# Date 2008-01-16 Time 03:16:10 PST -0800 (1200482170.46 s)
#phil __OFF__

Command line arguments: "../1173.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 = 14873
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1173

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 47.3993, 87.2539, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 2.02038
Completeness in resolution range: 0.976618
Completeness with d_max=infinity: 0.973608

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2528
                             d_min =   2.0204

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 2.02038
Completeness in resolution range: 0.976618
Completeness with d_max=infinity: 0.973608

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2532 -  4.3228 [2099/2124]  1889   210  10.0%
  bin  2:  4.3228 -  3.4442 [2031/2051]  1828   203  10.0%
  bin  3:  3.4442 -  3.0126 [1997/2016]  1795   202  10.1%
  bin  4:  3.0126 -  2.7389 [1971/2001]  1777   194   9.8%
  bin  5:  2.7389 -  2.5436 [1977/1996]  1780   197  10.0%
  bin  6:  2.5436 -  2.3942 [1957/1982]  1762   195  10.0%
  bin  7:  2.3942 -  2.2747 [1946/1974]  1746   200  10.3%
  bin  8:  2.2747 -  2.1760 [1940/1976]  1747   193   9.9%
  bin  9:  2.1760 -  2.0924 [1932/1974]  1744   188   9.7%
  bin 10:  2.0924 -  2.0204 [1739/1964]  1562   177  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1173/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: 0.13 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:
        1.54 -     2.21: 2
        2.21 -     2.89: 1254
        2.89 -     3.56: 4361
        3.56 -     4.23: 9030
        4.23 -     4.90: 13120
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.543 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
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.368 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27762 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_1173/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1173/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.3993 87.2539 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 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4708   r_free= 0.4554   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.270842                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.8213 0.99   1372  152 0.3847 0.3562      6.5727      6.4733|
|  2:  4.8213 -  3.8471 0.99   1315  146 0.3815 0.4096      6.7642       6.831|
|  3:  3.8471 -  3.3667 0.99   1287  144 0.4239 0.4014      6.6618      6.6471|
|  4:  3.3667 -  3.0616 0.99   1278  144 0.4603 0.3958      6.5276      6.4315|
|  5:  3.0616 -  2.8437 0.99   1279  141 0.4863 0.4808      6.3601       6.391|
|  6:  2.8437 -  2.6770 0.99   1269  139 0.5060 0.5212      6.2993      6.2148|
|  7:  2.6770 -  2.5436 0.99   1269  140 0.5091 0.4871      6.2265      6.2408|
|  8:  2.5436 -  2.4333 0.98   1255  143 0.5198 0.4712      6.1993      6.1387|
|  9:  2.4333 -  2.3400 0.98   1244  134 0.5170 0.5294      6.1177      6.1719|
| 10:  2.3400 -  2.2595 1.00   1248  144 0.5212 0.5031      6.1214      6.1392|
| 11:  2.2595 -  2.1890 0.97   1261  136 0.5060 0.4915      6.0414       6.055|
| 12:  2.1890 -  2.1266 0.98   1231  138 0.5300 0.5289      6.0027      6.0126|
| 13:  2.1266 -  2.0708 0.99   1241  142 0.5233 0.5011      5.9078      5.8724|
| 14:  2.0708 -  2.0204 0.84   1081  116 0.5363 0.4698      5.8532      5.7411|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2532 -  4.8213  1372   152  0.72  32.04   0.79     0.75      62757.74|
|  2:  4.8213 -  3.8471  1315   146  0.73  32.24   0.88     0.77      91017.32|
|  3:  3.8471 -  3.3667  1287   144  0.65  39.63   0.82     0.73      98798.88|
|  4:  3.3667 -  3.0616  1278   144  0.56  47.02   0.80     0.64      89357.68|
|  5:  3.0616 -  2.8437  1279   141  0.47  54.06   0.73     0.55      75513.51|
|  6:  2.8437 -  2.6770  1269   139  0.44  56.74   0.73     0.49      67024.48|
|  7:  2.6770 -  2.5436  1269   140  0.40  60.06   0.71     0.44      62894.76|
|  8:  2.5436 -  2.4333  1255   143  0.36  62.95   0.73     0.41      59438.91|
|  9:  2.4333 -  2.3400  1244   134  0.35  63.79   0.70     0.39      54967.01|
| 10:  2.3400 -  2.2595  1248   144  0.36  62.77   0.74     0.41      50020.26|
| 11:  2.2595 -  2.1890  1261   136  0.37  62.40   0.74     0.43      44898.09|
| 12:  2.1890 -  2.1266  1231   138  0.37  62.05   0.74     0.45      40961.95|
| 13:  2.1266 -  2.0708  1241   142  0.39  61.04   0.71     0.44      34239.92|
| 14:  2.0708 -  2.0204  1081   116  0.42  58.57   0.69     0.45      26563.97|
|alpha:            min =        0.39 max =            0.77 mean =         0.53|
|beta:             min =    26563.97 max =        98798.88 mean =     61953.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.64|
|phase err.(test): min =        0.00 max =           89.97 mean =        53.37|
|-----------------------------------------------------------------------------|

