# Date 2008-01-16 Time 02:57:58 PST -0800 (1200481078.61 s)
#phil __OFF__

Command line arguments: "../1053.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6025
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1053

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.3993, 87.6859, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.02158
Completeness in resolution range: 0.978325
Completeness with d_max=infinity: 0.975256

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2189
                             d_min =   2.0216

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.02158
Completeness in resolution range: 0.978325
Completeness with d_max=infinity: 0.975256

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2193 -  4.3252 [2100/2124]  1890   210  10.0%
  bin  2:  4.3252 -  3.4461 [2028/2048]  1824   204  10.1%
  bin  3:  3.4461 -  3.0144 [1993/2012]  1795   198   9.9%
  bin  4:  3.0144 -  2.7405 [1962/1992]  1764   198  10.1%
  bin  5:  2.7405 -  2.5450 [1978/1997]  1783   195   9.9%
  bin  6:  2.5450 -  2.3956 [1955/1980]  1758   197  10.1%
  bin  7:  2.3956 -  2.2760 [1942/1970]  1747   195  10.0%
  bin  8:  2.2760 -  2.1773 [1932/1968]  1739   193  10.0%
  bin  9:  2.1773 -  2.0937 [1913/1955]  1722   191  10.0%
  bin 10:  2.0937 -  2.0216 [1786/1977]  1608   178  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1053/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:
        1.74 -     2.37: 7
        2.37 -     3.00: 1907
        3.00 -     3.64: 4496
        3.64 -     4.27: 8920
        4.27 -     4.90: 12432
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.740 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.282 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27757 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_1053/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1053/model_refine_001.geo

CPU time processing inputs: 9.44


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.3993 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4717   r_free= 0.4596   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.270742                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8238 0.99   1374  152 0.3849 0.3544      6.5752      6.4733|
|  2:  4.8238 -  3.8492 0.99   1303  146 0.3804 0.4080      6.7573      6.8509|
|  3:  3.8492 -  3.3686 0.99   1287  144 0.4270 0.4109      6.6691      6.6477|
|  4:  3.3686 -  3.0634 0.99   1284  142 0.4590 0.4014      6.5328      6.4243|
|  5:  3.0634 -  2.8453 0.99   1267  139 0.4910 0.4668      6.3693      6.3845|
|  6:  2.8453 -  2.6785 0.99   1272  143 0.5095 0.5461      6.2918      6.2188|
|  7:  2.6785 -  2.5450 0.99   1269  139 0.5055 0.4694      6.2317      6.1948|
|  8:  2.5450 -  2.4347 0.98   1248  141 0.5172 0.4644      6.1968      6.1689|
|  9:  2.4347 -  2.3413 0.98   1251  138 0.5141 0.5696      6.1206      6.1571|
| 10:  2.3413 -  2.2608 1.00   1241  141 0.5293 0.5117      6.1265      6.1346|
| 11:  2.2608 -  2.1903 0.97   1254  135 0.5094 0.4997      6.0346      6.0701|
| 12:  2.1903 -  2.1279 0.98   1242  140 0.5225 0.5131      5.9992      6.0267|
| 13:  2.1279 -  2.0720 0.99   1243  136 0.5264 0.4816      5.8988      5.8592|
| 14:  2.0720 -  2.0216 0.86   1095  123 0.5380 0.5122      5.8609      5.7592|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2193 -  4.8238  1374   152  0.73  32.01   0.79     0.75      62208.26|
|  2:  4.8238 -  3.8492  1303   146  0.73  32.20   0.88     0.77      91990.43|
|  3:  3.8492 -  3.3686  1287   144  0.65  39.60   0.82     0.73      97974.95|
|  4:  3.3686 -  3.0634  1284   142  0.56  46.66   0.80     0.63      88031.07|
|  5:  3.0634 -  2.8453  1267   139  0.49  53.09   0.73     0.55      73166.78|
|  6:  2.8453 -  2.6785  1272   143  0.45  56.34   0.72     0.50      66506.35|
|  7:  2.6785 -  2.5450  1269   139  0.41  58.82   0.71     0.46      61415.24|
|  8:  2.5450 -  2.4347  1248   141  0.38  61.15   0.74     0.44      57777.32|
|  9:  2.4347 -  2.3413  1251   138  0.37  62.39   0.71     0.41      53807.17|
| 10:  2.3413 -  2.2608  1241   141  0.37  62.37   0.72     0.42      49629.61|
| 11:  2.2608 -  2.1903  1254   135  0.37  62.52   0.74     0.43      45099.74|
| 12:  2.1903 -  2.1279  1242   140  0.38  61.72   0.74     0.45      40836.02|
| 13:  2.1279 -  2.0720  1243   136  0.37  62.30   0.72     0.43      34782.10|
| 14:  2.0720 -  2.0216  1095   123  0.37  62.70   0.70     0.38      28452.86|
|alpha:            min =        0.38 max =            0.77 mean =         0.53|
|beta:             min =    28452.86 max =        97974.95 mean =     61393.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.51|
|phase err.(test): min =        0.00 max =           89.91 mean =        53.44|
|-----------------------------------------------------------------------------|

