# Date 2008-01-16 Time 01:21:41 PST -0800 (1200475301.25 s)
#phil __OFF__

Command line arguments: "../387.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27742
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 387

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.2261, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.97037
Completeness in resolution range: 0.981118
Completeness with d_max=infinity: 0.978032

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8236
                             d_min =   1.9704

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.97037
Completeness in resolution range: 0.981118
Completeness with d_max=infinity: 0.978032

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8240 -  4.2155 [2095/2119]  1886   209  10.0%
  bin  2:  4.2155 -  3.3588 [2023/2043]  1820   203  10.0%
  bin  3:  3.3588 -  2.9380 [1983/2002]  1784   199  10.0%
  bin  4:  2.9380 -  2.6711 [1954/1984]  1759   195  10.0%
  bin  5:  2.6711 -  2.4806 [1963/1982]  1769   194   9.9%
  bin  6:  2.4806 -  2.3349 [1955/1980]  1759   196  10.0%
  bin  7:  2.3349 -  2.2184 [1950/1978]  1752   198  10.2%
  bin  8:  2.2184 -  2.1221 [1918/1954]  1727   191  10.0%
  bin  9:  2.1221 -  2.0406 [1917/1959]  1727   190   9.9%
  bin 10:  2.0406 -  1.9704 [1831/1965]  1647   184  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_387/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:
        1.55 -     2.22: 18
        2.22 -     2.89: 1368
        2.89 -     3.56: 4593
        3.56 -     4.23: 9383
        4.23 -     4.90: 13522
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.548 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.800 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.800 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 178 " - " O   HOH Z 403 "  1.869 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28879 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_387/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_387/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.22605 85.09415 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: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4818   r_free= 0.4726   ksol= 0.00   Bsol= 0.00   scale= 0.804    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.279280                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7015 0.99   1367  152 0.3986 0.4065      6.5826      6.6159|
|  2:  4.7015 -  3.7516 0.99   1310  145 0.4128 0.3702      6.7941      6.7565|
|  3:  3.7516 -  3.2833 0.99   1274  143 0.4384 0.4304      6.6822      6.7396|
|  4:  3.2833 -  2.9858 0.99   1280  144 0.4614 0.4228      6.5389      6.4742|
|  5:  2.9858 -  2.7733 0.99   1263  138 0.5087 0.5163      6.3862      6.3686|
|  6:  2.7733 -  2.6107 0.99   1265  141 0.5155 0.5746      6.2975      6.2703|
|  7:  2.6107 -  2.4806 0.99   1259  137 0.5083 0.4475      6.2451      6.1723|
|  8:  2.4806 -  2.3730 0.98   1258  140 0.5277 0.5004      6.2066      6.2241|
|  9:  2.3730 -  2.2820 0.98   1242  136 0.5208 0.5584       6.121      6.1614|
| 10:  2.2820 -  2.2035 1.00   1239  140 0.5279 0.5289      6.1356      6.1012|
| 11:  2.2035 -  2.1348 0.97   1249  142 0.5124 0.4702      6.0421      6.0865|
| 12:  2.1348 -  2.0740 0.97   1232  133 0.5171 0.5198      6.0087      6.0224|
| 13:  2.0740 -  2.0195 0.99   1227  141 0.5399 0.5508      5.9059      5.9016|
| 14:  2.0195 -  1.9704 0.91   1165  127 0.5454 0.5004      5.8535      5.7585|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7015  1367   152  0.65  38.63   0.80     0.70      85206.63|
|  2:  4.7015 -  3.7516  1310   145  0.69  36.21   0.88     0.77     112116.72|
|  3:  3.7516 -  3.2833  1274   143  0.60  43.92   0.87     0.74     116680.10|
|  4:  3.2833 -  2.9858  1280   144  0.52  50.34   0.82     0.62     102506.27|
|  5:  2.9858 -  2.7733  1263   138  0.42  58.54   0.75     0.50      84428.90|
|  6:  2.7733 -  2.6107  1265   141  0.38  61.63   0.73     0.43      74122.97|
|  7:  2.6107 -  2.4806  1259   137  0.33  65.19   0.74     0.38      69160.07|
|  8:  2.4806 -  2.3730  1258   140  0.31  66.54   0.75     0.37      64126.13|
|  9:  2.3730 -  2.2820  1242   136  0.33  65.36   0.73     0.38      56443.64|
| 10:  2.2820 -  2.2035  1239   140  0.37  62.62   0.77     0.43      49273.17|
| 11:  2.2035 -  2.1348  1249   142  0.36  63.24   0.78     0.44      45806.72|
| 12:  2.1348 -  2.0740  1232   133  0.33  65.42   0.78     0.41      44070.37|
| 13:  2.0740 -  2.0195  1227   141  0.27  69.97   0.75     0.33      39245.84|
| 14:  2.0195 -  1.9704  1165   127  0.23  73.05   0.73     0.25      32344.15|
|alpha:            min =        0.25 max =            0.77 mean =         0.49|
|beta:             min =    32344.15 max =       116680.10 mean =     70325.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.29|
|phase err.(test): min =        0.00 max =           90.00 mean =        58.33|
|-----------------------------------------------------------------------------|

