# Date 2008-01-16 Time 02:37:45 PST -0800 (1200479865.73 s)
#phil __OFF__

Command line arguments: "../908.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4692
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 908

-------------------------------------------------------------------------------
  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: (70.9525, 46.93, 86.822, 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: (70.9525, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 2.00158
Completeness in resolution range: 0.97356
Completeness with d_max=infinity: 0.970521

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1235
                             d_min =   2.0016

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: (70.9525, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 2.00158
Completeness in resolution range: 0.97356
Completeness with d_max=infinity: 0.970521

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1239 -  4.2827 [2108/2132]  1898   210  10.0%
  bin  2:  4.2827 -  3.4121 [2033/2053]  1829   204  10.0%
  bin  3:  3.4121 -  2.9846 [2003/2022]  1801   202  10.1%
  bin  4:  2.9846 -  2.7134 [1987/2017]  1792   195   9.8%
  bin  5:  2.7134 -  2.5199 [1981/2000]  1783   198  10.0%
  bin  6:  2.5199 -  2.3719 [1959/1984]  1757   202  10.3%
  bin  7:  2.3719 -  2.2535 [1948/1976]  1755   193   9.9%
  bin  8:  2.2535 -  2.1557 [1953/1989]  1760   193   9.9%
  bin  9:  2.1557 -  2.0729 [1928/1970]  1736   192  10.0%
  bin 10:  2.0729 -  2.0016 [1689/1978]  1519   170  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_908/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 7
        2.42 -     3.04: 2180
        3.04 -     3.66: 4603
        3.66 -     4.28: 8986
        4.28 -     4.90: 12269
  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 207 " - " O   HOH Z 341 "  2.077 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 28040 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_908/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_908/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 70.9525 46.93 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4171   r_free= 0.4021   ksol= 0.00   Bsol= 0.00   scale= 0.826    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.203511                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7766 0.99   1378  152 0.3565 0.3303      6.5151      6.4007|
|  2:  4.7766 -  3.8113 0.99   1314  147 0.3042 0.3027      6.5931       6.613|
|  3:  3.8113 -  3.3354 0.99   1294  143 0.3535 0.3253      6.5109      6.5171|
|  4:  3.3354 -  3.0331 0.99   1277  146 0.3905 0.3345      6.4237      6.3135|
|  5:  3.0331 -  2.8172 0.99   1289  142 0.4314 0.4240      6.2877      6.3216|
|  6:  2.8172 -  2.6521 0.99   1276  139 0.4418 0.4769      6.2205      6.1612|
|  7:  2.6521 -  2.5199 0.99   1275  140 0.4763 0.4857        6.19      6.2281|
|  8:  2.5199 -  2.4106 0.98   1245  142 0.4666 0.4191      6.1409      6.0821|
|  9:  2.4106 -  2.3182 0.98   1265  139 0.4533 0.4753      6.0635      6.0719|
| 10:  2.3182 -  2.2384 1.00   1254  143 0.4807 0.4697      6.0827      6.0676|
| 11:  2.2384 -  2.1687 0.97   1251  133 0.4855 0.4157      6.0166      5.9608|
| 12:  2.1687 -  2.1068 0.98   1243  141 0.4701 0.4670      5.9547      5.9815|
| 13:  2.1068 -  2.0515 0.99   1268  141 0.4930 0.4971      5.8825      5.8669|
| 14:  2.0515 -  2.0016 0.79   1001  111 0.4781 0.4252      5.8273      5.6815|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7766  1378   152  0.76  29.11   0.81     0.78      51964.37|
|  2:  4.7766 -  3.8113  1314   147  0.81  25.70   0.92     0.84      62906.19|
|  3:  3.8113 -  3.3354  1294   143  0.74  31.47   0.88     0.82      65067.82|
|  4:  3.3354 -  3.0331  1277   146  0.69  36.38   0.85     0.74      59714.13|
|  5:  3.0331 -  2.8172  1289   142  0.60  44.20   0.78     0.67      55261.42|
|  6:  2.8172 -  2.6521  1276   139  0.56  47.64   0.77     0.61      52281.30|
|  7:  2.6521 -  2.5199  1275   140  0.51  50.91   0.75     0.57      50190.81|
|  8:  2.5199 -  2.4106  1245   142  0.51  51.55   0.77     0.57      46395.25|
|  9:  2.4106 -  2.3182  1265   139  0.53  49.80   0.75     0.58      40463.88|
| 10:  2.3182 -  2.2384  1254   143  0.54  49.26   0.78     0.60      35453.93|
| 11:  2.2384 -  2.1687  1251   133  0.52  50.47   0.77     0.59      33362.31|
| 12:  2.1687 -  2.1068  1243   141  0.50  52.51   0.80     0.58      32880.09|
| 13:  2.1068 -  2.0515  1268   141  0.49  52.90   0.75     0.57      28609.90|
| 14:  2.0515 -  2.0016  1001   111  0.58  46.32   0.74     0.59      19967.44|
|alpha:            min =        0.57 max =            0.84 mean =         0.65|
|beta:             min =    19967.44 max =        65067.82 mean =     45883.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.97 mean =        43.93|
|phase err.(test): min =        0.00 max =           89.88 mean =        44.06|
|-----------------------------------------------------------------------------|

============================== 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 = 6.586686              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.269   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.539129              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.985   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      680 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1486 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2589 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3921 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5002 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6531 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7693 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.067 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.615 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4261   r_free= 0.4086   ksol= 0.00   Bsol= 0.00   scale= 0.794    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.210877                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4101   r_free= 0.3879   ksol= 0.34   Bsol= 20.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.12,7.93,8.71,0.00,0.00,0.00); trace/3= 8.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.199262                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.204401              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.223   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.541013              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.354   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4101      final r-factor (work) = 0.2948          |
| start r-factor (free) = 0.3879      final r-factor (free) = 0.3131          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 73.3764 = 6.20 * 0.50 * 6.2243 + 1.00 * 54.0672                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7827 = 6.20 * 0.50 * 6.0193 + 1.00 * 0.1097                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2948      final r-factor (work) = 0.2219          |
