# Date 2008-01-16 Time 02:49:33 PST -0800 (1200480573.41 s)
#phil __OFF__

Command line arguments: "../986.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 = 17087
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 986

-------------------------------------------------------------------------------
  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, 45.9914, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, 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, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.9639
Completeness in resolution range: 0.929666
Completeness with d_max=infinity: 0.927027

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   1.9639

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, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.9639
Completeness in resolution range: 0.929666
Completeness with d_max=infinity: 0.927027

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.2041 [2208/2235]  1987   221  10.0%
  bin  2:  4.2041 -  3.3486 [2136/2156]  1923   213  10.0%
  bin  3:  3.3486 -  2.9288 [2101/2120]  1892   209   9.9%
  bin  4:  2.9288 -  2.6625 [2068/2098]  1855   213  10.3%
  bin  5:  2.6625 -  2.4726 [2072/2091]  1876   196   9.5%
  bin  6:  2.4726 -  2.3273 [2070/2095]  1856   214  10.3%
  bin  7:  2.3273 -  2.2112 [2046/2074]  1836   210  10.3%
  bin  8:  2.2112 -  2.1152 [2025/2061]  1822   203  10.0%
  bin  9:  2.1152 -  2.0339 [2043/2085]  1847   196   9.6%
  bin 10:  2.0339 -  1.9639 [ 820/2056]   736    84  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_986/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: 35
        2.42 -     3.04: 2198
        3.04 -     3.66: 4695
        3.66 -     4.28: 9006
        4.28 -     4.90: 12296
  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
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.850 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28225 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_986/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_986/model_refine_001.geo

CPU time processing inputs: 9.26


============================ 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 45.9914 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4954   r_free= 0.4859   ksol= 0.00   Bsol= 0.00   scale= 0.779    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.297976                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.6898 0.99   1431  160 0.4214 0.4028      6.6282      6.6359|
|  2:  4.6898 -  3.7407 0.99   1390  153 0.4225 0.4012      6.8446      6.7992|
|  3:  3.7407 -  3.2733 0.99   1343  150 0.4465 0.4271      6.6758       6.664|
|  4:  3.2733 -  2.9764 0.99   1360  153 0.4882 0.4694      6.5481      6.5067|
|  5:  2.9764 -  2.7645 0.99   1344  147 0.5294 0.5208      6.3784      6.3891|
|  6:  2.7645 -  2.6023 0.99   1336  150 0.5247 0.5329      6.2797      6.2252|
|  7:  2.6023 -  2.4726 0.99   1329  139 0.5405 0.4824      6.2481      6.1711|
|  8:  2.4726 -  2.3654 0.98   1316  156 0.5408 0.5245      6.1748      6.1932|
|  9:  2.3654 -  2.2746 0.98   1312  142 0.5389 0.5284      6.1394      6.1936|
| 10:  2.2746 -  2.1964 1.00   1323  159 0.5311 0.5283      6.0774      6.0614|
| 11:  2.1964 -  2.1279 0.98   1316  133 0.5171 0.5610       6.039      6.0694|
| 12:  2.1279 -  2.0672 0.98   1287  148 0.5410 0.5496      5.9412      5.9645|
| 13:  2.0672 -  2.0129 0.92   1220  131 0.5510 0.5487      5.8867      5.8022|
| 14:  2.0129 -  1.9639 0.24    323   38 0.5663 0.4862      5.8845       5.865|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.6898  1431   160  0.66  37.75   0.78     0.71      84450.13|
|  2:  4.6898 -  3.7407  1390   153  0.69  35.86   0.85     0.77     113383.48|
|  3:  3.7407 -  3.2733  1343   150  0.57  46.03   0.84     0.71     121878.68|
|  4:  3.2733 -  2.9764  1360   153  0.47  54.00   0.77     0.58     110706.30|
|  5:  2.9764 -  2.7645  1344   147  0.37  62.24   0.72     0.46      91554.65|
|  6:  2.7645 -  2.6023  1336   150  0.34  64.37   0.70     0.41      77906.57|
|  7:  2.6023 -  2.4726  1329   139  0.30  67.87   0.73     0.35      70573.93|
|  8:  2.4726 -  2.3654  1316   156  0.26  70.34   0.71     0.32      65278.92|
|  9:  2.3654 -  2.2746  1312   142  0.25  71.34   0.72     0.30      60949.98|
| 10:  2.2746 -  2.1964  1323   159  0.25  71.21   0.74     0.31      54826.68|
| 11:  2.1964 -  2.1279  1316   133  0.24  72.12   0.76     0.30      52816.75|
| 12:  2.1279 -  2.0672  1287   148  0.23  72.86   0.73     0.31      47507.04|
| 13:  2.0672 -  2.0129  1220   131  0.25  71.35   0.71     0.33      40243.15|
| 14:  2.0129 -  1.9639   323    38  0.38  61.83   0.70     0.41      28332.33|
|alpha:            min =        0.30 max =            0.77 mean =         0.45|
|beta:             min =    28332.33 max =       121878.68 mean =     76059.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.98|
|phase err.(test): min =        0.00 max =           89.98 mean =        61.17|
|-----------------------------------------------------------------------------|