============================== 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 = 12.348717             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.523   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.115990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.313   (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:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      158 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1475 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2570 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3841 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4966 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6469 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7593 |
|-----------------------------------------------------------------------------|
|-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 |       54.553 |
| 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 |       1.619 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.381)------------------------------------------|
|    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 = 12.381)------------------------------------------|
|    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 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4757   r_free= 0.4574   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| 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: 6.272155                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4635   r_free= 0.4459   ksol= 0.29   Bsol= 20.00   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.29,8.06,8.23,0.00,0.00,0.00); trace/3= 8.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.265039                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.224170             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.679   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.967560              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.950   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4635      final r-factor (work) = 0.3642          |
| start r-factor (free) = 0.4459      final r-factor (free) = 0.3903          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 89.7602 = 11.22 * 0.50 * 6.2734 + 1.00 * 54.5533                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.6720 = 11.22 * 0.50 * 6.1520 + 1.00 * 0.1466                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3642      final r-factor (work) = 0.3193          |
| start r-factor (free) = 0.3903      final r-factor (free) = 0.3627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9668 = 0.97 * 1.00 * 6.1520 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8681 = 0.97 * 1.00 * 6.0497 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.381)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.08  11.54    None  None   None       |
|    all(noH): 2823   0      0.00    108.08  11.54    None  None   None       |
|    Sol.    : 438    0      0.00    108.08  26.83    None  None   None       |
|    Mac.    : 2385   0      0.00    71.13   8.73     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 -  10.808: 1780   |   5:    54.038 -  64.845:   19        |
|      1:    10.808 -  21.615:  645   |   6:    64.845 -  75.653:    7        |
|      2:    21.615 -  32.423:  200   |   7:    75.653 -  86.460:    1        |
|      3:    32.423 -  43.230:  108   |   8:    86.460 -  97.268:    0        |
|      4:    43.230 -  54.038:   62   |   9:    97.268 - 108.075:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3193 r_free = 0.3627             target_work(ml) = 6.021         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3185 r_free = 0.3632             target_work(ml) = 6.020         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3185   r_free= 0.3632   ksol= 0.29   Bsol= 20.00   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.29,8.06,8.23,0.00,0.00,0.00); trace/3= 8.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.020094                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3174   r_free= 0.3593   ksol= 0.33   Bsol= 59.12   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.79,5.59,5.82,0.00,0.00,0.00); trace/3= 5.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.020658                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.448587              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.377   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.554669              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.909  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3174      final r-factor (work) = 0.2313          |
| start r-factor (free) = 0.3593      final r-factor (free) = 0.2806          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5928 = 4.45 * 0.50 * 6.0452 + 1.00 * 0.1466                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1753 = 4.45 * 0.50 * 5.8908 + 1.00 * 0.0725                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2313      final r-factor (work) = 0.2115          |
| start r-factor (free) = 0.2806      final r-factor (free) = 0.2591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2890 = 0.55 * 1.00 * 5.8908 + 1.00 * 0.0216                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2036 = 0.55 * 1.00 * 5.7134 + 1.00 * 0.0346                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.381)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.19  12.14    None  None   None       |
|    all(noH): 2823   0      0.00    108.19  12.14    None  None   None       |
|    Sol.    : 438    0      0.00    108.19  33.80    None  None   None       |
|    Mac.    : 2385   0      0.00    74.54   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 -  10.819: 1865   |   5:    54.096 -  64.915:   46        |
|      1:    10.819 -  21.638:  492   |   6:    64.915 -  75.734:   14        |
|      2:    21.638 -  32.457:  189   |   7:    75.734 -  86.553:    4        |
|      3:    32.457 -  43.277:  125   |   8:    86.553 -  97.372:    0        |
|      4:    43.277 -  54.096:   87   |   9:    97.372 - 108.191:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2115 r_free = 0.2591             target_work(ml) = 5.683         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2112 r_free = 0.2591             target_work(ml) = 5.682         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2112   r_free= 0.2591   ksol= 0.33   Bsol= 59.12   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.79,5.59,5.82,0.00,0.00,0.00); trace/3= 5.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.682184                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2099   r_free= 0.2578   ksol= 0.32   Bsol= 74.25   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,3.77,4.34,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.682998                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.688370              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.241  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.379010              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.987   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2099      final r-factor (work) = 0.1547          |
| start r-factor (free) = 0.2578      final r-factor (free) = 0.2001          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6162 = 3.69 * 0.50 * 5.7173 + 1.00 * 0.0725                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3242 = 3.69 * 0.50 * 5.5572 + 1.00 * 0.0757                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1547      final r-factor (work) = 0.1406          |
| start r-factor (free) = 0.2001      final r-factor (free) = 0.1899          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6789 = 1.38 * 1.00 * 5.5572 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4157 = 1.38 * 1.00 * 5.3655 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.381)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.50  13.06    None  None   None       |
|    all(noH): 2823   0      0.00    101.50  13.06    None  None   None       |
|    Sol.    : 438    0      0.00    101.50  39.50    None  None   None       |
|    Mac.    : 2385   0      0.00    86.37   8.20     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 -  10.150: 1831   |   5:    50.748 -  60.898:   90        |
|      1:    10.150 -  20.299:  470   |   6:    60.898 -  71.048:   51        |
|      2:    20.299 -  30.449:  149   |   7:    71.048 -  81.197:   15        |
|      3:    30.449 -  40.599:  114   |   8:    81.197 -  91.347:    9        |
|      4:    40.599 -  50.748:   93   |   9:    91.347 - 101.497:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1406 r_free = 0.1899             target_work(ml) = 5.340         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1406 r_free = 0.1897             target_work(ml) = 5.339         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1406   r_free= 0.1897   ksol= 0.32   Bsol= 74.25   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,3.77,4.34,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.339474                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1407   r_free= 0.1900   ksol= 0.34   Bsol= 74.25   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.22,4.09,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.340167                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.009978              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.505  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.416704              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.113  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1407      final r-factor (work) = 0.1256          |
| start r-factor (free) = 0.1900      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1527 = 3.01 * 0.50 * 5.3668 + 1.00 * 0.0757                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0451 = 3.01 * 0.50 * 5.2926 + 1.00 * 0.0798                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1256      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1762      final r-factor (free) = 0.1718          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2220 = 0.42 * 1.00 * 5.2926 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1991 = 0.42 * 1.00 * 5.2437 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.381)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.18   12.63    None  None   None       |