| start r-factor (free) = 0.3131      final r-factor (free) = 0.2515          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2713 = 0.54 * 1.00 * 6.0193 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1491 = 0.54 * 1.00 * 5.8004 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    58.26   10.19    None  None   None       |
|    all(noH): 2823   0      0.00    58.26   10.19    None  None   None       |
|    Sol.    : 438    0      0.00    57.89   27.68    None  None   None       |
|    Mac.    : 2385   0      0.00    58.26   6.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.826: 1335   |   5:    29.129 -  34.954:  109        |
|      1:     5.826 -  11.651:  732   |   6:    34.954 -  40.780:   71        |
|      2:    11.651 -  17.477:  251   |   7:    40.780 -  46.606:   46        |
|      3:    17.477 -  23.303:  132   |   8:    46.606 -  52.431:   23        |
|      4:    23.303 -  29.129:  116   |   9:    52.431 -  58.257:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2219 r_free = 0.2515             target_work(ml) = 5.701         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2213 r_free = 0.2516             target_work(ml) = 5.699         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2213   r_free= 0.2516   ksol= 0.34   Bsol= 20.00   scale= 1.084   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.12,7.93,8.71,0.00,0.00,0.00); trace/3= 8.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.699352                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2152   r_free= 0.2452   ksol= 0.34   Bsol= 48.77   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.67,4.33,5.41,0.00,0.00,0.00); trace/3= 4.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.695591                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.360852              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.812   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.275709              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.389  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2152      final r-factor (work) = 0.1532          |
| start r-factor (free) = 0.2452      final r-factor (free) = 0.1914          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9735 = 2.36 * 0.50 * 5.8149 + 1.00 * 0.1095                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5895 = 2.36 * 0.50 * 5.5313 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1532      final r-factor (work) = 0.1420          |
| start r-factor (free) = 0.1914      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5361 = 0.28 * 1.00 * 5.5313 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4862 = 0.28 * 1.00 * 5.3535 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    58.79   10.55    None  None   None       |
|    all(noH): 2823   0      0.00    58.79   10.55    None  None   None       |
|    Sol.    : 438    0      0.00    58.79   30.24    None  None   None       |
|    Mac.    : 2385   0      0.00    57.45   6.93     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 -   5.879: 1400   |   5:    29.396 -  35.275:   87        |
|      1:     5.879 -  11.758:  675   |   6:    35.275 -  41.154:  119        |
|      2:    11.758 -  17.637:  236   |   7:    41.154 -  47.033:   51        |
|      3:    17.637 -  23.516:  110   |   8:    47.033 -  52.912:   33        |
|      4:    23.516 -  29.396:  102   |   9:    52.912 -  58.791:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1420 r_free = 0.1821             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1420 r_free = 0.1822             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1420   r_free= 0.1822   ksol= 0.34   Bsol= 48.77   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.67,4.33,5.41,0.00,0.00,0.00); trace/3= 4.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.329349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1420   r_free= 0.1821   ksol= 0.33   Bsol= 48.77   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,3.64,4.80,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.330979                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.009883              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.920  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.568286              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.251  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1420      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1821      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4440 = 2.01 * 0.50 * 5.3574 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3548 = 2.01 * 0.50 * 5.2649 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1656      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.7967 = 3.57 * 1.00 * 5.2649 + 1.00 * 0.0101                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.5710 = 3.57 * 1.00 * 5.2001 + 1.00 * 0.0156                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.46   11.60    None  None   None       |
|    all(noH): 2823   0      0.00    76.46   11.60    None  None   None       |
|    Sol.    : 438    0      0.00    76.46   35.24    None  None   None       |
|    Mac.    : 2385   0      0.00    73.27   7.25     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.646: 1668   |   5:    38.230 -  45.876:   83        |
|      1:     7.646 -  15.292:  554   |   6:    45.876 -  53.522:   84        |
|      2:    15.292 -  22.938:  157   |   7:    53.522 -  61.167:   52        |
|      3:    22.938 -  30.584:  110   |   8:    61.167 -  68.813:   19        |
|      4:    30.584 -  38.230:   88   |   9:    68.813 -  76.459:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1637             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1637             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1637   ksol= 0.33   Bsol= 48.77   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,3.64,4.80,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195308                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1637   ksol= 0.32   Bsol= 48.77   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,3.60,4.74,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195015                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.812679              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.497  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.337421              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.612   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3761 = 2.81 * 0.50 * 5.1994 + 1.00 * 0.0639                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3430 = 2.81 * 0.50 * 5.1702 + 1.00 * 0.0719                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7596 = 0.34 * 1.00 * 5.1702 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7579 = 0.34 * 1.00 * 5.1631 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.09   11.09    None  None   None       |
|    all(noH): 2823   0      0.00    75.09   11.09    None  None   None       |
|    Sol.    : 438    0      0.54    72.95   33.03    None  None   None       |
|    Mac.    : 2385   0      0.00    75.09   7.06     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.509: 1693   |   5:    37.547 -  45.056:   76        |
