# Date 2008-01-16 Time 02:52:17 PST -0800 (1200480737.25 s)
#phil __OFF__

Command line arguments: "../1009.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19326
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1009

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.4607, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 1.9833
Completeness in resolution range: 0.943094
Completeness with d_max=infinity: 0.940287

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2189
                             d_min =   1.9833

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 1.9833
Completeness in resolution range: 0.943094
Completeness with d_max=infinity: 0.940287

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2193 -  4.2449 [2184/2209]  1964   220  10.1%
  bin  2:  4.2449 -  3.3814 [2098/2118]  1891   207   9.9%
  bin  3:  3.3814 -  2.9576 [2073/2092]  1866   207  10.0%
  bin  4:  2.9576 -  2.6888 [2049/2079]  1840   209  10.2%
  bin  5:  2.6888 -  2.4970 [2029/2048]  1835   194   9.6%
  bin  6:  2.4970 -  2.3503 [2030/2055]  1819   211  10.4%
  bin  7:  2.3503 -  2.2330 [2025/2053]  1819   206  10.2%
  bin  8:  2.2330 -  2.1360 [2002/2038]  1803   199   9.9%
  bin  9:  2.1360 -  2.0540 [2006/2048]  1813   193   9.6%
  bin 10:  2.0540 -  1.9833 [1093/2031]   980   113  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1009/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 20
        2.42 -     3.04: 2167
        3.04 -     3.66: 4661
        3.66 -     4.28: 8925
        4.28 -     4.90: 12271
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.252 3.040 -x,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.329 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28039 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_1009/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1009/model_refine_001.geo

CPU time processing inputs: 9.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.4607 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4741   r_free= 0.4583   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.273761                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.7351 0.99   1413  157 0.3939 0.3649      6.5942      6.5279|
|  2:  4.7351 -  3.7773 0.99   1363  153 0.3806 0.3945      6.7594       6.782|
|  3:  3.7773 -  3.3054 0.99   1343  144 0.4228 0.3862      6.6386      6.5907|
|  4:  3.3054 -  3.0057 0.99   1327  151 0.4645 0.4242      6.5173      6.4615|
|  5:  3.0057 -  2.7917 0.99   1323  149 0.5076 0.4783      6.3643      6.3659|
|  6:  2.7917 -  2.6280 0.99   1316  144 0.4981 0.4937      6.2573      6.1958|
|  7:  2.6280 -  2.4970 0.99   1311  139 0.5303 0.5163      6.2503      6.2126|
|  8:  2.4970 -  2.3887 0.98   1291  151 0.5234 0.4865      6.1653      6.1776|
|  9:  2.3887 -  2.2971 0.98   1293  146 0.5158 0.5416      6.1146      6.1845|
| 10:  2.2971 -  2.2180 1.00   1303  146 0.5240 0.4860      6.0996      6.0567|
| 11:  2.2180 -  2.1489 0.98   1311  138 0.5142 0.5067      6.0386       6.004|
| 12:  2.1489 -  2.0876 0.98   1268  142 0.5286 0.5162      5.9552      6.0071|
| 13:  2.0876 -  2.0328 0.99   1287  141 0.5277 0.5094      5.8735      5.7824|
| 14:  2.0328 -  1.9833 0.36    481   58 0.5413 0.4715      5.8682      5.8136|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2193 -  4.7351  1413   157  0.71  33.21   0.79     0.75      67828.37|
|  2:  4.7351 -  3.7773  1363   153  0.74  31.74   0.87     0.80      92591.43|
|  3:  3.7773 -  3.3054  1343   144  0.65  39.89   0.85     0.76      97507.42|
|  4:  3.3054 -  3.0057  1327   151  0.57  46.26   0.78     0.66      86846.01|
|  5:  3.0057 -  2.7917  1323   149  0.48  53.40   0.73     0.57      73066.43|
|  6:  2.7917 -  2.6280  1316   144  0.44  56.80   0.72     0.50      65739.43|
|  7:  2.6280 -  2.4970  1311   139  0.38  61.15   0.73     0.44      63918.51|
|  8:  2.4970 -  2.3887  1291   151  0.35  63.75   0.71     0.40      58905.54|
|  9:  2.3887 -  2.2971  1293   146  0.35  63.40   0.72     0.41      54751.41|
| 10:  2.2971 -  2.2180  1303   146  0.36  62.88   0.74     0.42      48111.93|
| 11:  2.2180 -  2.1489  1311   138  0.36  63.28   0.77     0.44      45874.56|
| 12:  2.1489 -  2.0876  1268   142  0.36  63.06   0.73     0.45      41232.39|
| 13:  2.0876 -  2.0328  1287   141  0.36  63.50   0.71     0.45      35287.42|
| 14:  2.0328 -  1.9833   481    58  0.42  58.53   0.71     0.45      27472.45|
|alpha:            min =        0.40 max =            0.80 mean =         0.54|
|beta:             min =    27472.45 max =        97507.42 mean =     63289.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.87|
|phase err.(test): min =        0.00 max =           89.99 mean =        53.92|
|-----------------------------------------------------------------------------|