|    all(noH): 2823   0      0.00    97.18   12.63    None  None   None       |
|    Sol.    : 438    0      0.98    97.18   38.14    None  None   None       |
|    Mac.    : 2385   0      0.00    86.10   7.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.718: 1826   |   5:    48.588 -  58.306:   83        |
|      1:     9.718 -  19.435:  488   |   6:    58.306 -  68.024:   57        |
|      2:    19.435 -  29.153:  137   |   7:    68.024 -  77.741:   16        |
|      3:    29.153 -  38.871:  117   |   8:    77.741 -  87.459:   11        |
|      4:    38.871 -  48.588:   86   |   9:    87.459 -  97.177:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1235 r_free = 0.1718             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1235 r_free = 0.1716             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1716   ksol= 0.34   Bsol= 74.25   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.22,4.09,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.229084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1715   ksol= 0.33   Bsol= 66.10   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.22,4.09,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.228945                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.272252              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.885  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.229991              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.490  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1234      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1715      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0368 = 2.27 * 0.50 * 5.2433 + 1.00 * 0.0798                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0030 = 2.27 * 0.50 * 5.2203 + 1.00 * 0.0720                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1214          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1674          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2145 = 0.23 * 1.00 * 5.2203 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2302 = 0.23 * 1.00 * 5.2145 + 1.00 * 0.0309                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.381)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.71   12.37    None  None   None       |
|    all(noH): 2823   0      0.00    95.71   12.37    None  None   None       |
|    Sol.    : 438    0      1.27    95.71   37.21    None  None   None       |
|    Mac.    : 2385   0      0.00    85.37   7.81     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 -   9.571: 1838   |   5:    47.853 -  57.424:   83        |
|      1:     9.571 -  19.141:  477   |   6:    57.424 -  66.994:   52        |
|      2:    19.141 -  28.712:  142   |   7:    66.994 -  76.565:   17        |
|      3:    28.712 -  38.283:  118   |   8:    76.565 -  86.136:   11        |
|      4:    38.283 -  47.853:   83   |   9:    86.136 -  95.706:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1214 r_free = 0.1674             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1213 r_free = 0.1673             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1673   ksol= 0.33   Bsol= 66.10   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.22,4.09,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209807                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.8213 0.99   1372  152 0.1038 0.1370      5.4247       5.556|
|  2:  4.8213 -  3.8471 0.99   1315  146 0.0879 0.1162      5.4689      5.6712|
|  3:  3.8471 -  3.3667 0.99   1287  144 0.1106 0.1544      5.5203      5.8608|
|  4:  3.3667 -  3.0616 0.99   1278  144 0.1301 0.1659      5.5122      5.6728|
|  5:  3.0616 -  2.8437 0.99   1279  141 0.1480 0.1862        5.42        5.61|
|  6:  2.8437 -  2.6770 0.99   1269  139 0.1335 0.1997         5.3      5.5138|
|  7:  2.6770 -  2.5436 0.99   1269  140 0.1414 0.1786      5.2536       5.461|
|  8:  2.5436 -  2.4333 0.98   1255  143 0.1309 0.1734      5.1569      5.3653|
|  9:  2.4333 -  2.3400 0.98   1244  134 0.1264 0.1787      5.1021      5.3269|
| 10:  2.3400 -  2.2595 1.00   1248  144 0.1277 0.1962      5.0568      5.3311|
| 11:  2.2595 -  2.1890 0.97   1261  136 0.1284 0.1853      5.0298      5.2924|
| 12:  2.1890 -  2.1266 0.98   1231  138 0.1230 0.1924      4.9483      5.3043|
| 13:  2.1266 -  2.0708 0.99   1241  142 0.1272 0.1824      4.8726      5.1156|
| 14:  2.0708 -  2.0204 0.84   1081  116 0.1197 0.1822      4.7456      4.9688|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2532 -  4.8213  1372   152  0.94   9.51   0.97     0.94       7895.10|
|  2:  4.8213 -  3.8471  1315   146  0.95   8.47   1.00     0.98       9661.50|
|  3:  3.8471 -  3.3667  1287   144  0.93  11.84   1.01     1.00      11347.84|
|  4:  3.3667 -  3.0616  1278   144  0.92  14.13   1.00     0.98      11138.41|
|  5:  3.0616 -  2.8437  1279   141  0.89  17.04   0.99     0.97       9514.33|
|  6:  2.8437 -  2.6770  1269   139  0.90  16.75   0.98     0.96       8133.92|
|  7:  2.6770 -  2.5436  1269   140  0.89  17.11   0.98     0.97       7169.90|
|  8:  2.5436 -  2.4333  1255   143  0.90  16.25   0.98     0.96       6031.27|
|  9:  2.4333 -  2.3400  1244   134  0.90  16.32   1.00     0.96       5639.03|
| 10:  2.3400 -  2.2595  1248   144  0.90  16.14   0.99     0.95       4890.91|
| 11:  2.2595 -  2.1890  1261   136  0.89  17.67   0.99     0.95       5024.69|
| 12:  2.1890 -  2.1266  1231   138  0.91  15.86   0.99     0.98       4371.20|
| 13:  2.1266 -  2.0708  1241   142  0.90  16.75   0.99     0.97       3776.00|
| 14:  2.0708 -  2.0204  1081   116  0.91  15.51   0.96     0.92       2780.92|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2780.92 max =        11347.84 mean =      7037.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.89|
|phase err.(test): min =        0.00 max =           89.73 mean =        14.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1673   ksol= 0.33   Bsol= 69.58   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-0.26,0.61,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209807                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1673   ksol= 0.33   Bsol= 69.58   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-0.26,0.61,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209807                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.8213 0.99   1372  152 0.1038 0.1370      5.4247       5.556|
|  2:  4.8213 -  3.8471 0.99   1315  146 0.0879 0.1162      5.4689      5.6712|
|  3:  3.8471 -  3.3667 0.99   1287  144 0.1106 0.1544      5.5203      5.8608|
|  4:  3.3667 -  3.0616 0.99   1278  144 0.1301 0.1659      5.5122      5.6728|
|  5:  3.0616 -  2.8437 0.99   1279  141 0.1480 0.1862        5.42        5.61|
|  6:  2.8437 -  2.6770 0.99   1269  139 0.1335 0.1997         5.3      5.5138|
|  7:  2.6770 -  2.5436 0.99   1269  140 0.1414 0.1786      5.2536       5.461|
|  8:  2.5436 -  2.4333 0.98   1255  143 0.1309 0.1734      5.1569      5.3653|
|  9:  2.4333 -  2.3400 0.98   1244  134 0.1264 0.1787      5.1021      5.3269|
| 10:  2.3400 -  2.2595 1.00   1248  144 0.1277 0.1962      5.0568      5.3311|
| 11:  2.2595 -  2.1890 0.97   1261  136 0.1284 0.1853      5.0298      5.2924|
| 12:  2.1890 -  2.1266 0.98   1231  138 0.1230 0.1924      4.9483      5.3043|
| 13:  2.1266 -  2.0708 0.99   1241  142 0.1272 0.1824      4.8726      5.1156|
| 14:  2.0708 -  2.0204 0.84   1081  116 0.1197 0.1822      4.7456      4.9688|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2532 -  4.8213  1372   152  0.94   9.51   0.97     0.94       7895.10|
|  2:  4.8213 -  3.8471  1315   146  0.95   8.47   1.00     0.98       9661.50|
|  3:  3.8471 -  3.3667  1287   144  0.93  11.84   1.01     1.00      11347.84|
|  4:  3.3667 -  3.0616  1278   144  0.92  14.13   1.00     0.98      11138.41|
|  5:  3.0616 -  2.8437  1279   141  0.89  17.04   0.99     0.97       9514.33|
|  6:  2.8437 -  2.6770  1269   139  0.90  16.75   0.98     0.96       8133.92|
|  7:  2.6770 -  2.5436  1269   140  0.89  17.11   0.98     0.97       7169.90|
|  8:  2.5436 -  2.4333  1255   143  0.90  16.25   0.98     0.96       6031.27|
|  9:  2.4333 -  2.3400  1244   134  0.90  16.32   1.00     0.96       5639.03|
| 10:  2.3400 -  2.2595  1248   144  0.90  16.14   0.99     0.95       4890.91|
| 11:  2.2595 -  2.1890  1261   136  0.89  17.67   0.99     0.95       5024.69|
| 12:  2.1890 -  2.1266  1231   138  0.91  15.86   0.99     0.98       4371.20|
| 13:  2.1266 -  2.0708  1241   142  0.90  16.75   0.99     0.97       3776.00|
| 14:  2.0708 -  2.0204  1081   116  0.91  15.51   0.96     0.92       2780.92|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2780.92 max =        11347.84 mean =      7037.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.89|
|phase err.(test): min =        0.00 max =           89.73 mean =        14.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.381)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.48    99.18   15.85    None  None   None       |
|    all(noH): 2823   0      3.48    99.18   15.85    None  None   None       |
|    Sol.    : 438    0      4.74    99.18   40.69    None  None   None       |
|    Mac.    : 2385   0      3.48    88.85   11.29    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:     3.477 -  13.047: 1838   |   5:    51.330 -  60.900:   83        |
|      1:    13.047 -  22.618:  477   |   6:    60.900 -  70.471:   52        |
|      2:    22.618 -  32.188:  142   |   7:    70.471 -  80.041:   17        |
|      3:    32.188 -  41.759:  118   |   8:    80.041 -  89.612:   11        |
|      4:    41.759 -  51.330:   83   |   9:    89.612 -  99.183:    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)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.371 - 4.867
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 339
   mapped sites are within: 0.733 - 4.867