============================== 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 = 19.059333             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.106   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.625201              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.355   (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:       32 |
| 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:      690 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1504 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2644 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3922 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5058 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6545 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7685 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.843 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.979 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4996   r_free= 0.4876   ksol= 0.00   Bsol= 0.00   scale= 0.750    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.298925                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4875   r_free= 0.4728   ksol= 0.30   Bsol= 20.00   scale= 0.962   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,8.72,8.04,0.00,0.00,0.00); trace/3= 8.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.293342                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.985241             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.200   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.547678              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.503   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4875      final r-factor (work) = 0.4156          |
| start r-factor (free) = 0.4728      final r-factor (free) = 0.4342          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.1305 = 15.99 * 0.50 * 6.2917 + 1.00 * 53.8433                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.9399 = 15.99 * 0.50 * 6.2294 + 1.00 * 0.1504                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4156      final r-factor (work) = 0.3732          |
| start r-factor (free) = 0.4342      final r-factor (free) = 0.4364          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6556 = 1.55 * 1.00 * 6.2294 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5613 = 1.55 * 1.00 * 6.1647 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.57   15.52    None  None   None       |
|    all(noH): 2823   0      0.00    85.57   15.52    None  None   None       |
|    Sol.    : 438    0      0.00    85.57   26.63    None  None   None       |
|    Mac.    : 2385   0      0.00    80.47   13.48    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 -   8.557: 1014   |   5:    42.784 -  51.341:   73        |
|      1:     8.557 -  17.114:  811   |   6:    51.341 -  59.898:   34        |
|      2:    17.114 -  25.671:  479   |   7:    59.898 -  68.455:   16        |
|      3:    25.671 -  34.227:  254   |   8:    68.455 -  77.012:    8        |
|      4:    34.227 -  42.784:  131   |   9:    77.012 -  85.568:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3732 r_free = 0.4364             target_work(ml) = 6.157         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3728 r_free = 0.4363             target_work(ml) = 6.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3728   r_free= 0.4363   ksol= 0.30   Bsol= 20.00   scale= 1.105   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,8.72,8.04,0.00,0.00,0.00); trace/3= 8.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.156842                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3707   r_free= 0.4331   ksol= 0.35   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.26,4.98,4.70,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.158166                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.781179             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.608  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.662385              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.183  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3707      final r-factor (work) = 0.2982          |
| start r-factor (free) = 0.4331      final r-factor (free) = 0.3627          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.4373 = 11.78 * 0.50 * 6.1602 + 1.00 * 0.1504                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.9088 = 11.78 * 0.50 * 6.0790 + 1.00 * 0.0998                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2982      final r-factor (work) = 0.2766          |
| start r-factor (free) = 0.3627      final r-factor (free) = 0.3466          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0470 = 0.66 * 1.00 * 6.0790 + 1.00 * 0.0204                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9617 = 0.66 * 1.00 * 5.9567 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.03   15.26    None  None   None       |
|    all(noH): 2823   0      0.00    81.03   15.26    None  None   None       |
|    Sol.    : 438    0      0.00    81.03   30.97    None  None   None       |
|    Mac.    : 2385   0      0.00    73.51   12.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.103: 1009   |   5:    40.513 -  48.616:   74        |
|      1:     8.103 -  16.205:  785   |   6:    48.616 -  56.719:   32        |
|      2:    16.205 -  24.308:  451   |   7:    56.719 -  64.821:   17        |
|      3:    24.308 -  32.411:  290   |   8:    64.821 -  72.924:    8        |
|      4:    32.411 -  40.513:  152   |   9:    72.924 -  81.026:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2766 r_free = 0.3466             target_work(ml) = 5.936         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2763 r_free = 0.3463             target_work(ml) = 5.936         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2763   r_free= 0.3463   ksol= 0.35   Bsol= 50.00   scale= 1.071   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.26,4.98,4.70,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.935715                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2750   r_free= 0.3441   ksol= 0.33   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.25,2.32,3.13,0.00,0.00,0.00); trace/3= 2.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.936405                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.901272              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.939  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.490411              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.729  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2750      final r-factor (work) = 0.2266          |
| start r-factor (free) = 0.3441      final r-factor (free) = 0.2908          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7183 = 3.90 * 0.50 * 5.9563 + 1.00 * 0.0998                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4928 = 3.90 * 0.50 * 5.8580 + 1.00 * 0.0660                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2266      final r-factor (work) = 0.2090          |
| start r-factor (free) = 0.2908      final r-factor (free) = 0.2679          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9017 = 0.49 * 1.00 * 5.8580 + 1.00 * 0.0289                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8235 = 0.49 * 1.00 * 5.7330 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.43   14.95    None  None   None       |
|    all(noH): 2823   0      0.00    80.43   14.95    None  None   None       |
|    Sol.    : 438    0      1.98    80.43   35.32    None  None   None       |
|    Mac.    : 2385   0      0.00    68.12   11.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.043: 1079   |   5:    40.213 -  48.255:  111        |
|      1:     8.043 -  16.085:  875   |   6:    48.255 -  56.298:   58        |
|      2:    16.085 -  24.128:  337   |   7:    56.298 -  64.341:   21        |
|      3:    24.128 -  32.170:  183   |   8:    64.341 -  72.383:    6        |
|      4:    32.170 -  40.213:  148   |   9:    72.383 -  80.426:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2090 r_free = 0.2679             target_work(ml) = 5.696         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2088 r_free = 0.2674             target_work(ml) = 5.695         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2088   r_free= 0.2674   ksol= 0.33   Bsol= 50.00   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.25,2.32,3.13,0.00,0.00,0.00); trace/3= 2.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.695349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2083   r_free= 0.2674   ksol= 0.32   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.00,1.02,2.25,0.00,0.00,0.00); trace/3= 1.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.695571                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.704619              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.868  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.015816              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.665  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2083      final r-factor (work) = 0.1603          |
| start r-factor (free) = 0.2674      final r-factor (free) = 0.2132          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5582 = 4.70 * 0.50 * 5.7357 + 1.00 * 0.0660                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2032 = 4.70 * 0.50 * 5.5816 + 1.00 * 0.0736                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1603      final r-factor (work) = 0.1455          |
| start r-factor (free) = 0.2132      final r-factor (free) = 0.2015          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6816 = 1.02 * 1.00 * 5.5816 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5166 = 1.02 * 1.00 * 5.4181 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.22   15.02    None  None   None       |
|    all(noH): 2823   0      0.00    83.22   15.02    None  None   None       |