============================== 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 = 12.112690             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.739   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.141513              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.282   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      157 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      677 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1468 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2571 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3826 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4986 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6431 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7617 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.573 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.628 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4766   r_free= 0.4616   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.272792                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4638   r_free= 0.4495   ksol= 0.30   Bsol= 20.00   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.83,8.47,9.97,0.00,0.00,0.00); trace/3= 8.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.265186                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.042415             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.780   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.994478              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.435   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4638      final r-factor (work) = 0.3656          |
| start r-factor (free) = 0.4495      final r-factor (free) = 0.3904          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 89.2178 = 11.04 * 0.50 * 6.2749 + 1.00 * 54.5725                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.1082 = 11.04 * 0.50 * 6.1510 + 1.00 * 0.1473                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3656      final r-factor (work) = 0.3203          |
| start r-factor (free) = 0.3904      final r-factor (free) = 0.3665          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1314 = 0.99 * 1.00 * 6.1510 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0277 = 0.99 * 1.00 * 6.0456 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.61  11.73    None  None   None       |
|    all(noH): 2823   0      0.00    111.61  11.73    None  None   None       |
|    Sol.    : 438    0      0.00    111.61  27.46    None  None   None       |
|    Mac.    : 2385   0      0.00    73.48   8.85     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.161: 1772   |   5:    55.805 -  66.966:   17        |
|      1:    11.161 -  22.322:  642   |   6:    66.966 -  78.127:    7        |
|      2:    22.322 -  33.483:  217   |   7:    78.127 -  89.288:    1        |
|      3:    33.483 -  44.644:  104   |   8:    89.288 - 100.449:    0        |
|      4:    44.644 -  55.805:   62   |   9:   100.449 - 111.610:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3203 r_free = 0.3665             target_work(ml) = 6.017         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3198 r_free = 0.3670             target_work(ml) = 6.016         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3198   r_free= 0.3670   ksol= 0.30   Bsol= 20.00   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.83,8.47,9.97,0.00,0.00,0.00); trace/3= 8.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.016248                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3175   r_free= 0.3612   ksol= 0.33   Bsol= 60.08   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.79,5.51,6.56,0.00,0.00,0.00); trace/3= 5.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.016743                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.092292              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.209   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.539396              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.530  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3175      final r-factor (work) = 0.2317          |
| start r-factor (free) = 0.3612      final r-factor (free) = 0.2777          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5087 = 4.09 * 0.50 * 6.0413 + 1.00 * 0.1473                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1129 = 4.09 * 0.50 * 5.8843 + 1.00 * 0.0728                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2317      final r-factor (work) = 0.2122          |
| start r-factor (free) = 0.2777      final r-factor (free) = 0.2583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1992 = 0.54 * 1.00 * 5.8843 + 1.00 * 0.0253                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1221 = 0.54 * 1.00 * 5.7128 + 1.00 * 0.0406                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.38  12.16    None  None   None       |
|    all(noH): 2823   0      0.00    114.38  12.16    None  None   None       |
|    Sol.    : 438    0      0.00    114.38  33.93    None  None   None       |
|    Mac.    : 2385   0      0.00    75.69   8.16     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.438: 1914   |   5:    57.191 -  68.630:   33        |
|      1:    11.438 -  22.877:  467   |   6:    68.630 -  80.068:    8        |
|      2:    22.877 -  34.315:  187   |   7:    80.068 -  91.506:    1        |
|      3:    34.315 -  45.753:  120   |   8:    91.506 - 102.944:    0        |
|      4:    45.753 -  57.191:   92   |   9:   102.944 - 114.383:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2122 r_free = 0.2583             target_work(ml) = 5.685         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2119 r_free = 0.2585             target_work(ml) = 5.684         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2119   r_free= 0.2585   ksol= 0.33   Bsol= 60.08   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.79,5.51,6.56,0.00,0.00,0.00); trace/3= 5.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.684481                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2111   r_free= 0.2581   ksol= 0.33   Bsol= 70.57   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,3.91,4.84,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.686583                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.701535              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.140  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.800441              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.238   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2111      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2581      final r-factor (free) = 0.1963          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6504 = 3.70 * 0.50 * 5.7151 + 1.00 * 0.0730                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3588 = 3.70 * 0.50 * 5.5565 + 1.00 * 0.0751                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1528      final r-factor (work) = 0.1407          |
| start r-factor (free) = 0.1963      final r-factor (free) = 0.1884          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0250 = 1.80 * 1.00 * 5.5565 + 1.00 * 0.0209                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6956 = 1.80 * 1.00 * 5.3566 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.02  12.44    None  None   None       |
|    all(noH): 2823   0      0.00    113.02  12.44    None  None   None       |
|    Sol.    : 438    0      0.00    113.02  36.42    None  None   None       |
|    Mac.    : 2385   0      0.00    104.92  8.03     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.302: 1927   |   5:    56.509 -  67.811:   45        |
|      1:    11.302 -  22.604:  419   |   6:    67.811 -  79.113:    9        |
|      2:    22.604 -  33.906:  171   |   7:    79.113 -  90.415:    3        |
|      3:    33.906 -  45.207:  147   |   8:    90.415 - 101.716:    0        |
|      4:    45.207 -  56.509:  100   |   9:   101.716 - 113.018:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1407 r_free = 0.1884             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1406 r_free = 0.1885             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1406   r_free= 0.1885   ksol= 0.33   Bsol= 70.57   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,3.91,4.84,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.336979                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1409   r_free= 0.1884   ksol= 0.34   Bsol= 70.57   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,3.29,4.42,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.337413                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.198816              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.214  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.360150              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.984   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1409      final r-factor (work) = 0.1296          |
| start r-factor (free) = 0.1884      final r-factor (free) = 0.1789          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9659 = 2.20 * 0.50 * 5.3582 + 1.00 * 0.0751                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8981 = 2.20 * 0.50 * 5.3027 + 1.00 * 0.0683                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1296      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.1789      final r-factor (free) = 0.1739          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9468 = 0.36 * 1.00 * 5.3027 + 1.00 * 0.0370                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9142 = 0.36 * 1.00 * 5.2689 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.24  12.13    None  None   None       |
|    all(noH): 2823   0      0.00    106.24  12.13    None  None   None       |
|    Sol.    : 438    0      0.40    106.24  35.94    None  None   None       |
|    Mac.    : 2385   0      0.00    75.84   7.76     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 -  10.625: 1927   |   5:    53.123 -  63.747:   55        |
|      1:    10.625 -  21.249:  421   |   6:    63.747 -  74.371:   18        |
|      2:    21.249 -  31.874:  149   |   7:    74.371 -  84.996:    5        |
|      3:    31.874 -  42.498:  131   |   8:    84.996 -  95.620:    0        |
|      4:    42.498 -  53.123:  116   |   9:    95.620 - 106.245:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1275 r_free = 0.1739             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1274 r_free = 0.1737             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1274   r_free= 0.1737   ksol= 0.34   Bsol= 70.57   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,3.29,4.42,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252975                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1274   r_free= 0.1737   ksol= 0.33   Bsol= 65.13   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,3.29,4.42,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252853                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.252554              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.108  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.777604              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.597   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1737      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0021 = 2.25 * 0.50 * 5.2685 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9672 = 2.25 * 0.50 * 5.2307 + 1.00 * 0.0760                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0823 = 0.78 * 1.00 * 5.2307 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0848 = 0.78 * 1.00 * 5.2055 + 1.00 * 0.0370                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.55   12.23    None  None   None       |
|    all(noH): 2823   0      0.00    94.55   12.23    None  None   None       |
|    Sol.    : 438    0      0.75    94.55   36.70    None  None   None       |
|    Mac.    : 2385   0      0.00    82.79   7.74     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 -   9.456: 1820   |   5:    47.277 -  56.733:   95        |
|      1:     9.456 -  18.911:  484   |   6:    56.733 -  66.188:   40        |
|      2:    18.911 -  28.366:  143   |   7:    66.188 -  75.644:   18        |
|      3:    28.366 -  37.822:  122   |   8:    75.644 -  85.099:    8        |
|      4:    37.822 -  47.277:   91   |   9:    85.099 -  94.555:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1202 r_free = 0.1676             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1201 r_free = 0.1676             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1676   ksol= 0.33   Bsol= 65.13   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,3.29,4.42,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.208095                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8238 0.99   1374  152 0.1051 0.1354      5.4286      5.5476|
|  2:  4.8238 -  3.8492 0.99   1303  146 0.0878 0.1140      5.4651      5.6618|
|  3:  3.8492 -  3.3686 0.99   1287  144 0.1103 0.1529      5.5193      5.8533|
|  4:  3.3686 -  3.0634 0.99   1284  142 0.1260 0.1674      5.4923      5.6738|
|  5:  3.0634 -  2.8453 0.99   1267  139 0.1450 0.1791      5.4166      5.5811|
|  6:  2.8453 -  2.6785 0.99   1272  143 0.1332 0.2171      5.2994      5.6038|
|  7:  2.6785 -  2.5450 0.99   1269  139 0.1402 0.1753      5.2543      5.4156|
|  8:  2.5450 -  2.4347 0.98   1248  141 0.1276 0.1808      5.1615      5.4354|
|  9:  2.4347 -  2.3413 0.98   1251  138 0.1238 0.1897       5.104      5.3324|
| 10:  2.3413 -  2.2608 1.00   1241  141 0.1245 0.1920      5.0587      5.3246|
| 11:  2.2608 -  2.1903 0.97   1254  135 0.1269 0.1810       5.024      5.2686|
| 12:  2.1903 -  2.1279 0.98   1242  140 0.1242 0.1920      4.9596      5.3184|
| 13:  2.1279 -  2.0720 0.99   1243  136 0.1238 0.1738      4.8713      5.0885|
| 14:  2.0720 -  2.0216 0.86   1095  123 0.1147 0.1904      4.7421      5.0342|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2193 -  4.8238  1374   152  0.94   9.58   0.97     0.94       7871.72|
|  2:  4.8238 -  3.8492  1303   146  0.95   8.32   1.00     0.98       9513.64|
|  3:  3.8492 -  3.3686  1287   144  0.93  11.69   1.01     1.01      11236.66|
|  4:  3.3686 -  3.0634  1284   142  0.92  13.90   1.00     0.98      10926.14|
|  5:  3.0634 -  2.8453  1267   139  0.89  17.09   0.99     0.97       9750.54|
|  6:  2.8453 -  2.6785  1272   143  0.89  17.39   0.98     0.95       8397.53|
|  7:  2.6785 -  2.5450  1269   139  0.89  17.35   0.98     0.95       7352.25|
|  8:  2.5450 -  2.4347  1248   141  0.90  16.48   0.98     0.95       6333.16|
|  9:  2.4347 -  2.3413  1251   138  0.90  16.67   0.99     0.95       5812.03|
| 10:  2.3413 -  2.2608  1241   141  0.89  16.86   0.99     0.94       5199.53|
| 11:  2.2608 -  2.1903  1254   135  0.89  17.48   0.98     0.94       5053.45|
| 12:  2.1903 -  2.1279  1242   140  0.90  16.69   0.99     0.97       4569.88|
| 13:  2.1279 -  2.0720  1243   136  0.90  16.94   0.98     0.96       3862.47|
| 14:  2.0720 -  2.0216  1095   123  0.91  15.78   0.96     0.91       2876.84|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2876.84 max =        11236.66 mean =      7127.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.09|
|phase err.(test): min =        0.00 max =           89.84 mean =        14.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1676   ksol= 0.33   Bsol= 68.75   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.31,0.88,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.208044                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1676   ksol= 0.33   Bsol= 68.75   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.31,0.88,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.208044                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8238 0.99   1374  152 0.1051 0.1354      5.4288       5.548|
|  2:  4.8238 -  3.8492 0.99   1303  146 0.0878 0.1140      5.4654      5.6621|
|  3:  3.8492 -  3.3686 0.99   1287  144 0.1103 0.1530      5.5196      5.8536|
|  4:  3.3686 -  3.0634 0.99   1284  142 0.1260 0.1674      5.4923       5.674|
|  5:  3.0634 -  2.8453 0.99   1267  139 0.1451 0.1791      5.4164      5.5807|
|  6:  2.8453 -  2.6785 0.99   1272  143 0.1332 0.2170      5.2991      5.6033|
|  7:  2.6785 -  2.5450 0.99   1269  139 0.1402 0.1755      5.2542      5.4158|
|  8:  2.5450 -  2.4347 0.98   1248  141 0.1276 0.1808      5.1615      5.4353|
|  9:  2.4347 -  2.3413 0.98   1251  138 0.1238 0.1896      5.1039      5.3319|
| 10:  2.3413 -  2.2608 1.00   1241  141 0.1245 0.1921      5.0586      5.3252|
| 11:  2.2608 -  2.1903 0.97   1254  135 0.1269 0.1809      5.0238      5.2685|
| 12:  2.1903 -  2.1279 0.98   1242  140 0.1242 0.1919      4.9595      5.3181|
| 13:  2.1279 -  2.0720 0.99   1243  136 0.1238 0.1738      4.8712      5.0884|
| 14:  2.0720 -  2.0216 0.86   1095  123 0.1147 0.1902      4.7417      5.0336|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2193 -  4.8238  1374   152  0.94   9.59   0.97     0.94       7877.44|
|  2:  4.8238 -  3.8492  1303   146  0.95   8.33   1.00     0.98       9519.94|
|  3:  3.8492 -  3.3686  1287   144  0.93  11.70   1.02     1.01      11243.69|
|  4:  3.3686 -  3.0634  1284   142  0.92  13.90   1.00     0.98      10924.48|
|  5:  3.0634 -  2.8453  1267   139  0.89  17.08   0.99     0.97       9744.94|
|  6:  2.8453 -  2.6785  1272   143  0.89  17.38   0.98     0.95       8393.11|
|  7:  2.6785 -  2.5450  1269   139  0.89  17.34   0.98     0.96       7349.61|
|  8:  2.5450 -  2.4347  1248   141  0.90  16.47   0.98     0.95       6330.51|
|  9:  2.4347 -  2.3413  1251   138  0.90  16.67   1.00     0.95       5812.47|
| 10:  2.3413 -  2.2608  1241   141  0.89  16.86   0.99     0.94       5197.23|
| 11:  2.2608 -  2.1903  1254   135  0.89  17.48   0.99     0.94       5054.36|
| 12:  2.1903 -  2.1279  1242   140  0.90  16.69   1.00     0.98       4568.58|
| 13:  2.1279 -  2.0720  1243   136  0.90  16.94   0.98     0.96       3860.36|
| 14:  2.0720 -  2.0216  1095   123  0.91  15.77   0.96     0.92       2872.87|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2872.87 max =        11243.69 mean =      7127.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.09|
|phase err.(test): min =        0.00 max =           89.84 mean =        14.45|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.62    98.17   15.85    None  None   None       |
|    all(noH): 2823   0      3.62    98.17   15.85    None  None   None       |
|    Sol.    : 438    0      4.37    98.17   40.32    None  None   None       |
|    Mac.    : 2385   0      3.62    86.41   11.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.620 -  13.076: 1820   |   5:    50.898 -  60.353:   95        |
|      1:    13.076 -  22.531:  484   |   6:    60.353 -  69.809:   40        |
|      2:    22.531 -  31.987:  143   |   7:    69.809 -  79.264:   18        |
|      3:    31.987 -  41.442:  122   |   8:    79.264 -  88.719:    8        |
|      4:    41.442 -  50.898:   91   |   9:    88.719 -  98.175:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.318 - 4.881
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 335 from: 346
   mapped sites are within: 0.706 - 4.881