============================== 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 = 14.704922             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.244   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.595691              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.235   (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 |  1.085 -  1.467:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.467 -  1.848:        9 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.848 -  2.230:      138 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.230 -  2.611:      605 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.611 -  2.993:     1414 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.993 -  3.374:     2593 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.374 -  3.756:     4018 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.756 -  4.137:     5252 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.137 -  4.518:     6801 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.518 -  4.900:     8063 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.901 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.085 |       2.196 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.440)------------------------------------------|
|    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 = 11.440)------------------------------------------|
|    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: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4874   r_free= 0.4747   ksol= 0.00   Bsol= 0.00   scale= 0.773    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.281288                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4728   r_free= 0.4598   ksol= 0.40   Bsol= 20.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.56,9.38,8.05,0.00,0.00,0.00); trace/3= 8.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.272000                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.115921             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.279   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.354299              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.562   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4728      final r-factor (work) = 0.3950          |
| start r-factor (free) = 0.4598      final r-factor (free) = 0.4141          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 90.9386 = 12.12 * 0.50 * 6.2790 + 1.00 * 52.9009                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6789 = 12.12 * 0.50 * 6.1970 + 1.00 * 0.1375                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3950      final r-factor (work) = 0.3501          |
| start r-factor (free) = 0.4141      final r-factor (free) = 0.3932          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4070 = 1.35 * 1.00 * 6.1970 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2938 = 1.35 * 1.00 * 6.1102 + 1.00 * 0.0188                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.440)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.26   13.61    None  None   None       |
|    all(noH): 2823   0      0.00    93.26   13.61    None  None   None       |
|    Sol.    : 438    0      0.00    91.35   26.83    None  None   None       |
|    Mac.    : 2385   0      0.00    93.26   11.18    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 -   9.326: 1269   |   5:    46.630 -  55.956:   40        |
|      1:     9.326 -  18.652:  848   |   6:    55.956 -  65.282:   17        |
|      2:    18.652 -  27.978:  363   |   7:    65.282 -  74.608:    7        |
|      3:    27.978 -  37.304:  186   |   8:    74.608 -  83.934:    1        |
|      4:    37.304 -  46.630:   90   |   9:    83.934 -  93.261:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3501 r_free = 0.3932             target_work(ml) = 6.090         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3495 r_free = 0.3939             target_work(ml) = 6.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3495   r_free= 0.3939   ksol= 0.40   Bsol= 20.00   scale= 1.108   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.56,9.38,8.05,0.00,0.00,0.00); trace/3= 8.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.089792                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3464   r_free= 0.3895   ksol= 0.36   Bsol= 30.84   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,5.12,4.91,0.00,0.00,0.00); trace/3= 4.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.089543                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.474286              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.860   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.529632              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.945  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3464      final r-factor (work) = 0.2448          |
| start r-factor (free) = 0.3895      final r-factor (free) = 0.2970          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.0044 = 8.47 * 0.50 * 6.1048 + 1.00 * 0.1375                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.3055 = 8.47 * 0.50 * 5.9495 + 1.00 * 0.0967                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2448      final r-factor (work) = 0.2150          |
| start r-factor (free) = 0.2970      final r-factor (free) = 0.2708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1700 = 0.53 * 1.00 * 5.9495 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0531 = 0.53 * 1.00 * 5.7415 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.440)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.47   13.18    None  None   None       |
|    all(noH): 2823   0      0.00    93.47   13.18    None  None   None       |
|    Sol.    : 438    0      0.20    87.77   32.24    None  None   None       |
|    Mac.    : 2385   0      0.00    93.47   9.68     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.347: 1521   |   5:    46.736 -  56.083:   40        |
|      1:     9.347 -  18.694:  660   |   6:    56.083 -  65.430:   16        |
|      2:    18.694 -  28.041:  246   |   7:    65.430 -  74.777:    4        |
|      3:    28.041 -  37.389:  212   |   8:    74.777 -  84.124:    2        |
|      4:    37.389 -  46.736:  120   |   9:    84.124 -  93.471:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2150 r_free = 0.2708             target_work(ml) = 5.696         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2144 r_free = 0.2704             target_work(ml) = 5.695         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2144   r_free= 0.2704   ksol= 0.36   Bsol= 30.84   scale= 1.065   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,5.12,4.91,0.00,0.00,0.00); trace/3= 4.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.695359                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2125   r_free= 0.2681   ksol= 0.34   Bsol= 30.84   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.16,2.79,3.30,0.00,0.00,0.00); trace/3= 2.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.690946                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.221204              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.106   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.467803              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.825  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2125      final r-factor (work) = 0.1594          |
| start r-factor (free) = 0.2681      final r-factor (free) = 0.2085          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3474 = 3.22 * 0.50 * 5.7437 + 1.00 * 0.0967                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0368 = 3.22 * 0.50 * 5.5724 + 1.00 * 0.0619                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1594      final r-factor (work) = 0.1435          |
| start r-factor (free) = 0.2085      final r-factor (free) = 0.1940          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6189 = 0.47 * 1.00 * 5.5724 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5324 = 0.47 * 1.00 * 5.3896 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.440)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.38   13.33    None  None   None       |
|    all(noH): 2823   0      0.00    94.38   13.33    None  None   None       |
|    Sol.    : 438    0      2.04    81.90   36.65    None  None   None       |
|    Mac.    : 2385   0      0.00    94.38   9.04     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 -   9.438: 1689   |   5:    47.192 -  56.630:   90        |
|      1:     9.438 -  18.877:  564   |   6:    56.630 -  66.068:   43        |
|      2:    18.877 -  28.315:  182   |   7:    66.068 -  75.507:    6        |
|      3:    28.315 -  37.753:  129   |   8:    75.507 -  84.945:    4        |
|      4:    37.753 -  47.192:  115   |   9:    84.945 -  94.383:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1435 r_free = 0.1940             target_work(ml) = 5.351         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1434 r_free = 0.1939             target_work(ml) = 5.351         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1434   r_free= 0.1939   ksol= 0.34   Bsol= 30.84   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.16,2.79,3.30,0.00,0.00,0.00); trace/3= 2.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.350979                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1433   r_free= 0.1940   ksol= 0.33   Bsol= 33.25   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,1.89,2.79,0.00,0.00,0.00); trace/3= 2.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.349248                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.558449              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.690  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.220266              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.785  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1433      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.1940      final r-factor (free) = 0.1725          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2638 = 1.56 * 0.50 * 5.3924 + 1.00 * 0.0619                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1831 = 1.56 * 0.50 * 5.3025 + 1.00 * 0.0513                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1282      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1725      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1790 = 0.22 * 1.00 * 5.3025 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1636 = 0.22 * 1.00 * 5.2388 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.440)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.84   13.00    None  None   None       |