peak=    9.774 closest distance to " CG2 VAL A 230 " =    1.451
peak=    7.114 closest distance to " CG2 VAL A 296 " =    1.132
peak=    5.941 closest distance to " CG  LEU A   5 " =    1.246
peak=    5.623 closest distance to " O   HOH Z 111 " =    2.074
peak=    5.556 closest distance to " CB  GLN A 223 " =    1.456
peak=    5.279 closest distance to " CG  LEU A 228 " =    1.243
peak=    5.186 closest distance to " O   HOH Z 232 " =    2.206
peak=    5.150 closest distance to " CB  SER A  63 " =    1.331
peak=    4.984 closest distance to " CA  VAL A 230 " =    1.269
peak=    4.776 closest distance to " CD2 LEU A   5 " =    1.159
peak=    4.710 closest distance to " O   PRO A 198 " =    1.590
peak=    4.710 closest distance to " CG  PRO A 198 " =    1.315
peak=    4.655 closest distance to " CZ  PHE A 218 " =    1.108
peak=    4.630 closest distance to " O   HOH Z 265 " =    2.214
peak=    4.565 closest distance to " CB  GLN A 183 " =    1.242
peak=    4.522 closest distance to " CB  TRP A 266 " =    0.989
peak=    4.427 closest distance to " CG  PRO A 243 " =    1.146
peak=    4.396 closest distance to " CB  ASP A 124 " =    0.759
peak=    4.379 closest distance to " O   HOH Z 425 " =    1.521
peak=    4.371 closest distance to " O   HOH Z 369 " =    2.017
peak=    4.323 closest distance to " O   HOH Z 184 " =    1.659
peak=    4.308 closest distance to " CG  PRO A 213 " =    1.272
peak=    4.302 closest distance to " O   HOH Z 368 " =    2.301
peak=    4.298 closest distance to " O   HOH Z 411 " =    3.664
peak=    4.295 closest distance to " CB  VAL A 296 " =    1.095
peak=    4.292 closest distance to " NH1AARG A 145 " =    1.212
peak=    4.264 closest distance to " CB  ARG A 190 " =    1.694
peak=    4.244 closest distance to " CD2 LEU A 228 " =    1.193
peak=    4.187 closest distance to " O   HOH Z 303 " =    2.188
peak=    4.179 closest distance to " NE2 GLN A  11 " =    1.082
peak=    4.166 closest distance to " O   HOH Z 236 " =    1.946
peak=    4.165 closest distance to " O   HOH Z 126 " =    1.609
peak=    4.152 closest distance to " CG2 THR A 221 " =    0.981
peak=    4.146 closest distance to " CB  ASP A 140 " =    0.820
peak=    4.143 closest distance to " CZ  PHE A 192 " =    1.061
peak=    4.121 closest distance to " O   HOH Z 298 " =    1.867
peak=    4.100 closest distance to " O   HOH Z 102 " =    1.422
peak=    4.090 closest distance to " O   HOH Z 261 " =    1.772
peak=    4.077 closest distance to " O   SER A  87 " =    2.369
peak=    4.062 closest distance to " O   HOH Z 247 " =    1.470
peak=    4.052 closest distance to " CB  GLU A 128 " =    1.090
peak=    4.049 closest distance to " CA  ALA A  51 " =    0.953
peak=    4.048 closest distance to " CB  ARG A  79 " =    1.506
peak=    4.034 closest distance to " CB  ASN A  39 " =    0.834
peak=    4.004 closest distance to " O   HOH Z 234 " =    3.835
peak=    3.986 closest distance to " CB  GLU A 152 " =    1.164
peak=    3.986 closest distance to " CD1AILE A 234 " =    0.925
peak=    3.982 closest distance to " CG  MET A 185 " =    1.329
peak=    3.971 closest distance to " CB  GLU A 277 " =    3.744
peak=    3.970 closest distance to " CB  ASN A 142 " =    0.932
peak=    3.968 closest distance to " CD  ARG A  66 " =    2.478
peak=    3.963 closest distance to " CB  ASN A 148 " =    1.360
peak=    3.961 closest distance to " O   ASP A 124 " =    1.178
peak=    3.955 closest distance to " CB  TYR A 169 " =    0.733
peak=    3.944 closest distance to " CA  ALA A 295 " =    1.079
peak=    3.912 closest distance to " CG1 VAL A 153 " =    1.011
peak=    3.908 closest distance to " CA  TYR A  30 " =    0.989
peak=    3.901 closest distance to " O   HOH Z  78 " =    2.233
peak=    3.900 closest distance to " O   HOH Z 427 " =    3.195
peak=    3.891 closest distance to " O   HOH Z 316 " =    3.212
peak=    3.873 closest distance to " O   HOH Z  48 " =    1.739
peak=    3.871 closest distance to " ND2 ASN A 249 " =    1.998
peak=    3.860 closest distance to " O   HOH Z 403 " =    1.700
peak=    3.854 closest distance to " CB  ARG A 275 " =    0.871
peak=    3.849 closest distance to " CD ALYS A 290 " =    1.090
peak=    3.832 closest distance to " OD1 ASN A  69 " =    2.520
peak=    3.827 closest distance to " CB  ALA A   9 " =    1.649
peak=    3.817 closest distance to " O   HOH Z  57 " =    1.462
peak=    3.816 closest distance to " CD  ARG A 159 " =    0.767
peak=    3.809 closest distance to " CB  ALA A 291 " =    1.330
peak=    3.800 closest distance to " CG1 ILE A  33 " =    1.309
peak=    3.797 closest distance to " O   HOH Z 126 " =    2.016
peak=    3.793 closest distance to " CB AVAL A  41 " =    1.152
peak=    3.787 closest distance to " O   HOH Z  88 " =    3.302
peak=    3.782 closest distance to " CB  PRO A  54 " =    0.820
peak=    3.781 closest distance to " CD  LYS A 166 " =    1.282
peak=    3.776 closest distance to " CB  SER A   3 " =    1.434
peak=    3.773 closest distance to " O   HOH Z 272 " =    2.001
peak=    3.762 closest distance to " O   HOH Z 346 " =    1.544
peak=    3.761 closest distance to " O   HOH Z 437 " =    1.825
peak=    3.757 closest distance to " O   HOH Z 423 " =    1.711
peak=    3.754 closest distance to " CB  GLU A  46 " =    0.933
peak=    3.750 closest distance to " CA  LEU A 282 " =    1.068
peak=    3.744 closest distance to " N   SER A 135 " =    1.422
peak=    3.739 closest distance to " O   HOH Z  49 " =    1.012
peak=    3.726 closest distance to " CD1 LEU A  96 " =    0.778
peak=    3.720 closest distance to " O   HOH Z 214 " =    2.396
peak=    3.719 closest distance to " CB  VAL A 202 " =    1.559
peak=    3.713 closest distance to " CA  SER A  87 " =    0.893
peak=    3.712 closest distance to " CD  ARG A 269 " =    0.968
peak=    3.706 closest distance to " CB  LEU A 143 " =    1.248
peak=    3.706 closest distance to " CG  ARG A 138 " =    1.245
peak=    3.704 closest distance to " OD1 ASN A 217 " =    1.610
peak=    3.685 closest distance to " O   HOH Z 422 " =    2.635
peak=    3.683 closest distance to " O   HOH Z  15 " =    1.939
peak=    3.680 closest distance to " CB  VAL A 265 " =    1.328
peak=    3.675 closest distance to " O   HOH Z  63 " =    1.910
peak=    3.674 closest distance to " CA  ASP A 191 " =    0.776
peak=    3.664 closest distance to " O   HOH Z  43 " =    1.933
peak=    3.664 closest distance to " NZ  LYS A  48 " =    1.347
peak=    3.654 closest distance to " O   HOH Z  80 " =    1.881
peak=    3.646 closest distance to " CG1 ILE A  49 " =    1.614
peak=    3.642 closest distance to " CA  GLU A 152 " =    0.908
peak=    3.635 closest distance to " NH1 ARG A  56 " =    1.035
peak=    3.634 closest distance to " CA  THR A 264 " =    0.779
peak=    3.632 closest distance to " O   HOH Z 285 " =    2.835
peak=    3.629 closest distance to " CA  ILE A 106 " =    0.770
peak=    3.627 closest distance to " O   HOH Z 359 " =    1.577
peak=    3.627 closest distance to " O   HOH Z  21 " =    1.754
peak=    3.626 closest distance to " ND2 ASN A 187 " =    1.455
peak=    3.614 closest distance to " CB  ALA A 242 " =    0.799
peak=    3.612 closest distance to " ND1 HIS A  81 " =    1.691
peak=    3.611 closest distance to " CB  ALA A 248 " =    1.186
peak=    3.606 closest distance to " CB  ALA A 104 " =    0.793
peak=    3.603 closest distance to " CA  ALA A  21 " =    1.215
peak=    3.600 closest distance to " NH2 ARG A 156 " =    1.134
peak=    3.600 closest distance to " CG  LEU A 167 " =    1.168
peak=    3.599 closest distance to " OG BSER A 164 " =    2.183
peak=    3.599 closest distance to " N   ASN A  39 " =    1.178
peak=    3.598 closest distance to " CA  ARG A 195 " =    1.201
peak=    3.593 closest distance to " CG BARG A 275 " =    1.481
peak=    3.591 closest distance to " O   HOH Z 183 " =    1.153
peak=    3.580 closest distance to " O   MET A 105 " =    1.767
peak=    3.578 closest distance to " O   HOH Z  68 " =    1.680
peak=    3.576 closest distance to " CG AARG A 275 " =    1.256
peak=    3.574 closest distance to " O   HOH Z 188 " =    2.995
peak=    3.573 closest distance to " O   HOH Z 433 " =    1.418
peak=    3.572 closest distance to " O   HOH Z 201 " =    2.885
peak=    3.561 closest distance to " O   HOH Z 193 " =    2.240
peak=    3.551 closest distance to " CD1 LEU A   5 " =    1.314
peak=    3.549 closest distance to " O   HOH Z 404 " =    1.513
peak=    3.549 closest distance to " O   HOH Z   4 " =    1.752
peak=    3.549 closest distance to " O   HOH Z 213 " =    1.911
peak=    3.540 closest distance to " CB  THR A  82 " =    1.415
peak=    3.537 closest distance to " O   HOH Z 134 " =    1.427
peak=    3.534 closest distance to " CB  LEU A 228 " =    1.180
peak=    3.530 closest distance to " O   HOH Z 158 " =    3.075
peak=    3.522 closest distance to " CD2 TRP A 179 " =    1.321
peak=    3.521 closest distance to " N   PHE A 130 " =    1.220
peak=    3.504 closest distance to " CD1 LEU A 300 " =    1.193
peak=    3.504 closest distance to " O   HOH Z 163 " =    1.671
peak=    3.503 closest distance to " CA  GLY A 211 " =    1.367
peak=    3.500 closest distance to " OG  SER A  22 " =    2.900
peak=    3.499 closest distance to " O   HOH Z 227 " =    1.774
peak=    3.490 closest distance to " NH1 ARG A  14 " =    1.015
peak=    3.482 closest distance to " O   HOH Z  19 " =    2.318
peak=    3.479 closest distance to " CG2 VAL A 296 " =    1.589
peak=    3.475 closest distance to " O   HOH Z 393 " =    3.957
peak=    3.469 closest distance to " CB  ASN A 187 " =    1.023
peak=    3.468 closest distance to " O   HOH Z 250 " =    1.380
peak=    3.467 closest distance to " O   HOH Z 112 " =    1.563
peak=    3.464 closest distance to " O   HOH Z  61 " =    1.625
peak=    3.464 closest distance to " N   VAL A 126 " =    1.483
peak=    3.461 closest distance to " CA  VAL A  41 " =    0.800
peak=    3.456 closest distance to " CE3 TRP A  85 " =    1.183
peak=    3.453 closest distance to " CA  ALA A 158 " =    1.136
peak=    3.452 closest distance to " O   HOH Z 402 " =    1.509
peak=    3.452 closest distance to " O   HOH Z 280 " =    2.944
peak=    3.448 closest distance to " CA  GLN A  88 " =    1.367
peak=    3.445 closest distance to " O   HOH Z 104 " =    2.545
peak=    3.442 closest distance to " CB  SER A 273 " =    0.912
peak=    3.435 closest distance to " O   HOH Z 132 " =    2.687
peak=    3.433 closest distance to " CA  LYS A 181 " =    1.077
peak=    3.427 closest distance to " CB  LEU A  83 " =    0.757