|      1:     7.509 -  15.019:  543   |   6:    45.056 -  52.566:   79        |
|      2:    15.019 -  22.528:  151   |   7:    52.566 -  60.075:   32        |
|      3:    22.528 -  30.038:  110   |   8:    60.075 -  67.584:   16        |
|      4:    30.038 -  37.547:  117   |   9:    67.584 -  75.094:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1128 r_free = 0.1589             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1589             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1589   ksol= 0.32   Bsol= 48.77   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,3.60,4.74,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154723                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1586   ksol= 0.32   Bsol= 48.77   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,3.60,4.74,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154751                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.544934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.346  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.365227              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.532   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6416 = 2.54 * 0.50 * 5.1630 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6223 = 2.54 * 0.50 * 5.1498 + 1.00 * 0.0694                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1116      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8963 = 0.37 * 1.00 * 5.1498 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9254 = 0.37 * 1.00 * 5.1481 + 1.00 * 0.0452                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.59   11.01    None  None   None       |
|    all(noH): 2823   0      0.00    75.59   11.01    None  None   None       |
|    Sol.    : 438    0      0.70    72.40   32.76    None  None   None       |
|    Mac.    : 2385   0      0.00    75.59   7.01     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.559: 1708   |   5:    37.795 -  45.354:   82        |
|      1:     7.559 -  15.118:  530   |   6:    45.354 -  52.913:   73        |
|      2:    15.118 -  22.677:  154   |   7:    52.913 -  60.472:   28        |
|      3:    22.677 -  30.236:  111   |   8:    60.472 -  68.031:   18        |
|      4:    30.236 -  37.795:  114   |   9:    68.031 -  75.590:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1582             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1582             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1582   ksol= 0.32   Bsol= 48.77   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,3.60,4.74,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147098                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7766 0.99   1378  152 0.1003 0.1317      5.3849       5.511|
|  2:  4.7766 -  3.8113 0.99   1314  147 0.0864 0.1134      5.4472      5.6475|
|  3:  3.8113 -  3.3354 0.99   1294  143 0.1046 0.1495      5.4765      5.8525|
|  4:  3.3354 -  3.0331 0.99   1277  146 0.1183 0.1556      5.4488      5.5928|
|  5:  3.0331 -  2.8172 0.99   1289  142 0.1309 0.1762      5.3299      5.5767|
|  6:  2.8172 -  2.6521 0.99   1276  139 0.1176 0.1918      5.2105      5.4828|
|  7:  2.6521 -  2.5199 0.99   1275  140 0.1285 0.1550      5.1808      5.3449|
|  8:  2.5199 -  2.4106 0.98   1245  142 0.1165 0.1755      5.0793      5.3831|
|  9:  2.4106 -  2.3182 0.98   1265  139 0.1164 0.1731      5.0462      5.2693|
| 10:  2.3182 -  2.2384 1.00   1254  143 0.1137 0.1695      4.9718      5.2496|
| 11:  2.2384 -  2.1687 0.97   1251  133 0.1147 0.1752       4.949      5.2399|
| 12:  2.1687 -  2.1068 0.98   1243  141 0.1113 0.1747      4.8752      5.2354|
| 13:  2.1068 -  2.0515 0.99   1268  141 0.1144 0.1687      4.8086      5.0614|
| 14:  2.0515 -  2.0016 0.79   1001  111 0.1084 0.1785      4.7016       4.947|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7766  1378   152  0.94   9.03   0.97     0.95       7040.60|
|  2:  4.7766 -  3.8113  1314   147  0.95   8.02   1.01     0.99       9153.84|
|  3:  3.8113 -  3.3354  1294   143  0.93  11.26   1.02     1.01      10546.83|
|  4:  3.3354 -  3.0331  1277   146  0.92  13.30   1.00     0.98      10235.60|
|  5:  3.0331 -  2.8172  1289   142  0.90  15.76   0.99     0.96       8366.57|
|  6:  2.8172 -  2.6521  1276   139  0.90  15.83   0.98     0.95       7183.41|
|  7:  2.6521 -  2.5199  1275   140  0.90  15.97   0.98     0.96       6360.80|
|  8:  2.5199 -  2.4106  1245   142  0.91  14.76   0.99     0.97       5321.84|
|  9:  2.4106 -  2.3182  1265   139  0.91  15.53   1.00     0.97       5176.36|
| 10:  2.3182 -  2.2384  1254   143  0.91  15.25   1.00     0.96       4364.70|
| 11:  2.2384 -  2.1687  1251   133  0.90  16.51   1.00     0.96       4446.99|
| 12:  2.1687 -  2.1068  1243   141  0.91  14.96   1.01     0.99       3877.89|
| 13:  2.1068 -  2.0515  1268   141  0.90  16.04   1.00     0.98       3457.83|
| 14:  2.0515 -  2.0016  1001   111  0.91  15.10   0.98     0.94       2742.09|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2742.09 max =        10546.83 mean =      6390.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.03|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.54|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1582   ksol= 0.32   Bsol= 51.59   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.37,0.78,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147143                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1582   ksol= 0.32   Bsol= 51.59   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.37,0.78,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147143                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7766 0.99   1378  152 0.1002 0.1316      5.3843      5.5104|
|  2:  4.7766 -  3.8113 0.99   1314  147 0.0863 0.1133      5.4464      5.6464|
|  3:  3.8113 -  3.3354 0.99   1294  143 0.1046 0.1495      5.4761      5.8524|
|  4:  3.3354 -  3.0331 0.99   1277  146 0.1184 0.1556       5.449       5.593|
|  5:  3.0331 -  2.8172 0.99   1289  142 0.1309 0.1763      5.3303      5.5773|
|  6:  2.8172 -  2.6521 0.99   1276  139 0.1176 0.1919       5.211      5.4832|
|  7:  2.6521 -  2.5199 0.99   1275  140 0.1285 0.1551      5.1811      5.3451|
|  8:  2.5199 -  2.4106 0.98   1245  142 0.1165 0.1756      5.0796      5.3834|
|  9:  2.4106 -  2.3182 0.98   1265  139 0.1164 0.1731      5.0463      5.2693|
| 10:  2.3182 -  2.2384 1.00   1254  143 0.1137 0.1695      4.9719      5.2499|
| 11:  2.2384 -  2.1687 0.97   1251  133 0.1147 0.1753      4.9491        5.24|
| 12:  2.1687 -  2.1068 0.98   1243  141 0.1113 0.1748      4.8753      5.2355|
| 13:  2.1068 -  2.0515 0.99   1268  141 0.1144 0.1687      4.8087      5.0615|
| 14:  2.0515 -  2.0016 0.79   1001  111 0.1084 0.1785      4.7017      4.9471|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7766  1378   152  0.94   9.02   0.97     0.95       7030.29|
|  2:  4.7766 -  3.8113  1314   147  0.95   8.00   1.01     0.99       9141.29|
|  3:  3.8113 -  3.3354  1294   143  0.93  11.26   1.02     1.01      10538.45|