peak=    9.836 closest distance to " CG2 VAL A 230 " =    1.443
peak=    5.916 closest distance to " CG  LEU A   5 " =    1.185
peak=    5.870 closest distance to " CB  GLN A 223 " =    1.445
peak=    5.858 closest distance to " O   HOH Z 111 " =    2.223
peak=    5.286 closest distance to " CG  LEU A 228 " =    1.212
peak=    5.057 closest distance to " CB  VAL A 296 " =    1.077
peak=    4.925 closest distance to " CG2 VAL A 296 " =    1.013
peak=    4.921 closest distance to " CD1AILE A 234 " =    1.046
peak=    4.865 closest distance to " NH1 ARG A 138 " =    1.037
peak=    4.847 closest distance to " CG  PRO A 198 " =    1.269
peak=    4.842 closest distance to " O   HOH Z 232 " =    2.236
peak=    4.772 closest distance to " CB  GLN A 183 " =    1.262
peak=    4.745 closest distance to " CB  VAL A 230 " =    1.256
peak=    4.736 closest distance to " CB  SER A  63 " =    1.274
peak=    4.624 closest distance to " O   HOH Z 369 " =    2.071
peak=    4.594 closest distance to " CZ  PHE A 218 " =    1.112
peak=    4.511 closest distance to " CD2 LEU A   5 " =    1.100
peak=    4.459 closest distance to " O   HOH Z 265 " =    2.105
peak=    4.453 closest distance to " CB  ARG A 190 " =    1.643
peak=    4.425 closest distance to " CG  PRO A 213 " =    1.239
peak=    4.399 closest distance to " O   HOH Z 298 " =    1.986
peak=    4.392 closest distance to " CB  TRP A 266 " =    1.045
peak=    4.391 closest distance to " NE2 GLN A  11 " =    1.090
peak=    4.350 closest distance to " O   HOH Z 425 " =    1.514
peak=    4.293 closest distance to " O   HOH Z 303 " =    2.196
peak=    4.288 closest distance to " CB  ASP A 124 " =    0.773
peak=    4.237 closest distance to " CG1 VAL A 296 " =    1.189
peak=    4.229 closest distance to " O   PRO A 198 " =    1.567
peak=    4.181 closest distance to " O   HOH Z 427 " =    3.177
peak=    4.177 closest distance to " O   SER A  87 " =    2.351
peak=    4.157 closest distance to " O   HOH Z 411 " =    3.758
peak=    4.157 closest distance to " CG2 THR A 221 " =    1.073
peak=    4.145 closest distance to " CD  LYS A 166 " =    1.335
peak=    4.130 closest distance to " O   HOH Z 236 " =    1.997
peak=    4.116 closest distance to " CG  PRO A 243 " =    1.139
peak=    4.094 closest distance to " CD2 LEU A 228 " =    1.249
peak=    4.081 closest distance to " CA  TYR A  30 " =    0.943
peak=    4.078 closest distance to " O   HOH Z 126 " =    1.673
peak=    4.067 closest distance to " CB  ARG A 275 " =    0.915
peak=    4.062 closest distance to " O   HOH Z 184 " =    1.594
peak=    4.061 closest distance to " NH1AARG A 145 " =    1.241
peak=    4.052 closest distance to " O   HOH Z 261 " =    1.794
peak=    4.048 closest distance to " CG  MET A 185 " =    1.326
peak=    4.026 closest distance to " CB  VAL A 202 " =    1.635
peak=    4.015 closest distance to " O   HOH Z 368 " =    2.387
peak=    4.009 closest distance to " CA  ALA A  51 " =    0.973
peak=    4.007 closest distance to " CB  GLU A 128 " =    1.082
peak=    3.980 closest distance to " O   HOH Z 234 " =    3.739
peak=    3.972 closest distance to " CB  ASP A 140 " =    0.995
peak=    3.968 closest distance to " CB  GLU A 277 " =    3.769
peak=    3.968 closest distance to " CA  ALA A 295 " =    1.134
peak=    3.964 closest distance to " O   HOH Z 102 " =    1.415
peak=    3.950 closest distance to " O   HOH Z 359 " =    1.654
peak=    3.912 closest distance to " CB  ASN A 142 " =    0.984
peak=    3.910 closest distance to " OG BSER A 164 " =    2.177
peak=    3.895 closest distance to " CA  ARG A 195 " =    1.223
peak=    3.895 closest distance to " O   HOH Z 247 " =    1.505
peak=    3.891 closest distance to " O   HOH Z  78 " =    1.748
peak=    3.890 closest distance to " CB  ARG A  79 " =    1.449
peak=    3.886 closest distance to " CB  ASN A 148 " =    1.408
peak=    3.885 closest distance to " CD  ARG A  66 " =    2.583
peak=    3.882 closest distance to " CD  ARG A 159 " =    0.779
peak=    3.881 closest distance to " O   HOH Z  19 " =    2.167
peak=    3.852 closest distance to " CD1 LEU A  96 " =    0.749
peak=    3.851 closest distance to " O   HOH Z 126 " =    2.083
peak=    3.843 closest distance to " CB  GLU A 152 " =    1.131
peak=    3.839 closest distance to " O   HOH Z  43 " =    2.017
peak=    3.836 closest distance to " O   HOH Z 142 " =    1.572
peak=    3.833 closest distance to " CB BVAL A  41 " =    1.185
peak=    3.833 closest distance to " O   HOH Z 422 " =    2.681
peak=    3.804 closest distance to " O   ASP A 124 " =    1.156
peak=    3.798 closest distance to " O   HOH Z 158 " =    3.074
peak=    3.798 closest distance to " O   HOH Z  80 " =    1.827
peak=    3.793 closest distance to " O   HOH Z 403 " =    1.702
peak=    3.792 closest distance to " O   HOH Z   4 " =    1.691
peak=    3.790 closest distance to " CB  ALA A   9 " =    1.655
peak=    3.781 closest distance to " O   HOH Z  63 " =    1.853
peak=    3.778 closest distance to " ND2 ASN A 187 " =    1.473
peak=    3.775 closest distance to " O   HOH Z 248 " =    1.510
peak=    3.774 closest distance to " O   MET A 105 " =    1.817
peak=    3.767 closest distance to " OD1 ASN A  69 " =    2.600
peak=    3.757 closest distance to " ND2 ASN A 249 " =    1.894
peak=    3.745 closest distance to " O   HOH Z 214 " =    2.616
peak=    3.740 closest distance to " O   HOH Z 188 " =    3.054
peak=    3.739 closest distance to " CA  ALA A  21 " =    1.248
peak=    3.738 closest distance to " CD2 TRP A 179 " =    1.315
peak=    3.736 closest distance to " O   HOH Z 285 " =    2.626
peak=    3.730 closest distance to " CZ3 TRP A 266 " =    1.138
peak=    3.724 closest distance to " O   HOH Z 227 " =    1.759
peak=    3.710 closest distance to " O   HOH Z 402 " =    1.506
peak=    3.704 closest distance to " O   HOH Z  48 " =    1.707
peak=    3.702 closest distance to " O   HOH Z 272 " =    1.949
peak=    3.685 closest distance to " O   HOH Z 346 " =    1.594
peak=    3.681 closest distance to " CB  PRO A  54 " =    0.767
peak=    3.669 closest distance to " CG1 VAL A 153 " =    0.977
peak=    3.666 closest distance to " CD1 LEU A   5 " =    1.345
peak=    3.660 closest distance to " CB  GLN A  88 " =    1.231
peak=    3.656 closest distance to " CA  SER A  87 " =    0.959
peak=    3.641 closest distance to " O   HOH Z 313 " =    1.767
peak=    3.639 closest distance to " CB  LEU A 143 " =    1.266
peak=    3.624 closest distance to " O   HOH Z 193 " =    2.198
peak=    3.620 closest distance to " CZ  PHE A 192 " =    0.997
peak=    3.619 closest distance to " O   HOH Z 280 " =    2.962
peak=    3.619 closest distance to " CB  GLU A  46 " =    0.944
peak=    3.617 closest distance to " CA  ARG A  36 " =    1.136
peak=    3.615 closest distance to " O   HOH Z 250 " =    1.332
peak=    3.611 closest distance to " CD ALYS A 290 " =    1.072
peak=    3.605 closest distance to " O   HOH Z 437 " =    1.689
peak=    3.603 closest distance to " CB  TRP A 179 " =    1.436
peak=    3.601 closest distance to " O   HOH Z 316 " =    3.174
peak=    3.600 closest distance to " O   ALA A 165 " =    1.423
peak=    3.599 closest distance to " CG2 ILE A 234 " =    0.835