============================== 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 = 11.920513             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.686   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.029478              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.420   (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:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1480 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2607 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3882 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5044 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6512 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7603 |
|-----------------------------------------------------------------------------|
|-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 |       54.200 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.698 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.118)------------------------------------------|
|    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 = 12.118)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4801   r_free= 0.4646   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.275885                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4662   r_free= 0.4482   ksol= 0.33   Bsol= 20.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.13,8.02,9.94,0.00,0.00,0.00); trace/3= 8.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.268791                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.574772             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.994   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.975242              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.705   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4662      final r-factor (work) = 0.3745          |
| start r-factor (free) = 0.4482      final r-factor (free) = 0.3911          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.3586 = 10.57 * 0.50 * 6.2713 + 1.00 * 54.1996                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.7464 = 10.57 * 0.50 * 6.1671 + 1.00 * 0.1387                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3745      final r-factor (work) = 0.3247          |
| start r-factor (free) = 0.3911      final r-factor (free) = 0.3736          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0288 = 0.98 * 1.00 * 6.1671 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9235 = 0.98 * 1.00 * 6.0582 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.118)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.87   12.75    None  None   None       |
|    all(noH): 2823   0      0.00    79.87   12.75    None  None   None       |
|    Sol.    : 438    0      0.00    79.87   27.88    None  None   None       |
|    Mac.    : 2385   0      0.00    65.39   9.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.987: 1235   |   5:    39.937 -  47.924:   69        |
|      1:     7.987 -  15.975:  795   |   6:    47.924 -  55.912:   45        |
|      2:    15.975 -  23.962:  383   |   7:    55.912 -  63.899:   13        |
|      3:    23.962 -  31.950:  183   |   8:    63.899 -  71.886:    7        |
|      4:    31.950 -  39.937:   92   |   9:    71.886 -  79.874:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3247 r_free = 0.3736             target_work(ml) = 6.036         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3242 r_free = 0.3741             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3242   r_free= 0.3741   ksol= 0.33   Bsol= 20.00   scale= 1.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.13,8.02,9.94,0.00,0.00,0.00); trace/3= 8.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.034823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3205   r_free= 0.3692   ksol= 0.34   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.91,4.35,6.53,0.00,0.00,0.00); trace/3= 5.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.034170                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.756223              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.125   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.461083              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.603  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3205      final r-factor (work) = 0.2277          |
| start r-factor (free) = 0.3692      final r-factor (free) = 0.2797          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5379 = 4.76 * 0.50 * 6.0549 + 1.00 * 0.1387                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0974 = 4.76 * 0.50 * 5.8970 + 1.00 * 0.0737                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2277      final r-factor (work) = 0.2055          |
| start r-factor (free) = 0.2797      final r-factor (free) = 0.2572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7344 = 0.46 * 1.00 * 5.8970 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6421 = 0.46 * 1.00 * 5.7039 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.118)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.57   12.48    None  None   None       |
|    all(noH): 2823   0      0.00    82.57   12.48    None  None   None       |
|    Sol.    : 438    0      0.00    82.57   33.23    None  None   None       |
|    Mac.    : 2385   0      0.00    66.56   8.67     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 -   8.257: 1467   |   5:    41.284 -  49.541:   87        |
|      1:     8.257 -  16.514:  721   |   6:    49.541 -  57.798:   41        |
|      2:    16.514 -  24.771:  222   |   7:    57.798 -  66.055:   21        |
|      3:    24.771 -  33.027:  127   |   8:    66.055 -  74.312:    3        |
|      4:    33.027 -  41.284:  132   |   9:    74.312 -  82.569:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2055 r_free = 0.2572             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2053 r_free = 0.2574             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2053   r_free= 0.2574   ksol= 0.34   Bsol= 50.00   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.91,4.35,6.53,0.00,0.00,0.00); trace/3= 5.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.663906                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2038   r_free= 0.2569   ksol= 0.32   Bsol= 57.14   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,2.54,4.41,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.665453                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.440092              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.551   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.680135              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.032  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2038      final r-factor (work) = 0.1559          |
| start r-factor (free) = 0.2569      final r-factor (free) = 0.2039          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0432 = 2.44 * 0.50 * 5.7125 + 1.00 * 0.0737                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8391 = 2.44 * 0.50 * 5.5545 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1559      final r-factor (work) = 0.1442          |
| start r-factor (free) = 0.2039      final r-factor (free) = 0.1960          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3445 = 1.68 * 1.00 * 5.5545 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0876 = 1.68 * 1.00 * 5.3881 + 1.00 * 0.0349                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.118)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.24   13.77    None  None   None       |
|    all(noH): 2823   0      0.00    93.24   13.77    None  None   None       |
|    Sol.    : 438    0      1.03    93.24   40.38    None  None   None       |
|    Mac.    : 2385   0      0.00    81.88   8.88     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.324: 1656   |   5:    46.618 -  55.942:   91        |
|      1:     9.324 -  18.647:  587   |   6:    55.942 -  65.266:   58        |
|      2:    18.647 -  27.971:  167   |   7:    65.266 -  74.589:   39        |
|      3:    27.971 -  37.295:  113   |   8:    74.589 -  83.913:   16        |
|      4:    37.295 -  46.618:   92   |   9:    83.913 -  93.237:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1442 r_free = 0.1960             target_work(ml) = 5.371         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1442 r_free = 0.1962             target_work(ml) = 5.371         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1442   r_free= 0.1962   ksol= 0.32   Bsol= 57.14   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,2.54,4.41,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.371335                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1441   r_free= 0.1959   ksol= 0.33   Bsol= 67.29   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.50,2.17,3.99,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.371200                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.377704              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.263   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.627955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.903   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1441      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1959      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8577 = 4.38 * 0.50 * 5.3889 + 1.00 * 0.0623                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6984 = 4.38 * 0.50 * 5.3071 + 1.00 * 0.0820                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1227      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1761      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3490 = 0.63 * 1.00 * 5.3071 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3017 = 0.63 * 1.00 * 5.2356 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.118)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.03   13.26    None  None   None       |