|  4:  3.3354 -  3.0331  1277   146  0.92  13.31   1.00     0.98      10240.27|
|  5:  3.0331 -  2.8172  1289   142  0.90  15.76   0.99     0.96       8373.36|
|  6:  2.8172 -  2.6521  1276   139  0.90  15.84   0.98     0.95       7190.29|
|  7:  2.6521 -  2.5199  1275   140  0.90  15.97   0.98     0.96       6365.85|
|  8:  2.5199 -  2.4106  1245   142  0.91  14.77   0.99     0.97       5324.40|
|  9:  2.4106 -  2.3182  1265   139  0.91  15.54   1.00     0.97       5177.93|
| 10:  2.3182 -  2.2384  1254   143  0.91  15.25   1.00     0.96       4365.91|
| 11:  2.2384 -  2.1687  1251   133  0.90  16.52   1.00     0.96       4448.48|
| 12:  2.1687 -  2.1068  1243   141  0.91  14.96   1.01     0.99       3879.22|
| 13:  2.1068 -  2.0515  1268   141  0.90  16.04   1.00     0.98       3458.90|
| 14:  2.0515 -  2.0016  1001   111  0.91  15.10   0.98     0.94       2742.67|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2742.67 max =        10538.45 mean =      6390.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.03|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.97    79.55   14.97    None  None   None       |
|    all(noH): 2823   0      3.97    79.55   14.97    None  None   None       |
|    Sol.    : 438    0      4.66    76.37   36.72    None  None   None       |
|    Mac.    : 2385   0      3.97    79.55   10.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.966 -  11.524: 1708   |   5:    41.760 -  49.319:   82        |
|      1:    11.524 -  19.083:  530   |   6:    49.319 -  56.878:   73        |
|      2:    19.083 -  26.642:  154   |   7:    56.878 -  64.437:   28        |
|      3:    26.642 -  34.201:  111   |   8:    64.437 -  71.996:   18        |
|      4:    34.201 -  41.760:  114   |   9:    71.996 -  79.555:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.307 - 4.815
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 311 from: 319
   mapped sites are within: 0.717 - 4.815

peak=   10.833 closest distance to " CG2 VAL A 230 " =    1.387
peak=    6.648 closest distance to " CG2 VAL A 296 " =    1.090
peak=    6.388 closest distance to " NH2 ARG A  56 " =    2.264
peak=    6.285 closest distance to " CG  LEU A   5 " =    1.253
peak=    5.752 closest distance to " CG  LEU A 228 " =    1.170
peak=    5.526 closest distance to " CB  GLN A 223 " =    1.451
peak=    5.467 closest distance to " CD2 LEU A   5 " =    1.200
peak=    5.142 closest distance to " CB  VAL A 296 " =    1.117
peak=    5.069 closest distance to " CB  GLN A 183 " =    1.258
peak=    5.032 closest distance to " NE2 GLN A  11 " =    1.167
peak=    4.890 closest distance to " CB  VAL A 230 " =    1.200
peak=    4.851 closest distance to " CB  SER A  63 " =    1.290
peak=    4.815 closest distance to " O   HOH Z 232 " =    2.353
peak=    4.770 closest distance to " O   HOH Z 142 " =    1.683
peak=    4.761 closest distance to " O   HOH Z 126 " =    1.977
peak=    4.517 closest distance to " CB  ARG A 275 " =    0.888
peak=    4.489 closest distance to " O   HOH Z 369 " =    2.054
peak=    4.420 closest distance to " CG  PRO A 243 " =    1.113
peak=    4.415 closest distance to " O   HOH Z 298 " =    1.795
peak=    4.410 closest distance to " O   HOH Z 427 " =    3.092
peak=    4.406 closest distance to " CZ  PHE A 218 " =    1.097
peak=    4.403 closest distance to " CG  PRO A 213 " =    1.204
peak=    4.399 closest distance to " C   PRO A 198 " =    1.513
peak=    4.365 closest distance to " O   HOH Z  78 " =    1.801
peak=    4.324 closest distance to " O   HOH Z 368 " =    2.174
peak=    4.317 closest distance to " O   HOH Z 265 " =    2.403
peak=    4.295 closest distance to " CB  TRP A 266 " =    0.946
peak=    4.284 closest distance to " O   HOH Z  61 " =    1.705
peak=    4.279 closest distance to " O   HOH Z 209 " =    2.277
peak=    4.277 closest distance to " O   HOH Z 236 " =    1.945
peak=    4.263 closest distance to " O   HOH Z 316 " =    3.144
peak=    4.260 closest distance to " O   HOH Z 261 " =    2.174
peak=    4.240 closest distance to " CB  ASN A 148 " =    1.347
peak=    4.239 closest distance to " CB  ARG A  79 " =    1.430
peak=    4.211 closest distance to " O   HOH Z 423 " =    1.744
peak=    4.177 closest distance to " O   HOH Z 346 " =    1.610
peak=    4.170 closest distance to " O   SER A  87 " =    2.298
peak=    4.168 closest distance to " CB  GLU A 152 " =    1.185
peak=    4.160 closest distance to " OD1 ASN A  69 " =    2.636
peak=    4.132 closest distance to " O   HOH Z 303 " =    2.078
peak=    4.120 closest distance to " CB  VAL A 265 " =    1.305
peak=    4.119 closest distance to " ND2 ASN A 187 " =    1.468
peak=    4.111 closest distance to " CD2 LEU A 228 " =    1.130
peak=    4.087 closest distance to " CB  GLU A 128 " =    1.095
peak=    4.082 closest distance to " O   HOH Z 158 " =    3.223
peak=    4.063 closest distance to " O   HOH Z 272 " =    1.903
peak=    4.056 closest distance to " CB  ASP A 140 " =    0.917
peak=    4.050 closest distance to " CA  TYR A  30 " =    0.972
peak=    4.022 closest distance to " CG  PRO A 198 " =    1.252
peak=    4.021 closest distance to " CB  SER A   3 " =    1.296
peak=    4.016 closest distance to " O   HOH Z  43 " =    1.902
peak=    3.969 closest distance to " O   HOH Z 411 " =    3.763
peak=    3.963 closest distance to " CB  GLU A 277 " =    3.624
peak=    3.953 closest distance to " ND2 ASN A 249 " =    1.920
peak=    3.952 closest distance to " CB  ASN A  39 " =    0.879
peak=    3.933 closest distance to " O   HOH Z 248 " =    1.690
peak=    3.928 closest distance to " O   HOH Z 403 " =    1.647
peak=    3.916 closest distance to " O   HOH Z 234 " =    3.744
peak=    3.908 closest distance to " O   HOH Z 203 " =    1.719
peak=    3.907 closest distance to " O   HOH Z  15 " =    2.148
peak=    3.877 closest distance to " CB  LEU A 143 " =    1.164
peak=    3.855 closest distance to " NH1AARG A 145 " =    1.172
peak=    3.848 closest distance to " O   HOH Z 214 " =    2.077
peak=    3.846 closest distance to " CB  ARG A 190 " =    1.541
peak=    3.844 closest distance to " CB  ASN A 187 " =    1.252
peak=    3.838 closest distance to " O   HOH Z 126 " =    1.993
peak=    3.835 closest distance to " CB  ALA A   9 " =    1.627
peak=    3.829 closest distance to " O   HOH Z 193 " =    1.927
peak=    3.819 closest distance to " CA  ALA A  51 " =    0.954
peak=    3.811 closest distance to " CD  ARG A 159 " =    0.738
peak=    3.811 closest distance to " CB  ASN A 142 " =    1.045
peak=    3.797 closest distance to " NH2 ARG A 156 " =    1.112
peak=    3.790 closest distance to " OG  SER A  97 " =    2.929
peak=    3.782 closest distance to " CA  SER A  87 " =    0.968
peak=    3.778 closest distance to " CG1 VAL A 153 " =    0.958
peak=    3.778 closest distance to " CB  VAL A 202 " =    1.578
peak=    3.775 closest distance to " O   HOH Z 425 " =    1.378
peak=    3.771 closest distance to " CB  PRO A  54 " =    0.801
peak=    3.769 closest distance to " CA  THR A 264 " =    0.784
peak=    3.751 closest distance to " O   HOH Z 280 " =    3.025
peak=    3.736 closest distance to " O   HOH Z 126 " =    1.567
peak=    3.733 closest distance to " CG  LEU A 167 " =    1.221
