.041  0.560 83.376  0.031  2.338   4.6087e-02
   5_bss:   7.663  0.041  0.560 83.376  0.031  2.338   4.6087e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  79.66   0.00  12.76  73.13   0.00  10.33  79.66   0.00  25.99
   1_occ:  79.66   0.00  12.76  73.13   0.00  10.33  79.66   0.00  25.99
   2_bss:  79.66   0.00  12.76  73.13   0.00  10.33  79.66   0.00  25.99
   2_xyz:  79.66   0.00  12.76  73.13   0.00  10.33  79.66   0.00  25.99
   2_adp:  78.29   0.00  13.18  70.64   0.00   9.38  78.29   1.49  33.87
   2_occ:  78.29   0.00  13.18  70.64   0.00   9.38  78.29   1.49  33.87
   3_bss:  78.29   0.00  13.18  70.64   0.00   9.38  78.29   1.49  33.87
   3_xyz:  78.29   0.00  13.18  70.64   0.00   9.38  78.29   1.49  33.87
   3_adp:  90.90   0.00  13.81  90.90   0.00   9.21  81.39   1.21  38.88
   3_occ:  90.90   0.00  13.81  90.90   0.00   9.21  81.39   1.21  38.88
   4_bss:  90.90   0.00  13.81  90.90   0.00   9.21  81.39   1.21  38.88
   4_xyz:  90.90   0.00  13.81  90.90   0.00   9.21  81.39   1.21  38.88
   4_adp:  93.97   0.00  13.54  93.97   0.00   9.03  82.12   1.76  38.07
   4_occ:  93.97   0.00  13.54  93.97   0.00   9.03  82.12   1.76  38.07
   5_bss:  93.97   0.00  13.54  93.97   0.00   9.03  82.12   1.76  38.07
   5_xyz:  93.97   0.00  13.54  93.97   0.00   9.03  82.12   1.76  38.07
   5_adp:  96.37   0.00  13.22  96.37   0.00   8.88  81.91   1.73  36.83
   5_occ:  96.37   0.00  13.22  96.37   0.00   8.88  81.91   1.73  36.83
   5_bss:  98.43   2.05  15.27  98.43   2.05  10.94  83.96   3.78  38.88
------------------------------------------------------------------------
 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:    1.217    0.041    0.416
   1_adp:    1.217    0.041    0.416
   1_occ:    1.217    0.041    0.416
   2_bss:    1.217    0.041    0.416
   2_xyz:    1.554    0.023    0.626
   2_adp:    1.554    0.023    0.626
   2_occ:    1.554    0.023    0.626
   3_bss:    1.554    0.023    0.626
   3_xyz:    1.656    0.032    0.681
   3_adp:    1.656    0.032    0.681
   3_occ:    1.656    0.032    0.681
   4_bss:    1.656    0.032    0.681
   4_xyz:    1.644    0.028    0.727
   4_adp:    1.644    0.028    0.727
   4_occ:    1.644    0.028    0.727
   5_bss:    1.644    0.028    0.727
   5_xyz:    1.704    0.031    0.739
   5_adp:    1.704    0.031    0.739
   5_occ:    1.704    0.031    0.739
   5_bss:    1.704    0.031    0.739
------------------------------------------------------------------------

CPU time actual refinement: 368.49


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1046/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1046/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1046/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1046/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1046/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 368.33 
  Macro-tasks:
    bulk solvent and scale       = 41.33  
    individual site refinement   = 165.85 
    weights calculation          = 32.12  
    collect and process          = 6.33   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 245.73 
  Micro-tasks:
    mask                            = 2.50   
    f_calc                          = 118.52 
    alpha_beta                      = 8.29   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 131.21 
    fmodel                         = 7.06   
    r_factors                      = 0.29   
    phase_errors                   = 10.09  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 279.34 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.031 micro seconds
Total CPU time: 6.37 minutes
from_scatterers_fft:    669 calls, 118.16 s
gradients_fft:          613 calls, 116.31 s

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

# Date 2008-01-16 Time 03:03:46 PST -0800 (1200481426.02 s)
Start R-work = 0.4780, R-free = 0.4727 (no bulk solvent and anisotropic scale)
Final R-work = 0.1319, R-free = 0.1805 (no bulk solvent and anisotropic scale)

Start R-work = 0.4694, R-free = 0.4619
Final R-work = 0.1155, R-free = 0.1639