|    all(noH): 2823   0      0.00    92.03   13.26    None  None   None       |
|    Sol.    : 438    0      1.75    92.03   38.90    None  None   None       |
|    Mac.    : 2385   0      0.00    82.66   8.55     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 -   9.203: 1702   |   5:    46.016 -  55.220:   91        |
|      1:     9.203 -  18.407:  569   |   6:    55.220 -  64.423:   54        |
|      2:    18.407 -  27.610:  152   |   7:    64.423 -  73.626:   27        |
|      3:    27.610 -  36.813:  121   |   8:    73.626 -  82.830:   20        |
|      4:    36.813 -  46.016:   83   |   9:    82.830 -  92.033:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1195 r_free = 0.1694             target_work(ml) = 5.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1194 r_free = 0.1693             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1693   ksol= 0.33   Bsol= 67.29   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.50,2.17,3.99,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.212425                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1693   ksol= 0.33   Bsol= 67.29   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.47,2.12,3.91,0.00,0.00,0.00); trace/3= 2.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.212386                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.599145              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.246  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.180473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.318  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1194      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1693      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2680 = 1.60 * 0.50 * 5.2353 + 1.00 * 0.0820                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2343 = 1.60 * 0.50 * 5.2234 + 1.00 * 0.0578                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1687      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9565 = 0.18 * 1.00 * 5.2234 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9587 = 0.18 * 1.00 * 5.2319 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.118)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.04   12.72    None  None   None       |
|    all(noH): 2823   0      0.00    87.04   12.72    None  None   None       |
|    Sol.    : 438    0      2.22    87.04   36.48    None  None   None       |
|    Mac.    : 2385   0      0.00    80.67   8.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.704: 1673   |   5:    43.521 -  52.225:   77        |
|      1:     8.704 -  17.408:  602   |   6:    52.225 -  60.930:   60        |
|      2:    17.408 -  26.113:  156   |   7:    60.930 -  69.634:   23        |
|      3:    26.113 -  34.817:  117   |   8:    69.634 -  78.338:   18        |
|      4:    34.817 -  43.521:   90   |   9:    78.338 -  87.042:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1230 r_free = 0.1675             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1229 r_free = 0.1673             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1673   ksol= 0.33   Bsol= 67.29   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.47,2.12,3.91,0.00,0.00,0.00); trace/3= 2.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.225601                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.7351 0.99   1413  157 0.1019 0.1366      5.4092      5.5782|
|  2:  4.7351 -  3.7773 0.99   1363  153 0.0914 0.1222      5.4854      5.6894|
|  3:  3.7773 -  3.3054 0.99   1343  144 0.1135 0.1571      5.5336      5.8566|
|  4:  3.3054 -  3.0057 0.99   1327  151 0.1323 0.1728      5.5113      5.6613|
|  5:  3.0057 -  2.7917 0.99   1323  149 0.1485 0.1847      5.4127      5.6271|
|  6:  2.7917 -  2.6280 0.99   1316  144 0.1356 0.2109      5.2763      5.5485|
|  7:  2.6280 -  2.4970 0.99   1311  139 0.1415 0.1724      5.2642      5.3856|
|  8:  2.4970 -  2.3887 0.98   1291  151 0.1334 0.1748       5.168      5.3709|
|  9:  2.3887 -  2.2971 0.98   1293  146 0.1349 0.2001      5.1364      5.4088|
| 10:  2.2971 -  2.2180 1.00   1303  146 0.1288 0.1666       5.032      5.1937|
| 11:  2.2180 -  2.1489 0.98   1311  138 0.1257 0.2053      5.0184      5.3879|
| 12:  2.1489 -  2.0876 0.98   1268  142 0.1272 0.1778      4.9338      5.1982|
| 13:  2.0876 -  2.0328 0.99   1287  141 0.1285 0.1714      4.8627      5.0534|
| 14:  2.0328 -  1.9833 0.36    481   58 0.1195 0.1541       4.767       4.902|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2193 -  4.7351  1413   157  0.94   9.44   0.97     0.95       7555.14|
|  2:  4.7351 -  3.7773  1363   153  0.95   8.44   1.00     0.99       9750.38|
|  3:  3.7773 -  3.3054  1343   144  0.93  12.16   1.02     1.02      11586.97|
|  4:  3.3054 -  3.0057  1327   151  0.91  14.84   1.01     0.98      11402.01|
|  5:  3.0057 -  2.7917  1323   149  0.89  17.30   1.00     0.98       9494.04|
|  6:  2.7917 -  2.6280  1316   144  0.89  17.15   0.98     0.95       7821.51|
|  7:  2.6280 -  2.4970  1311   139  0.89  16.92   0.99     0.96       7249.51|
|  8:  2.4970 -  2.3887  1291   151  0.89  17.06   0.99     0.97       6344.02|
|  9:  2.3887 -  2.2971  1293   146  0.89  17.35   1.00     0.96       6004.31|
| 10:  2.2971 -  2.2180  1303   146  0.89  16.71   1.00     0.97       4871.59|
| 11:  2.2180 -  2.1489  1311   138  0.90  16.77   1.00     0.95       4748.47|
| 12:  2.1489 -  2.0876  1268   142  0.90  16.47   1.01     1.01       4298.14|
| 13:  2.0876 -  2.0328  1287   141  0.89  17.78   1.00     0.98       3818.74|
| 14:  2.0328 -  1.9833   481    58  0.91  15.48   0.98     0.96       2980.78|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2980.78 max =        11586.97 mean =      7222.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.20|
|phase err.(test): min =        0.00 max =           89.67 mean =        14.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1667   ksol= 0.33   Bsol= 69.88   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.70,1.09,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.225519                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1667   ksol= 0.33   Bsol= 69.88   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.70,1.09,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.225519                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.7351 0.99   1413  157 0.1026 0.1319       5.406      5.5589|
|  2:  4.7351 -  3.7773 0.99   1363  153 0.0922 0.1207       5.487      5.6871|
|  3:  3.7773 -  3.3054 0.99   1343  144 0.1136 0.1574      5.5318      5.8563|
|  4:  3.3054 -  3.0057 0.99   1327  151 0.1322 0.1735      5.5119      5.6641|
|  5:  3.0057 -  2.7917 0.99   1323  149 0.1485 0.1848      5.4138      5.6292|
|  6:  2.7917 -  2.6280 0.99   1316  144 0.1357 0.2108      5.2765      5.5488|
|  7:  2.6280 -  2.4970 0.99   1311  139 0.1415 0.1724      5.2648      5.3864|
|  8:  2.4970 -  2.3887 0.98   1291  151 0.1334 0.1750      5.1679      5.3711|
|  9:  2.3887 -  2.2971 0.98   1293  146 0.1349 0.2002      5.1362      5.4083|
| 10:  2.2971 -  2.2180 1.00   1303  146 0.1288 0.1668      5.0318      5.1946|
| 11:  2.2180 -  2.1489 0.98   1311  138 0.1257 0.2054      5.0184      5.3877|
| 12:  2.1489 -  2.0876 0.98   1268  142 0.1272 0.1779      4.9342      5.1987|
| 13:  2.0876 -  2.0328 0.99   1287  141 0.1285 0.1713      4.8628      5.0537|
| 14:  2.0328 -  1.9833 0.36    481   58 0.1195 0.1542       4.767      4.9016|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2193 -  4.7351  1413   157  0.94   9.39   0.97     0.94       7309.99|
|  2:  4.7351 -  3.7773  1363   153  0.95   8.32   1.00     0.98       9556.00|
|  3:  3.7773 -  3.3054  1343   144  0.93  12.12   1.01     1.01      11535.02|
|  4:  3.3054 -  3.0057  1327   151  0.91  14.87   1.00     0.98      11426.48|
|  5:  3.0057 -  2.7917  1323   149  0.89  17.32   0.99     0.98       9540.60|
|  6:  2.7917 -  2.6280  1316   144  0.89  17.16   0.97     0.94       7836.11|
|  7:  2.6280 -  2.4970  1311   139  0.89  16.94   0.99     0.95       7266.78|
|  8:  2.4970 -  2.3887  1291   151  0.89  17.05   0.98     0.96       6346.03|
|  9:  2.3887 -  2.2971  1293   146  0.89  17.33   0.99     0.95       6001.11|
| 10:  2.2971 -  2.2180  1303   146  0.89  16.70   0.99     0.96       4872.87|
| 11:  2.2180 -  2.1489  1311   138  0.90  16.78   0.98     0.93       4753.62|
| 12:  2.1489 -  2.0876  1268   142  0.90  16.48   0.99     0.99       4302.15|
| 13:  2.0876 -  2.0328  1287   141  0.89  17.77   0.98     0.97       3819.29|
| 14:  2.0328 -  1.9833   481    58  0.91  15.48   0.97     0.95       2980.21|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2980.21 max =        11535.02 mean =      7192.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        15.19|
|phase err.(test): min =        0.00 max =           88.64 mean =        14.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.118)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.59    89.63   15.31    None  None   None       |
|    all(noH): 2823   0      2.59    89.63   15.31    None  None   None       |
|    Sol.    : 438    0      4.81    89.63   39.07    None  None   None       |
|    Mac.    : 2385   0      2.59    83.26   10.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.591 -  11.295: 1673   |   5:    46.112 -  54.816:   77        |
|      1:    11.295 -  19.999:  602   |   6:    54.816 -  63.520:   60        |
|      2:    19.999 -  28.703:  156   |   7:    63.520 -  72.224:   23        |
|      3:    28.703 -  37.407:  117   |   8:    72.224 -  80.928:   18        |
|      4:    37.407 -  46.112:   90   |   9:    80.928 -  89.633:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.271 - 4.762
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 330
   mapped sites are within: 0.701 - 4.762