|    Sol.    : 438    0      3.09    83.22   39.57    None  None   None       |
|    Mac.    : 2385   0      0.00    74.52   10.51    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 -   8.323: 1240   |   5:    41.612 -  49.935:  117        |
|      1:     8.323 -  16.645:  848   |   6:    49.935 -  58.257:   82        |
|      2:    16.645 -  24.968:  231   |   7:    58.257 -  66.580:   45        |
|      3:    24.968 -  33.290:  133   |   8:    66.580 -  74.902:    8        |
|      4:    33.290 -  41.612:  116   |   9:    74.902 -  83.225:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1455 r_free = 0.2015             target_work(ml) = 5.386         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1454 r_free = 0.2013             target_work(ml) = 5.385         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1454   r_free= 0.2013   ksol= 0.32   Bsol= 50.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.00,1.02,2.25,0.00,0.00,0.00); trace/3= 1.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.385157                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.2006   ksol= 0.32   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.78,0.31,1.97,0.00,0.00,0.00); trace/3= 1.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.383474                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.184759              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.467  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.379802              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.366  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1458      final r-factor (work) = 0.1296          |
| start r-factor (free) = 0.2006      final r-factor (free) = 0.1834          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7034 = 3.18 * 0.50 * 5.4194 + 1.00 * 0.0736                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5718 = 3.18 * 0.50 * 5.3407 + 1.00 * 0.0674                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1296      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1834      final r-factor (free) = 0.1793          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.7444 = 5.38 * 1.00 * 5.3407 + 1.00 * 0.0127                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.3878 = 5.38 * 1.00 * 5.2740 + 1.00 * 0.0148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.36  15.42    None  None   None       |
|    all(noH): 2823   0      0.00    103.36  15.42    None  None   None       |
|    Sol.    : 438    0      3.33    103.36  42.83    None  None   None       |
|    Mac.    : 2385   0      0.00    93.10   10.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.336: 1605   |   5:    51.680 -  62.016:   89        |
|      1:    10.336 -  20.672:  647   |   6:    62.016 -  72.352:   67        |
|      2:    20.672 -  31.008:  183   |   7:    72.352 -  82.688:   25        |
|      3:    31.008 -  41.344:  104   |   8:    82.688 -  93.024:    6        |
|      4:    41.344 -  51.680:   93   |   9:    93.024 - 103.360:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1249 r_free = 0.1793             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1249 r_free = 0.1792             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1249   r_free= 0.1792   ksol= 0.32   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.78,0.31,1.97,0.00,0.00,0.00); trace/3= 1.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.260932                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.6898 0.99   1431  160 0.0970 0.1344      5.3789       5.604|
|  2:  4.6898 -  3.7407 0.99   1390  153 0.0862 0.1178      5.4582        5.67|
|  3:  3.7407 -  3.2733 0.99   1343  150 0.1129 0.1612      5.5278      5.8692|
|  4:  3.2733 -  2.9764 0.99   1360  153 0.1382 0.1877      5.5406      5.7031|
|  5:  2.9764 -  2.7645 0.99   1344  147 0.1465 0.1964      5.4263      5.6795|
|  6:  2.7645 -  2.6023 0.99   1336  150 0.1451 0.2237      5.3338       5.604|
|  7:  2.6023 -  2.4726 0.99   1329  139 0.1426 0.1823      5.2876      5.4217|
|  8:  2.4726 -  2.3654 0.98   1316  156 0.1378 0.2042      5.2121      5.4826|
|  9:  2.3654 -  2.2746 0.98   1312  142 0.1423 0.2170      5.1882      5.4663|
| 10:  2.2746 -  2.1964 1.00   1323  159 0.1299 0.1924      5.0882      5.3048|
| 11:  2.1964 -  2.1279 0.98   1316  133 0.1301 0.2161      5.0738      5.4702|
| 12:  2.1279 -  2.0672 0.98   1287  148 0.1321 0.2082      5.0125      5.2588|
| 13:  2.0672 -  2.0129 0.92   1220  131 0.1278 0.1899       4.909      5.1307|
| 14:  2.0129 -  1.9639 0.24    323   38 0.1172 0.1697      4.7868      5.0043|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.6898  1431   160  0.94   9.59   0.97     0.95       7596.21|
|  2:  4.6898 -  3.7407  1390   153  0.95   8.46   1.02     1.00       9814.54|
|  3:  3.7407 -  3.2733  1343   150  0.92  12.58   1.04     1.04      11791.35|
|  4:  3.2733 -  2.9764  1360   153  0.90  16.23   1.02     1.00      12570.98|
|  5:  2.9764 -  2.7645  1344   147  0.88  17.91   1.00     0.98      10429.33|
|  6:  2.7645 -  2.6023  1336   150  0.87  19.45   0.98     0.94       9262.80|
|  7:  2.6023 -  2.4726  1329   139  0.88  18.36   0.99     0.96       8320.65|
|  8:  2.4726 -  2.3654  1316   156  0.87  19.23   0.98     0.95       7414.21|
|  9:  2.3654 -  2.2746  1312   142  0.87  19.27   0.99     0.93       6877.11|
| 10:  2.2746 -  2.1964  1323   159  0.88  18.88   0.99     0.94       6032.16|
| 11:  2.1964 -  2.1279  1316   133  0.87  19.54   0.99     0.93       5912.61|
| 12:  2.1279 -  2.0672  1287   148  0.87  19.51   1.00     0.99       5498.07|
| 13:  2.0672 -  2.0129  1220   131  0.87  20.18   0.99     0.96       4596.83|
| 14:  2.0129 -  1.9639   323    38  0.90  16.68   0.98     0.94       3420.80|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3420.80 max =        12570.98 mean =      8123.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.90 mean =        16.75|
|phase err.(test): min =        0.00 max =           89.86 mean =        16.15|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1790   ksol= 0.32   Bsol= 58.50   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.21,-0.76,0.98,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.260595                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1790   ksol= 0.32   Bsol= 58.50   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.21,-0.76,0.98,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.260595                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.6898 0.99   1431  160 0.0970 0.1347      5.3772      5.6067|
|  2:  4.6898 -  3.7407 0.99   1390  153 0.0866 0.1185      5.4616      5.6759|
|  3:  3.7407 -  3.2733 0.99   1343  150 0.1132 0.1615      5.5306      5.8723|
|  4:  3.2733 -  2.9764 0.99   1360  153 0.1380 0.1875      5.5402      5.7016|
|  5:  2.9764 -  2.7645 0.99   1344  147 0.1463 0.1962      5.4253      5.6786|
|  6:  2.7645 -  2.6023 0.99   1336  150 0.1447 0.2232      5.3321      5.6019|
|  7:  2.6023 -  2.4726 0.99   1329  139 0.1424 0.1823      5.2859      5.4208|
|  8:  2.4726 -  2.3654 0.98   1316  156 0.1378 0.2037      5.2109      5.4812|
|  9:  2.3654 -  2.2746 0.98   1312  142 0.1423 0.2167      5.1874      5.4657|
| 10:  2.2746 -  2.1964 1.00   1323  159 0.1298 0.1923      5.0874      5.3044|
| 11:  2.1964 -  2.1279 0.98   1316  133 0.1301 0.2160      5.0735      5.4702|
| 12:  2.1279 -  2.0672 0.98   1287  148 0.1320 0.2081      5.0122      5.2586|
| 13:  2.0672 -  2.0129 0.92   1220  131 0.1278 0.1895      4.9083      5.1296|
| 14:  2.0129 -  1.9639 0.24    323   38 0.1173 0.1695      4.7858      5.0032|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.6898  1431   160  0.94   9.57   0.97     0.95       7570.66|
|  2:  4.6898 -  3.7407  1390   153  0.95   8.48   1.02     1.00       9869.33|
|  3:  3.7407 -  3.2733  1343   150  0.92  12.65   1.04     1.04      11905.53|
|  4:  3.2733 -  2.9764  1360   153  0.90  16.26   1.02     1.00      12600.74|
|  5:  2.9764 -  2.7645  1344   147  0.88  17.90   1.01     0.99      10412.88|
|  6:  2.7645 -  2.6023  1336   150  0.87  19.40   0.99     0.95       9227.94|
|  7:  2.6023 -  2.4726  1329   139  0.88  18.33   1.00     0.97       8288.69|
|  8:  2.4726 -  2.3654  1316   156  0.87  19.20   0.99     0.95       7389.56|
|  9:  2.3654 -  2.2746  1312   142  0.87  19.24   1.00     0.94       6857.88|
| 10:  2.2746 -  2.1964  1323   159  0.88  18.86   1.00     0.95       6023.17|
| 11:  2.1964 -  2.1279  1316   133  0.87  19.54   0.99     0.94       5907.24|
| 12:  2.1279 -  2.0672  1287   148  0.87  19.51   1.01     0.99       5493.82|
| 13:  2.0672 -  2.0129  1220   131  0.87  20.17   1.00     0.97       4590.45|
| 14:  2.0129 -  1.9639   323    38  0.90  16.65   0.98     0.95       3411.74|
|alpha:            min =        0.94 max =            1.04 mean =         0.97|
|beta:             min =     3411.74 max =        12600.74 mean =      8125.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.74|
|phase err.(test): min =        0.00 max =           89.88 mean =        16.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.13    104.49  16.55    None  None   None       |
|    all(noH): 2823   0      1.13    104.49  16.55    None  None   None       |
|    Sol.    : 438    0      4.46    104.49  43.96    None  None   None       |
|    Mac.    : 2385   0      1.13    94.23   11.51    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:     1.130 -  11.466: 1605   |   5:    52.810 -  63.146:   89        |
|      1:    11.466 -  21.802:  647   |   6:    63.146 -  73.482:   67        |
|      2:    21.802 -  32.138:  183   |   7:    73.482 -  83.818:   25        |
|      3:    32.138 -  42.474:  104   |   8:    83.818 -  94.154:    6        |
|      4:    42.474 -  52.810:   93   |   9:    94.154 - 104.490:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.431 - 5.864
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 335 from: 341
   mapped sites are within: 0.703 - 5.864