|    all(noH): 2823   0      0.00    92.84   13.00    None  None   None       |
|    Sol.    : 438    0      2.78    80.56   35.95    None  None   None       |
|    Mac.    : 2385   0      0.00    92.84   8.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.284: 1703   |   5:    46.420 -  55.704:   89        |
|      1:     9.284 -  18.568:  582   |   6:    55.704 -  64.988:   40        |
|      2:    18.568 -  27.852:  151   |   7:    64.988 -  74.272:    9        |
|      3:    27.852 -  37.136:  131   |   8:    74.272 -  83.556:    3        |
|      4:    37.136 -  46.420:  113   |   9:    83.556 -  92.840:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1260 r_free = 0.1675             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1259 r_free = 0.1676             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1676   ksol= 0.33   Bsol= 33.25   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,1.89,2.79,0.00,0.00,0.00); trace/3= 2.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.223204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1676   ksol= 0.33   Bsol= 33.25   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,1.73,2.71,0.00,0.00,0.00); trace/3= 2.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.223082                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.591376              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.974  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.772734              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.585  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2195 = 1.59 * 0.50 * 5.2384 + 1.00 * 0.0513                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1833 = 1.59 * 0.50 * 5.1900 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2101 = 1.77 * 1.00 * 5.1900 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1593 = 1.77 * 1.00 * 5.1599 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.440)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.99   13.24    None  None   None       |
|    all(noH): 2823   0      0.00    96.99   13.24    None  None   None       |
|    Sol.    : 438    0      2.20    84.64   37.48    None  None   None       |
|    Mac.    : 2385   0      0.00    96.99   8.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.700: 1747   |   5:    48.497 -  58.197:   88        |
|      1:     9.700 -  19.399:  552   |   6:    58.197 -  67.896:   51        |
|      2:    19.399 -  29.098:  141   |   7:    67.896 -  77.596:   11        |
|      3:    29.098 -  38.798:  126   |   8:    77.596 -  87.295:    4        |
|      4:    38.798 -  48.497:  102   |   9:    87.295 -  96.995:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1613             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1152 r_free = 0.1613             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1613   ksol= 0.33   Bsol= 33.25   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,1.73,2.71,0.00,0.00,0.00); trace/3= 2.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164044                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7015 0.99   1367  152 0.1056 0.1268       5.428      5.5248|
|  2:  4.7015 -  3.7516 0.99   1310  145 0.0884 0.1168       5.459      5.6679|
|  3:  3.7516 -  3.2833 0.99   1274  143 0.1104 0.1447      5.5136      5.8172|
|  4:  3.2833 -  2.9858 0.99   1280  144 0.1270 0.1713      5.4888      5.6607|
|  5:  2.9858 -  2.7733 0.99   1263  138 0.1325 0.1747      5.3357      5.5088|
|  6:  2.7733 -  2.6107 0.99   1265  141 0.1209 0.1767      5.2162      5.4434|
|  7:  2.6107 -  2.4806 0.99   1259  137 0.1306 0.1760      5.1904      5.4337|
|  8:  2.4806 -  2.3730 0.98   1258  140 0.1204 0.1729      5.1101      5.3889|
|  9:  2.3730 -  2.2820 0.98   1242  136 0.1199 0.1720      5.0634      5.2679|
| 10:  2.2820 -  2.2035 1.00   1239  140 0.1101 0.1978      4.9816      5.3067|
| 11:  2.2035 -  2.1348 0.97   1249  142 0.1167 0.1660      4.9668      5.2744|
| 12:  2.1348 -  2.0740 0.97   1232  133 0.1160 0.1861      4.9154      5.2736|
| 13:  2.0740 -  2.0195 0.99   1227  141 0.1129 0.1737      4.8347      5.0657|
| 14:  2.0195 -  1.9704 0.91   1165  127 0.1051 0.1832      4.6933      4.9855|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7015  1367   152  0.94   9.21   0.99     0.96       7337.88|
|  2:  4.7015 -  3.7516  1310   145  0.95   8.00   1.03     1.02       9077.30|
|  3:  3.7516 -  3.2833  1274   143  0.93  11.44   1.05     1.04      10746.18|
|  4:  3.2833 -  2.9858  1280   144  0.92  13.53   1.02     1.02      10422.99|
|  5:  2.9858 -  2.7733  1263   138  0.90  15.51   1.00     0.96       8100.93|
|  6:  2.7733 -  2.6107  1265   141  0.90  15.61   0.99     0.96       7027.60|
|  7:  2.6107 -  2.4806  1259   137  0.90  16.58   1.00     0.97       6599.07|
|  8:  2.4806 -  2.3730  1258   140  0.91  15.54   1.00     0.97       5651.21|
|  9:  2.3730 -  2.2820  1242   136  0.91  15.61   1.01     0.99       5339.34|
| 10:  2.2820 -  2.2035  1239   140  0.91  15.39   1.01     0.97       4583.91|
| 11:  2.2035 -  2.1348  1249   142  0.89  16.85   1.01     0.98       4728.65|
| 12:  2.1348 -  2.0740  1232   133  0.91  15.89   1.02     1.00       4227.56|
| 13:  2.0740 -  2.0195  1227   141  0.90  16.05   1.02     1.01       3663.08|
| 14:  2.0195 -  1.9704  1165   127  0.91  15.32   1.00     0.97       2767.10|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2767.10 max =        10746.18 mean =      6502.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.26|
|phase err.(test): min =        0.00 max =           89.77 mean =        13.79|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1612   ksol= 0.32   Bsol= 37.75   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,-0.28,0.70,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163520                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1612   ksol= 0.32   Bsol= 37.75   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,-0.28,0.70,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163520                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7015 0.99   1367  152 0.1052 0.1263       5.416      5.5201|
|  2:  4.7015 -  3.7516 0.99   1310  145 0.0909 0.1176      5.4742      5.6756|
|  3:  3.7516 -  3.2833 0.99   1274  143 0.1119 0.1436      5.5198      5.8131|
|  4:  3.2833 -  2.9858 0.99   1280  144 0.1271 0.1701      5.4887      5.6533|
|  5:  2.9858 -  2.7733 0.99   1263  138 0.1322 0.1748      5.3354      5.5077|
|  6:  2.7733 -  2.6107 0.99   1265  141 0.1205 0.1775      5.2143      5.4455|
|  7:  2.6107 -  2.4806 0.99   1259  137 0.1305 0.1754      5.1886      5.4303|
|  8:  2.4806 -  2.3730 0.98   1258  140 0.1202 0.1720      5.1076      5.3838|
|  9:  2.3730 -  2.2820 0.98   1242  136 0.1197 0.1716      5.0613      5.2678|
| 10:  2.2820 -  2.2035 1.00   1239  140 0.1098 0.1975      4.9795      5.3048|
| 11:  2.2035 -  2.1348 0.97   1249  142 0.1163 0.1656      4.9647      5.2728|
| 12:  2.1348 -  2.0740 0.97   1232  133 0.1156 0.1866      4.9141      5.2751|
| 13:  2.0740 -  2.0195 0.99   1227  141 0.1125 0.1744      4.8338      5.0657|
| 14:  2.0195 -  1.9704 0.91   1165  127 0.1053 0.1826      4.6916      4.9837|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7015  1367   152  0.94   9.00   0.98     0.96       7222.01|
|  2:  4.7015 -  3.7516  1310   145  0.95   8.08   1.03     1.02       9098.85|
|  3:  3.7516 -  3.2833  1274   143  0.93  11.50   1.05     1.04      10806.29|
|  4:  3.2833 -  2.9858  1280   144  0.92  13.45   1.03     1.02      10349.62|
|  5:  2.9858 -  2.7733  1263   138  0.90  15.51   1.00     0.96       8086.94|
|  6:  2.7733 -  2.6107  1265   141  0.90  15.60   0.99     0.96       7015.58|
|  7:  2.6107 -  2.4806  1259   137  0.90  16.52   1.00     0.97       6566.72|
|  8:  2.4806 -  2.3730  1258   140  0.91  15.47   1.00     0.97       5612.54|
|  9:  2.3730 -  2.2820  1242   136  0.91  15.56   1.01     1.00       5314.76|
| 10:  2.2820 -  2.2035  1239   140  0.91  15.36   1.01     0.97       4566.41|
| 11:  2.2035 -  2.1348  1249   142  0.89  16.82   1.01     0.98       4715.88|
| 12:  2.1348 -  2.0740  1232   133  0.91  15.87   1.02     1.00       4221.48|
| 13:  2.0740 -  2.0195  1227   141  0.90  16.04   1.02     1.01       3659.67|
| 14:  2.0195 -  1.9704  1165   127  0.91  15.28   1.00     0.97       2755.78|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2755.78 max =        10806.29 mean =      6481.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.22|
|phase err.(test): min =        0.00 max =           89.49 mean =        13.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.440)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.03    99.02   15.27    None  None   None       |
|    all(noH): 2823   0      2.03    99.02   15.27    None  None   None       |
|    Sol.    : 438    0      4.23    86.67   39.50    None  None   None       |
|    Mac.    : 2385   0      2.03    99.02   10.82    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:     2.027 -  11.727: 1747   |   5:    50.525 -  60.224:   88        |
|      1:    11.727 -  21.426:  552   |   6:    60.224 -  69.924:   51        |
|      2:    21.426 -  31.126:  141   |   7:    69.924 -  79.623:   11        |
|      3:    31.126 -  40.825:  126   |   8:    79.623 -  89.323:    4        |
|      4:    40.825 -  50.525:  102   |   9:    89.323 -  99.022:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.377 - 5.581
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 304
   mapped sites are within: 0.708 - 5.581