peak=   10.610 closest distance to " CB  VAL A 230 " =    1.463
peak=    7.676 closest distance to " CG2 VAL A 296 " =    1.251
peak=    6.534 closest distance to " CD2 LEU A   5 " =    1.319
peak=    6.191 closest distance to " CG  ARG A 138 " =    1.180
peak=    5.953 closest distance to " NH1 ARG A 138 " =    1.089
peak=    5.512 closest distance to " O   HOH Z 232 " =    2.275
peak=    5.501 closest distance to " CG  PRO A  54 " =    1.473
peak=    5.472 closest distance to " CD1AILE A 234 " =    1.131
peak=    5.401 closest distance to " CB  GLN A 223 " =    1.434
peak=    5.210 closest distance to " CG  LEU A   5 " =    1.277
peak=    5.209 closest distance to " NE2 GLN A  11 " =    1.116
peak=    5.199 closest distance to " O   HOH Z 111 " =    2.013
peak=    5.110 closest distance to " O   HOH Z 142 " =    2.193
peak=    5.026 closest distance to " CD  ARG A 138 " =    1.154
peak=    4.889 closest distance to " CB  ASP A 124 " =    0.780
peak=    4.861 closest distance to " CG  PRO A 198 " =    1.332
peak=    4.847 closest distance to " CB  ASN A 148 " =    1.379
peak=    4.752 closest distance to " CB  PRO A  54 " =    1.057
peak=    4.742 closest distance to " O   HOH Z 369 " =    2.020
peak=    4.725 closest distance to " CG  LEU A 228 " =    1.227
peak=    4.664 closest distance to " O   HOH Z   9 " =    1.694
peak=    4.637 closest distance to " O   HOH Z 298 " =    1.907
peak=    4.606 closest distance to " CZ  PHE A 218 " =    1.094
peak=    4.565 closest distance to " CG  PRO A 243 " =    1.167
peak=    4.536 closest distance to " CA  VAL A 230 " =    1.275
peak=    4.532 closest distance to " CG  LEU A 167 " =    1.241
peak=    4.474 closest distance to " CB  GLN A 183 " =    1.186
peak=    4.452 closest distance to " O   HOH Z 222 " =    1.281
peak=    4.409 closest distance to " ND2 ASN A 187 " =    1.639
peak=    4.408 closest distance to " O   HOH Z 265 " =    2.103
peak=    4.391 closest distance to " CB  SER A  63 " =    1.249
peak=    4.381 closest distance to " CB  ASN A 142 " =    0.897
peak=    4.308 closest distance to " CB  TRP A 266 " =    0.947
peak=    4.305 closest distance to " O   HOH Z 316 " =    3.034
peak=    4.281 closest distance to " O   PRO A 198 " =    1.584
peak=    4.258 closest distance to " CB  ASN A  39 " =    0.944
peak=    4.255 closest distance to " CB  ARG A 275 " =    0.908
peak=    4.246 closest distance to " O   HOH Z   7 " =    1.261
peak=    4.244 closest distance to " O   HOH Z 368 " =    2.080
peak=    4.240 closest distance to " CD2 LEU A 228 " =    1.186
peak=    4.236 closest distance to " O   HOH Z 287 " =    2.140
peak=    4.233 closest distance to " O   HOH Z 427 " =    2.801
peak=    4.222 closest distance to " CG  PRO A 213 " =    1.308
peak=    4.196 closest distance to " CB  SER A   3 " =    1.425
peak=    4.153 closest distance to " CA  VAL A 296 " =    1.077
peak=    4.133 closest distance to " CA  SER A  87 " =    0.874
peak=    4.128 closest distance to " O   HOH Z 272 " =    1.867
peak=    4.103 closest distance to " CB  VAL A 265 " =    1.330
peak=    4.066 closest distance to " O   HOH Z  78 " =    1.685
peak=    4.044 closest distance to " CB  SER A 216 " =    0.924
peak=    4.003 closest distance to " O   HOH Z 303 " =    2.215
peak=    4.000 closest distance to " CB  SER A 210 " =    0.829
peak=    3.992 closest distance to " O   HOH Z 353 " =    2.579
peak=    3.971 closest distance to " O   HOH Z 130 " =    1.034
peak=    3.960 closest distance to " NH1AARG A 145 " =    1.200
peak=    3.958 closest distance to " O   HOH Z 425 " =    1.551
peak=    3.938 closest distance to " CD  ARG A  66 " =    2.251
peak=    3.935 closest distance to " O   HOH Z 214 " =    2.104
peak=    3.933 closest distance to " O   HOH Z  44 " =    2.202
peak=    3.931 closest distance to " O   HOH Z 126 " =    1.940
peak=    3.910 closest distance to " CD1 LEU A 300 " =    1.167
peak=    3.905 closest distance to " CG1 ILE A 151 " =    1.241
peak=    3.902 closest distance to " O   SER A  87 " =    2.354
peak=    3.900 closest distance to " CB  ASN A 187 " =    1.053
peak=    3.889 closest distance to " O   TYR A 116 " =    1.233
peak=    3.877 closest distance to " CD  LYS A 166 " =    1.240
peak=    3.876 closest distance to " NH2AARG A 190 " =    1.779
peak=    3.853 closest distance to " O   HOH Z 290 " =    1.207
peak=    3.849 closest distance to " NH2AARG A 145 " =    1.129
peak=    3.847 closest distance to " CB  LEU A 143 " =    1.220
peak=    3.847 closest distance to " CB  GLU A 128 " =    0.993
peak=    3.836 closest distance to " O   HOH Z  88 " =    3.092
peak=    3.833 closest distance to " O   HOH Z 126 " =    1.524
peak=    3.831 closest distance to " O   HOH Z 184 " =    1.518
peak=    3.829 closest distance to " CB  GLU A 152 " =    1.183
peak=    3.814 closest distance to " CB  ARG A 138 " =    1.375
peak=    3.811 closest distance to " O   HOH Z 158 " =    3.130
peak=    3.798 closest distance to " O   HOH Z 261 " =    2.047
peak=    3.795 closest distance to " CD  ARG A 269 " =    0.972
peak=    3.794 closest distance to " O   HOH Z 183 " =    1.347
peak=    3.786 closest distance to " CZ3 TRP A 266 " =    1.134
peak=    3.772 closest distance to " CD  ARG A 159 " =    0.762
peak=    3.767 closest distance to " CB  VAL A 202 " =    1.561
peak=    3.766 closest distance to " O   HOH Z 148 " =    2.323
peak=    3.763 closest distance to " O   HOH Z 234 " =    3.763
peak=    3.753 closest distance to " CD1 ILE A  33 " =    1.844
peak=    3.750 closest distance to " O   HOH Z 188 " =    2.956
peak=    3.734 closest distance to " O   HOH Z 437 " =    1.766
peak=    3.724 closest distance to " O   HOH Z  68 " =    2.093
peak=    3.723 closest distance to " O   HOH Z 193 " =    1.892
peak=    3.717 closest distance to " CA  PRO A  54 " =    1.362
peak=    3.716 closest distance to " CB  GLN A  89 " =    1.166
peak=    3.714 closest distance to " CB  ARG A  79 " =    1.446
peak=    3.707 closest distance to " O   HOH Z 156 " =    2.929
peak=    3.705 closest distance to " CG1 VAL A 153 " =    0.931
peak=    3.700 closest distance to " CA  ILE A 234 " =    0.961
peak=    3.698 closest distance to " CA  ALA A  51 " =    1.035
peak=    3.691 closest distance to " NE2 HIS A 207 " =    1.025
peak=    3.689 closest distance to " O   HOH Z 423 " =    1.585
peak=    3.679 closest distance to " N   PHE A 130 " =    1.250
peak=    3.679 closest distance to " CB  ALA A 104 " =    0.775
peak=    3.678 closest distance to " N   SER A 271 " =    0.984
peak=    3.676 closest distance to " O   ASN A 209 " =    1.395
peak=    3.672 closest distance to " CB  GLN A  88 " =    1.252
peak=    3.670 closest distance to " O   HOH Z   1 " =    1.904
peak=    3.668 closest distance to " CG2 THR A 221 " =    1.037
peak=    3.667 closest distance to " NH1 ARG A  14 " =    0.925
peak=    3.660 closest distance to " CG BARG A 102 " =    1.915
peak=    3.656 closest distance to " O   HOH Z 128 " =    2.237
peak=    3.653 closest distance to " CB  SER A 212 " =    1.306
peak=    3.650 closest distance to " CB  ALA A 160 " =    1.399
peak=    3.644 closest distance to " O   HOH Z 411 " =    3.376
peak=    3.639 closest distance to " CB  GLU A 277 " =    3.664
peak=    3.627 closest distance to " CA  ILE A 106 " =    0.802
peak=    3.624 closest distance to " O   HOH Z 346 " =    1.565
peak=    3.621 closest distance to " CE3 TRP A 274 " =    1.362
peak=    3.615 closest distance to " O   HOH Z 410 " =    1.502
peak=    3.606 closest distance to " CB  LEU A 228 " =    1.222
peak=    3.604 closest distance to " O   HOH Z  61 " =    1.652
peak=    3.599 closest distance to " ND1 HIS A  86 " =    1.767
peak=    3.593 closest distance to " CA  ALA A 160 " =    1.161
peak=    3.586 closest distance to " CA  GLY A 267 " =    0.957
peak=    3.585 closest distance to " O   HOH Z 380 " =    1.821
peak=    3.582 closest distance to " O   PRO A 198 " =    1.378
peak=    3.573 closest distance to " CB  GLU A  46 " =    0.923
peak=    3.570 closest distance to " CB  ARG A 190 " =    1.559
peak=    3.568 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.563 closest distance to " CD  GLN A 240 " =    1.649
peak=    3.560 closest distance to " O   HOH Z 294 " =    1.523
peak=    3.558 closest distance to " O   HOH Z 180 " =    2.090
peak=    3.556 closest distance to " CA  ASN A 127 " =    1.120
peak=    3.555 closest distance to " CA  TYR A  30 " =    1.002
peak=    3.554 closest distance to " CA  LEU A 282 " =    1.063
peak=    3.551 closest distance to " CD1 LEU A   5 " =    1.351
peak=    3.547 closest distance to " O   HOH Z  30 " =    1.585
peak=    3.544 closest distance to " O   HOH Z  78 " =    1.900
peak=    3.544 closest distance to " CA  ALA A 295 " =    1.114
peak=    3.538 closest distance to " OD1 ASN A  69 " =    2.574
peak=    3.522 closest distance to " CB  LEU A  83 " =    0.717
peak=    3.515 closest distance to " ND2 ASN A 249 " =    1.898
peak=    3.515 closest distance to " CA  THR A 264 " =    0.788
peak=    3.509 closest distance to " CE3 TRP A  85 " =    1.128
peak=    3.509 closest distance to " CB  ILE A 120 " =    1.269
peak=    3.508 closest distance to " CG2 VAL A 257 " =    0.956
peak=    3.501 closest distance to " O   HOH Z 368 " =    3.535
peak=    3.495 closest distance to " O   HOH Z 258 " =    2.120
peak=    3.486 closest distance to " CD2 TRP A 179 " =    1.275
peak=    3.486 closest distance to " O   HOH Z  10 " =    1.830
peak=    3.482 closest distance to " ND2 ASN A 249 " =    0.908
peak=    3.482 closest distance to " N   SER A 135 " =    1.309
peak=    3.479 closest distance to " CB  MET A  40 " =    0.819
peak=    3.470 closest distance to " CZ3 TRP A  92 " =    1.389
peak=    3.470 closest distance to " CB AVAL A  41 " =    1.286
peak=    3.469 closest distance to " O   HOH Z 273 " =    2.757
peak=    3.468 closest distance to " CA  ARG A  36 " =    1.140
peak=    3.465 closest distance to " O   HOH Z 193 " =    1.688
peak=    3.462 closest distance to " CE1 TYR A 186 " =    1.321
peak=    3.461 closest distance to " NE AARG A 275 " =    1.429
peak=    3.460 closest distance to " CB  LEU A 237 " =    0.830
peak=    3.450 closest distance to " CA  ARG A 195 " =    1.204
peak=    3.446 closest distance to " O   HOH Z   2 " =    1.671
peak=    3.438 closest distance to " OE2 GLU A   2 " =    1.971