peak=    9.309 closest distance to " CB  VAL A 230 " =    1.441
peak=    8.003 closest distance to " O   HOH Z 130 " =    1.698
peak=    7.510 closest distance to " CG2 VAL A 296 " =    1.220
peak=    6.923 closest distance to " CG  ARG A 138 " =    1.199
peak=    6.835 closest distance to " CD2 LEU A   5 " =    1.293
peak=    5.831 closest distance to " O   HOH Z  65 " =    1.437
peak=    5.704 closest distance to " O   HOH Z 222 " =    1.523
peak=    5.458 closest distance to " CD1AILE A 234 " =    1.049
peak=    5.385 closest distance to " NE2 GLN A  11 " =    1.162
peak=    5.346 closest distance to " CG  LEU A 228 " =    1.141
peak=    5.257 closest distance to " CG  PRO A  54 " =    1.452
peak=    5.211 closest distance to " NH1 ARG A 138 " =    1.059
peak=    5.178 closest distance to " O   HOH Z 268 " =    1.030
peak=    5.065 closest distance to " O   HOH Z 127 " =    1.186
peak=    4.893 closest distance to " O   HOH Z 232 " =    2.155
peak=    4.891 closest distance to " CG  LEU A   5 " =    1.166
peak=    4.887 closest distance to " O   HOH Z   7 " =    1.670
peak=    4.841 closest distance to " O   HOH Z 427 " =    2.374
peak=    4.806 closest distance to " O   HOH Z 287 " =    1.773
peak=    4.804 closest distance to " CB  VAL A 230 " =    1.226
peak=    4.802 closest distance to " O   HOH Z 427 " =    1.140
peak=    4.801 closest distance to " O   HOH Z   9 " =    1.992
peak=    4.749 closest distance to " CB  PRO A  54 " =    1.093
peak=    4.700 closest distance to " O   HOH Z 425 " =    1.745
peak=    4.687 closest distance to " O   HOH Z  63 " =    1.578
peak=    4.660 closest distance to " O   HOH Z 139 " =    1.384
peak=    4.640 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.613 closest distance to " O   HOH Z 143 " =    2.181
peak=    4.567 closest distance to " O   HOH Z 417 " =    1.647
peak=    4.512 closest distance to " CB  GLN A 223 " =    1.542
peak=    4.507 closest distance to " CB  ASN A 148 " =    1.437
peak=    4.495 closest distance to " O   HOH Z   2 " =    1.832
peak=    4.494 closest distance to " O   HOH Z 375 " =    1.018
peak=    4.448 closest distance to " CB  SER A 216 " =    1.088
peak=    4.427 closest distance to " O   HOH Z 298 " =    1.917
peak=    4.427 closest distance to " O   HOH Z 126 " =    2.236
peak=    4.410 closest distance to " O   HOH Z  59 " =    1.813
peak=    4.403 closest distance to " O   HOH Z 369 " =    2.096
peak=    4.396 closest distance to " O   HOH Z 361 " =    1.426
peak=    4.391 closest distance to " CB  GLN A 183 " =    1.221
peak=    4.382 closest distance to " O   HOH Z  69 " =    2.402
peak=    4.339 closest distance to " O   HOH Z 225 " =    1.545
peak=    4.317 closest distance to " O   HOH Z 410 " =    1.615
peak=    4.315 closest distance to " O   HOH Z 414 " =    1.393
peak=    4.311 closest distance to " O   HOH Z 424 " =    1.196
peak=    4.304 closest distance to " O   PRO A 198 " =    1.250
peak=    4.264 closest distance to " NZ BLYS A 290 " =    1.026
peak=    4.209 closest distance to " CB  LEU A 237 " =    0.851
peak=    4.208 closest distance to " CG  LEU A 167 " =    1.292
peak=    4.208 closest distance to " O   HOH Z 193 " =    1.630
peak=    4.189 closest distance to " CA  VAL A 296 " =    0.990
peak=    4.146 closest distance to " CB  SER A  63 " =    1.284
peak=    4.123 closest distance to " O   HOH Z 316 " =    3.045
peak=    4.106 closest distance to " CD2 TRP A 179 " =    2.265
peak=    4.087 closest distance to " O   HOH Z 218 " =    2.104
peak=    4.085 closest distance to " CA  ALA A  51 " =    1.098
peak=    4.082 closest distance to " O   HOH Z 411 " =    3.143
peak=    4.076 closest distance to " O   HOH Z 389 " =    1.412
peak=    4.071 closest distance to " O   HOH Z 133 " =    1.433
peak=    4.023 closest distance to " CB  SER A   3 " =    1.547
peak=    4.013 closest distance to " O   HOH Z 111 " =    1.485
peak=    4.008 closest distance to " O   HOH Z 392 " =    1.289
peak=    4.004 closest distance to " O   HOH Z  78 " =    1.674
peak=    3.997 closest distance to " CB  ASP A 124 " =    0.850
peak=    3.991 closest distance to " O   HOH Z 373 " =    1.491
peak=    3.977 closest distance to " CE3 TRP A 274 " =    1.341
peak=    3.974 closest distance to " CG  LYS A  76 " =    1.731
peak=    3.954 closest distance to " CB  MET A  47 " =    1.167
peak=    3.950 closest distance to " NH1AARG A 145 " =    1.139
peak=    3.949 closest distance to " CD  GLN A 240 " =    1.730
peak=    3.948 closest distance to " CA  ASN A 127 " =    1.209
peak=    3.932 closest distance to " O   HOH Z 236 " =    1.656
peak=    3.922 closest distance to " CB  VAL A 202 " =    1.594
peak=    3.921 closest distance to " C   ASN A 209 " =    1.620
peak=    3.917 closest distance to " CD  ARG A 138 " =    1.120
peak=    3.915 closest distance to " O   HOH Z 425 " =    2.101
peak=    3.898 closest distance to " O   HOH Z  97 " =    1.374
peak=    3.894 closest distance to " O   HOH Z 167 " =    1.801
peak=    3.880 closest distance to " O   HOH Z 133 " =    2.660
peak=    3.879 closest distance to " CA  ILE A 234 " =    1.054
peak=    3.850 closest distance to " CG  PRO A 243 " =    1.066
peak=    3.850 closest distance to " CG  PRO A 213 " =    1.261
peak=    3.846 closest distance to " O   HOH Z 423 " =    1.659
peak=    3.841 closest distance to " O   HOH Z  57 " =    1.222
peak=    3.835 closest distance to " O   HOH Z 245 " =    1.219
peak=    3.832 closest distance to " CD  ARG A  66 " =    2.435
peak=    3.828 closest distance to " CD2 LEU A 228 " =    1.322
peak=    3.801 closest distance to " CB  ASN A  39 " =    1.032
peak=    3.800 closest distance to " O   HOH Z  68 " =    2.096
peak=    3.800 closest distance to " CB  ASP A 132 " =    3.879
peak=    3.798 closest distance to " O   HOH Z 214 " =    2.196
peak=    3.789 closest distance to " OG BSER A 210 " =    1.266
peak=    3.784 closest distance to " CB  MET A  40 " =    0.882
peak=    3.784 closest distance to " O   HOH Z 385 " =    0.980
peak=    3.775 closest distance to " O   HOH Z 195 " =    1.710
peak=    3.772 closest distance to " O   HOH Z 258 " =    2.001
peak=    3.769 closest distance to " CG2 THR A 221 " =    1.223
peak=    3.768 closest distance to " O   HOH Z 425 " =    2.107
peak=    3.768 closest distance to " CG  GLN A  11 " =    2.205
peak=    3.764 closest distance to " ND1 HIS A  81 " =    1.676
peak=    3.761 closest distance to " O   HOH Z  30 " =    1.412
peak=    3.759 closest distance to " O   HOH Z 193 " =    1.667
peak=    3.752 closest distance to " N   GLN A 278 " =    1.221
peak=    3.743 closest distance to " CE3 TRP A 150 " =    1.125
peak=    3.741 closest distance to " CD  ARG A 269 " =    1.049
peak=    3.740 closest distance to " O   HOH Z  55 " =    1.875
peak=    3.740 closest distance to " O   HOH Z  91 " =    2.481
peak=    3.735 closest distance to " CB  GLU A 128 " =    1.112
peak=    3.735 closest distance to " O   HOH Z 158 " =    2.925
peak=    3.732 closest distance to " CD  ARG A 159 " =    0.756
peak=    3.732 closest distance to " CB  HIS A 108 " =    0.872
peak=    3.729 closest distance to " NH2AARG A 145 " =    1.138
peak=    3.728 closest distance to " CD1 ILE A  33 " =    1.831
peak=    3.722 closest distance to " CB  TRP A 266 " =    1.077
peak=    3.720 closest distance to " O   HOH Z   1 " =    2.084
peak=    3.710 closest distance to " N   SER A 271 " =    0.991
peak=    3.704 closest distance to " N   TYR A  15 " =    1.018
peak=    3.696 closest distance to " O   HOH Z  61 " =    1.692
peak=    3.693 closest distance to " O   HOH Z 375 " =    2.469
peak=    3.693 closest distance to " O   HOH Z  39 " =    1.161
peak=    3.691 closest distance to " O   HOH Z 418 " =    0.981
peak=    3.679 closest distance to " O   HOH Z  88 " =    3.256
peak=    3.676 closest distance to " CB  GLU A 277 " =    3.642
peak=    3.662 closest distance to " CB  ARG A 275 " =    1.074
peak=    3.662 closest distance to " O   HOH Z 368 " =    3.522
peak=    3.659 closest distance to " CG2 ILE A 234 " =    1.057
peak=    3.655 closest distance to " O   HOH Z 438 " =    1.947
peak=    3.655 closest distance to " N   SER A  97 " =    0.813
peak=    3.652 closest distance to " O   HOH Z 362 " =    1.991
peak=    3.648 closest distance to " O   MET A 105 " =    1.754
peak=    3.647 closest distance to " CA  GLY A 267 " =    1.207
peak=    3.642 closest distance to " O   HOH Z 380 " =    2.048
peak=    3.640 closest distance to " O   HOH Z 259 " =    2.376
peak=    3.640 closest distance to " O   HOH Z 422 " =    2.676
peak=    3.635 closest distance to " OG  SER A  62 " =    2.751
peak=    3.632 closest distance to " O   HOH Z 233 " =    1.434
peak=    3.625 closest distance to " O   HOH Z 217 " =    2.973
peak=    3.617 closest distance to " CB  ASN A 142 " =    0.905
peak=    3.617 closest distance to " OG ASER A 212 " =    1.694
peak=    3.617 closest distance to " CD BLYS A 290 " =    1.080
peak=    3.615 closest distance to " O   HOH Z 211 " =    1.139
peak=    3.615 closest distance to " CB  SER A 276 " =    1.051
peak=    3.614 closest distance to " OE2 GLU A   2 " =    2.022
peak=    3.612 closest distance to " O   HOH Z 153 " =    3.742
peak=    3.606 closest distance to " CA  ALA A 160 " =    0.977
peak=    3.603 closest distance to " O   HOH Z 346 " =    1.673
peak=    3.602 closest distance to " CB  LEU A 228 " =    1.365
peak=    3.595 closest distance to " O   HOH Z 154 " =    2.055
peak=    3.592 closest distance to " O   HOH Z  24 " =    2.076
peak=    3.585 closest distance to " CG1 ILE A 151 " =    1.114
peak=    3.585 closest distance to " O   HOH Z 419 " =    1.825
peak=    3.571 closest distance to " OD2 ASP A 286 " =    2.598
peak=    3.561 closest distance to " CZ3 TRP A 266 " =    1.217
peak=    3.557 closest distance to " O   HOH Z 371 " =    2.703
peak=    3.555 closest distance to " O   HOH Z 359 " =    1.308
peak=    3.553 closest distance to " NH2AARG A 190 " =    1.658
peak=    3.550 closest distance to " O   HOH Z  56 " =    1.896
peak=    3.543 closest distance to " O   HOH Z 109 " =    2.327
peak=    3.541 closest distance to " O   HOH Z 222 " =    1.741
peak=    3.539 closest distance to " O   HOH Z 305 " =    3.438
peak=    3.534 closest distance to " O   HOH Z 290 " =    0.970
peak=    3.531 closest distance to " CG  GLN A  88 " =    1.108
peak=    3.523 closest distance to " CZ3 TRP A  92 " =    1.150
peak=    3.511 closest distance to " CB  VAL A 250 " =    1.097
peak=    3.511 closest distance to " CA  ARG A 156 " =    1.035
peak=    3.503 closest distance to " O   HOH Z 146 " =    1.524
peak=    3.503 closest distance to " O   HOH Z 148 " =    2.422
peak=    3.501 closest distance to " CB  LYS A 290 " =    0.943