peak=    3.415 closest distance to " O  BHOH Z 338 " =    2.443
peak=    3.410 closest distance to " N   ARG A 190 " =    1.047
peak=    3.405 closest distance to " O   HOH Z 148 " =    2.045
peak=    3.403 closest distance to " CB  SER A 216 " =    0.850
peak=    3.402 closest distance to " O   HOH Z 313 " =    1.806
peak=    3.398 closest distance to " CB  ILE A 120 " =    1.390
peak=    3.397 closest distance to " O   HOH Z 193 " =    1.737
peak=    3.395 closest distance to " O   HOH Z 368 " =    3.505
peak=    3.389 closest distance to " CA  THR A 221 " =    0.844
peak=    3.387 closest distance to " CA  ASP A 162 " =    1.081
peak=    3.386 closest distance to " O   HOH Z 371 " =    3.005
peak=    3.385 closest distance to " CG  GLN A  88 " =    1.045
peak=    3.384 closest distance to " O   ALA A 165 " =    1.380
peak=    3.383 closest distance to " O   HOH Z 109 " =    2.580
peak=    3.381 closest distance to " O   HOH Z 139 " =    4.867
peak=    3.380 closest distance to " CZ3 TRP A 274 " =    4.772
peak=    3.376 closest distance to " O   HOH Z 383 " =    2.141
peak=    3.376 closest distance to " CZ3 TRP A  85 " =    0.944
peak=    3.369 closest distance to " CA  ASP A 124 " =    0.739
peak=    3.367 closest distance to " O   HOH Z 290 " =    1.226
peak=    3.365 closest distance to " O   HOH Z 185 " =    2.009
peak=    3.364 closest distance to " CB  SER A 210 " =    0.931
peak=    3.361 closest distance to " CB  ALA A 161 " =    0.884
peak=    3.361 closest distance to " ND2 ASN A 249 " =    0.824
peak=    3.360 closest distance to " O   HOH Z 133 " =    2.437
peak=    3.357 closest distance to " CA  ILE A  33 " =    1.675
peak=    3.357 closest distance to " CA  MET A 105 " =    0.940
peak=    3.354 closest distance to " O   HOH Z 188 " =    1.998
peak=    3.352 closest distance to " O   HOH Z 295 " =    1.528
peak=    3.350 closest distance to " O   HOH Z 293 " =    1.822
peak=    3.346 closest distance to " CB  PRO A 243 " =    1.222
peak=    3.344 closest distance to " CB  MET A  40 " =    0.766
peak=    3.343 closest distance to " CG  GLU A  37 " =    0.921
peak=    3.342 closest distance to " CB  GLN A  89 " =    1.127
peak=    3.341 closest distance to " CD2 LEU A 255 " =    1.568
peak=    3.340 closest distance to " NE2 HIS A 207 " =    1.168
peak=    3.337 closest distance to " CA  VAL A 112 " =    1.112
peak=    3.337 closest distance to " CD  PRO A  54 " =    0.912
peak=    3.336 closest distance to " CB  TRP A 150 " =    1.425
peak=    3.336 closest distance to " CA  ASN A 127 " =    1.094
peak=    3.335 closest distance to " O   HOH Z 313 " =    1.789
peak=    3.327 closest distance to " O   HOH Z 344 " =    3.108
peak=    3.326 closest distance to " O   HOH Z  48 " =    1.389
peak=    3.325 closest distance to " CA  MET A  40 " =    1.188
peak=    3.323 closest distance to " CA  ASP A 140 " =    1.374
peak=    3.321 closest distance to " O   HOH Z 291 " =    1.591
peak=    3.319 closest distance to " CG2 ILE A 234 " =    0.947
peak=    3.317 closest distance to " O   GLN A 278 " =    1.208
peak=    3.315 closest distance to " O   HOH Z 133 " =    1.716
peak=    3.308 closest distance to " CD  ARG A 219 " =    1.113
peak=    3.308 closest distance to " CB  PHE A 204 " =    0.943
peak=    3.308 closest distance to " CG  ARG A 269 " =    1.765
peak=    3.306 closest distance to " O   HOH Z 353 " =    2.767
peak=    3.306 closest distance to " CG1 VAL A 296 " =    1.248
peak=    3.304 closest distance to " O   HOH Z 141 " =    1.705
peak=    3.302 closest distance to " O   HOH Z  56 " =    1.708
peak=    3.302 closest distance to " O   ASN A  74 " =    1.555
peak=    3.301 closest distance to " O   HOH Z 125 " =    3.875
peak=    3.299 closest distance to " O   HOH Z  89 " =    1.806
peak=    3.296 closest distance to " O   HOH Z 172 " =    3.964
peak=    3.295 closest distance to " O   HOH Z 180 " =    2.037
peak=    3.294 closest distance to " O   HOH Z 271 " =    2.738
peak=    3.293 closest distance to " O   PRO A 213 " =    1.532
peak=    3.291 closest distance to " O   HOH Z 355 " =    1.779
peak=    3.286 closest distance to " O   TRP A 274 " =    1.819
peak=    3.285 closest distance to " CB  PRO A  54 " =    1.280
peak=    3.278 closest distance to " CA  PHE A  59 " =    1.096
peak=    3.274 closest distance to " CZ3 TRP A  92 " =    1.360
peak=    3.272 closest distance to " CB  TYR A  30 " =    1.075
peak=    3.268 closest distance to " CA  ALA A 160 " =    1.036
peak=    3.268 closest distance to " CG1 ILE A 151 " =    1.217
peak=    3.266 closest distance to " CA  ARG A  36 " =    1.120
peak=    3.263 closest distance to " CG  MET A 185 " =    0.994
peak=    3.262 closest distance to " CA  ARG A 139 " =    1.210
peak=    3.262 closest distance to " CA  VAL A 125 " =    1.166
peak=    3.261 closest distance to " CZ  PHE A  38 " =    1.189
peak=    3.261 closest distance to " CG2 THR A 220 " =    0.829
peak=    3.260 closest distance to " O   HOH Z  30 " =    1.141
peak=    3.259 closest distance to " OE1 GLN A  55 " =    1.316
peak=    3.258 closest distance to " O   HOH Z 281 " =    4.793
peak=    3.254 closest distance to " CG2 ILE A 106 " =    0.853
peak=    3.251 closest distance to " N   ASN A 127 " =    1.209
peak=    3.246 closest distance to " CB  TRP A 179 " =    1.396
peak=    3.241 closest distance to " O   HOH Z 187 " =    2.347
peak=    3.241 closest distance to " O   HOH Z 193 " =    2.051
peak=    3.241 closest distance to " CA  GLU A  46 " =    0.786
peak=    3.240 closest distance to " O   HOH Z  44 " =    1.888
peak=    3.240 closest distance to " CA  ASN A 215 " =    1.115
peak=    3.239 closest distance to " O   HOH Z 406 " =    1.537
peak=    3.238 closest distance to " CB  THR A  31 " =    1.529
peak=    3.238 closest distance to " CB  SER A 212 " =    1.294
peak=    3.237 closest distance to " O   ASN A 209 " =    1.297
peak=    3.233 closest distance to " CG1 VAL A 174 " =    1.104
peak=    3.229 closest distance to " CZ3 TRP A 266 " =    1.127
peak=    3.226 closest distance to " OG  SER A  28 " =    1.589
peak=    3.226 closest distance to " O   HOH Z 435 " =    2.038
peak=    3.224 closest distance to " CA  ALA A 154 " =    1.033
peak=    3.224 closest distance to " CA  ALA A 100 " =    1.096
peak=    3.223 closest distance to " CB  ALA A 100 " =    1.332
peak=    3.223 closest distance to " O   ASP A 200 " =    1.568
peak=    3.220 closest distance to " CB  ALA A 248 " =    1.390
peak=    3.216 closest distance to " CA  LYS A 117 " =    1.188
peak=    3.213 closest distance to " O   HOH Z 326 " =    2.239
peak=    3.208 closest distance to " CA  GLY A  98 " =    1.141
peak=    3.208 closest distance to " CA  TYR A 116 " =    1.461
peak=    3.206 closest distance to " O   HOH Z 263 " =    1.614
peak=    3.205 closest distance to " N   ALA A 256 " =    1.119
peak=    3.204 closest distance to " O   HOH Z 199 " =    1.717
peak=    3.203 closest distance to " O   HOH Z  22 " =    2.345
peak=    3.200 closest distance to " CE2 TYR A 186 " =    0.932
peak=    3.199 closest distance to " O   ALA A 158 " =    1.376
peak=    3.196 closest distance to " CB  SER A 288 " =    1.325
peak=    3.189 closest distance to " ND1 HIS A  86 " =    1.561
peak=    3.186 closest distance to " O   HOH Z 197 " =    1.874
peak=    3.186 closest distance to " CG  PHE A 204 " =    0.962
peak=    3.183 closest distance to " O   HOH Z 134 " =    2.505
peak=    3.180 closest distance to " CA  ASN A 217 " =    1.415
peak=    3.180 closest distance to " CD1 ILE A 106 " =    0.943
peak=    3.177 closest distance to " O   HOH Z 128 " =    2.322
peak=    3.177 closest distance to " O   HOH Z 394 " =    1.350
peak=    3.176 closest distance to " O   HOH Z 116 " =    1.876
peak=    3.176 closest distance to " CE  MET A 113 " =    1.809
peak=    3.174 closest distance to " O   HOH Z 130 " =    2.239
peak=    3.169 closest distance to " O   TYR A 116 " =    1.242
peak=    3.169 closest distance to " O   HOH Z 155 " =    3.341
peak=    3.168 closest distance to " CB  ASN A 215 " =    1.209
peak=    3.168 closest distance to " O   HOH Z 403 " =    2.210
peak=    3.163 closest distance to " CE2 TYR A  30 " =    0.825
peak=    3.162 closest distance to " O   HOH Z 203 " =    1.870
peak=    3.161 closest distance to " O   HOH Z  40 " =    1.835
peak=    3.155 closest distance to " NH1BARG A 275 " =    1.317
peak=    3.154 closest distance to " CB  ALA A  43 " =    1.022
peak=    3.154 closest distance to " NH2 ARG A  79 " =    1.373
peak=    3.150 closest distance to " CG1BVAL A  72 " =    1.747
peak=    3.147 closest distance to " O   HOH Z 298 " =    2.409
peak=    3.146 closest distance to " O   HOH Z 409 " =    2.853
peak=    3.144 closest distance to " CE  LYS A  76 " =    0.852
peak=    3.142 closest distance to " CA  ASN A  74 " =    1.250
peak=    3.136 closest distance to " CB  SER A  62 " =    0.742
peak=    3.136 closest distance to " CG2 THR A  29 " =    1.439
peak=    3.134 closest distance to " CB  ALA A 227 " =    1.046
peak=    3.129 closest distance to " O   HOH Z 329 " =    2.923
peak=    3.129 closest distance to " O   THR A  31 " =    1.545
peak=    3.126 closest distance to " CB  SER A  26 " =    1.809
peak=    3.122 closest distance to " CB  ALA A  10 " =    0.980
peak=    3.117 closest distance to " C   ALA A 299 " =    0.949
peak=    3.116 closest distance to " CB  GLN A 103 " =    0.929
peak=    3.113 closest distance to " O   HOH Z  49 " =    3.558
peak=    3.111 closest distance to " O   HOH Z 327 " =    1.810
peak=    3.110 closest distance to " N   ARG A 156 " =    1.459
peak=    3.108 closest distance to " O   HOH Z 391 " =    3.059
peak=    3.102 closest distance to " O   HOH Z 294 " =    1.572
peak=    3.099 closest distance to " N   GLN A 278 " =    1.040
peak=    3.095 closest distance to " OD1 ASN A 301 " =    1.726
peak=    3.094 closest distance to " O   HOH Z 215 " =    3.157
peak=    3.087 closest distance to " NE2 HIS A 115 " =    1.019
peak=    3.085 closest distance to " CA  LYS A 290 " =    1.277
peak=    3.073 closest distance to " CG  GLN A 144 " =    0.829
peak=    3.070 closest distance to " O   HOH Z 156 " =    2.901
peak=    3.062 closest distance to " CG2 VAL A 257 " =    0.827
peak=    3.032 closest distance to " O   HOH Z 152 " =    2.291
peak=    3.026 closest distance to " CB  ARG A 138 " =    1.003
peak=    3.020 closest distance to " O   HOH Z  63 " =    0.978