peak=    3.597 closest distance to " CB  GLN A  89 " =    1.147
peak=    3.596 closest distance to " CZ  PHE A  38 " =    1.235
peak=    3.596 closest distance to " OD2 ASP A 298 " =    3.898
peak=    3.594 closest distance to " OG  SER A 276 " =    1.479
peak=    3.585 closest distance to " O   HOH Z 393 " =    3.894
peak=    3.582 closest distance to " O   HOH Z 423 " =    1.737
peak=    3.582 closest distance to " CA  VAL A 125 " =    1.259
peak=    3.580 closest distance to " CD  ARG A 269 " =    0.906
peak=    3.576 closest distance to " N   VAL A 126 " =    1.407
peak=    3.569 closest distance to " CB  ASN A  39 " =    0.855
peak=    3.567 closest distance to " CE  LYS A  76 " =    0.867
peak=    3.557 closest distance to " CA  MET A 105 " =    0.967
peak=    3.557 closest distance to " O   ALA A 158 " =    1.386
peak=    3.551 closest distance to " CB  THR A  82 " =    1.370
peak=    3.544 closest distance to " CG  GLU A  37 " =    0.898
peak=    3.540 closest distance to " O   HOH Z 130 " =    1.080
peak=    3.536 closest distance to " CA  ALA A 291 " =    0.892
peak=    3.533 closest distance to " O   HOH Z 406 " =    1.509
peak=    3.530 closest distance to " CZ3 TRP A  85 " =    1.013
peak=    3.530 closest distance to " O   HOH Z  49 " =    1.130
peak=    3.523 closest distance to " O   HOH Z 163 " =    1.644
peak=    3.522 closest distance to " O  BHOH Z 338 " =    2.297
peak=    3.517 closest distance to " O   HOH Z  40 " =    1.652
peak=    3.512 closest distance to " CA  ILE A 106 " =    0.779
peak=    3.509 closest distance to " O   HOH Z 147 " =    1.709
peak=    3.509 closest distance to " CB  TRP A 150 " =    1.401
peak=    3.508 closest distance to " CA  THR A 264 " =    0.739
peak=    3.505 closest distance to " CA  LEU A 282 " =    1.114
peak=    3.500 closest distance to " CB  LEU A  83 " =    0.736
peak=    3.496 closest distance to " NH1 ARG A  14 " =    0.950
peak=    3.492 closest distance to " CB  SER A   3 " =    1.455
peak=    3.491 closest distance to " CD2 LEU A 297 " =    0.907
peak=    3.490 closest distance to " CB  ALA A 248 " =    1.158
peak=    3.490 closest distance to " CB  SER A 212 " =    1.196
peak=    3.488 closest distance to " CD1 LEU A 300 " =    1.145
peak=    3.486 closest distance to " O   HOH Z 155 " =    3.332
peak=    3.482 closest distance to " CB  PRO A 243 " =    1.199
peak=    3.480 closest distance to " CA  ARG A 139 " =    1.134
peak=    3.479 closest distance to " CE1 TYR A 186 " =    1.223
peak=    3.478 closest distance to " CG1 ILE A  33 " =    1.256
peak=    3.478 closest distance to " CB  VAL A 265 " =    1.319
peak=    3.476 closest distance to " O   HOH Z 353 " =    2.624
peak=    3.472 closest distance to " O   HOH Z 128 " =    1.779
peak=    3.469 closest distance to " O   HOH Z 146 " =    1.448
peak=    3.461 closest distance to " O   HOH Z 273 " =    2.936
peak=    3.460 closest distance to " O   HOH Z  44 " =    2.009
peak=    3.459 closest distance to " O   HOH Z  61 " =    1.610
peak=    3.458 closest distance to " CG1 ILE A  49 " =    1.598
peak=    3.457 closest distance to " CG  PHE A 204 " =    0.895
peak=    3.456 closest distance to " O   HOH Z 383 " =    2.193
peak=    3.455 closest distance to " O   HOH Z  59 " =    2.445
peak=    3.454 closest distance to " CG1 ILE A 151 " =    1.129
peak=    3.451 closest distance to " OG  SER A  22 " =    2.904
peak=    3.448 closest distance to " CB  THR A  31 " =    1.595
peak=    3.445 closest distance to " CG  LEU A 167 " =    1.111
peak=    3.443 closest distance to " NZ  LYS A  48 " =    1.352
peak=    3.437 closest distance to " N   SER A 135 " =    1.477
peak=    3.434 closest distance to " CB  SER A 288 " =    1.378
peak=    3.430 closest distance to " CA  MET A  40 " =    1.242
peak=    3.429 closest distance to " CA  GLU A 152 " =    0.885
peak=    3.428 closest distance to " OD1 ASN A 217 " =    1.570
peak=    3.425 closest distance to " O   HOH Z 180 " =    2.073
peak=    3.424 closest distance to " CD  ARG A  66 " =    2.402
peak=    3.420 closest distance to " CA  ASP A 191 " =    0.894
peak=    3.417 closest distance to " O   HOH Z 326 " =    2.316
peak=    3.415 closest distance to " O   HOH Z 261 " =    1.799
peak=    3.413 closest distance to " CZ3 TRP A 274 " =    4.637
peak=    3.409 closest distance to " CB  ASN A 187 " =    1.140
peak=    3.409 closest distance to " N   PHE A 130 " =    1.244
peak=    3.406 closest distance to " O   HOH Z 201 " =    2.893
peak=    3.404 closest distance to " CB  SER A 273 " =    0.909
peak=    3.403 closest distance to " O   HOH Z 290 " =    1.141
peak=    3.401 closest distance to " O   HOH Z 193 " =    1.749
peak=    3.401 closest distance to " O   PRO A  90 " =    1.418
peak=    3.401 closest distance to " CB  MET A  40 " =    0.785
peak=    3.399 closest distance to " O   ASP A 200 " =    1.665
peak=    3.398 closest distance to " CB  LYS A 117 " =    1.164
peak=    3.396 closest distance to " CB  ALA A 100 " =    1.312
peak=    3.395 closest distance to " N   ASN A  39 " =    1.300
peak=    3.390 closest distance to " O   HOH Z 109 " =    2.712
peak=    3.384 closest distance to " ND1 HIS A  81 " =    1.718
peak=    3.383 closest distance to " CB  ALA A  43 " =    0.929
peak=    3.382 closest distance to " O   HOH Z 213 " =    1.773
peak=    3.379 closest distance to " CB  ALA A 104 " =    0.821
peak=    3.374 closest distance to " CZ3 TRP A  92 " =    1.349
peak=    3.374 closest distance to " CB  MET A  47 " =    1.055
peak=    3.374 closest distance to " O   HOH Z  21 " =    1.731
peak=    3.363 closest distance to " O   HOH Z 251 " =    1.493
peak=    3.362 closest distance to " CB  ALA A 161 " =    0.957
peak=    3.361 closest distance to " O   HOH Z 365 " =    2.921
peak=    3.360 closest distance to " CA  ALA A 160 " =    0.942
peak=    3.359 closest distance to " CA  TYR A 116 " =    1.484
peak=    3.357 closest distance to " NH2 ARG A 156 " =    1.041
peak=    3.356 closest distance to " CG2 VAL A 257 " =    0.869
peak=    3.349 closest distance to " CA  ASN A 215 " =    1.223
peak=    3.346 closest distance to " OG  SER A 245 " =    1.615
peak=    3.345 closest distance to " CG2 ILE A 151 " =    0.787
peak=    3.342 closest distance to " CB  SER A  26 " =    1.876
peak=    3.341 closest distance to " O   GLN A 278 " =    1.345
peak=    3.338 closest distance to " CB  ALA A  34 " =    0.856
peak=    3.331 closest distance to " O   HOH Z 130 " =    2.225
peak=    3.329 closest distance to " O   HOH Z 368 " =    3.513
peak=    3.327 closest distance to " CB  ALA A 242 " =    0.811
peak=    3.325 closest distance to " O   HOH Z  88 " =    3.253
peak=    3.323 closest distance to " CG BARG A 275 " =    1.447
peak=    3.323 closest distance to " O   HOH Z 133 " =    2.471
peak=    3.320 closest distance to " O   HOH Z 371 " =    3.122
peak=    3.318 closest distance to " O   HOH Z 203 " =    1.757
peak=    3.317 closest distance to " CA  GLY A 211 " =    1.361
peak=    3.312 closest distance to " O   ASN A  74 " =    1.520
peak=    3.307 closest distance to " O   HOH Z 193 " =    2.036