peak=    3.495 closest distance to " O   HOH Z  88 " =    2.759
peak=    3.492 closest distance to " CA  ASP A 124 " =    0.703
peak=    3.492 closest distance to " O   HOH Z 350 " =    1.496
peak=    3.490 closest distance to " O   HOH Z 365 " =    2.976
peak=    3.489 closest distance to " O   HOH Z  10 " =    1.816
peak=    3.487 closest distance to " CE  LYS A  76 " =    0.836
peak=    3.484 closest distance to " O   HOH Z  78 " =    2.099
peak=    3.479 closest distance to " CD1 LEU A   5 " =    1.440
peak=    3.472 closest distance to " CB  LEU A 143 " =    1.107
peak=    3.472 closest distance to " CB  ALA A 114 " =    1.593
peak=    3.471 closest distance to " O   HOH Z  76 " =    1.100
peak=    3.466 closest distance to " CE  MET A  93 " =    1.484
peak=    3.466 closest distance to " CB  GLU A 236 " =    1.359
peak=    3.461 closest distance to " ND2 ASN A 249 " =    0.770
peak=    3.461 closest distance to " NE2 GLN A  58 " =    4.005
peak=    3.438 closest distance to " CE3 TRP A  85 " =    1.156
peak=    3.436 closest distance to " CG  ARG A 159 " =    0.998
peak=    3.433 closest distance to " NE1 TRP A 274 " =    0.946
peak=    3.431 closest distance to " O   HOH Z  20 " =    1.879
peak=    3.424 closest distance to " O   HOH Z 148 " =    1.462
peak=    3.424 closest distance to " CA  ASN A 215 " =    1.315
peak=    3.420 closest distance to " O   HOH Z  51 " =    1.758
peak=    3.417 closest distance to " O   HOH Z 207 " =    2.548
peak=    3.415 closest distance to " CG1 VAL A 296 " =    1.206
peak=    3.415 closest distance to " CB  ARG A 138 " =    1.277
peak=    3.413 closest distance to " CG BARG A 102 " =    2.033
peak=    3.411 closest distance to " OG ASER A 212 " =    1.482
peak=    3.405 closest distance to " CA  ALA A 295 " =    1.048
peak=    3.402 closest distance to " N   ALA A 256 " =    0.950
peak=    3.401 closest distance to " N   CYS A 260 " =    0.920
peak=    3.400 closest distance to " O   HOH Z 303 " =    2.597
peak=    3.399 closest distance to " CA  SER A  87 " =    0.999
peak=    3.394 closest distance to " O   HOH Z 128 " =    2.131
peak=    3.388 closest distance to " O   HOH Z 183 " =    1.324
peak=    3.387 closest distance to " O   HOH Z 133 " =    1.188
peak=    3.381 closest distance to " OD1 ASN A 217 " =    1.692
peak=    3.373 closest distance to " CD1 LEU A 300 " =    1.126
peak=    3.373 closest distance to " CB  VAL A 265 " =    1.332
peak=    3.371 closest distance to " CG  GLN A  89 " =    1.475
peak=    3.371 closest distance to " O   HOH Z 368 " =    2.031
peak=    3.370 closest distance to " CA  THR A 221 " =    0.925
peak=    3.361 closest distance to " ND2BASN A 224 " =    0.882
peak=    3.359 closest distance to " O   ASP A 200 " =    1.303
peak=    3.355 closest distance to " CB  ARG A 190 " =    1.746
peak=    3.350 closest distance to " CB  ASN A 110 " =    1.136
peak=    3.348 closest distance to " O   HOH Z 209 " =    2.464
peak=    3.344 closest distance to " O   HOH Z 310 " =    2.111
peak=    3.344 closest distance to " N   GLU A   2 " =    1.508
peak=    3.338 closest distance to " O   HOH Z  43 " =    1.175
peak=    3.334 closest distance to " O   HOH Z 143 " =    1.329
peak=    3.331 closest distance to " N   PHE A 130 " =    1.301
peak=    3.331 closest distance to " CB  LYS A 117 " =    1.267
peak=    3.329 closest distance to " O   HOH Z  44 " =    1.933
peak=    3.327 closest distance to " O   HOH Z 185 " =    1.908
peak=    3.324 closest distance to " O   HOH Z 424 " =    2.697
peak=    3.318 closest distance to " O   HOH Z 384 " =    1.550
peak=    3.313 closest distance to " NE AARG A 275 " =    1.484
peak=    3.311 closest distance to " O   HOH Z 412 " =    5.479
peak=    3.309 closest distance to " O   HOH Z 145 " =    2.427
peak=    3.308 closest distance to " O   HOH Z 217 " =    1.562
peak=    3.308 closest distance to " O   HOH Z 403 " =    1.496
peak=    3.306 closest distance to " CA  ARG A  36 " =    1.149
peak=    3.300 closest distance to " O   HOH Z 222 " =    2.086
peak=    3.299 closest distance to " CB  TRP A 179 " =    1.435
peak=    3.295 closest distance to " O   HOH Z 356 " =    1.351
peak=    3.295 closest distance to " O   HOH Z 145 " =    2.274
peak=    3.292 closest distance to " O   HOH Z  32 " =    2.178
peak=    3.291 closest distance to " CB  ARG A  79 " =    1.266
peak=    3.290 closest distance to " O   HOH Z 352 " =    1.576
peak=    3.287 closest distance to " O   HOH Z  44 " =    2.536
peak=    3.285 closest distance to " O   THR A 294 " =    0.973
peak=    3.283 closest distance to " CZ  PHE A 218 " =    1.196
peak=    3.279 closest distance to " O   ALA A 165 " =    1.410
peak=    3.276 closest distance to " NH1 ARG A  14 " =    1.094
peak=    3.274 closest distance to " O   GLY A 302 " =    2.373
peak=    3.273 closest distance to " O   HOH Z 392 " =    1.966
peak=    3.272 closest distance to " CA  ARG A 195 " =    1.328
peak=    3.271 closest distance to " O   HOH Z 115 " =    1.630
peak=    3.268 closest distance to " N   ARG A 156 " =    1.338
peak=    3.267 closest distance to " O   HOH Z 272 " =    1.869
peak=    3.262 closest distance to " ND2 ASN A  60 " =    3.039
peak=    3.259 closest distance to " O   HOH Z 360 " =    1.255
peak=    3.259 closest distance to " O   HOH Z 180 " =    2.240
peak=    3.253 closest distance to " CB  SER A 210 " =    0.963
peak=    3.249 closest distance to " CB  GLN A  88 " =    1.463
peak=    3.248 closest distance to " CD  LYS A 166 " =    1.491
peak=    3.248 closest distance to " O   HOH Z 213 " =    2.070
peak=    3.247 closest distance to " CZ  PHE A  38 " =    1.339
peak=    3.247 closest distance to " CZ3 TRP A 177 " =    0.987
peak=    3.246 closest distance to " OG BSER A 212 " =    2.690
peak=    3.245 closest distance to " CG BARG A 190 " =    1.374
peak=    3.240 closest distance to " CB  ALA A   1 " =    4.739
peak=    3.237 closest distance to " CA  ALA A 299 " =    0.978
peak=    3.236 closest distance to " CD  ARG A 195 " =    3.581
peak=    3.235 closest distance to " CA  TYR A  30 " =    1.044
peak=    3.231 closest distance to " O   HOH Z 193 " =    1.972
peak=    3.230 closest distance to " O   HOH Z 405 " =    1.553
peak=    3.227 closest distance to " O   HOH Z 368 " =    4.378
peak=    3.225 closest distance to " O   HOH Z 284 " =    1.522
peak=    3.223 closest distance to " CA  LYS A 117 " =    1.173
peak=    3.223 closest distance to " CG  MET A 188 " =    0.848
peak=    3.221 closest distance to " CA  MET A 105 " =    0.858
peak=    3.220 closest distance to " CB  LEU A 300 " =    0.901
peak=    3.220 closest distance to " CB  ALA A  43 " =    0.831
peak=    3.219 closest distance to " NH2BARG A 190 " =    1.424
peak=    3.215 closest distance to " O   ALA A 180 " =    1.295
peak=    3.214 closest distance to " O   HOH Z 329 " =    3.987
peak=    3.211 closest distance to " CA  ARG A 139 " =    0.961
peak=    3.210 closest distance to " CA  LEU A 282 " =    1.159
peak=    3.208 closest distance to " O   HOH Z 119 " =    1.548
peak=    3.208 closest distance to " O   HOH Z 172 " =    2.391
peak=    3.205 closest distance to " CA  ALA A 291 " =    0.914
peak=    3.204 closest distance to " O   HOH Z 438 " =    2.898
peak=    3.202 closest distance to " O   HOH Z 184 " =    1.574
peak=    3.200 closest distance to " O   CYS A 168 " =    1.462
peak=    3.196 closest distance to " O   HOH Z 189 " =    3.586
peak=    3.196 closest distance to " CB  GLN A  89 " =    1.204
peak=    3.190 closest distance to " CB  TYR A 169 " =    0.969
peak=    3.189 closest distance to " CG2 VAL A 268 " =    1.035
peak=    3.187 closest distance to " OG BSER A 258 " =    0.927
peak=    3.186 closest distance to " O   HOH Z 357 " =    2.157
peak=    3.184 closest distance to " CD1 LEU A 281 " =    1.013
peak=    3.184 closest distance to " O   HOH Z   1 " =    1.677
peak=    3.179 closest distance to " O   HOH Z 325 " =    2.093
peak=    3.179 closest distance to " O   HOH Z 132 " =    2.404
peak=    3.178 closest distance to " O   ALA A 233 " =    1.844
peak=    3.178 closest distance to " N   ALA A 292 " =    1.064
peak=    3.171 closest distance to " CZ  PHE A 192 " =    0.903
peak=    3.169 closest distance to " CD  ARG A  24 " =    1.172
peak=    3.169 closest distance to " ND2 ASN A 187 " =    1.590
peak=    3.168 closest distance to " O   HOH Z 201 " =    1.516
peak=    3.167 closest distance to " O   HOH Z 353 " =    1.603
peak=    3.163 closest distance to " O   HOH Z 409 " =    2.159
peak=    3.159 closest distance to " OD1 ASP A 200 " =    1.504
peak=    3.158 closest distance to " O   HOH Z 145 " =    1.876
peak=    3.157 closest distance to " CB AVAL A  41 " =    1.118
peak=    3.156 closest distance to " O   HOH Z 188 " =    3.162
peak=    3.156 closest distance to " OG BSER A  99 " =    2.176
peak=    3.147 closest distance to " O   HOH Z 302 " =    1.551
peak=    3.144 closest distance to " CD1 LEU A 167 " =    1.283
peak=    3.144 closest distance to " CB  TYR A  30 " =    1.319
peak=    3.143 closest distance to " O   HOH Z 285 " =    2.451
peak=    3.142 closest distance to " CG1 ILE A  49 " =    1.664
peak=    3.133 closest distance to " C   VAL A 153 " =    1.184
peak=    3.131 closest distance to " O   HOH Z 248 " =    1.945
peak=    3.130 closest distance to " CG2 ILE A  20 " =    1.746
peak=    3.130 closest distance to " N   PHE A 218 " =    0.857
peak=    3.130 closest distance to " N   ASP A 162 " =    1.558
peak=    3.117 closest distance to " CA  LEU A 222 " =    1.052
peak=    3.114 closest distance to " O   HOH Z 238 " =    1.476
peak=    3.111 closest distance to " O   HOH Z 119 " =    4.202
peak=    3.103 closest distance to " OD1 ASN A  45 " =    1.461
peak=    3.094 closest distance to " O   HOH Z 327 " =    1.656
peak=    3.094 closest distance to " O   HOH Z 435 " =    2.684
peak=    3.091 closest distance to " CG  GLN A  58 " =    1.140
peak=    3.087 closest distance to " CB  ALA A 104 " =    0.756
peak=    3.085 closest distance to " CB  TRP A 150 " =    0.720
peak=    3.081 closest distance to " NE2 GLN A  58 " =    5.864
peak=    3.075 closest distance to " CA  ILE A 106 " =    0.748
peak=    3.073 closest distance to " OE1 GLU A   2 " =    1.881
peak=    3.072 closest distance to " CA  THR A 264 " =    0.874
peak=    3.064 closest distance to " O   THR A 220 " =    1.779
peak=    3.048 closest distance to " O   HOH Z 130 " =    2.928
peak=    3.031 closest distance to " ND2 ASN A 170 " =    2.293
peak=    3.024 closest distance to " CB  ALA A 160 " =    1.513
peak=    3.021 closest distance to " CB  ARG A  79 " =    1.119
peak=    3.004 closest distance to " CB  LEU A 143 " =    0.912