peak=    3.427 closest distance to " N   ALA A 256 " =    1.139
peak=    3.423 closest distance to " CG2 ILE A 234 " =    0.951
peak=    3.415 closest distance to " O   HOH Z  92 " =    2.460
peak=    3.410 closest distance to " CA  ASP A 162 " =    0.872
peak=    3.402 closest distance to " CB  HIS A 108 " =    0.790
peak=    3.402 closest distance to " OG  SER A 135 " =    1.282
peak=    3.400 closest distance to " CB  VAL A 250 " =    1.106
peak=    3.400 closest distance to " O   HOH Z 185 " =    2.310
peak=    3.397 closest distance to " O   ASP A 200 " =    1.627
peak=    3.394 closest distance to " CA  ALA A  21 " =    1.192
peak=    3.392 closest distance to " O   HOH Z 285 " =    2.355
peak=    3.392 closest distance to " CA  ALA A 154 " =    1.084
peak=    3.390 closest distance to " CB  TRP A 150 " =    1.401
peak=    3.387 closest distance to " CA  TYR A 116 " =    1.437
peak=    3.386 closest distance to " O   HOH Z   1 " =    2.053
peak=    3.386 closest distance to " CD BLYS A 290 " =    1.064
peak=    3.383 closest distance to " CG  GLN A  89 " =    1.514
peak=    3.382 closest distance to " O   HOH Z 302 " =    1.775
peak=    3.381 closest distance to " CB  TRP A 179 " =    1.444
peak=    3.379 closest distance to " CB  SER A 273 " =    0.955
peak=    3.375 closest distance to " CB  GLN A 103 " =    1.044
peak=    3.373 closest distance to " CG AARG A 275 " =    1.305
peak=    3.372 closest distance to " O   HOH Z 133 " =    2.599
peak=    3.371 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.371 closest distance to " O   HOH Z 326 " =    2.193
peak=    3.368 closest distance to " CG  GLN A  88 " =    1.036
peak=    3.363 closest distance to " O   ASP A 124 " =    1.132
peak=    3.358 closest distance to " CZ  PHE A 192 " =    1.032
peak=    3.356 closest distance to " O   HOH Z 403 " =    1.563
peak=    3.356 closest distance to " OG  SER A 276 " =    1.149
peak=    3.355 closest distance to " O   HOH Z 422 " =    2.687
peak=    3.353 closest distance to " O   HOH Z 132 " =    2.575
peak=    3.351 closest distance to " CA  ALA A 184 " =    1.067
peak=    3.350 closest distance to " CD2 TYR A 186 " =    1.105
peak=    3.346 closest distance to " CA  ASP A 124 " =    0.701
peak=    3.342 closest distance to " O   HOH Z   3 " =    2.024
peak=    3.339 closest distance to " CZ  PHE A  38 " =    1.143
peak=    3.338 closest distance to " O   HOH Z 215 " =    2.920
peak=    3.330 closest distance to " CB  PRO A 243 " =    1.283
peak=    3.328 closest distance to " O   HOH Z 406 " =    1.534
peak=    3.326 closest distance to " O   HOH Z 332 " =    1.534
peak=    3.326 closest distance to " O   HOH Z 211 " =    0.922
peak=    3.320 closest distance to " O   HOH Z 409 " =    2.559
peak=    3.319 closest distance to " CA  PHE A 283 " =    1.076
peak=    3.318 closest distance to " O   HOH Z 171 " =    4.122
peak=    3.313 closest distance to " C   GLN A  88 " =    1.482
peak=    3.312 closest distance to " O   HOH Z 109 " =    2.603
peak=    3.310 closest distance to " CA  ASN A 215 " =    1.188
peak=    3.308 closest distance to " CB  ALA A  10 " =    0.886
peak=    3.305 closest distance to " O   HOH Z 145 " =    1.603
peak=    3.302 closest distance to " CB  MET A  47 " =    0.980
peak=    3.302 closest distance to " OG  SER A  62 " =    2.819
peak=    3.300 closest distance to " CA  TYR A 186 " =    1.537
peak=    3.300 closest distance to " ND1 HIS A  81 " =    1.838
peak=    3.299 closest distance to " O   HOH Z 110 " =    1.608
peak=    3.295 closest distance to " CA  LYS A 290 " =    1.316
peak=    3.294 closest distance to " CA  ASN A 217 " =    1.340
peak=    3.291 closest distance to " NH1 ARG A  56 " =    1.071
peak=    3.289 closest distance to " O   HOH Z 424 " =    2.720
peak=    3.289 closest distance to " O   HOH Z 172 " =    2.964
peak=    3.289 closest distance to " O   HOH Z 392 " =    1.264
peak=    3.288 closest distance to " OD2 ASP A 286 " =    2.875
peak=    3.288 closest distance to " O   MET A 105 " =    1.711
peak=    3.287 closest distance to " OG  SER A  62 " =    3.110
peak=    3.286 closest distance to " CG1 VAL A 296 " =    1.244
peak=    3.285 closest distance to " O   HOH Z 263 " =    1.688
peak=    3.282 closest distance to " O   HOH Z 175 " =    3.698
peak=    3.280 closest distance to " CB  SER A  62 " =    1.057
peak=    3.278 closest distance to " CG1 ILE A  49 " =    1.611
peak=    3.273 closest distance to " O   HOH Z 352 " =    1.819
peak=    3.266 closest distance to " CB  ALA A   1 " =    4.762
peak=    3.263 closest distance to " O   HOH Z 280 " =    3.088
peak=    3.263 closest distance to " O   HOH Z 359 " =    1.396
peak=    3.260 closest distance to " CG1BVAL A  72 " =    1.621
peak=    3.259 closest distance to " CB  ALA A 242 " =    0.811
peak=    3.258 closest distance to " O   HOH Z  43 " =    1.926
peak=    3.256 closest distance to " CG2 ILE A 120 " =    1.262
peak=    3.254 closest distance to " CD  LYS A  76 " =    1.895
peak=    3.254 closest distance to " O   HOH Z 185 " =    1.861
peak=    3.253 closest distance to " NZ BLYS A 290 " =    0.922
peak=    3.248 closest distance to " NZ  LYS A 117 " =    3.074
peak=    3.248 closest distance to " O   HOH Z 147 " =    1.706
peak=    3.243 closest distance to " O   HOH Z 248 " =    1.692
peak=    3.243 closest distance to " CE  MET A  93 " =    1.575
peak=    3.242 closest distance to " CB  LYS A 117 " =    1.237
peak=    3.240 closest distance to " N   SER A  12 " =    1.601
peak=    3.239 closest distance to " O   PHE A 192 " =    1.369
peak=    3.236 closest distance to " CA  LYS A 117 " =    1.128
peak=    3.235 closest distance to " O   HOH Z  21 " =    1.785
peak=    3.234 closest distance to " CD  GLN A 194 " =    1.488
peak=    3.232 closest distance to " CB  SER A 146 " =    0.934
peak=    3.232 closest distance to " OD2 ASP A  65 " =    3.089
peak=    3.228 closest distance to " NZ  LYS A  48 " =    1.393
peak=    3.228 closest distance to " O   THR A 294 " =    1.077
peak=    3.227 closest distance to " O   HOH Z  57 " =    1.227
peak=    3.226 closest distance to " CB  ASN A 173 " =    1.020
peak=    3.225 closest distance to " CA  ARG A 139 " =    1.057
peak=    3.225 closest distance to " O   HOH Z 340 " =    2.112
peak=    3.225 closest distance to " CG  GLU A  37 " =    0.931
peak=    3.222 closest distance to " CA  GLU A 152 " =    0.945
peak=    3.220 closest distance to " C   ALA A 299 " =    0.964
peak=    3.220 closest distance to " O   HOH Z 148 " =    3.582
peak=    3.217 closest distance to " O   HOH Z 350 " =    1.690
peak=    3.216 closest distance to " CB  ALA A   9 " =    1.578
peak=    3.214 closest distance to " CE3 TRP A 150 " =    1.002
peak=    3.208 closest distance to " O   HOH Z 119 " =    1.715
peak=    3.207 closest distance to " O   THR A 251 " =    1.159
peak=    3.196 closest distance to " O   HOH Z 166 " =    3.856
peak=    3.195 closest distance to " CB  ALA A 248 " =    1.254
peak=    3.193 closest distance to " OG BSER A 212 " =    2.719
peak=    3.191 closest distance to " O   HOH Z 344 " =    2.911
peak=    3.185 closest distance to " O   HOH Z 435 " =    2.029
peak=    3.185 closest distance to " O   HOH Z 291 " =    1.653
peak=    3.176 closest distance to " CB  ALA A 291 " =    1.143
peak=    3.176 closest distance to " CB  ASP A 140 " =    0.834
peak=    3.173 closest distance to " N   ASN A  39 " =    1.163
peak=    3.173 closest distance to " O   PHE A  61 " =    1.457
peak=    3.173 closest distance to " CA  VAL A 125 " =    1.125
peak=    3.171 closest distance to " O   HOH Z 419 " =    1.872
peak=    3.169 closest distance to " O   HOH Z 435 " =    2.097
peak=    3.167 closest distance to " CG  MET A 185 " =    1.153
peak=    3.166 closest distance to " CG2 VAL A 268 " =    1.044
peak=    3.162 closest distance to " NH2BARG A 190 " =    1.477
peak=    3.162 closest distance to " CG2 ILE A  20 " =    1.545
peak=    3.161 closest distance to " CA  ARG A 102 " =    1.188
peak=    3.160 closest distance to " CG  ARG A 159 " =    0.992
peak=    3.159 closest distance to " O   HOH Z 173 " =    1.798
peak=    3.156 closest distance to " CA  ALA A 158 " =    1.181
peak=    3.156 closest distance to " O   ASN A  74 " =    1.539
peak=    3.154 closest distance to " CA  MET A 105 " =    0.888
peak=    3.153 closest distance to " O   HOH Z 261 " =    1.432
peak=    3.149 closest distance to " O   HOH Z  80 " =    1.562
peak=    3.149 closest distance to " O  BHOH Z  74 " =    1.278
peak=    3.147 closest distance to " CD1 LEU A  96 " =    0.761
peak=    3.141 closest distance to " O   HOH Z 238 " =    3.652
peak=    3.140 closest distance to " O   HOH Z 368 " =    4.163
peak=    3.138 closest distance to " O   HOH Z  59 " =    1.915
peak=    3.133 closest distance to " CG1 ILE A  33 " =    1.323
peak=    3.132 closest distance to " O   HOH Z 153 " =    3.768
peak=    3.122 closest distance to " O   HOH Z  85 " =    2.043
peak=    3.121 closest distance to " O   HOH Z 200 " =    3.043
peak=    3.116 closest distance to " CB  ARG A 102 " =    0.747
peak=    3.115 closest distance to " OG ASER A 212 " =    1.981
peak=    3.115 closest distance to " OE2 GLU A  53 " =    2.097
peak=    3.114 closest distance to " CB  ALA A 291 " =    0.776
peak=    3.113 closest distance to " N   TYR A  15 " =    0.829
peak=    3.112 closest distance to " O   HOH Z 345 " =    3.496
peak=    3.110 closest distance to " O  BHOH Z 338 " =    2.482
peak=    3.108 closest distance to " O   HOH Z 152 " =    2.817
peak=    3.096 closest distance to " CB  ALA A  43 " =    0.951
peak=    3.091 closest distance to " O   PRO A  90 " =    1.687
peak=    3.087 closest distance to " CG  MET A 185 " =    0.929
peak=    3.081 closest distance to " O   HOH Z 371 " =    2.722
peak=    3.068 closest distance to " CB  ARG A 156 " =    1.179
peak=    3.060 closest distance to " CG1AVAL A 121 " =    0.755
peak=    3.056 closest distance to " CB  ALA A 114 " =    0.816
peak=    3.049 closest distance to " CB  GLU A 175 " =    0.972
peak=    3.044 closest distance to " CB  LEU A 300 " =    0.929
peak=    3.035 closest distance to " O   HOH Z 222 " =    2.263
peak=    3.030 closest distance to " CG  ARG A 269 " =    1.695
peak=    3.020 closest distance to " CA  TYR A  30 " =    1.089
peak=    3.001 closest distance to " O   HOH Z  88 " =    3.590