peak=    3.718 closest distance to " CG1 VAL A 296 " =    1.214
peak=    3.716 closest distance to " N   ASN A  39 " =    1.205
peak=    3.716 closest distance to " O   HOH Z  68 " =    2.206
peak=    3.709 closest distance to " CD  ARG A  66 " =    2.492
peak=    3.705 closest distance to " CB  TRP A 179 " =    1.467
peak=    3.705 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.695 closest distance to " CB BVAL A  41 " =    1.145
peak=    3.675 closest distance to " CB  GLU A  46 " =    0.997
peak=    3.668 closest distance to " CB  ARG A  79 " =    0.908
peak=    3.666 closest distance to " CD  LYS A 166 " =    1.300
peak=    3.659 closest distance to " CG1BVAL A  72 " =    1.687
peak=    3.648 closest distance to " CD BLYS A 290 " =    1.035
peak=    3.645 closest distance to " O   HOH Z 193 " =    2.012
peak=    3.624 closest distance to " CB  LEU A 228 " =    1.219
peak=    3.623 closest distance to " CG2 VAL A 257 " =    0.916
peak=    3.620 closest distance to " O   HOH Z 402 " =    1.456
peak=    3.618 closest distance to " N   PHE A 130 " =    1.205
peak=    3.614 closest distance to " CG  MET A 185 " =    1.166
peak=    3.613 closest distance to " O   HOH Z  21 " =    1.719
peak=    3.612 closest distance to " O   HOH Z 193 " =    1.712
peak=    3.605 closest distance to " CA  ASN A 215 " =    1.205
peak=    3.600 closest distance to " CB  ALA A 291 " =    1.348
peak=    3.600 closest distance to " CA  ALA A  21 " =    1.149
peak=    3.600 closest distance to " CG1 ILE A  49 " =    1.469
peak=    3.598 closest distance to " O   HOH Z 273 " =    2.716
peak=    3.597 closest distance to " O   HOH Z  92 " =    2.434
peak=    3.594 closest distance to " CD1 LEU A 300 " =    1.182
peak=    3.592 closest distance to " O   HOH Z 197 " =    3.189
peak=    3.592 closest distance to " CD  ARG A 269 " =    0.986
peak=    3.591 closest distance to " CA  ASP A 162 " =    1.011
peak=    3.590 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.585 closest distance to " O   MET A 105 " =    1.819
peak=    3.584 closest distance to " CA  ARG A 195 " =    1.210
peak=    3.580 closest distance to " CG BARG A 275 " =    1.467
peak=    3.568 closest distance to " CA  GLY A 267 " =    0.743
peak=    3.557 closest distance to " O   HOH Z 180 " =    2.135
peak=    3.554 closest distance to " O   TRP A 274 " =    1.911
peak=    3.553 closest distance to " CA  ALA A 158 " =    1.208
peak=    3.553 closest distance to " CB  SER A 212 " =    1.235
peak=    3.548 closest distance to " CA  ALA A 291 " =    0.912
peak=    3.548 closest distance to " O   HOH Z 371 " =    3.038
peak=    3.542 closest distance to " CG2 THR A 221 " =    1.184
peak=    3.542 closest distance to " O   HOH Z 344 " =    3.024
peak=    3.540 closest distance to " CB  THR A  31 " =    1.637
peak=    3.530 closest distance to " O   HOH Z 313 " =    1.798
peak=    3.526 closest distance to " O   HOH Z  88 " =    3.190
peak=    3.524 closest distance to " CB  MET A  40 " =    0.821
peak=    3.522 closest distance to " O   HOH Z  97 " =    2.504
peak=    3.519 closest distance to " O   HOH Z 359 " =    3.843
peak=    3.513 closest distance to " N   VAL A 126 " =    1.435
peak=    3.512 closest distance to " CG1 ILE A  33 " =    1.296
peak=    3.508 closest distance to " O   HOH Z 128 " =    2.149
peak=    3.502 closest distance to " CD1 LEU A  96 " =    0.717
peak=    3.501 closest distance to " O   HOH Z 128 " =    2.190
peak=    3.496 closest distance to " O   HOH Z 245 " =    1.390
peak=    3.494 closest distance to " CZ  PHE A 192 " =    0.957
peak=    3.491 closest distance to " O   HOH Z 133 " =    1.661
peak=    3.490 closest distance to " O   HOH Z 263 " =    1.683
peak=    3.487 closest distance to " O   HOH Z 141 " =    1.680
peak=    3.483 closest distance to " ND1 HIS A  81 " =    1.689
peak=    3.469 closest distance to " CB  ALA A 104 " =    0.728
peak=    3.461 closest distance to " OG  SER A  22 " =    2.821
peak=    3.461 closest distance to " O   HOH Z 305 " =    3.577
peak=    3.458 closest distance to " CB  SER A 216 " =    0.821
peak=    3.457 closest distance to " O   HOH Z  97 " =    2.008
peak=    3.452 closest distance to " OD2 ASP A 286 " =    2.857
peak=    3.451 closest distance to " CZ  PHE A  38 " =    1.149
peak=    3.450 closest distance to " CD1 ILE A  33 " =    1.661
peak=    3.448 closest distance to " O   HOH Z 285 " =    2.767
peak=    3.444 closest distance to " O   HOH Z  10 " =    1.813
peak=    3.439 closest distance to " O   HOH Z  48 " =    1.676
peak=    3.438 closest distance to " O   HOH Z 291 " =    1.681
peak=    3.437 closest distance to " O   HOH Z 250 " =    1.334
peak=    3.435 closest distance to " OG BSER A 164 " =    2.246
peak=    3.433 closest distance to " CD1 LEU A 228 " =    2.008
peak=    3.429 closest distance to " O   HOH Z  59 " =    2.113
peak=    3.423 closest distance to " O   HOH Z 132 " =    2.736
peak=    3.415 closest distance to " O   HOH Z 290 " =    1.088
peak=    3.414 closest distance to " CE1 TYR A 186 " =    1.325
peak=    3.409 closest distance to " NE2 HIS A 207 " =    1.346
peak=    3.408 closest distance to " O   HOH Z 353 " =    2.603
peak=    3.405 closest distance to " O   HOH Z 145 " =    1.956
peak=    3.404 closest distance to " CB  ALA A 242 " =    0.797
peak=    3.404 closest distance to " CB  HIS A 108 " =    0.766
peak=    3.402 closest distance to " CB  ARG A 139 " =    0.929
peak=    3.398 closest distance to " CB  THR A 157 " =    1.129
peak=    3.398 closest distance to " O   HOH Z 437 " =    1.810
peak=    3.396 closest distance to " O   HOH Z 435 " =    2.005
peak=    3.396 closest distance to " O   HOH Z 166 " =    3.758
peak=    3.395 closest distance to " O   HOH Z  40 " =    1.834
peak=    3.392 closest distance to " O   HOH Z 368 " =    3.538
peak=    3.388 closest distance to " CE  LYS A  76 " =    0.884
peak=    3.387 closest distance to " CB  ALA A  34 " =    0.907
peak=    3.377 closest distance to " CB  TRP A 150 " =    1.379
peak=    3.375 closest distance to " CB  ARG A 138 " =    0.977
peak=    3.375 closest distance to " O   HOH Z 112 " =    1.655
peak=    3.374 closest distance to " CB  THR A  82 " =    1.368
peak=    3.372 closest distance to " O   HOH Z 299 " =    4.220
peak=    3.372 closest distance to " O   HOH Z 426 " =    1.596
peak=    3.369 closest distance to " CB  ASN A 224 " =    1.018
peak=    3.366 closest distance to " O   ALA A 158 " =    1.401
peak=    3.363 closest distance to " O   HOH Z 187 " =    2.284
peak=    3.358 closest distance to " CA  PHE A 283 " =    1.222
peak=    3.358 closest distance to " CA  MET A  40 " =    1.113
peak=    3.355 closest distance to " N   SER A 135 " =    1.351
peak=    3.349 closest distance to " O   HOH Z 422 " =    2.692
peak=    3.347 closest distance to " CD2 TRP A 179 " =    1.347
peak=    3.346 closest distance to " O   HOH Z 172 " =    3.517
peak=    3.344 closest distance to " CB  GLN A  88 " =    1.207
peak=    3.344 closest distance to " O   HOH Z 227 " =    1.717
peak=    3.342 closest distance to " NZ  LYS A 117 " =    3.286
peak=    3.342 closest distance to " CA  ALA A 154 " =    0.979