peak=    3.302 closest distance to " CG  ARG A 269 " =    1.806
peak=    3.302 closest distance to " O   HOH Z 125 " =    3.812
peak=    3.301 closest distance to " O   HOH Z 293 " =    1.853
peak=    3.300 closest distance to " CA  ALA A 158 " =    1.219
peak=    3.299 closest distance to " O   HOH Z 197 " =    2.679
peak=    3.298 closest distance to " CG  GLN A  88 " =    1.084
peak=    3.298 closest distance to " CB  LEU A 228 " =    1.186
peak=    3.298 closest distance to " CE3 TRP A 150 " =    1.080
peak=    3.296 closest distance to " O   HOH Z 332 " =    1.559
peak=    3.293 closest distance to " O   HOH Z 132 " =    2.753
peak=    3.289 closest distance to " CB  ASN A 110 " =    1.221
peak=    3.288 closest distance to " CG2 THR A 220 " =    0.815
peak=    3.283 closest distance to " CA  GLN A  88 " =    1.332
peak=    3.282 closest distance to " O   HOH Z 435 " =    2.049
peak=    3.278 closest distance to " CB  ALA A 291 " =    1.328
peak=    3.278 closest distance to " CB  ILE A 120 " =    1.353
peak=    3.277 closest distance to " CB  VAL A 268 " =    0.866
peak=    3.275 closest distance to " O   PHE A 192 " =    1.537
peak=    3.274 closest distance to " CA  LYS A 181 " =    1.070
peak=    3.271 closest distance to " O   HOH Z 271 " =    2.647
peak=    3.269 closest distance to " N   GLY A  98 " =    1.198
peak=    3.269 closest distance to " NZ  LYS A 117 " =    3.091
peak=    3.268 closest distance to " CB  GLN A 205 " =    1.111
peak=    3.264 closest distance to " O   HOH Z 313 " =    1.685
peak=    3.262 closest distance to " CA  THR A 221 " =    0.888
peak=    3.258 closest distance to " O   TRP A 274 " =    1.807
peak=    3.250 closest distance to " CG BARG A 102 " =    1.794
peak=    3.247 closest distance to " CG1BVAL A  72 " =    1.717
peak=    3.247 closest distance to " CA  VAL A  41 " =    0.765
peak=    3.244 closest distance to " O   HOH Z   9 " =    1.979
peak=    3.243 closest distance to " CA  SER A  12 " =    1.467
peak=    3.243 closest distance to " O   HOH Z 187 " =    2.401
peak=    3.240 closest distance to " CB  GLN A 103 " =    1.007
peak=    3.239 closest distance to " O   HOH Z 166 " =    3.527
peak=    3.238 closest distance to " CA  ASP A 140 " =    1.307
peak=    3.232 closest distance to " O   HOH Z 391 " =    2.993
peak=    3.231 closest distance to " CA  VAL A 112 " =    1.155
peak=    3.229 closest distance to " O   HOH Z 117 " =    2.112
peak=    3.228 closest distance to " O   HOH Z 295 " =    1.503
peak=    3.228 closest distance to " O   HOH Z 394 " =    1.385
peak=    3.226 closest distance to " CA  ALA A 100 " =    1.048
peak=    3.224 closest distance to " O   HOH Z 298 " =    2.464
peak=    3.224 closest distance to " NE2 HIS A 207 " =    1.194
peak=    3.223 closest distance to " O   HOH Z   9 " =    1.169
peak=    3.220 closest distance to " O   THR A  31 " =    1.544
peak=    3.218 closest distance to " CA  ARG A 156 " =    1.141
peak=    3.217 closest distance to " O   GLN A  88 " =    1.636
peak=    3.213 closest distance to " CA  ASN A 217 " =    1.336
peak=    3.211 closest distance to " O   PRO A 213 " =    1.503
peak=    3.211 closest distance to " O   PHE A  61 " =    1.343
peak=    3.210 closest distance to " N   ALA A 256 " =    1.094
peak=    3.207 closest distance to " O   HOH Z 134 " =    1.339
peak=    3.206 closest distance to " CA  ASP A 124 " =    0.734
peak=    3.206 closest distance to " O   THR A 220 " =    1.220
peak=    3.202 closest distance to " O   HOH Z 305 " =    3.560
peak=    3.200 closest distance to " NH2AARG A 145 " =    1.246
peak=    3.197 closest distance to " CB  SER A  62 " =    0.881
peak=    3.192 closest distance to " CG  MET A 185 " =    0.964
peak=    3.188 closest distance to " O   HOH Z 148 " =    3.216
peak=    3.186 closest distance to " CA  ALA A 154 " =    1.004
peak=    3.185 closest distance to " CD1 LEU A  96 " =    1.337
peak=    3.184 closest distance to " O   HOH Z 148 " =    2.077
peak=    3.183 closest distance to " CD1 LEU A 101 " =    1.125
peak=    3.177 closest distance to " O   HOH Z 256 " =    2.100
peak=    3.176 closest distance to " O   HOH Z 294 " =    1.556
peak=    3.175 closest distance to " N   ASP A 162 " =    1.226
peak=    3.174 closest distance to " O   THR A 182 " =    1.446
peak=    3.173 closest distance to " O   HOH Z  57 " =    1.327
peak=    3.170 closest distance to " CG2 ILE A 106 " =    0.879
peak=    3.159 closest distance to " O   HOH Z 116 " =    1.929
peak=    3.158 closest distance to " CG  MET A 188 " =    0.822
peak=    3.157 closest distance to " O   HOH Z  44 " =    2.743
peak=    3.155 closest distance to " O   HOH Z 188 " =    1.940
peak=    3.149 closest distance to " CA  ASN A 127 " =    1.087
peak=    3.142 closest distance to " CB  ASP A 140 " =    0.706
peak=    3.140 closest distance to " ND2 ASN A 301 " =    1.736
peak=    3.133 closest distance to " OE1 GLN A  55 " =    1.401
peak=    3.131 closest distance to " CD2 LEU A 255 " =    1.621
peak=    3.129 closest distance to " O   GLY A 203 " =    1.498
peak=    3.128 closest distance to " CB  GLU A  37 " =    0.948
peak=    3.126 closest distance to " O   HOH Z  49 " =    3.626
peak=    3.126 closest distance to " O   HOH Z 329 " =    4.102
peak=    3.124 closest distance to " CB  VAL A 257 " =    0.767
peak=    3.122 closest distance to " CD1 LEU A 222 " =    0.727
peak=    3.117 closest distance to " CG2 VAL A 197 " =    1.107
peak=    3.114 closest distance to " CG2 ILE A 120 " =    1.084
peak=    3.113 closest distance to " CD1 ILE A 199 " =    0.822
peak=    3.107 closest distance to " O   HOH Z 185 " =    1.917
peak=    3.104 closest distance to " O   ASN A 209 " =    1.357
peak=    3.104 closest distance to " O   HOH Z 215 " =    3.132
peak=    3.104 closest distance to " N   ILE A  20 " =    2.277
peak=    3.101 closest distance to " O   THR A 251 " =    1.231
peak=    3.100 closest distance to " N   TYR A  15 " =    0.771
peak=    3.092 closest distance to " O   HOH Z 344 " =    3.013
peak=    3.089 closest distance to " CB  ALA A   1 " =    4.881
peak=    3.088 closest distance to " CB  LEU A  96 " =    1.281
peak=    3.088 closest distance to " O   HOH Z 409 " =    2.961
peak=    3.078 closest distance to " CG  MET A 113 " =    1.850
peak=    3.078 closest distance to " C   ALA A 299 " =    0.959
peak=    3.077 closest distance to " O   HOH Z 197 " =    1.962
peak=    3.070 closest distance to " O   HOH Z 172 " =    3.345
peak=    3.068 closest distance to " CE2 PHE A 204 " =    0.825
peak=    3.062 closest distance to " O   HOH Z 124 " =    2.012
peak=    3.057 closest distance to " CB  ASN A 285 " =    0.910
peak=    3.046 closest distance to " CB  TYR A  30 " =    1.091
peak=    3.043 closest distance to " O   HOH Z 130 " =    2.343
peak=    3.042 closest distance to " NH1 ARG A  56 " =    1.071
peak=    3.039 closest distance to " CB  ALA A 227 " =    1.054
peak=    3.030 closest distance to " CB  PRO A  54 " =    1.280
peak=    3.027 closest distance to " O   HOH Z 134 " =    2.580
peak=    3.018 closest distance to " CG2 ILE A 263 " =    0.922
peak=    3.007 closest distance to " N   GLY A 133 " =    3.760