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.540 - 5.410
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.733 - 5.410

peak=   -5.813 closest distance to " CG2 VAL A 230 " =    0.745
peak=   -4.934 closest distance to " CD  ARG A 138 " =    1.126
peak=   -4.470 closest distance to " O   PRO A 198 " =    1.186
peak=   -4.351 closest distance to " OE1 GLN A  88 " =    0.939
peak=   -4.303 closest distance to " CG  ARG A 138 " =    0.831
peak=   -4.264 closest distance to " O   HOH Z 211 " =    0.939
peak=   -4.207 closest distance to " CD  ARG A  14 " =    3.229
peak=   -4.161 closest distance to " O   HOH Z 162 " =    2.629
peak=   -4.138 closest distance to " CG1 VAL A 112 " =    2.649
peak=   -4.132 closest distance to " CD  ARG A 156 " =    2.059
peak=   -4.012 closest distance to " O   HOH Z 351 " =    1.410
peak=   -3.940 closest distance to " CA  GLY A 241 " =    2.365
peak=   -3.938 closest distance to " O   HOH Z 231 " =    1.873
peak=   -3.894 closest distance to " N   THR A 157 " =    1.531
peak=   -3.893 closest distance to " O   HOH Z 231 " =    0.879
peak=   -3.880 closest distance to " CG2 VAL A 202 " =    2.733
peak=   -3.878 closest distance to " CD2 LEU A   5 " =    0.903
peak=   -3.874 closest distance to " O   VAL A  67 " =    2.625
peak=   -3.837 closest distance to " O   GLY A  17 " =    1.370
peak=   -3.836 closest distance to " CG2 THR A 178 " =    2.371
peak=   -3.833 closest distance to " O   HOH Z 290 " =    1.172
peak=   -3.814 closest distance to " O   HOH Z 394 " =    1.511
peak=   -3.814 closest distance to " CG  TRP A 266 " =    1.780
peak=   -3.812 closest distance to " O   HOH Z 185 " =    2.250
peak=   -3.794 closest distance to " OG BSER A 134 " =    1.500
peak=   -3.770 closest distance to " O   HOH Z  52 " =    1.099
peak=   -3.766 closest distance to " O   PRO A 163 " =    1.966
peak=   -3.765 closest distance to " O   GLY A 203 " =    2.475
peak=   -3.753 closest distance to " CA  ASP A  27 " =    2.443
peak=   -3.751 closest distance to " O   HOH Z 359 " =    3.095
peak=   -3.751 closest distance to " CG2 VAL A 296 " =    0.854
peak=   -3.750 closest distance to " O   HOH Z 411 " =    5.325
peak=   -3.742 closest distance to " CG1 VAL A 296 " =    1.398
peak=   -3.728 closest distance to " CB  PRO A 163 " =    2.443
peak=   -3.726 closest distance to " O   HOH Z 100 " =    0.966
peak=   -3.709 closest distance to " OG  SER A  97 " =    2.265
peak=   -3.691 closest distance to " CB  ALA A  43 " =    2.597
peak=   -3.641 closest distance to " CD1 LEU A 101 " =    2.371
peak=   -3.624 closest distance to " C   LEU A 222 " =    0.968
peak=   -3.616 closest distance to " O   HOH Z 275 " =    1.840
peak=   -3.616 closest distance to " CD  GLN A  58 " =    0.861
peak=   -3.608 closest distance to " CD  GLN A 223 " =    2.344
peak=   -3.603 closest distance to " CE2 TYR A  30 " =    2.730
peak=   -3.599 closest distance to " CB  VAL A 230 " =    1.127
peak=   -3.595 closest distance to " O   HOH Z 166 " =    2.189
peak=   -3.575 closest distance to " CB  TRP A  85 " =    2.532
peak=   -3.574 closest distance to " CA  GLY A 241 " =    3.127
peak=   -3.564 closest distance to " CD1 LEU A 228 " =    2.373
peak=   -3.560 closest distance to " O   TYR A 247 " =    2.861
peak=   -3.551 closest distance to " O   HOH Z 359 " =    1.606
peak=   -3.551 closest distance to " O   HOH Z 166 " =    1.968
peak=   -3.546 closest distance to " O   HOH Z 201 " =    1.646
peak=   -3.542 closest distance to " C   ALA A 158 " =    1.407
peak=   -3.531 closest distance to " CG  GLN A  88 " =    0.846
peak=   -3.528 closest distance to " O   HOH Z 377 " =    0.745
peak=   -3.525 closest distance to " CG  MET A 105 " =    0.965
peak=   -3.522 closest distance to " C   GLU A 236 " =    0.955
peak=   -3.519 closest distance to " O   HOH Z 216 " =    1.285
peak=   -3.519 closest distance to " CB  PHE A 192 " =    1.851
peak=   -3.514 closest distance to " O   HOH Z 377 " =    1.584
peak=   -3.511 closest distance to " O   HOH Z 108 " =    1.351
peak=   -3.505 closest distance to " O   HOH Z  51 " =    1.079
peak=   -3.505 closest distance to " CE3 TRP A 150 " =    2.420
peak=   -3.500 closest distance to " OE1 GLU A  44 " =    0.850
peak=   -3.494 closest distance to " O   ILE A  49 " =    1.714
peak=   -3.491 closest distance to " C   ASN A 285 " =    2.438
peak=   -3.486 closest distance to " CZ2 TRP A  92 " =    2.868
peak=   -3.486 closest distance to " CB  TYR A  15 " =    2.215
peak=   -3.479 closest distance to " O   HOH Z 389 " =    1.452
peak=   -3.477 closest distance to " O   HOH Z  43 " =    1.668
peak=   -3.476 closest distance to " CB  ALA A 161 " =    2.584
peak=   -3.476 closest distance to " OD1 ASN A  60 " =    0.850
peak=   -3.475 closest distance to " CZ2 TRP A 274 " =    0.926
peak=   -3.474 closest distance to " OH  TYR A 172 " =    1.766
peak=   -3.460 closest distance to " O   HOH Z  11 " =    1.828
peak=   -3.459 closest distance to " CG2 ILE A 151 " =    2.611
peak=   -3.458 closest distance to " O   HOH Z 295 " =    1.535
peak=   -3.451 closest distance to " O   HOH Z  73 " =    2.030
peak=   -3.448 closest distance to " ND2 ASN A  45 " =    1.165
peak=   -3.448 closest distance to " CG  LEU A 228 " =    0.906
peak=   -3.446 closest distance to " O   HOH Z 435 " =    2.889
peak=   -3.443 closest distance to " CZ3 TRP A 179 " =    1.158
peak=   -3.438 closest distance to " NH2 ARG A  79 " =    2.049
peak=   -3.437 closest distance to " O   HOH Z 389 " =    2.143
peak=   -3.432 closest distance to " CB  VAL A 296 " =    0.982
peak=   -3.429 closest distance to " O   HOH Z 211 " =    1.167
peak=   -3.428 closest distance to " CD2 TYR A 293 " =    1.966
peak=   -3.425 closest distance to " OG BSER A 134 " =    1.918
peak=   -3.423 closest distance to " O   HOH Z   9 " =    1.732
peak=   -3.418 closest distance to " CG1 VAL A 250 " =    2.714
peak=   -3.407 closest distance to " CB  ALA A 248 " =    2.115
peak=   -3.406 closest distance to " CG  ASP A 231 " =    0.733
peak=   -3.405 closest distance to " N   ALA A 226 " =    2.121
peak=   -3.404 closest distance to " CG1 VAL A 265 " =    2.470
peak=   -3.394 closest distance to " CG2 VAL A 296 " =    1.642
peak=   -3.392 closest distance to " O   GLY A 211 " =    1.220
peak=   -3.387 closest distance to " NH2AARG A 275 " =    5.410
peak=   -3.384 closest distance to " CB  ASP A 132 " =    2.380
peak=   -3.382 closest distance to " O   HOH Z  65 " =    1.123
peak=   -3.380 closest distance to " O   HOH Z 198 " =    2.281
peak=   -3.374 closest distance to " O   HOH Z  60 " =    1.702
peak=   -3.374 closest distance to " O   MET A  40 " =    2.849
peak=   -3.371 closest distance to " C   PHE A  59 " =    1.115