peak=    3.340 closest distance to " CG  GLN A  88 " =    1.081
peak=    3.337 closest distance to " O   HOH Z 313 " =    1.715
peak=    3.335 closest distance to " CG1 ILE A 151 " =    1.080
peak=    3.333 closest distance to " O   HOH Z 133 " =    2.402
peak=    3.332 closest distance to " CA  ALA A 295 " =    1.080
peak=    3.330 closest distance to " O   ASP A 124 " =    1.128
peak=    3.328 closest distance to " CB  SER A 273 " =    0.877
peak=    3.325 closest distance to " N   ARG A 156 " =    1.373
peak=    3.324 closest distance to " CA  LEU A 282 " =    1.039
peak=    3.321 closest distance to " O  BHOH Z 338 " =    2.433
peak=    3.321 closest distance to " CA  THR A 221 " =    0.929
peak=    3.321 closest distance to " NE2 GLN A  77 " =    3.353
peak=    3.319 closest distance to " CD1 ILE A 106 " =    1.005
peak=    3.315 closest distance to " CB  ALA A 248 " =    1.436
peak=    3.315 closest distance to " O   HOH Z   1 " =    1.889
peak=    3.314 closest distance to " O   HOH Z 171 " =    2.276
peak=    3.312 closest distance to " CB  ILE A 120 " =    1.299
peak=    3.311 closest distance to " CB  ALA A 248 " =    1.042
peak=    3.309 closest distance to " CA  TYR A 116 " =    1.451
peak=    3.309 closest distance to " O   HOH Z 294 " =    1.561
peak=    3.309 closest distance to " CB  LYS A 117 " =    1.216
peak=    3.307 closest distance to " CA  VAL A  41 " =    0.810
peak=    3.306 closest distance to " O   HOH Z 365 " =    3.003
peak=    3.305 closest distance to " O   HOH Z 350 " =    1.661
peak=    3.304 closest distance to " O   HOH Z 425 " =    2.049
peak=    3.303 closest distance to " O   HOH Z 148 " =    3.297
peak=    3.303 closest distance to " CA  ARG A  36 " =    1.099
peak=    3.303 closest distance to " O   HOH Z 417 " =    3.253
peak=    3.302 closest distance to " CA  TYR A  30 " =    1.058
peak=    3.299 closest distance to " CA  LYS A 181 " =    1.046
peak=    3.296 closest distance to " ND1 HIS A  86 " =    1.650
peak=    3.294 closest distance to " CB  ASN A 110 " =    1.100
peak=    3.284 closest distance to " CA  MET A 105 " =    0.953
peak=    3.283 closest distance to " CA  VAL A 125 " =    1.123
peak=    3.280 closest distance to " CG  GLN A 278 " =    1.306
peak=    3.269 closest distance to " O   HOH Z 213 " =    1.834
peak=    3.269 closest distance to " CB  GLN A 278 " =    0.854
peak=    3.266 closest distance to " O   HOH Z 250 " =    1.301
peak=    3.264 closest distance to " O   HOH Z 409 " =    3.149
peak=    3.262 closest distance to " CE1 HIS A 108 " =    1.149
peak=    3.261 closest distance to " N   ARG A 190 " =    1.050
peak=    3.255 closest distance to " CG2 ILE A  20 " =    1.496
peak=    3.253 closest distance to " O   GLN A 278 " =    1.534
peak=    3.253 closest distance to " O   HOH Z 329 " =    3.907
peak=    3.252 closest distance to " N   SER A  12 " =    1.597
peak=    3.251 closest distance to " CG2 THR A 220 " =    0.813
peak=    3.247 closest distance to " O   HOH Z 407 " =    2.391
peak=    3.246 closest distance to " CA  ALA A 233 " =    1.404
peak=    3.242 closest distance to " CA  ASN A 127 " =    1.033
peak=    3.239 closest distance to " CB  GLN A  89 " =    1.153
peak=    3.235 closest distance to " NZ  LYS A  48 " =    1.332
peak=    3.231 closest distance to " O   HOH Z 417 " =    2.034
peak=    3.228 closest distance to " CB  ALA A 114 " =    1.326
peak=    3.228 closest distance to " N   GLN A 278 " =    1.139
peak=    3.226 closest distance to " O   LYS A 290 " =    2.438
peak=    3.222 closest distance to " CA  ILE A 106 " =    0.742
peak=    3.211 closest distance to " O   ARG A  56 " =    2.877
peak=    3.209 closest distance to " CB  GLN A 103 " =    0.985
peak=    3.207 closest distance to " CB  SER A  26 " =    1.703
peak=    3.207 closest distance to " O   HOH Z 175 " =    2.205
peak=    3.205 closest distance to " O   HOH Z 406 " =    1.529
peak=    3.201 closest distance to " CG  MET A 185 " =    1.034
peak=    3.200 closest distance to " CG BARG A 102 " =    1.794
peak=    3.195 closest distance to " CB  GLN A 205 " =    1.032
peak=    3.195 closest distance to " OG  SER A 245 " =    1.672
peak=    3.191 closest distance to " O   HOH Z  80 " =    1.597
peak=    3.191 closest distance to " O   HOH Z 327 " =    1.885
peak=    3.190 closest distance to " CA  SER A 146 " =    1.735
peak=    3.189 closest distance to " O   HOH Z  66 " =    2.246
peak=    3.182 closest distance to " O   TYR A 116 " =    1.336
peak=    3.182 closest distance to " OG BSER A 134 " =    2.948
peak=    3.181 closest distance to " O   HOH Z 403 " =    1.402
peak=    3.179 closest distance to " NE  ARG A  79 " =    1.239
peak=    3.175 closest distance to " CB  SER A 245 " =    3.222
peak=    3.174 closest distance to " O   HOH Z 135 " =    1.843
peak=    3.171 closest distance to " O   HOH Z   3 " =    1.760
peak=    3.165 closest distance to " CB  ALA A   1 " =    4.815
peak=    3.165 closest distance to " O   HOH Z 419 " =    1.795
peak=    3.165 closest distance to " O   HOH Z 251 " =    1.549
peak=    3.163 closest distance to " O   HOH Z  20 " =    1.575
peak=    3.162 closest distance to " CB  MET A  47 " =    1.155
peak=    3.161 closest distance to " CB  VAL A 268 " =    0.851
peak=    3.156 closest distance to " CG  ARG A 159 " =    1.006
peak=    3.156 closest distance to " CG2 VAL A 197 " =    1.027
peak=    3.156 closest distance to " CD  LYS A 119 " =    1.585
peak=    3.144 closest distance to " CZ3 TRP A 274 " =    4.658
peak=    3.143 closest distance to " O   HOH Z 302 " =    1.938
peak=    3.143 closest distance to " CA  ASP A 140 " =    1.260
peak=    3.141 closest distance to " CB  TYR A 116 " =    0.836
peak=    3.134 closest distance to " O   HOH Z  89 " =    1.788
peak=    3.131 closest distance to " OH  TYR A 214 " =    1.206
peak=    3.128 closest distance to " CD1 LEU A 261 " =    1.247
peak=    3.126 closest distance to " ND2 ASN A 110 " =    1.630
peak=    3.125 closest distance to " O   HOH Z 325 " =    2.279
peak=    3.119 closest distance to " CA  ALA A 248 " =    1.190
peak=    3.116 closest distance to " O   HOH Z 128 " =    1.802
peak=    3.116 closest distance to " O   HOH Z 156 " =    3.420
peak=    3.108 closest distance to " CB  LYS A 193 " =    1.049
peak=    3.095 closest distance to " N   ASN A 127 " =    1.228
peak=    3.092 closest distance to " OG  SER A  62 " =    2.919
peak=    3.089 closest distance to " O   HOH Z 345 " =    3.410
peak=    3.083 closest distance to " O   HOH Z 383 " =    2.086
peak=    3.083 closest distance to " OE2 GLU A  53 " =    2.013
peak=    3.073 closest distance to " CA  ASP A 191 " =    0.853
peak=    3.063 closest distance to " CA  GLY A 211 " =    1.330
peak=    3.060 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.058 closest distance to " CA  LYS A 290 " =    1.215
peak=    3.056 closest distance to " O   HOH Z  61 " =    1.598
peak=    3.053 closest distance to " CZ3 TRP A  85 " =    1.003
peak=    3.052 closest distance to " C   ALA A 299 " =    0.961
peak=    3.049 closest distance to " O   HOH Z 293 " =    1.779
peak=    3.044 closest distance to " CB  PHE A 204 " =    0.774