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.779 - 5.348
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.779 - 5.348

peak=   -5.447 closest distance to " CG2 VAL A 230 " =    0.782
peak=   -4.204 closest distance to " CG1 VAL A 112 " =    2.650
peak=   -4.194 closest distance to " CD2 LEU A 237 " =    2.774
peak=   -4.182 closest distance to " CB  ALA A 161 " =    2.610
peak=   -4.138 closest distance to " O   HOH Z 166 " =    1.786
peak=   -4.099 closest distance to " CD1 LEU A   5 " =    2.582
peak=   -4.088 closest distance to " O   HOH Z 211 " =    1.154
peak=   -4.085 closest distance to " CD  ARG A 156 " =    2.043
peak=   -4.065 closest distance to " CG  ASP A 231 " =    0.779
peak=   -4.004 closest distance to " CG  GLN A 223 " =    2.221
peak=   -3.996 closest distance to " CB  ALA A 291 " =    2.562
peak=   -3.972 closest distance to " O   HOH Z  52 " =    1.826
peak=   -3.967 closest distance to " O   SER A 271 " =    2.259
peak=   -3.939 closest distance to " CE2 TYR A  30 " =    2.788
peak=   -3.936 closest distance to " CB  PRO A 243 " =    2.686
peak=   -3.928 closest distance to " CD  GLN A  58 " =    0.965
peak=   -3.921 closest distance to " O   HOH Z  10 " =    1.610
peak=   -3.905 closest distance to " O   HOH Z 351 " =    1.548
peak=   -3.893 closest distance to " CA  ASP A 298 " =    1.085
peak=   -3.892 closest distance to " CG2BVAL A  41 " =    2.751
peak=   -3.887 closest distance to " O   HOH Z 231 " =    2.020
peak=   -3.869 closest distance to " O   HOH Z 290 " =    1.311
peak=   -3.865 closest distance to " CD1 PHE A  59 " =    2.020
peak=   -3.839 closest distance to " C   ALA A 158 " =    1.328
peak=   -3.830 closest distance to " O   HOH Z 411 " =    5.282
peak=   -3.822 closest distance to " O   HOH Z 231 " =    1.395
peak=   -3.802 closest distance to " OG  SER A  97 " =    2.261
peak=   -3.789 closest distance to " O   HOH Z 394 " =    1.577
peak=   -3.788 closest distance to " CE3 TRP A  70 " =    1.788
peak=   -3.771 closest distance to " OE1 GLN A  88 " =    1.282
peak=   -3.764 closest distance to " OD1 ASN A 148 " =    1.472
peak=   -3.760 closest distance to " O   HOH Z 103 " =    2.104
peak=   -3.756 closest distance to " O   HOH Z  73 " =    2.159
peak=   -3.752 closest distance to " CG1 VAL A 296 " =    1.401
peak=   -3.745 closest distance to " O   PRO A 198 " =    1.254
peak=   -3.738 closest distance to " O   GLY A 203 " =    2.341
peak=   -3.738 closest distance to " CG  ARG A 269 " =    2.353
peak=   -3.730 closest distance to " C   ASN A 285 " =    2.494
peak=   -3.728 closest distance to " O   HOH Z 216 " =    1.486
peak=   -3.722 closest distance to " NE2 GLN A 194 " =    1.896
peak=   -3.718 closest distance to " NH2 ARG A  66 " =    1.883
peak=   -3.711 closest distance to " CG  MET A 105 " =    0.934
peak=   -3.711 closest distance to " OG  SER A  87 " =    1.691
peak=   -3.704 closest distance to " CD  ARG A  14 " =    3.280
peak=   -3.700 closest distance to " CG1 VAL A 112 " =    2.775
peak=   -3.686 closest distance to " N   THR A  18 " =    1.286
peak=   -3.675 closest distance to " CZ2 TRP A  92 " =    2.842
peak=   -3.664 closest distance to " O   HOH Z 184 " =    1.381
peak=   -3.642 closest distance to " O   HOH Z 177 " =    1.651
peak=   -3.637 closest distance to " CA  GLY A 241 " =    2.338
peak=   -3.616 closest distance to " CD2 LEU A 167 " =    1.846
peak=   -3.613 closest distance to " CA  GLY A 241 " =    3.155
peak=   -3.612 closest distance to " CG  TRP A 266 " =    1.895
peak=   -3.608 closest distance to " O   HOH Z 185 " =    2.470
peak=   -3.605 closest distance to " N   SER A   3 " =    2.184
peak=   -3.603 closest distance to " O   GLY A  80 " =    2.574
peak=   -3.602 closest distance to " CD1 LEU A 101 " =    2.800
peak=   -3.586 closest distance to " N   ALA A 226 " =    2.310
peak=   -3.576 closest distance to " NH2AARG A 275 " =    5.348
peak=   -3.550 closest distance to " C   HIS A 108 " =    1.149
peak=   -3.546 closest distance to " CD2 TYR A 293 " =    1.936
peak=   -3.540 closest distance to " O   HOH Z  60 " =    2.239
peak=   -3.539 closest distance to " O   HOH Z 241 " =    1.079
peak=   -3.533 closest distance to " CZ3 TRP A 179 " =    1.116
peak=   -3.520 closest distance to " O   HOH Z  13 " =    1.620
peak=   -3.514 closest distance to " OD2 ASP A  50 " =    2.318
peak=   -3.512 closest distance to " O   HOH Z 113 " =    1.827
peak=   -3.511 closest distance to " O   HOH Z 174 " =    2.427
peak=   -3.510 closest distance to " CD1 ILE A 151 " =    2.435
peak=   -3.502 closest distance to " CD2 PHE A  59 " =    2.636
peak=   -3.502 closest distance to " CD  PRO A 213 " =    2.204
peak=   -3.500 closest distance to " O   PRO A 163 " =    2.164
peak=   -3.500 closest distance to " CD  GLN A  88 " =    0.860
peak=   -3.495 closest distance to " O   HOH Z  11 " =    1.855
peak=   -3.494 closest distance to " CG  PHE A  59 " =    2.109
peak=   -3.486 closest distance to " O   VAL A 189 " =    2.573
peak=   -3.467 closest distance to " CG  LEU A 101 " =    2.492
peak=   -3.464 closest distance to " O   HOH Z  17 " =    1.355
peak=   -3.462 closest distance to " O   HOH Z 111 " =    2.092
peak=   -3.462 closest distance to " CA  GLY A 203 " =    2.387
peak=   -3.461 closest distance to " O   HOH Z 407 " =    3.451
peak=   -3.456 closest distance to " CH2 TRP A 177 " =    2.299
peak=   -3.452 closest distance to " O   HOH Z  94 " =    2.093
peak=   -3.446 closest distance to " O   HOH Z 210 " =    0.973
peak=   -3.442 closest distance to " CD1 LEU A 228 " =    2.493
peak=   -3.439 closest distance to " O   HOH Z  19 " =    2.190
peak=   -3.426 closest distance to " CA  GLY A 133 " =    2.308
peak=   -3.426 closest distance to " O   HOH Z 377 " =    1.234
peak=   -3.425 closest distance to " NE2 GLN A  88 " =    0.956
peak=   -3.420 closest distance to " O   GLY A 211 " =    1.483
peak=   -3.420 closest distance to " CB  ALA A 114 " =    2.548
peak=   -3.410 closest distance to " O   HOH Z 113 " =    2.304
peak=   -3.406 closest distance to " OXT GLY A 302 " =    3.088
peak=   -3.404 closest distance to " CD1 LEU A 101 " =    2.565
peak=   -3.404 closest distance to " O   HOH Z 234 " =    4.545
peak=   -3.399 closest distance to " N   THR A 157 " =    1.575
peak=   -3.394 closest distance to " N   ALA A  43 " =    2.707
peak=   -3.392 closest distance to " O   HOH Z 426 " =    1.775
peak=   -3.390 closest distance to " CG2 VAL A 296 " =    1.507
peak=   -3.389 closest distance to " C   LEU A 143 " =    1.015