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.780 - 5.434
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 206
   mapped sites are within: 0.780 - 5.434

peak=   -5.229 closest distance to " CG2 VAL A 230 " =    0.860
peak=   -4.572 closest distance to " CD  GLN A  58 " =    0.920
peak=   -4.558 closest distance to " CG1 VAL A 296 " =    1.158
peak=   -4.445 closest distance to " O   HOH Z 211 " =    1.068
peak=   -4.214 closest distance to " CG1 VAL A 112 " =    2.640
peak=   -4.192 closest distance to " O   HOH Z 411 " =    5.434
peak=   -4.188 closest distance to " O   HOH Z 166 " =    1.628
peak=   -4.158 closest distance to " O   HOH Z 196 " =    2.515
peak=   -4.127 closest distance to " CG1 VAL A 250 " =    2.761
peak=   -4.119 closest distance to " CB  ALA A 161 " =    2.622
peak=   -4.091 closest distance to " CD  ARG A 156 " =    2.096
peak=   -4.061 closest distance to " CA  ASP A 298 " =    1.048
peak=   -4.024 closest distance to " O   HOH Z  37 " =    2.048
peak=   -4.002 closest distance to " CB  PRO A 243 " =    2.709
peak=   -3.979 closest distance to " O   HOH Z  52 " =    1.644
peak=   -3.975 closest distance to " O   HOH Z 210 " =    0.832
peak=   -3.954 closest distance to " O   HOH Z 394 " =    1.572
peak=   -3.946 closest distance to " OE1 GLN A 223 " =    2.250
peak=   -3.943 closest distance to " O   SER A 271 " =    2.232
peak=   -3.937 closest distance to " CG  ARG A 269 " =    2.375
peak=   -3.908 closest distance to " O   HOH Z  10 " =    1.612
peak=   -3.903 closest distance to " CE3 TRP A  70 " =    1.751
peak=   -3.896 closest distance to " O   HOH Z  73 " =    2.337
peak=   -3.880 closest distance to " CD  ARG A  14 " =    3.248
peak=   -3.877 closest distance to " O   HOH Z 231 " =    2.230
peak=   -3.869 closest distance to " CG2BVAL A  41 " =    2.770
peak=   -3.867 closest distance to " O   HOH Z 133 " =    1.107
peak=   -3.861 closest distance to " CE2 TYR A  30 " =    2.774
peak=   -3.839 closest distance to " CD2 TYR A 293 " =    1.830
peak=   -3.830 closest distance to " CZ2 TRP A  92 " =    2.825
peak=   -3.775 closest distance to " C   ALA A 158 " =    1.302
peak=   -3.739 closest distance to " OE1 GLN A  88 " =    0.919
peak=   -3.716 closest distance to " N   THR A  18 " =    1.289
peak=   -3.710 closest distance to " O   HOH Z 216 " =    1.218
peak=   -3.706 closest distance to " C   HIS A 108 " =    1.167
peak=   -3.704 closest distance to " O   VAL A  67 " =    2.669
peak=   -3.699 closest distance to " CA  GLY A 241 " =    2.303
peak=   -3.698 closest distance to " OD1 ASN A 148 " =    1.386
peak=   -3.697 closest distance to " O   HOH Z 351 " =    1.497
peak=   -3.696 closest distance to " CD2 LEU A 167 " =    1.782
peak=   -3.673 closest distance to " N   ALA A  43 " =    2.679
peak=   -3.664 closest distance to " CG  ASP A 231 " =    0.780
peak=   -3.657 closest distance to " OXT GLY A 302 " =    3.132
peak=   -3.656 closest distance to " NH2AARG A 275 " =    5.362
peak=   -3.649 closest distance to " CG  HIS A  86 " =    1.154
peak=   -3.648 closest distance to " CG1 VAL A 112 " =    2.768
peak=   -3.646 closest distance to " CD1 LEU A 101 " =    2.468
peak=   -3.641 closest distance to " C   LEU A 143 " =    1.080
peak=   -3.639 closest distance to " O   PRO A 198 " =    1.299
peak=   -3.635 closest distance to " OG  SER A  97 " =    2.256
peak=   -3.626 closest distance to " O   PRO A 163 " =    2.153
peak=   -3.607 closest distance to " O   HOH Z 350 " =    1.961
peak=   -3.604 closest distance to " CE3 TRP A 150 " =    2.273
peak=   -3.589 closest distance to " C   ASN A 285 " =    2.501
peak=   -3.587 closest distance to " CD1 PHE A  59 " =    2.032
peak=   -3.578 closest distance to " O   HOH Z 251 " =    4.931
peak=   -3.575 closest distance to " N   ALA A 226 " =    2.182
peak=   -3.570 closest distance to " O   HOH Z 183 " =    1.301
peak=   -3.561 closest distance to " CD  GLN A 223 " =    1.284
peak=   -3.556 closest distance to " O   HOH Z 431 " =    2.005
peak=   -3.547 closest distance to " O   HOH Z 238 " =    0.963
peak=   -3.545 closest distance to " O   HOH Z 177 " =    1.764
peak=   -3.536 closest distance to " NE2 GLN A 194 " =    1.939
peak=   -3.528 closest distance to " O   GLY A 203 " =    2.299
peak=   -3.528 closest distance to " O   HOH Z  43 " =    1.636
peak=   -3.520 closest distance to " CG  GLU A 277 " =    1.268
peak=   -3.515 closest distance to " O   HOH Z 185 " =    2.415
peak=   -3.511 closest distance to " O   GLY A  80 " =    2.676
peak=   -3.508 closest distance to " O   HOH Z 407 " =    3.350
peak=   -3.505 closest distance to " CA  SER A  62 " =    2.762
peak=   -3.489 closest distance to " O   HOH Z 290 " =    1.284
peak=   -3.481 closest distance to " OD2 ASP A  50 " =    2.367
peak=   -3.473 closest distance to " CE BMET A  47 " =    1.819
peak=   -3.472 closest distance to " O   HOH Z  19 " =    2.130
peak=   -3.460 closest distance to " O   HOH Z 368 " =    1.791
peak=   -3.454 closest distance to " O   HOH Z 113 " =    2.397
peak=   -3.448 closest distance to " CA  GLY A 241 " =    3.157
peak=   -3.441 closest distance to " CD1 ILE A 151 " =    2.488
peak=   -3.439 closest distance to " CG  TRP A 266 " =    1.860
peak=   -3.435 closest distance to " NH2 ARG A  66 " =    1.939
peak=   -3.433 closest distance to " CB  ALA A 248 " =    2.151
peak=   -3.429 closest distance to " CD1 ILE A  33 " =    2.563
peak=   -3.426 closest distance to " O   HOH Z 241 " =    1.218
peak=   -3.421 closest distance to " CA  GLY A 133 " =    2.269
peak=   -3.418 closest distance to " CD1 LEU A   5 " =    2.604
peak=   -3.416 closest distance to " CG1 VAL A  67 " =    2.895
peak=   -3.415 closest distance to " O   VAL A 189 " =    2.636
peak=   -3.409 closest distance to " O   GLY A 211 " =    1.444
peak=   -3.405 closest distance to " O   HOH Z 119 " =    2.142
peak=   -3.399 closest distance to " NE2 GLN A 103 " =    1.918
peak=   -3.397 closest distance to " NH2 ARG A  79 " =    1.616
peak=   -3.388 closest distance to " CB  VAL A 230 " =    1.060
peak=   -3.386 closest distance to " O   HOH Z 359 " =    2.850
peak=   -3.384 closest distance to " O   HOH Z  13 " =    1.558
peak=   -3.383 closest distance to " CG  MET A 105 " =    0.968
peak=   -3.381 closest distance to " O   HOH Z  44 " =    2.212
peak=   -3.380 closest distance to " O   HOH Z 295 " =    1.595
peak=   -3.379 closest distance to " O   HOH Z 198 " =    2.512
peak=   -3.375 closest distance to " O   HOH Z  11 " =    1.845
peak=   -3.373 closest distance to " O   ASP A  27 " =    2.141
peak=   -3.370 closest distance to " O   HOH Z  17 " =    1.357
peak=   -3.369 closest distance to " CD  LYS A 289 " =    2.468