peak=   10.892 closest distance to " CB  VAL A 296 " =    1.541
peak=   10.570 closest distance to " CB  VAL A 230 " =    1.415
peak=    7.037 closest distance to " O   HOH Z 130 " =    1.306
peak=    6.254 closest distance to " O   HOH Z 124 " =    1.834
peak=    6.057 closest distance to " NH2 ARG A  56 " =    2.048
peak=    5.970 closest distance to " CD2 LEU A   5 " =    1.244
peak=    5.766 closest distance to " NE2 GLN A  11 " =    1.190
peak=    5.632 closest distance to " O   HOH Z  65 " =    1.063
peak=    5.610 closest distance to " O   HOH Z 142 " =    2.048
peak=    5.606 closest distance to " CG  LEU A   5 " =    1.128
peak=    5.357 closest distance to " O   HOH Z 236 " =    1.429
peak=    5.306 closest distance to " O   HOH Z   7 " =    1.443
peak=    5.282 closest distance to " O   HOH Z 193 " =    1.734
peak=    5.154 closest distance to " CG  PRO A  54 " =    1.280
peak=    4.996 closest distance to " CB  ARG A 275 " =    0.949
peak=    4.988 closest distance to " CG  PRO A 213 " =    1.266
peak=    4.940 closest distance to " CB  VAL A 230 " =    1.118
peak=    4.903 closest distance to " O   HOH Z 278 " =    1.172
peak=    4.893 closest distance to " CB  PRO A  54 " =    1.017
peak=    4.859 closest distance to " O   HOH Z 126 " =    1.849
peak=    4.859 closest distance to " O   HOH Z 427 " =    2.491
peak=    4.778 closest distance to " CG  LEU A 228 " =    1.090
peak=    4.738 closest distance to " CB  SER A   3 " =    1.318
peak=    4.714 closest distance to " O   HOH Z 209 " =    2.296
peak=    4.703 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.688 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.656 closest distance to " CB  GLN A 223 " =    1.521
peak=    4.639 closest distance to " CG  PRO A 198 " =    1.190
peak=    4.630 closest distance to " O   HOH Z 423 " =    1.531
peak=    4.603 closest distance to " O   HOH Z 424 " =    1.085
peak=    4.560 closest distance to " O   HOH Z 369 " =    2.237
peak=    4.543 closest distance to " O   HOH Z   9 " =    1.275
peak=    4.505 closest distance to " CD2 LEU A 228 " =    1.155
peak=    4.493 closest distance to " O   HOH Z  78 " =    1.657
peak=    4.473 closest distance to " O   HOH Z 316 " =    2.782
peak=    4.463 closest distance to " O   HOH Z 263 " =    1.506
peak=    4.408 closest distance to " O   HOH Z 272 " =    1.851
peak=    4.329 closest distance to " O   HOH Z 298 " =    1.786
peak=    4.302 closest distance to " O   HOH Z 380 " =    1.657
peak=    4.267 closest distance to " O   SER A  87 " =    2.372
peak=    4.253 closest distance to " CB BVAL A  41 " =    1.181
peak=    4.252 closest distance to " CD1AILE A 234 " =    0.921
peak=    4.230 closest distance to " CB  ASN A 148 " =    1.350
peak=    4.221 closest distance to " O   HOH Z  44 " =    1.922
peak=    4.194 closest distance to " O   HOH Z  11 " =    1.631
peak=    4.158 closest distance to " O   HOH Z 203 " =    1.635
peak=    4.149 closest distance to " CB  SER A  63 " =    1.235
peak=    4.137 closest distance to " CA  PHE A 283 " =    1.459
peak=    4.137 closest distance to " O   HOH Z 403 " =    1.728
peak=    4.134 closest distance to " NZ  LYS A 117 " =    3.098
peak=    4.119 closest distance to " O   HOH Z 344 " =    1.204
peak=    4.106 closest distance to " O   HOH Z  59 " =    1.655
peak=    4.095 closest distance to " CG2 VAL A 257 " =    0.889
peak=    4.072 closest distance to " O   HOH Z 143 " =    1.093
peak=    4.060 closest distance to " O   HOH Z 250 " =    1.375
peak=    4.050 closest distance to " O   HOH Z  68 " =    2.191
peak=    4.031 closest distance to " O   HOH Z 425 " =    1.395
peak=    4.026 closest distance to " O   HOH Z 405 " =    1.443
peak=    4.025 closest distance to " CB  VAL A 265 " =    1.248
peak=    4.019 closest distance to " O   HOH Z 411 " =    3.613
peak=    4.009 closest distance to " O   HOH Z 389 " =    1.321
peak=    4.007 closest distance to " O   HOH Z 145 " =    1.512
peak=    4.007 closest distance to " O   HOH Z  93 " =    2.255
peak=    3.989 closest distance to " O   HOH Z 130 " =    2.207
peak=    3.981 closest distance to " NH1BARG A 145 " =    1.486
peak=    3.977 closest distance to " CB  ARG A  79 " =    1.378
peak=    3.969 closest distance to " CG  GLN A  11 " =    2.133
peak=    3.969 closest distance to " CB  TRP A 179 " =    1.270
peak=    3.955 closest distance to " O   HOH Z 287 " =    1.594
peak=    3.954 closest distance to " CB  GLU A 152 " =    1.193
peak=    3.933 closest distance to " CB  VAL A 202 " =    1.728
peak=    3.919 closest distance to " O   PRO A 198 " =    1.254
peak=    3.886 closest distance to " O   HOH Z 419 " =    2.005
peak=    3.886 closest distance to " CB  SER A 216 " =    0.878
peak=    3.879 closest distance to " CA  ASN A 127 " =    1.034
peak=    3.866 closest distance to " O   HOH Z 346 " =    1.554
peak=    3.863 closest distance to " O   HOH Z 260 " =    1.155
peak=    3.861 closest distance to " OD1 ASN A  69 " =    2.595
peak=    3.854 closest distance to " O   HOH Z 227 " =    1.834
peak=    3.849 closest distance to " O   HOH Z 189 " =    2.555
peak=    3.848 closest distance to " O   HOH Z 371 " =    2.837
peak=    3.842 closest distance to " O   HOH Z  61 " =    1.553
peak=    3.837 closest distance to " CB  ARG A 139 " =    1.048
peak=    3.828 closest distance to " O   HOH Z 123 " =    1.178
peak=    3.815 closest distance to " O   HOH Z 117 " =    1.952
peak=    3.815 closest distance to " O   HOH Z 303 " =    2.242
peak=    3.813 closest distance to " O   HOH Z 234 " =    3.421
peak=    3.799 closest distance to " N   PHE A 130 " =    1.323
peak=    3.797 closest distance to " O   HOH Z 137 " =    1.578
peak=    3.787 closest distance to " O   HOH Z 193 " =    1.856
peak=    3.786 closest distance to " CG  PRO A 243 " =    1.159
peak=    3.785 closest distance to " CE AMET A  47 " =    1.321
peak=    3.781 closest distance to " CB  TYR A 169 " =    0.990
peak=    3.780 closest distance to " CB  LEU A 255 " =    0.806
peak=    3.776 closest distance to " O   PRO A 198 " =    1.572
peak=    3.773 closest distance to " O   HOH Z 284 " =    1.621
peak=    3.762 closest distance to " CA  TYR A  30 " =    1.008
peak=    3.760 closest distance to " O   HOH Z 422 " =    2.351
peak=    3.750 closest distance to " OG  SER A  62 " =    2.997
peak=    3.745 closest distance to " O   HOH Z 108 " =    2.081
peak=    3.723 closest distance to " O   HOH Z 345 " =    3.227
peak=    3.720 closest distance to " O   HOH Z 371 " =    1.703
peak=    3.709 closest distance to " O   HOH Z 272 " =    2.269
peak=    3.706 closest distance to " CG  LEU A 167 " =    1.171
peak=    3.702 closest distance to " O   HOH Z  71 " =    1.415
peak=    3.692 closest distance to " CG1BVAL A  72 " =    1.249
peak=    3.692 closest distance to " CB  TRP A 266 " =    1.060
peak=    3.689 closest distance to " O   HOH Z 112 " =    1.129
peak=    3.687 closest distance to " CB  THR A 157 " =    1.006
peak=    3.683 closest distance to " CB  GLU A 277 " =    3.443
peak=    3.678 closest distance to " NH1 ARG A  14 " =    0.952
peak=    3.675 closest distance to " CG2 THR A 221 " =    1.302
peak=    3.674 closest distance to " O   HOH Z 146 " =    1.668
peak=    3.671 closest distance to " O   HOH Z  63 " =    1.180
peak=    3.671 closest distance to " O   HOH Z  85 " =    1.320
peak=    3.637 closest distance to " O   HOH Z 202 " =    1.038
peak=    3.631 closest distance to " O   HOH Z 423 " =    1.635
peak=    3.628 closest distance to " CZ AARG A 102 " =    1.805
peak=    3.625 closest distance to " CD  GLN A 194 " =    1.379
peak=    3.612 closest distance to " O   HOH Z 222 " =    2.223
peak=    3.608 closest distance to " O   HOH Z  22 " =    2.149
peak=    3.606 closest distance to " CB  ASN A 148 " =    1.884
peak=    3.595 closest distance to " OD2 ASP A 286 " =    2.548
peak=    3.590 closest distance to " O   HOH Z  55 " =    2.108
peak=    3.589 closest distance to " O   HOH Z 147 " =    1.380
peak=    3.581 closest distance to " CD  ARG A 269 " =    1.093
peak=    3.579 closest distance to " O   HOH Z 303 " =    1.638
peak=    3.576 closest distance to " CA  LYS A 290 " =    1.292
peak=    3.572 closest distance to " CG  GLN A  88 " =    1.059
peak=    3.563 closest distance to " O   HOH Z  43 " =    1.826
peak=    3.558 closest distance to " O   HOH Z 130 " =    1.843
peak=    3.553 closest distance to " CE3 TRP A 274 " =    2.320
peak=    3.552 closest distance to " CB  GLN A  88 " =    1.277
peak=    3.551 closest distance to " O   HOH Z 227 " =    2.231
peak=    3.548 closest distance to " N   ARG A 156 " =    1.301
peak=    3.545 closest distance to " O   HOH Z 344 " =    2.765
peak=    3.540 closest distance to " O   HOH Z 366 " =    2.765
peak=    3.540 closest distance to " O   HOH Z 359 " =    1.169
peak=    3.535 closest distance to " O   HOH Z 368 " =    3.637
peak=    3.535 closest distance to " NH2BARG A 145 " =    1.986
peak=    3.530 closest distance to " O   HOH Z 427 " =    1.408
peak=    3.524 closest distance to " O   HOH Z 196 " =    1.547
peak=    3.516 closest distance to " CG1 ILE A  33 " =    1.352
peak=    3.506 closest distance to " O   HOH Z 383 " =    2.206
peak=    3.505 closest distance to " OG BSER A 164 " =    2.227
peak=    3.505 closest distance to " CD  PRO A 243 " =    1.438
peak=    3.491 closest distance to " O   HOH Z   9 " =    1.881
peak=    3.491 closest distance to " CB  SER A 276 " =    1.080
peak=    3.491 closest distance to " CA  ILE A 234 " =    0.979
peak=    3.487 closest distance to " O   HOH Z  61 " =    1.553
peak=    3.486 closest distance to " CB  ALA A   1 " =    1.025
peak=    3.486 closest distance to " NE1 TRP A 274 " =    0.974