peak=   -3.389 closest distance to " CD  GLN A 223 " =    0.817
peak=   -3.384 closest distance to " CG  GLU A 277 " =    1.364
peak=   -3.380 closest distance to " O   SER A 276 " =    1.765
peak=   -3.380 closest distance to " O   HOH Z 317 " =    2.195
peak=   -3.375 closest distance to " O   HOH Z 114 " =    1.489
peak=   -3.373 closest distance to " NH2 ARG A  79 " =    1.653
peak=   -3.370 closest distance to " O   HOH Z 136 " =    2.452
peak=   -3.362 closest distance to " O   HOH Z 106 " =    1.985
peak=   -3.359 closest distance to " ND2 ASN A  60 " =    1.444
peak=   -3.345 closest distance to " O   HOH Z 232 " =    1.764
peak=   -3.339 closest distance to " O   HOH Z  44 " =    2.141
peak=   -3.338 closest distance to " OG BSER A 134 " =    1.349
peak=   -3.333 closest distance to " O   VAL A  67 " =    2.537
peak=   -3.332 closest distance to " O   HOH Z 368 " =    1.706
peak=   -3.332 closest distance to " CE  LYS A  76 " =    2.637
peak=   -3.320 closest distance to " N   TYR A  68 " =    2.908
peak=   -3.316 closest distance to " CG  ARG A  66 " =    2.461
peak=   -3.315 closest distance to " O   HOH Z  38 " =    1.202
peak=   -3.310 closest distance to " CG2 THR A 178 " =    2.191
peak=   -3.307 closest distance to " O   GLY A 262 " =    2.491
peak=   -3.306 closest distance to " O   HOH Z  43 " =    1.628
peak=   -3.303 closest distance to " O   HOH Z 308 " =    1.717
peak=   -3.298 closest distance to " CG2 VAL A 296 " =    0.908
peak=   -3.297 closest distance to " O   HOH Z 371 " =    1.613
peak=   -3.288 closest distance to " ND2 ASN A  45 " =    2.268
peak=   -3.288 closest distance to " O   HOH Z 396 " =    1.793
peak=   -3.287 closest distance to " O   ALA A   7 " =    1.530
peak=   -3.286 closest distance to " CG  PHE A 283 " =    2.872
peak=   -3.282 closest distance to " O   HOH Z 183 " =    1.345
peak=   -3.280 closest distance to " O   HOH Z 431 " =    1.905
peak=   -3.271 closest distance to " NH2 ARG A  79 " =    2.060
peak=   -3.269 closest distance to " CB  ALA A 248 " =    2.086
peak=   -3.266 closest distance to " C   ALA A 165 " =    2.020
peak=   -3.265 closest distance to " O   HOH Z 128 " =    2.677
peak=   -3.259 closest distance to " CB  ALA A  10 " =    2.223
peak=   -3.256 closest distance to " NH1AARG A 102 " =    1.507
peak=   -3.254 closest distance to " O   HOH Z 114 " =    3.455
peak=   -3.250 closest distance to " O   HOH Z 251 " =    5.006
peak=   -3.248 closest distance to " SG  CYS A 168 " =    1.177
peak=   -3.246 closest distance to " O   HOH Z 295 " =    1.511
peak=   -3.243 closest distance to " CB  ASN A  69 " =    1.480
peak=   -3.235 closest distance to " ND2 ASN A  45 " =    1.153
peak=   -3.233 closest distance to " CG  LEU A   5 " =    0.861
peak=   -3.220 closest distance to " O   HOH Z 411 " =    1.738
peak=   -3.217 closest distance to " O   HOH Z 252 " =    3.953
peak=   -3.217 closest distance to " CE BMET A  47 " =    2.060
peak=   -3.213 closest distance to " O   HOH Z  49 " =    1.159
peak=   -3.210 closest distance to " O   HOH Z 275 " =    1.592
peak=   -3.206 closest distance to " CB  TRP A  85 " =    2.612
peak=   -3.206 closest distance to " O   HOH Z 359 " =    2.983
peak=   -3.203 closest distance to " N   ALA A 248 " =    2.479
peak=   -3.199 closest distance to " O   HOH Z 409 " =    4.633
peak=   -3.198 closest distance to " CG2 VAL A 189 " =    2.002
peak=   -3.198 closest distance to " CB  ALA A 256 " =    2.753
peak=   -3.197 closest distance to " O   HOH Z 243 " =    1.609
peak=   -3.187 closest distance to " O   HOH Z 262 " =    2.815
peak=   -3.182 closest distance to " O   VAL A 125 " =    2.284
peak=   -3.176 closest distance to " OG ASER A 134 " =    1.406
peak=   -3.176 closest distance to " CG  LYS A 166 " =    2.160
peak=   -3.174 closest distance to " NE2 GLN A 103 " =    1.856
peak=   -3.172 closest distance to " OD1 ASP A 171 " =    1.642
peak=   -3.168 closest distance to " N   SER A 276 " =    1.453
peak=   -3.166 closest distance to " CG1 VAL A 125 " =    1.953
peak=   -3.165 closest distance to " N   SER A 212 " =    1.857
peak=   -3.160 closest distance to " C   ASP A 270 " =    1.266
peak=   -3.156 closest distance to " CD1 TYR A 247 " =    2.308
peak=   -3.155 closest distance to " O   HOH Z 236 " =    1.405
peak=   -3.155 closest distance to " O   HOH Z 165 " =    1.881
peak=   -3.145 closest distance to " O   HOH Z 222 " =    1.530
peak=   -3.145 closest distance to " CD2 PHE A  61 " =    2.493
peak=   -3.143 closest distance to " CB  ALA A 291 " =    2.296
peak=   -3.138 closest distance to " CB  TYR A  15 " =    2.152
peak=   -3.137 closest distance to " OG  SER A 206 " =    1.735
peak=   -3.131 closest distance to " O   HOH Z 353 " =    2.346
peak=   -3.129 closest distance to " ND2 ASN A  69 " =    1.816
peak=   -3.128 closest distance to " C   GLY A  13 " =    0.946
peak=   -3.125 closest distance to " O   PHE A 218 " =    1.448
peak=   -3.124 closest distance to " O   HOH Z 423 " =    2.127
peak=   -3.121 closest distance to " CG  PRO A 163 " =    2.347
peak=   -3.118 closest distance to " O   HOH Z 176 " =    0.925
peak=   -3.114 closest distance to " C   LEU A 222 " =    0.840
peak=   -3.114 closest distance to " OG  SER A  62 " =    1.896
peak=   -3.114 closest distance to " CB  ALA A  43 " =    2.713
peak=   -3.113 closest distance to " C   ASN A 187 " =    1.725
peak=   -3.110 closest distance to " O   HOH Z 190 " =    2.123
peak=   -3.109 closest distance to " O   HOH Z 111 " =    1.248
peak=   -3.108 closest distance to " O   HOH Z 227 " =    1.324
peak=   -3.107 closest distance to " O   HOH Z  60 " =    2.157
peak=   -3.106 closest distance to " CB  PRO A 163 " =    2.557
peak=   -3.106 closest distance to " O   HOH Z 166 " =    1.946
peak=   -3.105 closest distance to " CB  ALA A 227 " =    2.363
peak=   -3.104 closest distance to " O   HOH Z 285 " =    1.650
peak=   -3.101 closest distance to " O   HOH Z 198 " =    1.400
peak=   -3.096 closest distance to " O   HOH Z 389 " =    1.966
peak=   -3.092 closest distance to " ND2 ASN A  45 " =    1.602
peak=   -3.088 closest distance to " NH2 ARG A  66 " =    1.244
peak=   -3.088 closest distance to " O   HOH Z 189 " =    2.359
peak=   -3.079 closest distance to " O   ASP A  27 " =    1.999
peak=   -3.066 closest distance to " ND2 ASN A  60 " =    1.960
peak=   -3.042 closest distance to " O   HOH Z   6 " =    1.678
peak=   -3.036 closest distance to " CG2 THR A 221 " =    2.311
peak=   -3.002 closest distance to " O   HOH Z 193 " =    2.164