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.726 - 5.876
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 221
   mapped sites are within: 0.726 - 5.876

peak=   -4.552 closest distance to " CD  ARG A 138 " =    1.294
peak=   -4.456 closest distance to " OG BSER A 134 " =    1.643
peak=   -4.293 closest distance to " CB  VAL A 230 " =    1.026
peak=   -4.268 closest distance to " CG  ARG A 219 " =    2.450
peak=   -4.246 closest distance to " CG2 VAL A 230 " =    0.980
peak=   -4.160 closest distance to " N   ALA A  43 " =    2.716
peak=   -4.131 closest distance to " N   THR A 157 " =    1.605
peak=   -4.027 closest distance to " CB  PHE A 130 " =    1.312
peak=   -4.005 closest distance to " OG  SER A  87 " =    1.380
peak=   -4.000 closest distance to " O   HOH Z 415 " =    1.105
peak=   -3.963 closest distance to " O   HOH Z 411 " =    5.113
peak=   -3.962 closest distance to " CB  ALA A  43 " =    2.508
peak=   -3.922 closest distance to " O   HOH Z 131 " =    3.887
peak=   -3.913 closest distance to " O   HOH Z 286 " =    1.594
peak=   -3.913 closest distance to " CD  ARG A 156 " =    1.970
peak=   -3.911 closest distance to " CD  ARG A  14 " =    3.080
peak=   -3.908 closest distance to " CB  ASP A  27 " =    2.472
peak=   -3.901 closest distance to " O   PRO A 198 " =    1.291
peak=   -3.894 closest distance to " CB  ALA A 227 " =    2.433
peak=   -3.894 closest distance to " CG  MET A 105 " =    0.998
peak=   -3.893 closest distance to " O   HOH Z 198 " =    2.392
peak=   -3.846 closest distance to " CD  LYS A 289 " =    2.293
peak=   -3.842 closest distance to " CG  ARG A 138 " =    0.989
peak=   -3.816 closest distance to " O   HOH Z  39 " =    0.940
peak=   -3.782 closest distance to " O   HOH Z 185 " =    2.133
peak=   -3.755 closest distance to " O   HOH Z 292 " =    1.773
peak=   -3.742 closest distance to " CB  ALA A 248 " =    2.002
peak=   -3.738 closest distance to " CB  ALA A   9 " =    2.442
peak=   -3.730 closest distance to " OE1 GLN A  88 " =    0.940
peak=   -3.725 closest distance to " O   ARG A 145 " =    1.407
peak=   -3.717 closest distance to " O   HOH Z 350 " =    1.609
peak=   -3.716 closest distance to " O   HOH Z 359 " =    1.629
peak=   -3.694 closest distance to " O   HOH Z 389 " =    2.210
peak=   -3.689 closest distance to " NH2 ARG A  79 " =    2.067
peak=   -3.685 closest distance to " OG ASER A 134 " =    1.130
peak=   -3.678 closest distance to " CD2 TYR A 116 " =    2.305
peak=   -3.675 closest distance to " O   ALA A   1 " =    1.265
peak=   -3.673 closest distance to " O   HOH Z 298 " =    2.799
peak=   -3.670 closest distance to " CD1 LEU A 222 " =    2.476
peak=   -3.653 closest distance to " O   HOH Z 216 " =    1.572
peak=   -3.649 closest distance to " OG  SER A  28 " =    1.993
peak=   -3.646 closest distance to " O   HOH Z 389 " =    1.257
peak=   -3.645 closest distance to " CB  PRO A 243 " =    2.632
peak=   -3.644 closest distance to " CD2 TYR A 293 " =    1.869
peak=   -3.636 closest distance to " O   HOH Z  52 " =    0.801
peak=   -3.635 closest distance to " O   HOH Z 111 " =    1.787
peak=   -3.624 closest distance to " NH2AARG A 275 " =    5.584
peak=   -3.619 closest distance to " OE1 GLU A 277 " =    2.299
peak=   -3.612 closest distance to " O   HOH Z 377 " =    1.778
peak=   -3.612 closest distance to " CG2 VAL A 202 " =    2.759
peak=   -3.608 closest distance to " N   PRO A 163 " =    1.458
peak=   -3.595 closest distance to " O   SER A  22 " =    2.813
peak=   -3.590 closest distance to " O   HOH Z 275 " =    1.791
peak=   -3.586 closest distance to " O   ALA A  84 " =    1.753
peak=   -3.585 closest distance to " OD2 ASP A  50 " =    1.642
peak=   -3.584 closest distance to " O   HOH Z 385 " =    0.924
peak=   -3.583 closest distance to " CA  GLY A 203 " =    2.379
peak=   -3.581 closest distance to " O   HOH Z 231 " =    1.891
peak=   -3.581 closest distance to " CD  LYS A 166 " =    2.426
peak=   -3.576 closest distance to " CB  ASP A 132 " =    2.356
peak=   -3.574 closest distance to " NE2 GLN A  58 " =    2.944
peak=   -3.568 closest distance to " CA  GLY A  98 " =    1.916
peak=   -3.565 closest distance to " OD1 ASP A 191 " =    1.908
peak=   -3.557 closest distance to " CG  TRP A 266 " =    1.776
peak=   -3.556 closest distance to " O   HOH Z  60 " =    1.817
peak=   -3.543 closest distance to " CG2AVAL A  41 " =    2.813
peak=   -3.535 closest distance to " CA  GLY A 241 " =    2.207
peak=   -3.529 closest distance to " O   PRO A 163 " =    1.950
peak=   -3.529 closest distance to " OG  SER A  97 " =    2.185
peak=   -3.528 closest distance to " O   HOH Z 166 " =    1.738
peak=   -3.525 closest distance to " O   SER A 135 " =    1.520
peak=   -3.506 closest distance to " CE2 TYR A  30 " =    2.606
peak=   -3.504 closest distance to " O   PRO A 243 " =    2.345
peak=   -3.502 closest distance to " O   HOH Z 231 " =    0.726
peak=   -3.501 closest distance to " CG2 VAL A 296 " =    1.817
peak=   -3.496 closest distance to " O   SER A 141 " =    1.858
peak=   -3.490 closest distance to " CZ2 TRP A 274 " =    0.940
peak=   -3.486 closest distance to " CZ2 TRP A  92 " =    2.857
peak=   -3.485 closest distance to " CG2 ILE A 151 " =    2.548
peak=   -3.483 closest distance to " C   ARG A 269 " =    1.355
peak=   -3.477 closest distance to " CD2 LEU A   5 " =    0.951
peak=   -3.475 closest distance to " N   ARG A 138 " =    1.573
peak=   -3.472 closest distance to " CG2 THR A  52 " =    3.116
peak=   -3.471 closest distance to " O   GLY A  80 " =    2.521
peak=   -3.470 closest distance to " CG  GLN A  88 " =    0.815
peak=   -3.469 closest distance to " O   HOH Z  22 " =    2.978
peak=   -3.468 closest distance to " O   HOH Z  43 " =    1.738
peak=   -3.458 closest distance to " NH2 ARG A 219 " =    1.796
peak=   -3.450 closest distance to " CB  GLN A  55 " =    1.149
peak=   -3.449 closest distance to " ND2 ASN A 285 " =    1.885
peak=   -3.446 closest distance to " OG  SER A  26 " =    1.042
peak=   -3.444 closest distance to " C   ALA A 158 " =    1.407
peak=   -3.444 closest distance to " O   HOH Z 166 " =    1.325
peak=   -3.438 closest distance to " O   GLY A 203 " =    2.555
peak=   -3.416 closest distance to " OH  TYR A 247 " =    1.625
peak=   -3.403 closest distance to " CB  TRP A  85 " =    2.422
peak=   -3.402 closest distance to " O   TRP A  70 " =    1.548
peak=   -3.396 closest distance to " O   HOH Z  11 " =    1.829
peak=   -3.394 closest distance to " O   HOH Z 268 " =    0.766
peak=   -3.390 closest distance to " CG  GLN A 278 " =    2.269
peak=   -3.389 closest distance to " O   HOH Z  52 " =    2.025
peak=   -3.381 closest distance to " CD1 LEU A 101 " =    2.272
peak=   -3.377 closest distance to " O   ALA A  51 " =    1.352
peak=   -3.376 closest distance to " CG  PRO A 163 " =    2.521
peak=   -3.375 closest distance to " CB  TYR A  15 " =    2.161
peak=   -3.373 closest distance to " CE BMET A  47 " =    0.960
peak=   -3.372 closest distance to " O   HOH Z 407 " =    3.181
peak=   -3.370 closest distance to " OG  SER A 245 " =    1.387
peak=   -3.364 closest distance to " O   HOH Z 409 " =    5.876