peak=    3.043 closest distance to " C   ASN A  39 " =    1.027
peak=    3.041 closest distance to " O   HOH Z 271 " =    2.391
peak=    3.031 closest distance to " CB  ALA A 100 " =    1.229
peak=    3.029 closest distance to " OG  SER A 206 " =    1.204
peak=    3.011 closest distance to " CB  ILE A  20 " =    1.384

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.523 - 5.496
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 209
   mapped sites are within: 0.766 - 5.496

peak=   -5.511 closest distance to " CG2 VAL A 230 " =    0.766
peak=   -4.484 closest distance to " CB  PRO A 243 " =    2.662
peak=   -4.469 closest distance to " CD  ARG A 156 " =    2.031
peak=   -4.386 closest distance to " CD  ARG A  14 " =    3.386
peak=   -4.113 closest distance to " O   HOH Z 266 " =    5.277
peak=   -4.108 closest distance to " CD  GLN A  58 " =    1.026
peak=   -4.088 closest distance to " CZ3 TRP A 179 " =    1.182
peak=   -4.065 closest distance to " CG  GLN A 223 " =    2.070
peak=   -4.043 closest distance to " O   ILE A 109 " =    2.593
peak=   -3.984 closest distance to " C   HIS A 108 " =    1.187
peak=   -3.983 closest distance to " OG BSER A 134 " =    1.206
peak=   -3.937 closest distance to " O   HOH Z 351 " =    1.517
peak=   -3.905 closest distance to " O   HOH Z 114 " =    3.113
peak=   -3.900 closest distance to " O   VAL A  67 " =    2.674
peak=   -3.884 closest distance to " CG  ASP A 231 " =    0.776
peak=   -3.884 closest distance to " CG1 VAL A 112 " =    2.644
peak=   -3.865 closest distance to " CG2 VAL A 296 " =    1.266
peak=   -3.826 closest distance to " O   HOH Z 435 " =    2.808
peak=   -3.819 closest distance to " CE2 TYR A  30 " =    2.780
peak=   -3.817 closest distance to " CD2 LEU A 300 " =    2.804
peak=   -3.799 closest distance to " O   HOH Z 196 " =    2.142
peak=   -3.792 closest distance to " CG1 VAL A 250 " =    2.779
peak=   -3.788 closest distance to " OG  SER A  97 " =    2.315
peak=   -3.771 closest distance to " O   HOH Z 185 " =    2.357
peak=   -3.766 closest distance to " O   HOH Z 231 " =    2.021
peak=   -3.753 closest distance to " O   HOH Z 290 " =    1.244
peak=   -3.750 closest distance to " NH2AARG A 275 " =    5.301
peak=   -3.729 closest distance to " CB  PHE A 192 " =    1.957
peak=   -3.725 closest distance to " O   HOH Z  11 " =    1.928
peak=   -3.718 closest distance to " CA  GLY A 241 " =    3.137
peak=   -3.715 closest distance to " O   VAL A 189 " =    2.621
peak=   -3.715 closest distance to " O   VAL A  67 " =    2.718
peak=   -3.682 closest distance to " ND2 ASN A  45 " =    1.145
peak=   -3.680 closest distance to " OXT GLY A 302 " =    2.946
peak=   -3.663 closest distance to " O   HOH Z  52 " =    1.537
peak=   -3.661 closest distance to " O   PRO A 163 " =    2.141
peak=   -3.658 closest distance to " N   THR A 157 " =    1.503
peak=   -3.653 closest distance to " CG1 VAL A 296 " =    1.392
peak=   -3.645 closest distance to " OD1 ASN A 148 " =    1.495
peak=   -3.637 closest distance to " O   HOH Z 166 " =    2.052
peak=   -3.634 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.631 closest distance to " CB  ALA A 248 " =    2.125
peak=   -3.626 closest distance to " O   HOH Z 389 " =    1.992
peak=   -3.625 closest distance to " C   ALA A 158 " =    1.340
peak=   -3.624 closest distance to " N   ALA A  43 " =    2.475
peak=   -3.621 closest distance to " O   HOH Z  73 " =    2.158
peak=   -3.619 closest distance to " N   ASP A 171 " =    2.355
peak=   -3.618 closest distance to " N   ALA A 226 " =    2.132
peak=   -3.613 closest distance to " O   HOH Z 394 " =    1.517
peak=   -3.611 closest distance to " CB  ALA A  43 " =    2.563
peak=   -3.608 closest distance to " CE  MET A 105 " =    2.195
peak=   -3.607 closest distance to " O   HOH Z 426 " =    1.658
peak=   -3.599 closest distance to " O   HOH Z 198 " =    2.436
peak=   -3.596 closest distance to " OG  SER A  87 " =    1.462
peak=   -3.596 closest distance to " C   MET A 188 " =    1.336
peak=   -3.596 closest distance to " C   ILE A 239 " =    2.131
peak=   -3.590 closest distance to " CG2 ILE A 263 " =    2.400
peak=   -3.582 closest distance to " O   HOH Z  44 " =    2.252
peak=   -3.577 closest distance to " CB  ALA A 248 " =    2.415
peak=   -3.574 closest distance to " ND2 ASN A  45 " =    1.881
peak=   -3.571 closest distance to " O   PRO A 198 " =    1.228
peak=   -3.570 closest distance to " CD1 LEU A 228 " =    2.302
peak=   -3.558 closest distance to " CE3 TRP A 150 " =    2.047
peak=   -3.555 closest distance to " CB  PRO A 163 " =    2.553
peak=   -3.535 closest distance to " CA  GLY A 241 " =    2.340
peak=   -3.535 closest distance to " CG1 VAL A 197 " =    2.245
peak=   -3.533 closest distance to " CD1 LEU A 101 " =    2.424
peak=   -3.530 closest distance to " CG1 VAL A 112 " =    2.937
peak=   -3.529 closest distance to " O   HOH Z 211 " =    1.617
peak=   -3.514 closest distance to " O   HOH Z 407 " =    3.140
peak=   -3.506 closest distance to " CG  TRP A 266 " =    1.817
peak=   -3.490 closest distance to " CE2 PHE A 218 " =    2.565
peak=   -3.485 closest distance to " CB  ALA A 291 " =    2.179
peak=   -3.483 closest distance to " O   HOH Z 241 " =    1.268
peak=   -3.481 closest distance to " CD1 LEU A 101 " =    2.906
peak=   -3.476 closest distance to " NE2 GLN A  88 " =    1.955
peak=   -3.476 closest distance to " O   HOH Z 353 " =    2.116
peak=   -3.472 closest distance to " NH2 ARG A  79 " =    1.994
peak=   -3.466 closest distance to " OG BSER A 134 " =    1.784
peak=   -3.464 closest distance to " O   HOH Z 359 " =    3.228
peak=   -3.464 closest distance to " CE BMET A  47 " =    1.733
peak=   -3.448 closest distance to " CD2 TYR A 293 " =    2.082
peak=   -3.444 closest distance to " CB  ALA A 291 " =    2.262
peak=   -3.435 closest distance to " O   HOH Z 103 " =    1.842
peak=   -3.434 closest distance to " CD  ARG A 139 " =    1.647
peak=   -3.425 closest distance to " N   GLN A  58 " =    1.665
peak=   -3.424 closest distance to " CG  HIS A  86 " =    1.075
peak=   -3.420 closest distance to " CA  ASP A  27 " =    2.476
peak=   -3.416 closest distance to " O   GLY A  17 " =    1.341
peak=   -3.410 closest distance to " ND2 ASN A 249 " =    2.414
peak=   -3.404 closest distance to " CB  ASP A 132 " =    2.306
peak=   -3.404 closest distance to " CD2 LEU A 167 " =    1.880
peak=   -3.401 closest distance to " O   HOH Z  60 " =    2.204
peak=   -3.397 closest distance to " O   HOH Z 417 " =    2.882
peak=   -3.394 closest distance to " C   LEU A 222 " =    0.820
peak=   -3.394 closest distance to " CB  ASN A  69 " =    1.232
peak=   -3.390 closest distance to " NH2 ARG A 159 " =    2.360
peak=   -3.385 closest distance to " OH  TYR A 247 " =    2.106
peak=   -3.383 closest distance to " O   HOH Z  38 " =    1.558
peak=   -3.382 closest distance to " CB  ASP A 132 " =    2.355
peak=   -3.379 closest distance to " CB  VAL A 230 " =    1.038
peak=   -3.371 closest distance to " CD1 ILE A 239 " =    2.125
peak=   -3.365 closest distance to " OD1 ASN A 187 " =    1.605
peak=   -3.365 closest distance to " C   LEU A 143 " =    1.125
peak=   -3.364 closest distance to " OG  SER A  62 " =    1.714