peak=   -3.365 closest distance to " CE2 TRP A  70 " =    2.298
peak=   -3.363 closest distance to " O   HOH Z  60 " =    2.430
peak=   -3.362 closest distance to " O   HOH Z 282 " =    4.943
peak=   -3.357 closest distance to " O   HOH Z 102 " =    1.481
peak=   -3.355 closest distance to " O   HOH Z 144 " =    1.310
peak=   -3.355 closest distance to " CE BMET A  47 " =    1.493
peak=   -3.354 closest distance to " CG1 VAL A 112 " =    2.611
peak=   -3.353 closest distance to " CG1 VAL A 112 " =    2.951
peak=   -3.350 closest distance to " CZ  PHE A 130 " =    1.005
peak=   -3.343 closest distance to " O   VAL A 189 " =    2.508
peak=   -3.340 closest distance to " CG  GLU A 277 " =    1.265
peak=   -3.339 closest distance to " CA  GLY A  98 " =    1.983
peak=   -3.338 closest distance to " CB  PHE A 130 " =    1.294
peak=   -3.336 closest distance to " CZ  PHE A 192 " =    2.675
peak=   -3.335 closest distance to " CA  SER A  62 " =    2.622
peak=   -3.332 closest distance to " O   HOH Z 131 " =    4.093
peak=   -3.328 closest distance to " OG  SER A  87 " =    1.501
peak=   -3.328 closest distance to " CD  PRO A 243 " =    2.002
peak=   -3.324 closest distance to " CD1 LEU A 101 " =    2.577
peak=   -3.319 closest distance to " CD  LYS A 289 " =    2.387
peak=   -3.318 closest distance to " O   HOH Z 112 " =    1.309
peak=   -3.313 closest distance to " C   ASP A 270 " =    1.526
peak=   -3.312 closest distance to " O   HOH Z 111 " =    1.819
peak=   -3.311 closest distance to " O   HOH Z  39 " =    0.784
peak=   -3.309 closest distance to " OG  SER A  63 " =    1.058
peak=   -3.308 closest distance to " C   HIS A 108 " =    1.121
peak=   -3.300 closest distance to " O   HOH Z 238 " =    0.881
peak=   -3.300 closest distance to " O   HOH Z 350 " =    1.771
peak=   -3.296 closest distance to " ND2 ASN A  60 " =    1.689
peak=   -3.293 closest distance to " ND2 ASN A 187 " =    1.518
peak=   -3.290 closest distance to " CA  VAL A 296 " =    1.057
peak=   -3.290 closest distance to " O   ARG A 145 " =    1.404
peak=   -3.289 closest distance to " O   HOH Z 241 " =    1.325
peak=   -3.287 closest distance to " N   ASP A 191 " =    1.141
peak=   -3.281 closest distance to " O   HOH Z 281 " =    2.729
peak=   -3.272 closest distance to " C   SER A 273 " =    1.119
peak=   -3.271 closest distance to " N   ALA A  43 " =    2.730
peak=   -3.268 closest distance to " NE2 GLN A  88 " =    1.068
peak=   -3.268 closest distance to " CB  ALA A 227 " =    2.420
peak=   -3.266 closest distance to " CE3 TRP A  70 " =    1.758
peak=   -3.257 closest distance to " CE2 PHE A 218 " =    2.456
peak=   -3.255 closest distance to " O   ASP A  27 " =    1.699
peak=   -3.255 closest distance to " O   HOH Z  38 " =    1.567
peak=   -3.254 closest distance to " O   HOH Z 251 " =    4.824
peak=   -3.253 closest distance to " O   HOH Z 118 " =    1.638
peak=   -3.252 closest distance to " C   MET A 188 " =    1.515
peak=   -3.248 closest distance to " O   HOH Z 286 " =    1.640
peak=   -3.246 closest distance to " O   HOH Z 198 " =    1.062
peak=   -3.246 closest distance to " CB  HIS A  86 " =    1.092
peak=   -3.239 closest distance to " CB  HIS A  81 " =    0.992
peak=   -3.237 closest distance to " O   SER A  22 " =    2.376
peak=   -3.232 closest distance to " O   SER A 276 " =    1.753
peak=   -3.230 closest distance to " O   HOH Z 139 " =    0.970
peak=   -3.216 closest distance to " O   HOH Z 133 " =    1.294
peak=   -3.208 closest distance to " CD2 HIS A 207 " =    2.372
peak=   -3.206 closest distance to " CB  CYS A 254 " =    2.072
peak=   -3.206 closest distance to " O   HOH Z 368 " =    1.540
peak=   -3.205 closest distance to " O   GLY A  80 " =    2.536
peak=   -3.204 closest distance to " O   ALA A  51 " =    1.537
peak=   -3.198 closest distance to " CD1 ILE A  33 " =    2.569
peak=   -3.196 closest distance to " O   HOH Z 412 " =    4.362
peak=   -3.188 closest distance to " O   HOH Z 313 " =    1.337
peak=   -3.179 closest distance to " CB  ASP A 200 " =    2.730
peak=   -3.177 closest distance to " N   SER A 212 " =    1.897
peak=   -3.170 closest distance to " O   HOH Z 179 " =    2.238
peak=   -3.152 closest distance to " N   SER A 276 " =    1.325
peak=   -3.151 closest distance to " O   HOH Z 275 " =    1.527
peak=   -3.147 closest distance to " NH2 ARG A  79 " =    1.537
peak=   -3.145 closest distance to " O   HOH Z 407 " =    3.096
peak=   -3.143 closest distance to " OG ASER A 134 " =    1.607
peak=   -3.142 closest distance to " C   LYS A  76 " =    1.327
peak=   -3.141 closest distance to " O   HOH Z 253 " =    4.135
peak=   -3.141 closest distance to " CG2 THR A 178 " =    2.156
peak=   -3.140 closest distance to " O   HOH Z 406 " =    2.230
peak=   -3.138 closest distance to " O   HOH Z 166 " =    1.461
peak=   -3.133 closest distance to " OG  SER A 141 " =    1.926
peak=   -3.130 closest distance to " O   HOH Z 111 " =    4.573
peak=   -3.125 closest distance to " O   VAL A 125 " =    2.292
peak=   -3.122 closest distance to " O   HOH Z   2 " =    1.659
peak=   -3.121 closest distance to " OH  TYR A 247 " =    1.816
peak=   -3.112 closest distance to " OG  SER A 206 " =    1.779
peak=   -3.112 closest distance to " O   HOH Z 353 " =    2.001
peak=   -3.111 closest distance to " OD2 ASP A  50 " =    2.112
peak=   -3.109 closest distance to " O   TRP A  70 " =    1.458
peak=   -3.106 closest distance to " O   HOH Z  52 " =    1.879
peak=   -3.106 closest distance to " O   HOH Z 357 " =    1.886
peak=   -3.103 closest distance to " O   HOH Z 118 " =    1.112
peak=   -3.100 closest distance to " O   HOH Z 380 " =    1.158
peak=   -3.096 closest distance to " CA  ALA A 248 " =    2.480
peak=   -3.090 closest distance to " O   HOH Z 365 " =    1.394
peak=   -3.090 closest distance to " O   HOH Z 390 " =    2.217
peak=   -3.086 closest distance to " OD1 ASP A 171 " =    1.609
peak=   -3.082 closest distance to " CB  GLN A  55 " =    1.384
peak=   -3.079 closest distance to " CA  SER A 135 " =    1.349
peak=   -3.077 closest distance to " O   HOH Z 177 " =    1.909
peak=   -3.076 closest distance to " CB  ALA A   9 " =    2.555
peak=   -3.070 closest distance to " CA  GLY A 133 " =    2.199
peak=   -3.063 closest distance to " O   HOH Z 292 " =    1.870
peak=   -3.061 closest distance to " CD1 ILE A 239 " =    2.177
peak=   -3.059 closest distance to " CD1 ILE A 199 " =    2.627
peak=   -3.057 closest distance to " O   HOH Z  44 " =    1.120
peak=   -3.050 closest distance to " CE  MET A 105 " =    2.425
peak=   -3.049 closest distance to " NE2 GLN A 240 " =    1.639
peak=   -3.044 closest distance to " O   HOH Z 171 " =    2.283
peak=   -3.016 closest distance to " CB  CYS A 201 " =    2.328