peak=    3.475 closest distance to " C   ALA A 299 " =    1.005
peak=    3.468 closest distance to " NH1AARG A 145 " =    1.085
peak=    3.467 closest distance to " CB  GLU A 128 " =    1.045
peak=    3.460 closest distance to " CB  SER A  26 " =    1.535
peak=    3.457 closest distance to " ND2 ASN A 187 " =    1.675
peak=    3.456 closest distance to " CB  VAL A 126 " =    1.194
peak=    3.454 closest distance to " O   HOH Z  39 " =    1.167
peak=    3.453 closest distance to " O   HOH Z 148 " =    1.597
peak=    3.451 closest distance to " N   ASN A  39 " =    1.100
peak=    3.447 closest distance to " CG1 VAL A 153 " =    0.915
peak=    3.442 closest distance to " O   HOH Z 132 " =    1.197
peak=    3.441 closest distance to " CB  TYR A  30 " =    1.626
peak=    3.440 closest distance to " CG  LEU A 281 " =    0.980
peak=    3.439 closest distance to " O   HOH Z  59 " =    2.007
peak=    3.436 closest distance to " O   HOH Z 406 " =    1.556
peak=    3.431 closest distance to " O   HOH Z 357 " =    1.924
peak=    3.431 closest distance to " O   HOH Z 119 " =    1.528
peak=    3.429 closest distance to " O   HOH Z 366 " =    3.221
peak=    3.426 closest distance to " CG AARG A 275 " =    1.075
peak=    3.424 closest distance to " CA  LEU A 101 " =    1.419
peak=    3.421 closest distance to " O   HOH Z 368 " =    2.029
peak=    3.420 closest distance to " O   HOH Z 276 " =    1.239
peak=    3.418 closest distance to " O   HOH Z  89 " =    1.624
peak=    3.417 closest distance to " O   HOH Z 425 " =    1.962
peak=    3.416 closest distance to " O   HOH Z  58 " =    1.626
peak=    3.415 closest distance to " N   GLN A 278 " =    1.058
peak=    3.413 closest distance to " OE1 GLU A   2 " =    2.071
peak=    3.408 closest distance to " O   HOH Z  30 " =    1.425
peak=    3.406 closest distance to " CD2 LEU A 297 " =    0.999
peak=    3.404 closest distance to " O   HOH Z  88 " =    2.562
peak=    3.402 closest distance to " NE  ARG A  56 " =    3.425
peak=    3.399 closest distance to " O   HOH Z  48 " =    1.633
peak=    3.394 closest distance to " O   HOH Z   1 " =    1.541
peak=    3.393 closest distance to " O   HOH Z 106 " =    2.508
peak=    3.389 closest distance to " ND2 ASN A 110 " =    1.648
peak=    3.387 closest distance to " O   HOH Z 222 " =    2.267
peak=    3.385 closest distance to " CA  ASN A 215 " =    1.111
peak=    3.377 closest distance to " CB  HIS A 108 " =    0.863
peak=    3.372 closest distance to " O   HOH Z 118 " =    1.526
peak=    3.371 closest distance to " O   HOH Z 180 " =    2.094
peak=    3.371 closest distance to " O   HOH Z 281 " =    1.720
peak=    3.370 closest distance to " CB  ASN A 142 " =    1.061
peak=    3.368 closest distance to " O   HOH Z 392 " =    1.267
peak=    3.365 closest distance to " O   HOH Z 209 " =    2.313
peak=    3.361 closest distance to " CB  SER A 273 " =    0.805
peak=    3.358 closest distance to " OG1 THR A 294 " =    2.361
peak=    3.351 closest distance to " NH1 ARG A 138 " =    1.074
peak=    3.349 closest distance to " NZ  LYS A 117 " =    1.100
peak=    3.348 closest distance to " CB  ALA A 291 " =    1.422
peak=    3.346 closest distance to " O   HOH Z 389 " =    2.922
peak=    3.343 closest distance to " CA  ALA A 158 " =    1.208
peak=    3.340 closest distance to " CB  ILE A 234 " =    0.942
peak=    3.339 closest distance to " NE2 GLN A  58 " =    3.171
peak=    3.338 closest distance to " CE1 TYR A 186 " =    1.255
peak=    3.330 closest distance to " O   HOH Z 284 " =    2.765
peak=    3.329 closest distance to " O   HOH Z 128 " =    1.963
peak=    3.322 closest distance to " O   HOH Z 244 " =    1.591
peak=    3.321 closest distance to " N   VAL A 257 " =    1.646
peak=    3.318 closest distance to " OG ASER A 134 " =    1.488
peak=    3.315 closest distance to " CA  ALA A  51 " =    1.015
peak=    3.314 closest distance to " CG  GLN A  89 " =    1.375
peak=    3.312 closest distance to " O   HOH Z 410 " =    1.457
peak=    3.309 closest distance to " O   HOH Z 423 " =    1.286
peak=    3.309 closest distance to " O   HOH Z  10 " =    1.640
peak=    3.308 closest distance to " SD  MET A 185 " =    1.479
peak=    3.301 closest distance to " CE  MET A  93 " =    1.524
peak=    3.300 closest distance to " CB  ALA A 248 " =    1.395
peak=    3.296 closest distance to " CA  ALA A  21 " =    1.202
peak=    3.292 closest distance to " O   HOH Z 132 " =    2.249
peak=    3.289 closest distance to " O   HOH Z 118 " =    1.672
peak=    3.282 closest distance to " O   HOH Z 108 " =    1.043
peak=    3.281 closest distance to " O   GLN A  58 " =    1.420
peak=    3.281 closest distance to " CB  LYS A 117 " =    1.193
peak=    3.280 closest distance to " CB  ARG A 190 " =    1.764
peak=    3.278 closest distance to " O   HOH Z 134 " =    1.357
peak=    3.271 closest distance to " CG1BVAL A 121 " =    0.955
peak=    3.271 closest distance to " O   HOH Z 424 " =    2.429
peak=    3.270 closest distance to " CG1AVAL A 121 " =    0.848
peak=    3.269 closest distance to " CA  ASN A 217 " =    1.187
peak=    3.268 closest distance to " O   HOH Z 181 " =    2.115
peak=    3.263 closest distance to " O   HOH Z 153 " =    3.602
peak=    3.258 closest distance to " CB  PRO A 198 " =    0.992
peak=    3.257 closest distance to " O   HOH Z  80 " =    2.104
peak=    3.253 closest distance to " O   HOH Z 374 " =    2.409
peak=    3.252 closest distance to " NH2AARG A 190 " =    1.770
peak=    3.251 closest distance to " OE2 GLU A   2 " =    1.809
peak=    3.250 closest distance to " O   HOH Z 257 " =    2.325
peak=    3.247 closest distance to " O   HOH Z 151 " =    1.580
peak=    3.244 closest distance to " CB  GLN A 278 " =    0.861
peak=    3.242 closest distance to " O   HOH Z 261 " =    1.546
peak=    3.242 closest distance to " N   TYR A  15 " =    1.054
peak=    3.240 closest distance to " CE  LYS A  76 " =    0.894
peak=    3.239 closest distance to " O   HOH Z  64 " =    2.005
peak=    3.239 closest distance to " CD1 ILE A  33 " =    1.676
peak=    3.238 closest distance to " C   GLU A 277 " =    1.311
peak=    3.236 closest distance to " CD BLYS A 290 " =    1.204
peak=    3.234 closest distance to " O   HOH Z 220 " =    1.204
peak=    3.231 closest distance to " O   HOH Z 145 " =    1.924
peak=    3.231 closest distance to " O   HOH Z 417 " =    1.736
peak=    3.230 closest distance to " OG BSER A 134 " =    3.066
peak=    3.224 closest distance to " NZ  LYS A  48 " =    1.864
peak=    3.221 closest distance to " O   HOH Z 192 " =    1.554
peak=    3.218 closest distance to " O   HOH Z 213 " =    1.910
peak=    3.217 closest distance to " O   HOH Z 247 " =    1.257
peak=    3.216 closest distance to " O   HOH Z 305 " =    3.269
peak=    3.214 closest distance to " O   HOH Z 353 " =    2.510
peak=    3.212 closest distance to " OG  SER A  62 " =    2.709
peak=    3.210 closest distance to " O   HOH Z 158 " =    2.950
peak=    3.206 closest distance to " O   HOH Z 114 " =    3.979
peak=    3.203 closest distance to " CB  LEU A 300 " =    0.891
peak=    3.198 closest distance to " O   HOH Z 110 " =    1.575
peak=    3.196 closest distance to " O   HOH Z 172 " =    5.581
peak=    3.195 closest distance to " O   HOH Z   1 " =    1.700
peak=    3.177 closest distance to " NH2BARG A 145 " =    1.440
peak=    3.177 closest distance to " O   HOH Z   6 " =    1.966
peak=    3.165 closest distance to " O   HOH Z  43 " =    2.687
peak=    3.164 closest distance to " CG2 ILE A  20 " =    1.706
peak=    3.163 closest distance to " O   HOH Z 368 " =    2.461
peak=    3.162 closest distance to " OG  SER A  22 " =    2.709
peak=    3.156 closest distance to " CE  MET A  40 " =    1.038
peak=    3.151 closest distance to " CA  SER A  87 " =    1.039
peak=    3.150 closest distance to " CB  ALA A 114 " =    1.493
peak=    3.148 closest distance to " O   HOH Z 135 " =    1.853
peak=    3.148 closest distance to " O   HOH Z 193 " =    1.839
peak=    3.147 closest distance to " O   HOH Z 249 " =    1.071
peak=    3.142 closest distance to " CB  MET A  40 " =    0.869
peak=    3.140 closest distance to " CB  TYR A 169 " =    0.905
peak=    3.135 closest distance to " O   HOH Z 358 " =    1.485
peak=    3.132 closest distance to " CG1 ILE A 120 " =    1.332
peak=    3.125 closest distance to " CA  THR A 264 " =    0.780
peak=    3.124 closest distance to " CB  ARG A 138 " =    0.901
peak=    3.124 closest distance to " O   HOH Z 128 " =    2.015
peak=    3.118 closest distance to " O   HOH Z 273 " =    2.839
peak=    3.115 closest distance to " O   HOH Z 245 " =    1.322
peak=    3.113 closest distance to " CA  LEU A 282 " =    1.208
peak=    3.112 closest distance to " O   HOH Z 233 " =    1.622
peak=    3.109 closest distance to " OE2 GLU A  53 " =    2.031
peak=    3.108 closest distance to " CB  ARG A 102 " =    0.799
peak=    3.096 closest distance to " CG1 ILE A 151 " =    1.144
peak=    3.095 closest distance to " O   HOH Z 213 " =    1.647
peak=    3.090 closest distance to " O   HOH Z 128 " =    2.614
peak=    3.089 closest distance to " CD  ARG A 159 " =    0.708
peak=    3.085 closest distance to " O   HOH Z 234 " =    2.097
peak=    3.084 closest distance to " O   HOH Z 148 " =    2.417
peak=    3.084 closest distance to " O   HOH Z 189 " =    4.247
peak=    3.083 closest distance to " CD2 TYR A  30 " =    1.141
peak=    3.061 closest distance to " CA  GLN A 194 " =    1.167
peak=    3.061 closest distance to " CG  ARG A 269 " =    1.402
peak=    3.045 closest distance to " CD1 LEU A   5 " =    1.801
peak=    3.044 closest distance to " CA  TYR A 116 " =    1.575
peak=    3.036 closest distance to " N   GLU A   2 " =    1.309