peak=   -3.361 closest distance to " CB  ASP A 132 " =    2.320
peak=   -3.361 closest distance to " O   HOH Z   9 " =    1.674
peak=   -3.360 closest distance to " O   HOH Z 123 " =    2.583
peak=   -3.348 closest distance to " O   HOH Z 136 " =    2.441
peak=   -3.343 closest distance to " O   HOH Z 259 " =    4.188
peak=   -3.341 closest distance to " CD1 LEU A 101 " =    2.633
peak=   -3.337 closest distance to " CG2BVAL A  41 " =    1.792
peak=   -3.331 closest distance to " O   HOH Z  60 " =    1.963
peak=   -3.330 closest distance to " O   HOH Z 106 " =    1.911
peak=   -3.329 closest distance to " CZ3 TRP A 179 " =    1.158
peak=   -3.322 closest distance to " O   HOH Z 165 " =    1.768
peak=   -3.319 closest distance to " CG  GLU A  53 " =    1.539
peak=   -3.313 closest distance to " CD  GLN A  88 " =    0.844
peak=   -3.312 closest distance to " OG ASER A 134 " =    1.384
peak=   -3.311 closest distance to " CG  ARG A 269 " =    2.078
peak=   -3.309 closest distance to " SD BMET A  47 " =    1.050
peak=   -3.306 closest distance to " CD2 PHE A 192 " =    2.065
peak=   -3.306 closest distance to " O   HOH Z 145 " =    1.169
peak=   -3.304 closest distance to " CD2 LEU A 300 " =    2.639
peak=   -3.304 closest distance to " O   HOH Z 285 " =    1.715
peak=   -3.303 closest distance to " O   SER A 276 " =    1.863
peak=   -3.302 closest distance to " OG BSER A 134 " =    1.316
peak=   -3.301 closest distance to " O   HOH Z 377 " =    1.852
peak=   -3.301 closest distance to " OG  SER A  87 " =    1.687
peak=   -3.299 closest distance to " O   HOH Z 435 " =    2.663
peak=   -3.298 closest distance to " O   HOH Z 256 " =    1.320
peak=   -3.297 closest distance to " CG  GLN A  11 " =    1.595
peak=   -3.297 closest distance to " O   HOH Z 434 " =    1.770
peak=   -3.293 closest distance to " O   HOH Z   6 " =    1.601
peak=   -3.293 closest distance to " N   ASN A  60 " =    1.285
peak=   -3.291 closest distance to " ND2 ASN A  45 " =    1.142
peak=   -3.286 closest distance to " O   HOH Z 252 " =    3.912
peak=   -3.285 closest distance to " O   HOH Z 231 " =    1.537
peak=   -3.285 closest distance to " CD2 PHE A  61 " =    2.566
peak=   -3.285 closest distance to " O   HOH Z 149 " =    2.168
peak=   -3.284 closest distance to " O   HOH Z 184 " =    1.631
peak=   -3.278 closest distance to " SG  CYS A 260 " =    2.470
peak=   -3.278 closest distance to " O   HOH Z 234 " =    4.535
peak=   -3.278 closest distance to " N   SER A   3 " =    2.148
peak=   -3.277 closest distance to " O   HOH Z  44 " =    1.034
peak=   -3.277 closest distance to " O   HOH Z 411 " =    1.737
peak=   -3.273 closest distance to " CA  GLY A 203 " =    2.460
peak=   -3.271 closest distance to " O   HOH Z 292 " =    4.742
peak=   -3.270 closest distance to " O   VAL A 125 " =    2.367
peak=   -3.266 closest distance to " CB  ALA A  43 " =    2.630
peak=   -3.250 closest distance to " CG2 VAL A 189 " =    2.084
peak=   -3.248 closest distance to " O   HOH Z 189 " =    2.386
peak=   -3.238 closest distance to " N   LEU A  83 " =    1.515
peak=   -3.234 closest distance to " NH2 ARG A 159 " =    2.480
peak=   -3.233 closest distance to " CG  ARG A 259 " =    2.506
peak=   -3.232 closest distance to " CB  PRO A 163 " =    2.539
peak=   -3.229 closest distance to " CD  PRO A 213 " =    2.194
peak=   -3.224 closest distance to " O   HOH Z 111 " =    1.373
peak=   -3.222 closest distance to " O   HOH Z  38 " =    1.414
peak=   -3.220 closest distance to " O   GLY A  80 " =    2.350
peak=   -3.218 closest distance to " CE  LYS A  76 " =    2.588
peak=   -3.217 closest distance to " OD1 ASN A 173 " =    1.355
peak=   -3.215 closest distance to " CA  ASN A 127 " =    1.080
peak=   -3.211 closest distance to " O   HOH Z 396 " =    1.984
peak=   -3.210 closest distance to " O   HOH Z 377 " =    1.299
peak=   -3.200 closest distance to " ND2 ASN A  60 " =    1.362
peak=   -3.199 closest distance to " O   HOH Z 317 " =    2.142
peak=   -3.195 closest distance to " CG  PRO A 163 " =    2.166
peak=   -3.189 closest distance to " O   HOH Z 236 " =    1.435
peak=   -3.188 closest distance to " O   HOH Z 423 " =    2.054
peak=   -3.188 closest distance to " CB  ALA A 291 " =    2.290
peak=   -3.186 closest distance to " O   HOH Z  60 " =    2.197
peak=   -3.176 closest distance to " OD1 ASP A 171 " =    1.554
peak=   -3.176 closest distance to " O   HOH Z 409 " =    4.720
peak=   -3.171 closest distance to " CG1 VAL A  78 " =    2.650
peak=   -3.170 closest distance to " C   ASP A 270 " =    1.280
peak=   -3.170 closest distance to " OG  SER A 206 " =    1.836
peak=   -3.168 closest distance to " CD2 PHE A 225 " =    1.284
peak=   -3.168 closest distance to " NE  ARG A  66 " =    4.086
peak=   -3.165 closest distance to " O   HOH Z 102 " =    1.601
peak=   -3.164 closest distance to " CB  ALA A 248 " =    2.336
peak=   -3.162 closest distance to " CD1 TYR A 247 " =    2.354
peak=   -3.160 closest distance to " OG BSER A 134 " =    1.997
peak=   -3.160 closest distance to " CG2 VAL A 296 " =    1.302
peak=   -3.155 closest distance to " CE  MET A 105 " =    2.367
peak=   -3.153 closest distance to " O   SER A 210 " =    1.924
peak=   -3.151 closest distance to " CG2 VAL A 112 " =    2.506
peak=   -3.142 closest distance to " OH  TYR A 247 " =    1.839
peak=   -3.139 closest distance to " O   HOH Z 176 " =    0.781
peak=   -3.138 closest distance to " CG  LEU A   5 " =    0.962
peak=   -3.131 closest distance to " ND2 ASN A  69 " =    1.863
peak=   -3.129 closest distance to " O   HOH Z 111 " =    2.065
peak=   -3.122 closest distance to " NE2 GLN A  88 " =    1.051
peak=   -3.119 closest distance to " CD  PRO A 243 " =    1.955
peak=   -3.118 closest distance to " CA  SER A  62 " =    2.519
peak=   -3.117 closest distance to " C   ALA A 165 " =    1.952
peak=   -3.108 closest distance to " O   HOH Z 429 " =    2.084
peak=   -3.101 closest distance to " O   HOH Z 114 " =    1.599
peak=   -3.099 closest distance to " OE2 GLU A 277 " =    2.881
peak=   -3.098 closest distance to " NE  ARG A 138 " =    1.850
peak=   -3.097 closest distance to " CD1 LEU A 228 " =    2.419
peak=   -3.093 closest distance to " ND2 ASN A 187 " =    1.702
peak=   -3.089 closest distance to " CB  ASP A 171 " =    2.352
peak=   -3.088 closest distance to " O   HOH Z 177 " =    1.344
peak=   -3.073 closest distance to " CB  SER A 146 " =    2.230
peak=   -3.073 closest distance to " CD1 TRP A  70 " =    1.149
peak=   -3.064 closest distance to " O   HOH Z 389 " =    1.903
peak=   -3.054 closest distance to " OE1 GLN A  88 " =    1.203
peak=   -3.034 closest distance to " O   HOH Z 313 " =    1.185