peak=   -3.356 closest distance to " CB  PRO A 163 " =    2.300
peak=   -3.354 closest distance to " O   HOH Z 359 " =    3.359
peak=   -3.352 closest distance to " CD  GLN A  77 " =    1.433
peak=   -3.348 closest distance to " O   HOH Z 186 " =    1.355
peak=   -3.346 closest distance to " O   HOH Z 200 " =    3.416
peak=   -3.340 closest distance to " C   MET A 188 " =    1.564
peak=   -3.340 closest distance to " OH  TYR A 214 " =    1.084
peak=   -3.339 closest distance to " O   VAL A 197 " =    1.773
peak=   -3.339 closest distance to " CG2 THR A  31 " =    2.433
peak=   -3.337 closest distance to " CB  ARG A  79 " =    2.500
peak=   -3.337 closest distance to " O   HOH Z 238 " =    0.912
peak=   -3.336 closest distance to " CD2 LEU A 237 " =    2.803
peak=   -3.335 closest distance to " NE2 GLN A 223 " =    1.486
peak=   -3.334 closest distance to " CB  ALA A 291 " =    2.054
peak=   -3.330 closest distance to " O   HOH Z  53 " =    1.728
peak=   -3.328 closest distance to " O   HOH Z 427 " =    1.786
peak=   -3.328 closest distance to " O   HOH Z  60 " =    2.609
peak=   -3.327 closest distance to " O   HOH Z 420 " =    3.213
peak=   -3.321 closest distance to " O   ALA A  10 " =    1.863
peak=   -3.320 closest distance to " OG  SER A  63 " =    1.306
peak=   -3.318 closest distance to " OE1 GLU A   2 " =    1.962
peak=   -3.314 closest distance to " CA  GLY A 133 " =    2.016
peak=   -3.313 closest distance to " CD1 LEU A   5 " =    2.475
peak=   -3.311 closest distance to " CD1 ILE A  33 " =    2.439
peak=   -3.304 closest distance to " O   ILE A  49 " =    1.540
peak=   -3.304 closest distance to " CG  LEU A   5 " =    0.962
peak=   -3.303 closest distance to " O   HOH Z 352 " =    1.572
peak=   -3.297 closest distance to " O   ASP A  27 " =    2.026
peak=   -3.296 closest distance to " O   HOH Z 211 " =    1.318
peak=   -3.294 closest distance to " O   HOH Z 174 " =    2.852
peak=   -3.293 closest distance to " CB  PRO A  54 " =    2.458
peak=   -3.291 closest distance to " CG  ARG A 259 " =    2.487
peak=   -3.286 closest distance to " CB  SER A  63 " =    3.275
peak=   -3.284 closest distance to " O   HOH Z 325 " =    1.646
peak=   -3.282 closest distance to " C   GLU A 236 " =    0.976
peak=   -3.281 closest distance to " O   HOH Z 275 " =    1.602
peak=   -3.275 closest distance to " O   HOH Z 365 " =    1.776
peak=   -3.275 closest distance to " CG  LEU A 281 " =    1.799
peak=   -3.268 closest distance to " CZ  PHE A  59 " =    1.622
peak=   -3.268 closest distance to " O   HOH Z 368 " =    1.425
peak=   -3.258 closest distance to " O   HOH Z 435 " =    2.302
peak=   -3.256 closest distance to " CD1 PHE A  59 " =    2.108
peak=   -3.251 closest distance to " CA  ASN A 127 " =    1.033
peak=   -3.248 closest distance to " CA  ARG A 156 " =    1.132
peak=   -3.248 closest distance to " CD1 LEU A 297 " =    2.258
peak=   -3.248 closest distance to " OD2 ASP A 171 " =    1.765
peak=   -3.245 closest distance to " N   LEU A 282 " =    2.193
peak=   -3.244 closest distance to " O   HOH Z 163 " =    1.946
peak=   -3.244 closest distance to " O   HOH Z 426 " =    1.686
peak=   -3.232 closest distance to " O   HOH Z 134 " =    4.150
peak=   -3.231 closest distance to " O   HOH Z 201 " =    1.578
peak=   -3.229 closest distance to " O   HOH Z 165 " =    2.190
peak=   -3.228 closest distance to " OG  SER A 206 " =    1.760
peak=   -3.226 closest distance to " OG  SER A  62 " =    4.441
peak=   -3.226 closest distance to " C   GLU A   2 " =    1.874
peak=   -3.225 closest distance to " O   GLN A 194 " =    1.504
peak=   -3.222 closest distance to " O   HOH Z  73 " =    2.153
peak=   -3.212 closest distance to " OE1 GLN A  88 " =    1.445
peak=   -3.211 closest distance to " CD  PRO A 213 " =    2.109
peak=   -3.210 closest distance to " O   HOH Z 155 " =    1.107
peak=   -3.206 closest distance to " O   HOH Z 108 " =    1.702
peak=   -3.204 closest distance to " CG1 VAL A 125 " =    2.400
peak=   -3.203 closest distance to " CE  MET A 113 " =    2.236
peak=   -3.201 closest distance to " OE2 GLU A 152 " =    1.161
peak=   -3.199 closest distance to " O   HOH Z 105 " =    1.954
peak=   -3.197 closest distance to " O   HOH Z 353 " =    1.739
peak=   -3.194 closest distance to " O   HOH Z 128 " =    2.391
peak=   -3.192 closest distance to " O   HOH Z 348 " =    1.725
peak=   -3.191 closest distance to " NE2 GLN A 240 " =    1.366
peak=   -3.188 closest distance to " O   HOH Z 351 " =    1.573
peak=   -3.187 closest distance to " O   HOH Z  51 " =    0.955
peak=   -3.174 closest distance to " O   GLY A 211 " =    1.219
peak=   -3.174 closest distance to " CA  HIS A 207 " =    1.185
peak=   -3.172 closest distance to " O   HOH Z  32 " =    2.023
peak=   -3.170 closest distance to " CB  SER A 271 " =    1.124
peak=   -3.166 closest distance to " CB  ASN A  39 " =    2.118
peak=   -3.160 closest distance to " O   HOH Z  69 " =    1.719
peak=   -3.157 closest distance to " O   HOH Z 290 " =    1.325
peak=   -3.153 closest distance to " O   HOH Z  67 " =    3.132
peak=   -3.152 closest distance to " O   TYR A  30 " =    2.660
peak=   -3.149 closest distance to " O   HOH Z 103 " =    1.505
peak=   -3.147 closest distance to " O   HOH Z 318 " =    1.719
peak=   -3.145 closest distance to " O   HOH Z 121 " =    3.763
peak=   -3.143 closest distance to " N   VAL A  72 " =    2.030
peak=   -3.142 closest distance to " O   HOH Z 389 " =    4.817
peak=   -3.142 closest distance to " O   HOH Z 298 " =    0.970
peak=   -3.141 closest distance to " CZ  TYR A 169 " =    1.713
peak=   -3.139 closest distance to " C   ASN A 285 " =    2.281
peak=   -3.138 closest distance to " O   HOH Z 406 " =    2.430
peak=   -3.137 closest distance to " CB  ALA A 291 " =    1.911
peak=   -3.116 closest distance to " O   HOH Z 133 " =    1.595
peak=   -3.112 closest distance to " O   HOH Z  68 " =    1.464
peak=   -3.109 closest distance to " O   HOH Z 394 " =    1.572
peak=   -3.107 closest distance to " CD1 TRP A  85 " =    1.073
peak=   -3.104 closest distance to " O   HOH Z 165 " =    1.675
peak=   -3.099 closest distance to " O   HOH Z 257 " =    1.429
peak=   -3.098 closest distance to " CB  ALA A 161 " =    1.606
peak=   -3.097 closest distance to " C   SER A 206 " =    1.448
peak=   -3.096 closest distance to " N   VAL A 232 " =    2.149
peak=   -3.095 closest distance to " O   VAL A 189 " =    2.603
peak=   -3.095 closest distance to " O   SER A 271 " =    2.045
peak=   -3.095 closest distance to " CG2 VAL A 296 " =    0.997
peak=   -3.093 closest distance to " O   HOH Z  52 " =    0.982
peak=   -3.090 closest distance to " O   HOH Z 313 " =    1.451
peak=   -3.070 closest distance to " O   HOH Z 111 " =    1.286
peak=   -3.065 closest distance to " N   VAL A 125 " =    0.868
peak=   -3.053 closest distance to " O   HOH Z  52 " =    1.790
peak=   -3.048 closest distance to " CD2 HIS A 207 " =    2.371
peak=   -3.048 closest distance to " CB  ALA A 248 " =    2.375
peak=   -3.047 closest distance to " CG1 VAL A 112 " =    2.883
peak=   -3.008 closest distance to " O   HOH Z 193 " =    1.687