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 181         
Filter by distance & map next to the model:
   mapped sites are within: 0.726 - 5.959
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 181 from: 181
   mapped sites are within: 0.726 - 5.959

peak=   -4.834 closest distance to " CD  ARG A 156 " =    1.962
peak=   -4.543 closest distance to " CA  GLY A  23 " =    1.972
peak=   -4.438 closest distance to " CG2 VAL A 230 " =    0.726
peak=   -4.362 closest distance to " O   VAL A  67 " =    2.700
peak=   -4.308 closest distance to " CD  ARG A  14 " =    3.198
peak=   -4.299 closest distance to " O   PRO A 198 " =    1.228
peak=   -4.294 closest distance to " CD1 LEU A 255 " =    2.783
peak=   -4.199 closest distance to " NH2 ARG A  79 " =    1.930
peak=   -4.142 closest distance to " CB  ASN A  39 " =    2.210
peak=   -4.128 closest distance to " OG BSER A 134 " =    1.180
peak=   -4.100 closest distance to " C   HIS A 108 " =    1.144
peak=   -4.077 closest distance to " O   HOH Z 191 " =    5.300
peak=   -4.077 closest distance to " CB  ALA A 248 " =    2.049
peak=   -4.054 closest distance to " CB  TYR A  15 " =    2.104
peak=   -3.993 closest distance to " CG2 THR A   4 " =    1.892
peak=   -3.952 closest distance to " O   VAL A  67 " =    2.800
peak=   -3.942 closest distance to " O   HOH Z 266 " =    4.721
peak=   -3.939 closest distance to " O   ALA A 161 " =    1.663
peak=   -3.929 closest distance to " N   GLN A  58 " =    1.815
peak=   -3.908 closest distance to " OD2 ASP A 191 " =    1.331
peak=   -3.897 closest distance to " CA  GLY A 133 " =    1.892
peak=   -3.865 closest distance to " CE2 PHE A 218 " =    2.495
peak=   -3.852 closest distance to " O   HOH Z 388 " =    2.120
peak=   -3.846 closest distance to " O   HOH Z 231 " =    1.860
peak=   -3.821 closest distance to " CG2AVAL A  41 " =    2.914
peak=   -3.815 closest distance to " CA  GLY A  98 " =    1.869
peak=   -3.810 closest distance to " CD1 PHE A  59 " =    1.981
peak=   -3.792 closest distance to " C   ASN A 285 " =    2.143
peak=   -3.786 closest distance to " O   HOH Z 111 " =    4.297
peak=   -3.786 closest distance to " CB  PRO A 243 " =    2.599
peak=   -3.753 closest distance to " O   HOH Z 290 " =    1.095
peak=   -3.718 closest distance to " O   ALA A 292 " =    2.100
peak=   -3.716 closest distance to " O   ALA A  51 " =    1.255
peak=   -3.703 closest distance to " CB  ALA A   7 " =    2.013
peak=   -3.702 closest distance to " O   HOH Z  65 " =    0.961
peak=   -3.700 closest distance to " CE2 TYR A  30 " =    2.846
peak=   -3.692 closest distance to " CD  LYS A 289 " =    2.470
peak=   -3.670 closest distance to " CB  ALA A 100 " =    2.502
peak=   -3.660 closest distance to " CZ  PHE A  59 " =    1.385
peak=   -3.655 closest distance to " O   HOH Z 407 " =    3.046
peak=   -3.647 closest distance to " O   HOH Z 412 " =    5.959
peak=   -3.638 closest distance to " CG2 THR A 178 " =    2.045
peak=   -3.632 closest distance to " OG  SER A   3 " =    1.632
peak=   -3.628 closest distance to " N   HIS A 115 " =    1.973
peak=   -3.607 closest distance to " O   HOH Z 103 " =    1.683
peak=   -3.605 closest distance to " CG  PHE A 283 " =    2.542
peak=   -3.605 closest distance to " C   ASN A 187 " =    1.886
peak=   -3.604 closest distance to " O   PRO A 163 " =    1.857
peak=   -3.601 closest distance to " O   SER A 135 " =    1.502
peak=   -3.589 closest distance to " CG1 VAL A 112 " =    2.807
peak=   -3.589 closest distance to " O   HOH Z  47 " =    1.530
peak=   -3.587 closest distance to " O   HOH Z 102 " =    1.586
peak=   -3.586 closest distance to " O   HOH Z 427 " =    1.447
peak=   -3.577 closest distance to " O   HOH Z 193 " =    1.703
peak=   -3.576 closest distance to " OG ASER A 134 " =    1.062
peak=   -3.544 closest distance to " O   HOH Z 313 " =    1.634
peak=   -3.541 closest distance to " O   HOH Z 389 " =    1.984
peak=   -3.536 closest distance to " ND2 ASN A 187 " =    1.630
peak=   -3.535 closest distance to " OG  SER A 206 " =    1.586
peak=   -3.533 closest distance to " O   HOH Z 348 " =    1.717
peak=   -3.532 closest distance to " N   ALA A 248 " =    1.682
peak=   -3.527 closest distance to " O   HOH Z 351 " =    1.494
peak=   -3.526 closest distance to " CB  ALA A  43 " =    2.223
peak=   -3.525 closest distance to " O   HOH Z 423 " =    2.368
peak=   -3.522 closest distance to " N   THR A 157 " =    1.327
peak=   -3.514 closest distance to " O   GLN A 183 " =    1.228
peak=   -3.506 closest distance to " CB  PRO A 280 " =    2.134
peak=   -3.491 closest distance to " O   SER A  22 " =    2.353
peak=   -3.486 closest distance to " O   ASN A 187 " =    1.487
peak=   -3.485 closest distance to " O   MET A  40 " =    2.656
peak=   -3.481 closest distance to " CD  GLN A  88 " =    0.997
peak=   -3.475 closest distance to " O   HOH Z 185 " =    2.012
peak=   -3.474 closest distance to " O   SER A 146 " =    1.026
peak=   -3.464 closest distance to " O   HOH Z 250 " =    1.397
peak=   -3.446 closest distance to " CB  CYS A 201 " =    2.527
peak=   -3.440 closest distance to " O   HOH Z 198 " =    2.059
peak=   -3.438 closest distance to " O   HOH Z 137 " =    1.463
peak=   -3.431 closest distance to " O   HOH Z 140 " =    1.350
peak=   -3.429 closest distance to " CG  GLN A 223 " =    1.587
peak=   -3.428 closest distance to " O   HOH Z 130 " =    2.178
peak=   -3.424 closest distance to " O   HOH Z 165 " =    2.091
peak=   -3.414 closest distance to " CD1 LEU A 101 " =    2.274
peak=   -3.412 closest distance to " CG  ASP A 231 " =    0.807
peak=   -3.409 closest distance to " CB  ALA A 161 " =    2.513
peak=   -3.405 closest distance to " CD  GLU A 152 " =    2.160
peak=   -3.404 closest distance to " O   HOH Z 377 " =    0.980
peak=   -3.403 closest distance to " O   HOH Z 364 " =    2.510
peak=   -3.401 closest distance to " CB  ASP A 132 " =    2.276