================= 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    :  0.4708 0.4554   6.270842e+00   6.250754e+00
   1_bss:  0.4635 0.4459   6.265039e+00   6.242986e+00
   1_xyz:  0.3642 0.3903   6.117189e+00   6.158161e+00
   1_adp:  0.3193 0.3627   6.021293e+00   6.113168e+00
   1_occ:  0.3185 0.3632   6.020094e+00   6.114008e+00
   2_bss:  0.3174 0.3593   6.020658e+00   6.111536e+00
   2_xyz:  0.2313 0.2806   5.757640e+00   5.908599e+00
   2_adp:  0.2115 0.2591   5.682723e+00   5.846949e+00
   2_occ:  0.2112 0.2591   5.682184e+00   5.846090e+00
   3_bss:  0.2099 0.2578   5.682998e+00   5.845053e+00
   3_xyz:  0.1547 0.2001   5.407596e+00   5.611896e+00
   3_adp:  0.1406 0.1899   5.339941e+00   5.564266e+00
   3_occ:  0.1406 0.1897   5.339474e+00   5.563775e+00
   4_bss:  0.1407 0.1900   5.340167e+00   5.563352e+00
   4_xyz:  0.1256 0.1762   5.249136e+00   5.489772e+00
   4_adp:  0.1235 0.1718   5.229856e+00   5.466224e+00
   4_occ:  0.1235 0.1716   5.229084e+00   5.465405e+00
   5_bss:  0.1234 0.1715   5.228945e+00   5.465186e+00
   5_xyz:  0.1208 0.1683   5.211267e+00   5.447288e+00
   5_adp:  0.1214 0.1674   5.210339e+00   5.441312e+00
   5_occ:  0.1213 0.1673   5.209807e+00   5.440839e+00
   5_bss:  0.1213 0.1673   5.209807e+00   5.440839e+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:  0.294  20.000   8.287   8.058   8.233   0.000   0.000   0.000
   1_xyz:  0.294  20.000   8.287   8.058   8.233   0.000   0.000   0.000
   1_adp:  0.294  20.000   8.287   8.058   8.233   0.000   0.000   0.000
   1_occ:  0.294  20.000   8.287   8.058   8.233   0.000   0.000   0.000
   2_bss:  0.327  59.120   5.789   5.589   5.818   0.000   0.000   0.000
   2_xyz:  0.327  59.120   5.789   5.589   5.818   0.000   0.000   0.000
   2_adp:  0.327  59.120   5.789   5.589   5.818   0.000   0.000   0.000
   2_occ:  0.327  59.120   5.789   5.589   5.818   0.000   0.000   0.000
   3_bss:  0.323  74.246   3.683   3.765   4.336   0.000   0.000   0.000
   3_xyz:  0.323  74.246   3.683   3.765   4.336   0.000   0.000   0.000
   3_adp:  0.323  74.246   3.683   3.765   4.336   0.000   0.000   0.000
   3_occ:  0.323  74.246   3.683   3.765   4.336   0.000   0.000   0.000
   4_bss:  0.338  74.246   3.123   3.219   4.088   0.000   0.000   0.000
   4_xyz:  0.338  74.246   3.123   3.219   4.088   0.000   0.000   0.000
   4_adp:  0.338  74.246   3.123   3.219   4.088   0.000   0.000   0.000
   4_occ:  0.338  74.246   3.123   3.219   4.088   0.000   0.000   0.000
   5_bss:  0.328  66.100   3.123   3.219   4.088   0.000   0.000   0.000
   5_xyz:  0.328  66.100   3.123   3.219   4.088   0.000   0.000   0.000
   5_adp:  0.328  66.100   3.123   3.219   4.088   0.000   0.000   0.000
   5_occ:  0.328  66.100   3.123   3.219   4.088   0.000   0.000   0.000
   5_bss:  0.328  69.576  -0.354  -0.258   0.612   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.611 0.4757  0.5290    61958.448
   1_bss:  53.120 0.4810  0.6816    60420.687
   1_xyz:  44.869 0.5824  0.8014    43969.722
   1_adp:  40.060 0.6414  0.8868    37311.915
   1_occ:  40.058 0.6414  0.8854    37335.481
   2_bss:  39.892 0.6433  0.8156    37055.092
   2_xyz:  28.919 0.7692  0.9539    20913.590
   2_adp:  26.090 0.8005  0.9813    17841.299
   2_occ:  26.078 0.8006  0.9808    17817.725
   3_bss:  26.028 0.8012  0.9197    17780.629
   3_xyz:  19.088 0.8702  0.9696    10174.863
   3_adp:  17.753 0.8829  0.9714     9140.609
   3_occ:  17.743 0.8830  0.9713     9136.007
   4_bss:  17.718 0.8832  0.9557     9117.387
   4_xyz:  16.007 0.8985  0.9641     7762.351
   4_adp:  15.427 0.9037  0.9633     7426.344
   4_occ:  15.409 0.9038  0.9633     7412.775
   5_bss:  15.407 0.9038  0.9633     7408.368
   5_xyz:  15.020 0.9071  0.9647     7129.799
   5_adp:  14.831 0.9088  0.9635     7046.253
   5_occ:  14.821 0.9089  0.9635     7037.395
   5_bss:  14.821 0.9089  0.9635     7037.395
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4553e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4553e+01
   1_xyz:   1.725  0.014  0.111 18.129  0.007  4.111   1.4663e-01
   1_adp:   1.725  0.014  0.111 18.129  0.007  4.111   1.4663e-01
   1_occ:   1.725  0.014  0.111 18.129  0.007  4.111   1.4663e-01
   2_bss:   1.725  0.014  0.111 18.129  0.007  4.111   1.4663e-01
   2_xyz:   1.088  0.008  0.074 16.466  0.004  4.132   7.2494e-02
   2_adp:   1.088  0.008  0.074 16.466  0.004  4.132   7.2494e-02
   2_occ:   1.088  0.008  0.074 16.466  0.004  4.132   7.2494e-02
   3_bss:   1.088  0.008  0.074 16.466  0.004  4.132   7.2494e-02
   3_xyz:   1.119  0.009  0.085 16.249  0.004  4.116   7.5689e-02
   3_adp:   1.119  0.009  0.085 16.249  0.004  4.116   7.5689e-02
   3_occ:   1.119  0.009  0.085 16.249  0.004  4.116   7.5689e-02
   4_bss:   1.119  0.009  0.085 16.249  0.004  4.116   7.5689e-02
   4_xyz:   1.132  0.010  0.089 16.151  0.004  4.127   7.9777e-02
   4_adp:   1.132  0.010  0.089 16.151  0.004  4.127   7.9777e-02
   4_occ:   1.132  0.010  0.089 16.151  0.004  4.127   7.9777e-02
   5_bss:   1.132  0.010  0.089 16.151  0.004  4.127   7.9777e-02
   5_xyz:   1.076  0.010  0.086 15.737  0.004  4.130   7.2021e-02
   5_adp:   1.076  0.010  0.086 15.737  0.004  4.130   7.2021e-02
   5_occ:   1.076  0.010  0.086 15.737  0.004  4.130   7.2021e-02
   5_bss:   1.076  0.010  0.086 15.737  0.004  4.130   7.2021e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0738e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0738e+00
   1_xyz:  14.503  0.171  0.460 85.919  0.040  2.221   1.0934e-01
   1_adp:  14.503  0.171  0.460 85.919  0.040  2.221   1.0934e-01
   1_occ:  14.503  0.171  0.460 85.919  0.040  2.221   1.0934e-01
   2_bss:  14.503  0.171  0.460 85.919  0.040  2.221   1.0934e-01
   2_xyz:   6.930  0.068  0.254 85.273  0.037  2.232   6.1861e-02
   2_adp:   6.930  0.068  0.254 85.273  0.037  2.232   6.1861e-02
   2_occ:   6.930  0.068  0.254 85.273  0.037  2.232   6.1861e-02
   3_bss:   6.930  0.068  0.254 85.273  0.037  2.232   6.1861e-02
   3_xyz:   8.146  0.063  0.467 85.733  0.045  2.327   4.5060e-02
   3_adp:   8.146  0.063  0.467 85.733  0.045  2.327   4.5060e-02
   3_occ:   8.146  0.063  0.467 85.733  0.045  2.327   4.5060e-02
   4_bss:   8.146  0.063  0.467 85.733  0.045  2.327   4.5060e-02
   4_xyz:   9.562  0.064  0.542 82.233  0.041  2.285   6.1019e-02
   4_adp:   9.562  0.064  0.542 82.233  0.041  2.285   6.1019e-02
   4_occ:   9.562  0.064  0.542 82.233  0.041  2.285   6.1019e-02
   5_bss:   9.562  0.064  0.542 82.233  0.041  2.285   6.1019e-02
   5_xyz:   7.923  0.045  0.545 81.871  0.041  2.357   4.4742e-02
   5_adp:   7.923  0.045  0.545 81.871  0.041  2.357   4.4742e-02
   5_occ:   7.923  0.045  0.545 81.871  0.041  2.357   4.4742e-02
   5_bss:   7.923  0.045  0.545 81.871  0.041  2.357   4.4742e-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: 108.08   0.00  11.54  71.13   0.00   8.73 108.08   0.00  26.83
   1_occ: 108.08   0.00  11.54  71.13   0.00   8.73 108.08   0.00  26.83
   2_bss: 108.08   0.00  11.54  71.13   0.00   8.73 108.08   0.00  26.83
   2_xyz: 108.08   0.00  11.54  71.13   0.00   8.73 108.08   0.00  26.83
   2_adp: 108.19   0.00  12.14  74.54   0.00   8.16 108.19   0.00  33.80
   2_occ: 108.19   0.00  12.14  74.54   0.00   8.16 108.19   0.00  33.80
   3_bss: 108.19   0.00  12.14  74.54   0.00   8.16 108.19   0.00  33.80
   3_xyz: 108.19   0.00  12.14  74.54   0.00   8.16 108.19   0.00  33.80
   3_adp: 101.50   0.00  13.06  86.37   0.00   8.20 101.50   0.00  39.50
   3_occ: 101.50   0.00  13.06  86.37   0.00   8.20 101.50   0.00  39.50
   4_bss: 101.50   0.00  13.06  86.37   0.00   8.20 101.50   0.00  39.50
   4_xyz: 101.50   0.00  13.06  86.37   0.00   8.20 101.50   0.00  39.50
   4_adp:  97.18   0.00  12.63  86.10   0.00   7.94  97.18   0.98  38.14
   4_occ:  97.18   0.00  12.63  86.10   0.00   7.94  97.18   0.98  38.14
   5_bss:  97.18   0.00  12.63  86.10   0.00   7.94  97.18   0.98  38.14
   5_xyz:  97.18   0.00  12.63  86.10   0.00   7.94  97.18   0.98  38.14
   5_adp:  95.71   0.00  12.37  85.37   0.00   7.81  95.71   1.27  37.21
   5_occ:  95.71   0.00  12.37  85.37   0.00   7.81  95.71   1.27  37.21
   5_bss:  99.18   3.48  15.85  88.85   3.48  11.29  99.18   4.74  40.69
------------------------------------------------------------------------
 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:    1.249    0.028    0.416
   1_adp:    1.249    0.028    0.416
   1_occ:    1.249    0.028    0.416
   2_bss:    1.249    0.028    0.416
   2_xyz:    1.673    0.028    0.560
   2_adp:    1.673    0.028    0.560
   2_occ:    1.673    0.028    0.560
   3_bss:    1.673    0.028    0.560
   3_xyz:    1.560    0.035    0.635
   3_adp:    1.560    0.035    0.635
   3_occ:    1.560    0.035    0.635
   4_bss:    1.560    0.035    0.635
   4_xyz:    1.635    0.033    0.672
   4_adp:    1.635    0.033    0.672
   4_occ:    1.635    0.033    0.672
   5_bss:    1.635    0.033    0.672
   5_xyz:    1.709    0.048    0.681
   5_adp:    1.709    0.048    0.681
   5_occ:    1.709    0.048    0.681
   5_bss:    1.709    0.048    0.681
------------------------------------------------------------------------

CPU time actual refinement: 322.24


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1173/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_1173/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1173/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1173/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1173/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.09 
  Macro-tasks:
    bulk solvent and scale       = 41.25  
    individual site refinement   = 128.68 
    weights calculation          = 31.51  
    collect and process          = 6.47   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 208.03 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 98.07  
    alpha_beta                      = 8.21   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 107.80 
    fmodel                         = 7.16   
    r_factors                      = 0.25   
    phase_errors                   = 10.33  
    foms                           = 0.38   
    TOTAL for micro-tasks          = 235.07 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.600 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    629 calls, 97.77 s
gradients_fft:          574 calls, 95.02 s

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

# Date 2008-01-16 Time 03:21:45 PST -0800 (1200482505.89 s)
Start R-work = 0.4708, R-free = 0.4554 (no bulk solvent and anisotropic scale)
Final R-work = 0.1372, R-free = 0.1823 (no bulk solvent and anisotropic scale)

Start R-work = 0.4635, R-free = 0.4459
Final R-work = 0.1213, R-free = 0.1673