================= 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    :  0.4741 0.4583   6.273761e+00   6.250956e+00
   1_bss:  0.4662 0.4482   6.268791e+00   6.244411e+00
   1_xyz:  0.3745 0.3911   6.132980e+00   6.159365e+00
   1_adp:  0.3247 0.3736   6.035575e+00   6.126041e+00
   1_occ:  0.3242 0.3741   6.034823e+00   6.126292e+00
   2_bss:  0.3205 0.3692   6.034170e+00   6.123050e+00
   2_xyz:  0.2277 0.2797   5.754206e+00   5.909765e+00
   2_adp:  0.2055 0.2572   5.663881e+00   5.832028e+00
   2_occ:  0.2053 0.2574   5.663906e+00   5.832819e+00
   3_bss:  0.2038 0.2569   5.665453e+00   5.833741e+00
   3_xyz:  0.1559 0.2039   5.424022e+00   5.627181e+00
   3_adp:  0.1442 0.1960   5.371083e+00   5.591414e+00
   3_occ:  0.1442 0.1962   5.371335e+00   5.592015e+00
   4_bss:  0.1441 0.1959   5.371200e+00   5.591111e+00
   4_xyz:  0.1227 0.1761   5.245131e+00   5.490850e+00
   4_adp:  0.1195 0.1694   5.212868e+00   5.454034e+00
   4_occ:  0.1194 0.1693   5.212425e+00   5.453468e+00
   5_bss:  0.1194 0.1693   5.212386e+00   5.453450e+00
   5_xyz:  0.1217 0.1687   5.224551e+00   5.454564e+00
   5_adp:  0.1230 0.1675   5.226180e+00   5.446386e+00
   5_occ:  0.1229 0.1673   5.225601e+00   5.445621e+00
   5_bss:  0.1231 0.1667   5.225519e+00   5.444405e+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:  0.332  20.001   8.129   8.024   9.941   0.000   0.000   0.000
   1_xyz:  0.332  20.001   8.129   8.024   9.941   0.000   0.000   0.000
   1_adp:  0.332  20.001   8.129   8.024   9.941   0.000   0.000   0.000
   1_occ:  0.332  20.001   8.129   8.024   9.941   0.000   0.000   0.000
   2_bss:  0.336  50.000   4.911   4.347   6.530   0.000   0.000   0.000
   2_xyz:  0.336  50.000   4.911   4.347   6.530   0.000   0.000   0.000
   2_adp:  0.336  50.000   4.911   4.347   6.530   0.000   0.000   0.000
   2_occ:  0.336  50.000   4.911   4.347   6.530   0.000   0.000   0.000
   3_bss:  0.320  57.137   2.963   2.535   4.414   0.000   0.000   0.000
   3_xyz:  0.320  57.137   2.963   2.535   4.414   0.000   0.000   0.000
   3_adp:  0.320  57.137   2.963   2.535   4.414   0.000   0.000   0.000
   3_occ:  0.320  57.137   2.963   2.535   4.414   0.000   0.000   0.000
   4_bss:  0.333  67.287   2.497   2.167   3.987   0.000   0.000   0.000
   4_xyz:  0.333  67.287   2.497   2.167   3.987   0.000   0.000   0.000
   4_adp:  0.333  67.287   2.497   2.167   3.987   0.000   0.000   0.000
   4_occ:  0.333  67.287   2.497   2.167   3.987   0.000   0.000   0.000
   5_bss:  0.333  67.287   2.471   2.117   3.909   0.000   0.000   0.000
   5_xyz:  0.333  67.287   2.471   2.117   3.909   0.000   0.000   0.000
   5_adp:  0.333  67.287   2.471   2.117   3.909   0.000   0.000   0.000
   5_occ:  0.333  67.287   2.471   2.117   3.909   0.000   0.000   0.000
   5_bss:  0.335  69.878  -0.384  -0.701   1.085   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.874 0.4722  0.5439    63284.370
   1_bss:  54.039 0.4689  0.6991    62042.019
   1_xyz:  44.469 0.5875  0.8464    43953.695
   1_adp:  40.557 0.6356  0.9451    38961.538
   1_occ:  40.601 0.6349  0.9433    39001.730
   2_bss:  40.290 0.6385  0.8417    38477.936
   2_xyz:  28.912 0.7689  0.9749    20832.127
   2_adp:  25.682 0.8045  0.9953    17210.223
   2_occ:  25.709 0.8043  0.9945    17225.481
   3_bss:  25.716 0.8043  0.9281    17308.817
   3_xyz:  19.464 0.8666  0.9774    10555.596
   3_adp:  18.572 0.8752  0.9797     9854.198
   3_occ:  18.591 0.8751  0.9794     9859.156
   4_bss:  18.573 0.8752  0.9647     9836.623
   4_xyz:  16.335 0.8951  0.9752     7865.048
   4_adp:  15.447 0.9030  0.9752     7310.172
   4_occ:  15.440 0.9031  0.9752     7299.136
   5_bss:  15.438 0.9031  0.9734     7299.109
   5_xyz:  15.357 0.9042  0.9725     7298.771
   5_adp:  15.147 0.9062  0.9724     7236.423
   5_occ:  15.138 0.9062  0.9724     7222.394
   5_bss:  15.124 0.9063  0.9641     7192.172
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4200e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4200e+01
   1_xyz:   1.677  0.013  0.108 18.214  0.006  4.111   1.3868e-01
   1_adp:   1.677  0.013  0.108 18.214  0.006  4.111   1.3868e-01
   1_occ:   1.677  0.013  0.108 18.214  0.006  4.111   1.3868e-01
   2_bss:   1.677  0.013  0.108 18.214  0.006  4.111   1.3868e-01
   2_xyz:   1.091  0.008  0.076 16.243  0.005  4.111   7.3668e-02
   2_adp:   1.091  0.008  0.076 16.243  0.005  4.111   7.3668e-02
   2_occ:   1.091  0.008  0.076 16.243  0.005  4.111   7.3668e-02
   3_bss:   1.091  0.008  0.076 16.243  0.005  4.111   7.3668e-02
   3_xyz:   1.003  0.007  0.077 15.690  0.003  4.127   6.2276e-02
   3_adp:   1.003  0.007  0.077 15.690  0.003  4.127   6.2276e-02
   3_occ:   1.003  0.007  0.077 15.690  0.003  4.127   6.2276e-02
   4_bss:   1.003  0.007  0.077 15.690  0.003  4.127   6.2276e-02
   4_xyz:   1.171  0.011  0.090 15.860  0.004  4.137   8.2009e-02
   4_adp:   1.171  0.011  0.090 15.860  0.004  4.137   8.2009e-02
   4_occ:   1.171  0.011  0.090 15.860  0.004  4.137   8.2009e-02
   5_bss:   1.171  0.011  0.090 15.860  0.004  4.137   8.2009e-02
   5_xyz:   0.957  0.007  0.075 15.469  0.003  4.113   5.7846e-02
   5_adp:   0.957  0.007  0.075 15.469  0.003  4.113   5.7846e-02
   5_occ:   0.957  0.007  0.075 15.469  0.003  4.113   5.7846e-02
   5_bss:   0.957  0.007  0.075 15.469  0.003  4.113   5.7846e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0274e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0274e+00
   1_xyz:  13.942  0.169  0.421 85.274  0.035  2.265   1.0203e-01
   1_adp:  13.942  0.169  0.421 85.274  0.035  2.265   1.0203e-01
   1_occ:  13.942  0.169  0.421 85.274  0.035  2.265   1.0203e-01
   2_bss:  13.942  0.169  0.421 85.274  0.035  2.265   1.0203e-01
   2_xyz:   6.594  0.075  0.265 85.597  0.044  2.245   7.2560e-02
   2_adp:   6.594  0.075  0.265 85.597  0.044  2.245   7.2560e-02
   2_occ:   6.594  0.075  0.265 85.597  0.044  2.245   7.2560e-02
   3_bss:   6.594  0.075  0.265 85.597  0.044  2.245   7.2560e-02
   3_xyz:   8.184  0.050  0.377 88.628  0.027  2.374   9.2912e-02
   3_adp:   8.184  0.050  0.377 88.628  0.027  2.374   9.2912e-02
   3_occ:   8.184  0.050  0.377 88.628  0.027  2.374   9.2912e-02
   4_bss:   8.184  0.050  0.377 88.628  0.027  2.374   9.2912e-02
   4_xyz:   9.655  0.073  0.543 83.083  0.040  2.292   5.8631e-02
   4_adp:   9.655  0.073  0.543 83.083  0.040  2.292   5.8631e-02
   4_occ:   9.655  0.073  0.543 83.083  0.040  2.292   5.8631e-02
   5_bss:   9.655  0.073  0.543 83.083  0.040  2.292   5.8631e-02
   5_xyz:   8.121  0.047  0.376 82.589  0.037  2.399   3.1928e-02
   5_adp:   8.121  0.047  0.376 82.589  0.037  2.399   3.1928e-02
   5_occ:   8.121  0.047  0.376 82.589  0.037  2.399   3.1928e-02
   5_bss:   8.121  0.047  0.376 82.589  0.037  2.399   3.1928e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  79.87   0.00  12.75  65.39   0.00   9.98  79.87   0.00  27.88
   1_occ:  79.87   0.00  12.75  65.39   0.00   9.98  79.87   0.00  27.88
   2_bss:  79.87   0.00  12.75  65.39   0.00   9.98  79.87   0.00  27.88
   2_xyz:  79.87   0.00  12.75  65.39   0.00   9.98  79.87   0.00  27.88
   2_adp:  82.57   0.00  12.48  66.56   0.00   8.67  82.57   0.00  33.23
   2_occ:  82.57   0.00  12.48  66.56   0.00   8.67  82.57   0.00  33.23
   3_bss:  82.57   0.00  12.48  66.56   0.00   8.67  82.57   0.00  33.23
   3_xyz:  82.57   0.00  12.48  66.56   0.00   8.67  82.57   0.00  33.23
   3_adp:  93.24   0.00  13.77  81.88   0.00   8.88  93.24   1.03  40.38
   3_occ:  93.24   0.00  13.77  81.88   0.00   8.88  93.24   1.03  40.38
   4_bss:  93.24   0.00  13.77  81.88   0.00   8.88  93.24   1.03  40.38
   4_xyz:  93.24   0.00  13.77  81.88   0.00   8.88  93.24   1.03  40.38
   4_adp:  92.03   0.00  13.26  82.66   0.00   8.55  92.03   1.75  38.90
   4_occ:  92.03   0.00  13.26  82.66   0.00   8.55  92.03   1.75  38.90
   5_bss:  92.03   0.00  13.26  82.66   0.00   8.55  92.03   1.75  38.90
   5_xyz:  92.03   0.00  13.26  82.66   0.00   8.55  92.03   1.75  38.90
   5_adp:  87.04   0.00  12.72  80.67   0.00   8.36  87.04   2.22  36.48
   5_occ:  87.04   0.00  12.72  80.67   0.00   8.36  87.04   2.22  36.48
   5_bss:  89.63   2.59  15.31  83.26   2.59  10.95  89.63   4.81  39.07
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.240    0.017    0.410
   1_adp:    1.240    0.017    0.410
   1_occ:    1.240    0.017    0.410
   2_bss:    1.240    0.017    0.410
   2_xyz:    1.513    0.059    0.557
   2_adp:    1.513    0.059    0.557
   2_occ:    1.513    0.059    0.557
   3_bss:    1.513    0.059    0.557
   3_xyz:    1.487    0.035    0.619
   3_adp:    1.487    0.035    0.619
   3_occ:    1.487    0.035    0.619
   4_bss:    1.487    0.035    0.619
   4_xyz:    1.638    0.012    0.660
   4_adp:    1.638    0.012    0.660
   4_occ:    1.638    0.012    0.660
   5_bss:    1.638    0.012    0.660
   5_xyz:    1.722    0.041    0.666
   5_adp:    1.722    0.041    0.666
   5_occ:    1.722    0.041    0.666
   5_bss:    1.722    0.041    0.666
------------------------------------------------------------------------

CPU time actual refinement: 334.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1009/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_1009/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1009/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1009/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1009/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.22 
  Macro-tasks:
    bulk solvent and scale       = 39.76  
    individual site refinement   = 140.55 
    weights calculation          = 31.00  
    collect and process          = 6.43   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 217.84 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 102.96 
    alpha_beta                      = 8.11   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 114.70 
    fmodel                         = 7.55   
    r_factors                      = 0.22   
    phase_errors                   = 10.73  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 247.97 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.631 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    667 calls, 102.60 s
gradients_fft:          612 calls, 100.69 s

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

# Date 2008-01-16 Time 02:58:04 PST -0800 (1200481084.65 s)
Start R-work = 0.4741, R-free = 0.4583 (no bulk solvent and anisotropic scale)
Final R-work = 0.1395, R-free = 0.1838 (no bulk solvent and anisotropic scale)

Start R-work = 0.4662, R-free = 0.4482
Final R-work = 0.1231, R-free = 0.1667