peak=   -3.399 closest distance to " O   HOH Z 166 " =    1.562
peak=   -3.396 closest distance to " O   PRO A 243 " =    2.492
peak=   -3.392 closest distance to " O   GLY A  80 " =    2.451
peak=   -3.392 closest distance to " O   HOH Z  24 " =    1.273
peak=   -3.386 closest distance to " CA  GLY A  35 " =    1.992
peak=   -3.385 closest distance to " CB  ALA A 244 " =    2.110
peak=   -3.382 closest distance to " O   PRO A 198 " =    1.206
peak=   -3.381 closest distance to " CE3 TRP A 274 " =    2.261
peak=   -3.370 closest distance to " CG  TRP A 266 " =    1.834
peak=   -3.360 closest distance to " O   HOH Z 211 " =    1.496
peak=   -3.359 closest distance to " O   HOH Z 426 " =    2.214
peak=   -3.357 closest distance to " O   ALA A   8 " =    1.810
peak=   -3.355 closest distance to " CA  ASN A 127 " =    1.223
peak=   -3.354 closest distance to " O   HOH Z 166 " =    1.696
peak=   -3.349 closest distance to " CB  PHE A 192 " =    1.751
peak=   -3.342 closest distance to " O   HOH Z 131 " =    3.967
peak=   -3.327 closest distance to " CG  GLN A  58 " =    1.111
peak=   -3.327 closest distance to " O   HOH Z 143 " =    1.075
peak=   -3.326 closest distance to " O   PRO A 163 " =    0.953
peak=   -3.322 closest distance to " OE1 GLU A 277 " =    2.163
peak=   -3.322 closest distance to " O   HOH Z 298 " =    1.252
peak=   -3.321 closest distance to " CG2 ILE A 151 " =    2.542
peak=   -3.320 closest distance to " O   HOH Z  63 " =    1.310
peak=   -3.320 closest distance to " O   HOH Z 350 " =    1.937
peak=   -3.316 closest distance to " OXT GLY A 302 " =    2.913
peak=   -3.314 closest distance to " O   GLY A  57 " =    1.359
peak=   -3.312 closest distance to " CA  ASP A  27 " =    2.340
peak=   -3.302 closest distance to " O   HOH Z 385 " =    2.013
peak=   -3.302 closest distance to " O   HOH Z 426 " =    1.639
peak=   -3.289 closest distance to " O   HOH Z  13 " =    1.424
peak=   -3.286 closest distance to " ND2 ASN A  45 " =    1.139
peak=   -3.278 closest distance to " CD2 LEU A 237 " =    2.725
peak=   -3.274 closest distance to " C   GLY A 229 " =    1.258
peak=   -3.268 closest distance to " NE2 GLN A 223 " =    1.581
peak=   -3.268 closest distance to " O   HOH Z 256 " =    1.108
peak=   -3.267 closest distance to " CD2 LEU A   5 " =    1.132
peak=   -3.266 closest distance to " O   HOH Z   9 " =    1.518
peak=   -3.259 closest distance to " O   HOH Z 210 " =    1.923
peak=   -3.256 closest distance to " ND2BASN A 224 " =    1.688
peak=   -3.254 closest distance to " O   HOH Z 364 " =    1.631
peak=   -3.250 closest distance to " OE1 GLN A  88 " =    1.116
peak=   -3.247 closest distance to " O   HOH Z 392 " =    0.782
peak=   -3.241 closest distance to " O   HOH Z 134 " =    2.855
peak=   -3.238 closest distance to " O   HOH Z 231 " =    1.384
peak=   -3.230 closest distance to " OG  SER A  97 " =    2.093
peak=   -3.230 closest distance to " CZ2 TRP A 274 " =    0.886
peak=   -3.228 closest distance to " O   HOH Z 234 " =    3.770
peak=   -3.228 closest distance to " OE2 GLU A 152 " =    1.167
peak=   -3.228 closest distance to " CB  PRO A  90 " =    1.470
peak=   -3.221 closest distance to " C   GLN A 205 " =    1.965
peak=   -3.218 closest distance to " CG  MET A 105 " =    0.873
peak=   -3.216 closest distance to " CB  ASP A 132 " =    2.201
peak=   -3.213 closest distance to " C   ALA A 158 " =    1.276
peak=   -3.205 closest distance to " CG1 VAL A 197 " =    2.261
peak=   -3.205 closest distance to " O   ILE A  49 " =    1.725
peak=   -3.203 closest distance to " C   LEU A 143 " =    1.078
peak=   -3.202 closest distance to " CG1 VAL A 296 " =    2.045
peak=   -3.197 closest distance to " CG  ARG A 219 " =    2.325
peak=   -3.195 closest distance to " O   HOH Z 359 " =    3.431
peak=   -3.195 closest distance to " N   VAL A  72 " =    1.655
peak=   -3.194 closest distance to " CA  GLY A 241 " =    2.130
peak=   -3.194 closest distance to " N   ALA A 226 " =    1.916
peak=   -3.194 closest distance to " OH  TYR A 214 " =    1.193
peak=   -3.192 closest distance to " O   HOH Z  68 " =    1.859
peak=   -3.190 closest distance to " O   HOH Z 435 " =    1.804
peak=   -3.187 closest distance to " CG  PRO A 243 " =    1.355
peak=   -3.182 closest distance to " CB  TYR A 172 " =    2.112
peak=   -3.182 closest distance to " O   HOH Z 158 " =    2.117
peak=   -3.182 closest distance to " ND2 ASN A  60 " =    1.375
peak=   -3.177 closest distance to " O   HOH Z 137 " =    1.731
peak=   -3.175 closest distance to " O   HOH Z 368 " =    2.319
peak=   -3.167 closest distance to " CG  GLU A 277 " =    1.222
peak=   -3.160 closest distance to " CD2 TRP A 150 " =    0.812
peak=   -3.156 closest distance to " O   HOH Z  93 " =    1.474
peak=   -3.145 closest distance to " O   HOH Z 111 " =    1.135
peak=   -3.143 closest distance to " CG2 THR A  42 " =    1.680
peak=   -3.130 closest distance to " N   ALA A   1 " =    1.733
peak=   -3.124 closest distance to " O   HOH Z 175 " =    1.145
peak=   -3.121 closest distance to " CG  GLN A 278 " =    2.079
peak=   -3.121 closest distance to " CD2 TYR A 293 " =    1.936
peak=   -3.111 closest distance to " O   HOH Z 389 " =    1.390
peak=   -3.108 closest distance to " CZ  TYR A 169 " =    1.730
peak=   -3.104 closest distance to " CG  LYS A 193 " =    2.418
peak=   -3.090 closest distance to " N   TYR A 293 " =    2.137
peak=   -3.090 closest distance to " O   HOH Z 359 " =    1.707
peak=   -3.069 closest distance to " O   HOH Z 415 " =    1.480
peak=   -3.065 closest distance to " CZ  ARG A  24 " =    1.699
peak=   -3.061 closest distance to " OD1 ASP A 200 " =    1.273
peak=   -3.060 closest distance to " O   HOH Z  60 " =    2.269
peak=   -3.059 closest distance to " O   ASN A 249 " =    1.483
peak=   -3.054 closest distance to " O   TRP A  70 " =    1.418
peak=   -3.044 closest distance to " O   GLN A 240 " =    1.902
peak=   -3.029 closest distance to " CG  GLU A 152 " =    1.438