================= 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    :  0.4717 0.4596   6.270742e+00   6.250330e+00
   1_bss:  0.4638 0.4495   6.265186e+00   6.241420e+00
   1_xyz:  0.3656 0.3904   6.116867e+00   6.152697e+00
   1_adp:  0.3203 0.3665   6.017218e+00   6.104055e+00
   1_occ:  0.3198 0.3670   6.016248e+00   6.105187e+00
   2_bss:  0.3175 0.3612   6.016743e+00   6.102840e+00
   2_xyz:  0.2317 0.2777   5.754958e+00   5.898342e+00
   2_adp:  0.2122 0.2583   5.684968e+00   5.844859e+00
   2_occ:  0.2119 0.2585   5.684481e+00   5.844463e+00
   3_bss:  0.2111 0.2581   5.686583e+00   5.845010e+00
   3_xyz:  0.1528 0.1963   5.395914e+00   5.596680e+00
   3_adp:  0.1407 0.1884   5.336963e+00   5.559755e+00
   3_occ:  0.1406 0.1885   5.336979e+00   5.560174e+00
   4_bss:  0.1409 0.1884   5.337413e+00   5.559086e+00
   4_xyz:  0.1296 0.1789   5.273648e+00   5.505648e+00
   4_adp:  0.1275 0.1739   5.253716e+00   5.478213e+00
   4_occ:  0.1274 0.1737   5.252975e+00   5.477408e+00
   5_bss:  0.1274 0.1737   5.252853e+00   5.477250e+00
   5_xyz:  0.1215 0.1676   5.211508e+00   5.443759e+00
   5_adp:  0.1202 0.1676   5.208436e+00   5.446055e+00
   5_occ:  0.1201 0.1676   5.208095e+00   5.445843e+00
   5_bss:  0.1201 0.1676   5.208044e+00   5.445817e+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:  0.299  20.000   7.832   8.473   9.968   0.000   0.000   0.000
   1_xyz:  0.299  20.000   7.832   8.473   9.968   0.000   0.000   0.000
   1_adp:  0.299  20.000   7.832   8.473   9.968   0.000   0.000   0.000
   1_occ:  0.299  20.000   7.832   8.473   9.968   0.000   0.000   0.000
   2_bss:  0.329  60.084   4.791   5.511   6.565   0.000   0.000   0.000
   2_xyz:  0.329  60.084   4.791   5.511   6.565   0.000   0.000   0.000
   2_adp:  0.329  60.084   4.791   5.511   6.565   0.000   0.000   0.000
   2_occ:  0.329  60.084   4.791   5.511   6.565   0.000   0.000   0.000
   3_bss:  0.333  70.573   3.383   3.907   4.841   0.000   0.000   0.000
   3_xyz:  0.333  70.573   3.383   3.907   4.841   0.000   0.000   0.000
   3_adp:  0.333  70.573   3.383   3.907   4.841   0.000   0.000   0.000
   3_occ:  0.333  70.573   3.383   3.907   4.841   0.000   0.000   0.000
   4_bss:  0.337  70.573   2.960   3.294   4.421   0.000   0.000   0.000
   4_xyz:  0.337  70.573   2.960   3.294   4.421   0.000   0.000   0.000
   4_adp:  0.337  70.573   2.960   3.294   4.421   0.000   0.000   0.000
   4_occ:  0.337  70.573   2.960   3.294   4.421   0.000   0.000   0.000
   5_bss:  0.328  65.132   2.960   3.294   4.421   0.000   0.000   0.000
   5_xyz:  0.328  65.132   2.960   3.294   4.421   0.000   0.000   0.000
   5_adp:  0.328  65.132   2.960   3.294   4.421   0.000   0.000   0.000
   5_occ:  0.328  65.132   2.960   3.294   4.421   0.000   0.000   0.000
   5_bss:  0.328  68.752  -0.562  -0.314   0.876   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.500 0.4771  0.5300    61396.091
   1_bss:  52.495 0.4892  0.7067    59699.167
   1_xyz:  44.336 0.5891  0.8247    43023.748
   1_adp:  39.428 0.6492  0.9150    36375.336
   1_occ:  39.437 0.6491  0.9141    36431.838
   2_bss:  39.243 0.6514  0.8226    36179.543
   2_xyz:  28.734 0.7713  0.9521    20557.001
   2_adp:  26.104 0.8004  0.9742    17777.315
   2_occ:  26.109 0.8003  0.9736    17763.485
   3_bss:  26.115 0.8004  0.9200    17819.610
   3_xyz:  18.715 0.8738  0.9738     9835.384
   3_adp:  17.629 0.8842  0.9733     9096.647
   3_occ:  17.639 0.8841  0.9732     9104.411
   4_bss:  17.625 0.8842  0.9565     9087.443
   4_xyz:  16.381 0.8954  0.9616     8063.983
   4_adp:  15.699 0.9015  0.9598     7650.179
   4_occ:  15.680 0.9017  0.9599     7639.010
   5_bss:  15.682 0.9017  0.9598     7636.772
   5_xyz:  14.981 0.9075  0.9638     7114.906
   5_adp:  15.027 0.9071  0.9586     7129.083
   5_occ:  15.025 0.9071  0.9585     7127.579
   5_bss:  15.023 0.9072  0.9607     7127.231
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4573e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4573e+01
   1_xyz:   1.733  0.014  0.111 18.121  0.007  4.112   1.4733e-01
   1_adp:   1.733  0.014  0.111 18.121  0.007  4.112   1.4733e-01
   1_occ:   1.733  0.014  0.111 18.121  0.007  4.112   1.4733e-01
   2_bss:   1.733  0.014  0.111 18.121  0.007  4.112   1.4733e-01
   2_xyz:   1.116  0.008  0.075 16.512  0.004  4.131   7.2788e-02
   2_adp:   1.116  0.008  0.075 16.512  0.004  4.131   7.2788e-02
   2_occ:   1.116  0.008  0.075 16.512  0.004  4.131   7.2788e-02
   3_bss:   1.116  0.008  0.075 16.512  0.004  4.131   7.2788e-02
   3_xyz:   1.124  0.009  0.085 16.272  0.004  4.139   7.5082e-02
   3_adp:   1.124  0.009  0.085 16.272  0.004  4.139   7.5082e-02
   3_occ:   1.124  0.009  0.085 16.272  0.004  4.139   7.5082e-02
   4_bss:   1.124  0.009  0.085 16.272  0.004  4.139   7.5082e-02
   4_xyz:   1.047  0.009  0.081 16.026  0.004  4.147   6.8277e-02
   4_adp:   1.047  0.009  0.081 16.026  0.004  4.147   6.8277e-02
   4_occ:   1.047  0.009  0.081 16.026  0.004  4.147   6.8277e-02
   5_bss:   1.047  0.009  0.081 16.026  0.004  4.147   6.8277e-02
   5_xyz:   1.117  0.010  0.088 15.793  0.004  4.116   7.5951e-02
   5_adp:   1.117  0.010  0.088 15.793  0.004  4.116   7.5951e-02
   5_occ:   1.117  0.010  0.088 15.793  0.004  4.116   7.5951e-02
   5_bss:   1.117  0.010  0.088 15.793  0.004  4.116   7.5951e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0762e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0762e+00
   1_xyz:  14.709  0.174  0.466 85.832  0.039  2.308   1.0989e-01
   1_adp:  14.709  0.174  0.466 85.832  0.039  2.308   1.0989e-01
   1_occ:  14.709  0.174  0.466 85.832  0.039  2.308   1.0989e-01
   2_bss:  14.709  0.174  0.466 85.832  0.039  2.308   1.0989e-01
   2_xyz:   7.300  0.072  0.270 88.034  0.035  2.206   4.8039e-02
   2_adp:   7.300  0.072  0.270 88.034  0.035  2.206   4.8039e-02
   2_occ:   7.300  0.072  0.270 88.034  0.035  2.206   4.8039e-02
   3_bss:   7.300  0.072  0.270 88.034  0.035  2.206   4.8039e-02
   3_xyz:   8.300  0.064  0.351 85.118  0.043  2.334   4.8962e-02
   3_adp:   8.300  0.064  0.351 85.118  0.043  2.334   4.8962e-02
   3_occ:   8.300  0.064  0.351 85.118  0.043  2.334   4.8962e-02
   4_bss:   8.300  0.064  0.351 85.118  0.043  2.334   4.8962e-02
   4_xyz:   8.559  0.053  0.399 81.678  0.037  2.358   3.8594e-02
   4_adp:   8.559  0.053  0.399 81.678  0.037  2.358   3.8594e-02
   4_occ:   8.559  0.053  0.399 81.678  0.037  2.358   3.8594e-02
   5_bss:   8.559  0.053  0.399 81.678  0.037  2.358   3.8594e-02
   5_xyz:   8.237  0.046  0.482 82.340  0.042  2.362   4.5401e-02
   5_adp:   8.237  0.046  0.482 82.340  0.042  2.362   4.5401e-02
   5_occ:   8.237  0.046  0.482 82.340  0.042  2.362   4.5401e-02
   5_bss:   8.237  0.046  0.482 82.340  0.042  2.362   4.5401e-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: 111.61   0.00  11.73  73.48   0.00   8.85 111.61   0.00  27.46
   1_occ: 111.61   0.00  11.73  73.48   0.00   8.85 111.61   0.00  27.46
   2_bss: 111.61   0.00  11.73  73.48   0.00   8.85 111.61   0.00  27.46
   2_xyz: 111.61   0.00  11.73  73.48   0.00   8.85 111.61   0.00  27.46
   2_adp: 114.38   0.00  12.16  75.69   0.00   8.16 114.38   0.00  33.93
   2_occ: 114.38   0.00  12.16  75.69   0.00   8.16 114.38   0.00  33.93
   3_bss: 114.38   0.00  12.16  75.69   0.00   8.16 114.38   0.00  33.93
   3_xyz: 114.38   0.00  12.16  75.69   0.00   8.16 114.38   0.00  33.93
   3_adp: 113.02   0.00  12.44 104.92   0.00   8.03 113.02   0.00  36.42
   3_occ: 113.02   0.00  12.44 104.92   0.00   8.03 113.02   0.00  36.42
   4_bss: 113.02   0.00  12.44 104.92   0.00   8.03 113.02   0.00  36.42
   4_xyz: 113.02   0.00  12.44 104.92   0.00   8.03 113.02   0.00  36.42
   4_adp: 106.24   0.00  12.13  75.84   0.00   7.76 106.24   0.40  35.94
   4_occ: 106.24   0.00  12.13  75.84   0.00   7.76 106.24   0.40  35.94
   5_bss: 106.24   0.00  12.13  75.84   0.00   7.76 106.24   0.40  35.94
   5_xyz: 106.24   0.00  12.13  75.84   0.00   7.76 106.24   0.40  35.94
   5_adp:  94.55   0.00  12.23  82.79   0.00   7.74  94.55   0.75  36.70
   5_occ:  94.55   0.00  12.23  82.79   0.00   7.74  94.55   0.75  36.70
   5_bss:  98.17   3.62  15.85  86.41   3.62  11.36  98.17   4.37  40.32
------------------------------------------------------------------------
 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:    1.267    0.029    0.417
   1_adp:    1.267    0.029    0.417
   1_occ:    1.267    0.029    0.417
   2_bss:    1.267    0.029    0.417
   2_xyz:    1.742    0.022    0.549
   2_adp:    1.742    0.022    0.549
   2_occ:    1.742    0.022    0.549
   3_bss:    1.742    0.022    0.549
   3_xyz:    1.614    0.042    0.634
   3_adp:    1.614    0.042    0.634
   3_occ:    1.614    0.042    0.634
   4_bss:    1.614    0.042    0.634
   4_xyz:    1.751    0.021    0.662
   4_adp:    1.751    0.021    0.662
   4_occ:    1.751    0.021    0.662
   5_bss:    1.751    0.021    0.662
   5_xyz:    1.781    0.024    0.676
   5_adp:    1.781    0.024    0.676
   5_occ:    1.781    0.024    0.676
   5_bss:    1.781    0.024    0.676
------------------------------------------------------------------------

CPU time actual refinement: 323.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1053/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_1053/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1053/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1053/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1053/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.75 
  Macro-tasks:
    bulk solvent and scale       = 42.26  
    individual site refinement   = 129.64 
    weights calculation          = 32.72  
    collect and process          = 6.59   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 211.34 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 97.21  
    alpha_beta                      = 8.36   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 107.02 
    fmodel                         = 7.30   
    r_factors                      = 0.19   
    phase_errors                   = 10.53  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 233.83 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.631 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    623 calls, 96.86 s
gradients_fft:          569 calls, 94.04 s

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

# Date 2008-01-16 Time 03:03:34 PST -0800 (1200481414.37 s)
Start R-work = 0.4717, R-free = 0.4596 (no bulk solvent and anisotropic scale)
Final R-work = 0.1363, R-free = 0.1828 (no bulk solvent and anisotropic scale)

Start R-work = 0.4638, R-free = 0.4495
Final R-work = 0.1201, R-free = 0.1676