================= 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    :  0.4954 0.4859   6.297976e+00   6.283948e+00
   1_bss:  0.4875 0.4728   6.293342e+00   6.276896e+00
   1_xyz:  0.4156 0.4342   6.209615e+00   6.235705e+00
   1_adp:  0.3732 0.4364   6.157302e+00   6.233701e+00
   1_occ:  0.3728 0.4363   6.156842e+00   6.234005e+00
   2_bss:  0.3707 0.4331   6.158166e+00   6.233943e+00
   2_xyz:  0.2982 0.3627   5.983114e+00   6.113636e+00
   2_adp:  0.2766 0.3466   5.936237e+00   6.080859e+00
   2_occ:  0.2763 0.3463   5.935715e+00   6.080657e+00
   3_bss:  0.2750 0.3441   5.936405e+00   6.078300e+00
   3_xyz:  0.2266 0.2908   5.767493e+00   5.941636e+00
   3_adp:  0.2090 0.2679   5.696029e+00   5.880848e+00
   3_occ:  0.2088 0.2674   5.695349e+00   5.880096e+00
   4_bss:  0.2083 0.2674   5.695571e+00   5.879737e+00
   4_xyz:  0.1603 0.2132   5.460450e+00   5.679231e+00
   4_adp:  0.1455 0.2015   5.385803e+00   5.619535e+00
   4_occ:  0.1454 0.2013   5.385157e+00   5.618823e+00
   5_bss:  0.1458 0.2006   5.383474e+00   5.616297e+00
   5_xyz:  0.1296 0.1834   5.288020e+00   5.533143e+00
   5_adp:  0.1249 0.1793   5.261691e+00   5.508149e+00
   5_occ:  0.1249 0.1792   5.260932e+00   5.507552e+00
   5_bss:  0.1248 0.1790   5.260595e+00   5.507780e+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:  0.300  20.000   7.260   8.718   8.042   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.260   8.718   8.042   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.260   8.718   8.042   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.260   8.718   8.042   0.000   0.000   0.000
   2_bss:  0.346  50.000   4.261   4.981   4.702   0.000   0.000   0.000
   2_xyz:  0.346  50.000   4.261   4.981   4.702   0.000   0.000   0.000
   2_adp:  0.346  50.000   4.261   4.981   4.702   0.000   0.000   0.000
   2_occ:  0.346  50.000   4.261   4.981   4.702   0.000   0.000   0.000
   3_bss:  0.334  50.000   2.251   2.322   3.125   0.000   0.000   0.000
   3_xyz:  0.334  50.000   2.251   2.322   3.125   0.000   0.000   0.000
   3_adp:  0.334  50.000   2.251   2.322   3.125   0.000   0.000   0.000
   3_occ:  0.334  50.000   2.251   2.322   3.125   0.000   0.000   0.000
   4_bss:  0.323  50.000   1.000   1.019   2.248   0.000   0.000   0.000
   4_xyz:  0.323  50.000   1.000   1.019   2.248   0.000   0.000   0.000
   4_adp:  0.323  50.000   1.000   1.019   2.248   0.000   0.000   0.000
   4_occ:  0.323  50.000   1.000   1.019   2.248   0.000   0.000   0.000
   5_bss:  0.316  50.000   0.783   0.307   1.966   0.000   0.000   0.000
   5_xyz:  0.316  50.000   0.783   0.307   1.966   0.000   0.000   0.000
   5_adp:  0.316  50.000   0.783   0.307   1.966   0.000   0.000   0.000
   5_occ:  0.316  50.000   0.783   0.307   1.966   0.000   0.000   0.000
   5_bss:  0.318  58.504  -0.212  -0.763   0.975  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.997 0.3804  0.4543    76058.991
   1_bss:  60.561 0.3854  0.5800    74823.608
   1_xyz:  53.243 0.4780  0.6986    59891.931
   1_adp:  52.370 0.4887  0.7805    59157.667
   1_occ:  52.419 0.4881  0.7789    59301.188
   2_bss:  52.207 0.4907  0.7015    58979.247
   2_xyz:  40.509 0.6346  0.8875    37760.039
   2_adp:  37.618 0.6698  0.9347    34042.333
   2_occ:  37.596 0.6700  0.9341    33974.933
   3_bss:  37.417 0.6722  0.8711    33811.900
   3_xyz:  30.051 0.7559  0.9569    22769.889
   3_adp:  26.980 0.7903  0.9774    19129.991
   3_occ:  26.961 0.7904  0.9771    19079.301
   4_bss:  26.940 0.7907  0.9383    19057.567
   4_xyz:  21.127 0.8499  0.9798    11892.249
   4_adp:  19.533 0.8656  0.9796    10485.429
   4_occ:  19.516 0.8658  0.9794    10458.772
   5_bss:  19.446 0.8663  0.9660    10370.622
   5_xyz:  17.332 0.8860  0.9747     8538.274
   5_adp:  16.707 0.8919  0.9678     8148.076
   5_occ:  16.689 0.8921  0.9676     8123.853
   5_bss:  16.683 0.8921  0.9715     8125.528
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3843e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3843e+01
   1_xyz:   1.739  0.014  0.109 18.499  0.007  4.107   1.5037e-01
   1_adp:   1.739  0.014  0.109 18.499  0.007  4.107   1.5037e-01
   1_occ:   1.739  0.014  0.109 18.499  0.007  4.107   1.5037e-01
   2_bss:   1.739  0.014  0.109 18.499  0.007  4.107   1.5037e-01
   2_xyz:   1.262  0.009  0.091 16.905  0.006  4.107   9.9776e-02
   2_adp:   1.262  0.009  0.091 16.905  0.006  4.107   9.9776e-02
   2_occ:   1.262  0.009  0.091 16.905  0.006  4.107   9.9776e-02
   3_bss:   1.262  0.009  0.091 16.905  0.006  4.107   9.9776e-02
   3_xyz:   1.038  0.007  0.073 15.671  0.004  4.122   6.6016e-02
   3_adp:   1.038  0.007  0.073 15.671  0.004  4.122   6.6016e-02
   3_occ:   1.038  0.007  0.073 15.671  0.004  4.122   6.6016e-02
   4_bss:   1.038  0.007  0.073 15.671  0.004  4.122   6.6016e-02
   4_xyz:   1.104  0.008  0.082 15.754  0.004  4.109   7.3601e-02
   4_adp:   1.104  0.008  0.082 15.754  0.004  4.109   7.3601e-02
   4_occ:   1.104  0.008  0.082 15.754  0.004  4.109   7.3601e-02
   5_bss:   1.104  0.008  0.082 15.754  0.004  4.109   7.3601e-02
   5_xyz:   1.048  0.008  0.080 15.652  0.004  4.116   6.7401e-02
   5_adp:   1.048  0.008  0.080 15.652  0.004  4.116   6.7401e-02
   5_occ:   1.048  0.008  0.080 15.652  0.004  4.116   6.7401e-02
   5_bss:   1.048  0.008  0.080 15.652  0.004  4.116   6.7401e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9791e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9791e+00
   1_xyz:  13.601  0.194  0.423 88.528  0.036  2.182   1.0505e-01
   1_adp:  13.601  0.194  0.423 88.528  0.036  2.182   1.0505e-01
   1_occ:  13.601  0.194  0.423 88.528  0.036  2.182   1.0505e-01
   2_bss:  13.601  0.194  0.423 88.528  0.036  2.182   1.0505e-01
   2_xyz:   7.724  0.089  0.302 89.481  0.049  2.042   6.7813e-02
   2_adp:   7.724  0.089  0.302 89.481  0.049  2.042   6.7813e-02
   2_occ:   7.724  0.089  0.302 89.481  0.049  2.042   6.7813e-02
   3_bss:   7.724  0.089  0.302 89.481  0.049  2.042   6.7813e-02
   3_xyz:   7.437  0.069  0.328 81.550  0.026  2.323   5.5765e-02
   3_adp:   7.437  0.069  0.328 81.550  0.026  2.323   5.5765e-02
   3_occ:   7.437  0.069  0.328 81.550  0.026  2.323   5.5765e-02
   4_bss:   7.437  0.069  0.328 81.550  0.026  2.323   5.5765e-02
   4_xyz:   7.155  0.057  0.379 84.069  0.042  2.275   5.9011e-02
   4_adp:   7.155  0.057  0.379 84.069  0.042  2.275   5.9011e-02
   4_occ:   7.155  0.057  0.379 84.069  0.042  2.275   5.9011e-02
   5_bss:   7.155  0.057  0.379 84.069  0.042  2.275   5.9011e-02
   5_xyz:   8.021  0.057  0.436 81.110  0.039  2.312   4.3551e-02
   5_adp:   8.021  0.057  0.436 81.110  0.039  2.312   4.3551e-02
   5_occ:   8.021  0.057  0.436 81.110  0.039  2.312   4.3551e-02
   5_bss:   8.021  0.057  0.436 81.110  0.039  2.312   4.3551e-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:  85.57   0.00  15.52  80.47   0.00  13.48  85.57   0.00  26.63
   1_occ:  85.57   0.00  15.52  80.47   0.00  13.48  85.57   0.00  26.63
   2_bss:  85.57   0.00  15.52  80.47   0.00  13.48  85.57   0.00  26.63
   2_xyz:  85.57   0.00  15.52  80.47   0.00  13.48  85.57   0.00  26.63
   2_adp:  81.03   0.00  15.26  73.51   0.00  12.38  81.03   0.00  30.97
   2_occ:  81.03   0.00  15.26  73.51   0.00  12.38  81.03   0.00  30.97
   3_bss:  81.03   0.00  15.26  73.51   0.00  12.38  81.03   0.00  30.97
   3_xyz:  81.03   0.00  15.26  73.51   0.00  12.38  81.03   0.00  30.97
   3_adp:  80.43   0.00  14.95  68.12   0.00  11.21  80.43   1.98  35.32
   3_occ:  80.43   0.00  14.95  68.12   0.00  11.21  80.43   1.98  35.32
   4_bss:  80.43   0.00  14.95  68.12   0.00  11.21  80.43   1.98  35.32
   4_xyz:  80.43   0.00  14.95  68.12   0.00  11.21  80.43   1.98  35.32
   4_adp:  83.22   0.00  15.02  74.52   0.00  10.51  83.22   3.09  39.57
   4_occ:  83.22   0.00  15.02  74.52   0.00  10.51  83.22   3.09  39.57
   5_bss:  83.22   0.00  15.02  74.52   0.00  10.51  83.22   3.09  39.57
   5_xyz:  83.22   0.00  15.02  74.52   0.00  10.51  83.22   3.09  39.57
   5_adp: 103.36   0.00  15.42  93.10   0.00  10.38 103.36   3.33  42.83
   5_occ: 103.36   0.00  15.42  93.10   0.00  10.38 103.36   3.33  42.83
   5_bss: 104.49   1.13  16.55  94.23   1.13  11.51 104.49   4.46  43.96
------------------------------------------------------------------------
 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:    1.270    0.026    0.413
   1_adp:    1.270    0.026    0.413
   1_occ:    1.270    0.026    0.413
   2_bss:    1.270    0.026    0.413
   2_xyz:    1.532    0.044    0.599
   2_adp:    1.532    0.044    0.599
   2_occ:    1.532    0.044    0.599
   3_bss:    1.532    0.044    0.599
   3_xyz:    1.704    0.053    0.670
   3_adp:    1.704    0.053    0.670
   3_occ:    1.704    0.053    0.670
   4_bss:    1.704    0.053    0.670
   4_xyz:    1.884    0.045    0.781
   4_adp:    1.884    0.045    0.781
   4_occ:    1.884    0.045    0.781
   5_bss:    1.884    0.045    0.781
   5_xyz:    2.016    0.045    0.803
   5_adp:    2.016    0.045    0.803
   5_occ:    2.016    0.045    0.803
   5_bss:    2.016    0.045    0.803
------------------------------------------------------------------------

CPU time actual refinement: 342.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_986/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_986/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_986/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_986/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_986/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.87 
  Macro-tasks:
    bulk solvent and scale       = 41.10  
    individual site refinement   = 142.87 
    weights calculation          = 32.41  
    collect and process          = 6.47   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 222.97 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 107.76 
    alpha_beta                      = 8.27   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 116.88 
    fmodel                         = 7.21   
    r_factors                      = 0.15   
    phase_errors                   = 10.29  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 254.48 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.870 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    622 calls, 107.39 s
gradients_fft:          567 calls, 104.10 s

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

# Date 2008-01-16 Time 02:55:27 PST -0800 (1200480927.78 s)
Start R-work = 0.4954, R-free = 0.4859 (no bulk solvent and anisotropic scale)
Final R-work = 0.1406, R-free = 0.1941 (no bulk solvent and anisotropic scale)

Start R-work = 0.4875, R-free = 0.4728
Final R-work = 0.1248, R-free = 0.1790