================= 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    :  0.4818 0.4726   6.279280e+00   6.269595e+00
   1_bss:  0.4728 0.4598   6.272000e+00   6.257436e+00
   1_xyz:  0.3950 0.4141   6.170961e+00   6.192595e+00
   1_adp:  0.3501 0.3932   6.090420e+00   6.168196e+00
   1_occ:  0.3495 0.3939   6.089792e+00   6.169055e+00
   2_bss:  0.3464 0.3895   6.089543e+00   6.165958e+00
   2_xyz:  0.2448 0.2970   5.804923e+00   5.954915e+00
   2_adp:  0.2150 0.2708   5.696219e+00   5.873958e+00
   2_occ:  0.2144 0.2704   5.695359e+00   5.874095e+00
   3_bss:  0.2125 0.2681   5.690946e+00   5.869101e+00
   3_xyz:  0.1594 0.2085   5.436827e+00   5.648441e+00
   3_adp:  0.1435 0.1940   5.351183e+00   5.576594e+00
   3_occ:  0.1434 0.1939   5.350979e+00   5.576405e+00
   4_bss:  0.1433 0.1940   5.349248e+00   5.574029e+00
   4_xyz:  0.1282 0.1725   5.245783e+00   5.472316e+00
   4_adp:  0.1260 0.1675   5.223456e+00   5.442390e+00
   4_occ:  0.1259 0.1676   5.223204e+00   5.442017e+00
   5_bss:  0.1259 0.1676   5.223082e+00   5.441959e+00
   5_xyz:  0.1172 0.1603   5.169226e+00   5.402681e+00
   5_adp:  0.1152 0.1613   5.164425e+00   5.407642e+00
   5_occ:  0.1152 0.1613   5.164044e+00   5.407009e+00
   5_bss:  0.1155 0.1612   5.163520e+00   5.405584e+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:  0.403  20.000   6.555   9.382   8.049   0.000   0.000   0.000
   1_xyz:  0.403  20.000   6.555   9.382   8.049   0.000   0.000   0.000
   1_adp:  0.403  20.000   6.555   9.382   8.049   0.000   0.000   0.000
   1_occ:  0.403  20.000   6.555   9.382   8.049   0.000   0.000   0.000
   2_bss:  0.357  30.840   3.294   5.119   4.905   0.000   0.000   0.000
   2_xyz:  0.357  30.840   3.294   5.119   4.905   0.000   0.000   0.000
   2_adp:  0.357  30.840   3.294   5.119   4.905   0.000   0.000   0.000
   2_occ:  0.357  30.840   3.294   5.119   4.905   0.000   0.000   0.000
   3_bss:  0.340  30.840   2.161   2.794   3.303   0.000   0.000   0.000
   3_xyz:  0.340  30.840   2.161   2.794   3.303   0.000   0.000   0.000
   3_adp:  0.340  30.840   2.161   2.794   3.303   0.000   0.000   0.000
   3_occ:  0.340  30.840   2.161   2.794   3.303   0.000   0.000   0.000
   4_bss:  0.326  33.250   1.611   1.890   2.786   0.000   0.000   0.000
   4_xyz:  0.326  33.250   1.611   1.890   2.786   0.000   0.000   0.000
   4_adp:  0.326  33.250   1.611   1.890   2.786   0.000   0.000   0.000
   4_occ:  0.326  33.250   1.611   1.890   2.786   0.000   0.000   0.000
   5_bss:  0.326  33.250   1.566   1.735   2.711   0.000   0.000   0.000
   5_xyz:  0.326  33.250   1.566   1.735   2.711   0.000   0.000   0.000
   5_adp:  0.326  33.250   1.566   1.735   2.711   0.000   0.000   0.000
   5_occ:  0.326  33.250   1.566   1.735   2.711   0.000   0.000   0.000
   5_bss:  0.318  37.754  -0.423  -0.281   0.704   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.292 0.4160  0.4884    70327.128
   1_bss:  57.986 0.4182  0.6160    67183.428
   1_xyz:  47.484 0.5509  0.8015    50115.361
   1_adp:  43.302 0.6035  0.9265    45298.988
   1_occ:  43.447 0.6017  0.9228    45406.767
   2_bss:  43.116 0.6055  0.8159    44720.136
   2_xyz:  30.540 0.7516  0.9828    23077.868
   2_adp:  26.554 0.7960  1.0238    18713.548
   2_occ:  26.519 0.7963  1.0234    18688.469
   3_bss:  26.327 0.7980  0.9631    18340.636
   3_xyz:  19.842 0.8630  1.0039    10857.391
   3_adp:  17.997 0.8807  1.0070     9428.783
   3_occ:  17.992 0.8808  1.0067     9418.230
   4_bss:  17.935 0.8812  0.9820     9350.578
   4_xyz:  15.586 0.9019  0.9925     7455.852
   4_adp:  14.889 0.9080  0.9930     7077.130
   4_occ:  14.880 0.9081  0.9929     7066.952
   5_bss:  14.877 0.9081  0.9895     7065.244
   5_xyz:  14.119 0.9141  0.9925     6464.436
   5_adp:  14.220 0.9135  0.9874     6511.769
   5_occ:  14.209 0.9136  0.9873     6502.603
   5_bss:  14.177 0.9138  0.9884     6482.027
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.2901e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.2901e+01
   1_xyz:   1.677  0.013  0.105 18.178  0.006  4.106   1.3746e-01
   1_adp:   1.677  0.013  0.105 18.178  0.006  4.106   1.3746e-01
   1_occ:   1.677  0.013  0.105 18.178  0.006  4.106   1.3746e-01
   2_bss:   1.677  0.013  0.105 18.178  0.006  4.106   1.3746e-01
   2_xyz:   1.249  0.010  0.087 16.085  0.005  4.116   9.6655e-02
   2_adp:   1.249  0.010  0.087 16.085  0.005  4.116   9.6655e-02
   2_occ:   1.249  0.010  0.087 16.085  0.005  4.116   9.6655e-02
   3_bss:   1.249  0.010  0.087 16.085  0.005  4.116   9.6655e-02
   3_xyz:   1.000  0.006  0.072 15.777  0.004  4.107   6.1905e-02
   3_adp:   1.000  0.006  0.072 15.777  0.004  4.107   6.1905e-02
   3_occ:   1.000  0.006  0.072 15.777  0.004  4.107   6.1905e-02
   4_bss:   1.000  0.006  0.072 15.777  0.004  4.107   6.1905e-02
   4_xyz:   0.879  0.004  0.065 15.475  0.003  4.109   5.1285e-02
   4_adp:   0.879  0.004  0.065 15.475  0.003  4.109   5.1285e-02
   4_occ:   0.879  0.004  0.065 15.475  0.003  4.109   5.1285e-02
   5_bss:   0.879  0.004  0.065 15.475  0.003  4.109   5.1285e-02
   5_xyz:   0.912  0.005  0.068 15.355  0.003  4.111   5.3728e-02
   5_adp:   0.912  0.005  0.068 15.355  0.003  4.111   5.3728e-02
   5_occ:   0.912  0.005  0.068 15.355  0.003  4.111   5.3728e-02
   5_bss:   0.912  0.005  0.068 15.355  0.003  4.111   5.3728e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.085   6.8552e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.085   6.8552e+00
   1_xyz:  13.666  0.167  0.447 86.093  0.041  2.267   9.6638e-02
   1_adp:  13.666  0.167  0.447 86.093  0.041  2.267   9.6638e-02
   1_occ:  13.666  0.167  0.447 86.093  0.041  2.267   9.6638e-02
   2_bss:  13.666  0.167  0.447 86.093  0.041  2.267   9.6638e-02
   2_xyz:   8.852  0.130  0.332 83.131  0.042  2.218   1.6858e-01
   2_adp:   8.852  0.130  0.332 83.131  0.042  2.218   1.6858e-01
   2_occ:   8.852  0.130  0.332 83.131  0.042  2.218   1.6858e-01
   3_bss:   8.852  0.130  0.332 83.131  0.042  2.218   1.6858e-01
   3_xyz:   6.672  0.047  0.306 83.598  0.028  2.318   4.9296e-02
   3_adp:   6.672  0.047  0.306 83.598  0.028  2.318   4.9296e-02
   3_occ:   6.672  0.047  0.306 83.598  0.028  2.318   4.9296e-02
   4_bss:   6.672  0.047  0.306 83.598  0.028  2.318   4.9296e-02
   4_xyz:   6.263  0.037  0.253 83.651  0.028  2.333   2.7818e-02
   4_adp:   6.263  0.037  0.253 83.651  0.028  2.333   2.7818e-02
   4_occ:   6.263  0.037  0.253 83.651  0.028  2.333   2.7818e-02
   5_bss:   6.263  0.037  0.253 83.651  0.028  2.333   2.7818e-02
   5_xyz:   6.222  0.038  0.273 84.329  0.030  2.310   3.6967e-02
   5_adp:   6.222  0.038  0.273 84.329  0.030  2.310   3.6967e-02
   5_occ:   6.222  0.038  0.273 84.329  0.030  2.310   3.6967e-02
   5_bss:   6.222  0.038  0.273 84.329  0.030  2.310   3.6967e-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:  93.26   0.00  13.61  93.26   0.00  11.18  91.35   0.00  26.83
   1_occ:  93.26   0.00  13.61  93.26   0.00  11.18  91.35   0.00  26.83
   2_bss:  93.26   0.00  13.61  93.26   0.00  11.18  91.35   0.00  26.83
   2_xyz:  93.26   0.00  13.61  93.26   0.00  11.18  91.35   0.00  26.83
   2_adp:  93.47   0.00  13.18  93.47   0.00   9.68  87.77   0.20  32.24
   2_occ:  93.47   0.00  13.18  93.47   0.00   9.68  87.77   0.20  32.24
   3_bss:  93.47   0.00  13.18  93.47   0.00   9.68  87.77   0.20  32.24
   3_xyz:  93.47   0.00  13.18  93.47   0.00   9.68  87.77   0.20  32.24
   3_adp:  94.38   0.00  13.33  94.38   0.00   9.04  81.90   2.04  36.65
   3_occ:  94.38   0.00  13.33  94.38   0.00   9.04  81.90   2.04  36.65
   4_bss:  94.38   0.00  13.33  94.38   0.00   9.04  81.90   2.04  36.65
   4_xyz:  94.38   0.00  13.33  94.38   0.00   9.04  81.90   2.04  36.65
   4_adp:  92.84   0.00  13.00  92.84   0.00   8.79  80.56   2.78  35.95
   4_occ:  92.84   0.00  13.00  92.84   0.00   8.79  80.56   2.78  35.95
   5_bss:  92.84   0.00  13.00  92.84   0.00   8.79  80.56   2.78  35.95
   5_xyz:  92.84   0.00  13.00  92.84   0.00   8.79  80.56   2.78  35.95
   5_adp:  96.99   0.00  13.24  96.99   0.00   8.79  84.64   2.20  37.48
   5_occ:  96.99   0.00  13.24  96.99   0.00   8.79  84.64   2.20  37.48
   5_bss:  99.02   2.03  15.27  99.02   2.03  10.82  86.67   4.23  39.50
------------------------------------------------------------------------
 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:    1.240    0.013    0.409
   1_adp:    1.240    0.013    0.409
   1_occ:    1.240    0.013    0.409
   2_bss:    1.240    0.013    0.409
   2_xyz:    1.460    0.022    0.612
   2_adp:    1.460    0.022    0.612
   2_occ:    1.460    0.022    0.612
   3_bss:    1.460    0.022    0.612
   3_xyz:    1.565    0.043    0.675
   3_adp:    1.565    0.043    0.675
   3_occ:    1.565    0.043    0.675
   4_bss:    1.565    0.043    0.675
   4_xyz:    1.734    0.045    0.709
   4_adp:    1.734    0.045    0.709
   4_occ:    1.734    0.045    0.709
   5_bss:    1.734    0.045    0.709
   5_xyz:    1.764    0.048    0.726
   5_adp:    1.764    0.048    0.726
   5_occ:    1.764    0.048    0.726
   5_bss:    1.764    0.048    0.726
------------------------------------------------------------------------

CPU time actual refinement: 349.74


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_387/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_387/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_387/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_387/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_387/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.59 
  Macro-tasks:
    bulk solvent and scale       = 41.20  
    individual site refinement   = 152.80 
    weights calculation          = 31.75  
    collect and process          = 6.66   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 232.55 
  Micro-tasks:
    mask                            = 2.38   
    f_calc                          = 108.59 
    alpha_beta                      = 8.50   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 121.39 
    fmodel                         = 7.70   
    r_factors                      = 0.13   
    phase_errors                   = 10.57  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 260.76 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.796 micro seconds
Total CPU time: 6.06 minutes
from_scatterers_fft:    669 calls, 108.27 s
gradients_fft:          615 calls, 106.94 s

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

# Date 2008-01-16 Time 01:27:45 PST -0800 (1200475665.25 s)
Start R-work = 0.4818, R-free = 0.4726 (no bulk solvent and anisotropic scale)
Final R-work = 0.1319, R-free = 0.1776 (no bulk solvent and anisotropic scale)

Start R-work = 0.4728, R-free = 0.4598
Final R-work = 0.1155, R-free = 0.1612