peak=   -3.359 closest distance to " O   HOH Z  43 " =    1.783
peak=   -3.352 closest distance to " O   HOH Z 102 " =    1.668
peak=   -3.347 closest distance to " N   THR A 235 " =    1.310
peak=   -3.344 closest distance to " O   HOH Z 313 " =    1.095
peak=   -3.343 closest distance to " CD  LYS A 289 " =    2.521
peak=   -3.339 closest distance to " NE2 GLN A 194 " =    1.792
peak=   -3.337 closest distance to " O   MET A  40 " =    2.780
peak=   -3.337 closest distance to " CZ  TYR A 169 " =    1.674
peak=   -3.334 closest distance to " O   GLY A  80 " =    2.528
peak=   -3.332 closest distance to " CG  PHE A 283 " =    2.756
peak=   -3.332 closest distance to " CA  GLY A  98 " =    1.960
peak=   -3.329 closest distance to " O   HOH Z 191 " =    5.496
peak=   -3.322 closest distance to " CA  GLY A 203 " =    2.420
peak=   -3.318 closest distance to " O   GLY A 196 " =    1.240
peak=   -3.307 closest distance to " CD2 LEU A 237 " =    2.837
peak=   -3.294 closest distance to " NH2 ARG A  79 " =    1.603
peak=   -3.289 closest distance to " CB  VAL A 296 " =    1.152
peak=   -3.284 closest distance to " O   HOH Z 140 " =    1.785
peak=   -3.284 closest distance to " O   HOH Z 134 " =    2.827
peak=   -3.282 closest distance to " NZ  LYS A 119 " =    3.546
peak=   -3.281 closest distance to " CG  ARG A 269 " =    2.544
peak=   -3.279 closest distance to " O   HOH Z 222 " =    1.478
peak=   -3.276 closest distance to " CG  GLU A 277 " =    1.172
peak=   -3.270 closest distance to " CD2 PHE A  61 " =    2.478
peak=   -3.264 closest distance to " O   HOH Z 310 " =    1.919
peak=   -3.264 closest distance to " ND2 ASN A  60 " =    1.348
peak=   -3.259 closest distance to " O   HOH Z 166 " =    1.559
peak=   -3.258 closest distance to " N   ALA A 248 " =    2.462
peak=   -3.256 closest distance to " O   HOH Z 262 " =    2.905
peak=   -3.254 closest distance to " NE2 GLN A 278 " =    1.934
peak=   -3.251 closest distance to " CD1 TYR A 247 " =    2.374
peak=   -3.249 closest distance to " N   SER A 212 " =    1.922
peak=   -3.242 closest distance to " OG  SER A 206 " =    1.778
peak=   -3.242 closest distance to " O   HOH Z 275 " =    1.508
peak=   -3.242 closest distance to " N   ALA A 248 " =    1.837
peak=   -3.241 closest distance to " O   SER A 271 " =    2.246
peak=   -3.238 closest distance to " O   HOH Z  13 " =    1.497
peak=   -3.238 closest distance to " O   GLY A 211 " =    1.392
peak=   -3.232 closest distance to " O   HOH Z 176 " =    0.832
peak=   -3.227 closest distance to " O   SER A  22 " =    2.274
peak=   -3.227 closest distance to " O   HOH Z 174 " =    2.518
peak=   -3.226 closest distance to " O   HOH Z 311 " =    3.783
peak=   -3.225 closest distance to " O   HOH Z  10 " =    1.479
peak=   -3.222 closest distance to " O   PRO A 198 " =    1.348
peak=   -3.219 closest distance to " C   ASP A 231 " =    2.556
peak=   -3.218 closest distance to " OD1 ASP A 171 " =    1.610
peak=   -3.218 closest distance to " C   PHE A  59 " =    1.340
peak=   -3.215 closest distance to " O   HOH Z 326 " =    5.145
peak=   -3.214 closest distance to " CA  GLY A 133 " =    2.306
peak=   -3.213 closest distance to " CD1 PHE A  59 " =    1.996
peak=   -3.205 closest distance to " NE2 GLN A 103 " =    1.768
peak=   -3.200 closest distance to " O   HOH Z 396 " =    1.922
peak=   -3.189 closest distance to " O   LYS A 117 " =    1.810
peak=   -3.188 closest distance to " CD1 TYR A 247 " =    2.647
peak=   -3.188 closest distance to " O   HOH Z 175 " =    4.294
peak=   -3.188 closest distance to " CD1 ILE A 151 " =    2.414
peak=   -3.181 closest distance to " O   HOH Z 350 " =    1.898
peak=   -3.179 closest distance to " CG1 VAL A 230 " =    1.958
peak=   -3.175 closest distance to " N   MET A 188 " =    1.859
peak=   -3.175 closest distance to " N   PHE A  59 " =    2.092
peak=   -3.173 closest distance to " CG  LEU A 228 " =    0.971
peak=   -3.172 closest distance to " ND2 ASN A 187 " =    1.536
peak=   -3.163 closest distance to " O   HOH Z  47 " =    1.653
peak=   -3.162 closest distance to " O   HOH Z 252 " =    4.002
peak=   -3.161 closest distance to " O   HOH Z 369 " =    2.251
peak=   -3.160 closest distance to " O   HOH Z 256 " =    1.320
peak=   -3.160 closest distance to " O   HOH Z  51 " =    1.329
peak=   -3.158 closest distance to " N   SER A 276 " =    1.396
peak=   -3.157 closest distance to " CB  ASP A 171 " =    2.267
peak=   -3.156 closest distance to " N   SER A   3 " =    1.963
peak=   -3.153 closest distance to " CD1 ILE A 199 " =    2.578
peak=   -3.153 closest distance to " OD2 ASP A  50 " =    2.314
peak=   -3.152 closest distance to " CD  PRO A 213 " =    2.162
peak=   -3.151 closest distance to " OH  TYR A 214 " =    1.211
peak=   -3.149 closest distance to " CG2 THR A 178 " =    2.271
peak=   -3.148 closest distance to " O   HOH Z 436 " =    1.632
peak=   -3.146 closest distance to " CD2 TYR A 247 " =    2.318
peak=   -3.144 closest distance to " O   HOH Z 298 " =    2.835
peak=   -3.142 closest distance to " NH2BARG A 275 " =    1.783
peak=   -3.138 closest distance to " C   LYS A  76 " =    1.594
peak=   -3.138 closest distance to " O   HOH Z 123 " =    2.478
peak=   -3.136 closest distance to " O   HOH Z 313 " =    1.629
peak=   -3.130 closest distance to " CG1 VAL A  67 " =    2.963
peak=   -3.129 closest distance to " O   LYS A 289 " =    3.029
peak=   -3.124 closest distance to " O   HOH Z 390 " =    2.337
peak=   -3.119 closest distance to " O   HOH Z  41 " =    2.301
peak=   -3.117 closest distance to " O   HOH Z  90 " =    1.609
peak=   -3.104 closest distance to " OG ASER A 134 " =    1.343
peak=   -3.100 closest distance to " CB  TRP A  85 " =    2.515
peak=   -3.099 closest distance to " OE1 GLN A  88 " =    0.931
peak=   -3.097 closest distance to " CD  PRO A 243 " =    2.184
peak=   -3.088 closest distance to " O   VAL A 125 " =    2.355
peak=   -3.074 closest distance to " O   HOH Z 244 " =    1.951
peak=   -3.072 closest distance to " CD  GLN A  88 " =    0.820
peak=   -3.063 closest distance to " CD2 LEU A 300 " =    2.876
peak=   -3.063 closest distance to " CG2 VAL A 189 " =    2.018
peak=   -3.051 closest distance to " CB  TYR A  15 " =    2.198
peak=   -3.050 closest distance to " O   HOH Z 139 " =    3.032
peak=   -3.018 closest distance to " O   HOH Z   6 " =    1.707
peak=   -3.015 closest distance to " O   HOH Z 193 " =    2.067
peak=   -2.959 closest distance to " CG2 ILE A  20 " =    2.606

================= 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    :  0.4171 0.4021   6.203511e+00   6.173634e+00
   1_bss:  0.4101 0.3879   6.199262e+00   6.159360e+00
   1_xyz:  0.2948 0.3131   5.952769e+00   6.002289e+00
   1_adp:  0.2219 0.2515   5.700929e+00   5.822855e+00
   1_occ:  0.2213 0.2516   5.699352e+00   5.823934e+00
   2_bss:  0.2152 0.2452   5.695591e+00   5.817464e+00
   2_xyz:  0.1532 0.1914   5.391525e+00   5.569850e+00
   2_adp:  0.1420 0.1821   5.329641e+00   5.521383e+00
   2_occ:  0.1420 0.1822   5.329349e+00   5.521566e+00
   3_bss:  0.1420 0.1821   5.330979e+00   5.522485e+00
   3_xyz:  0.1241 0.1656   5.219355e+00   5.439344e+00
   3_adp:  0.1192 0.1637   5.195522e+00   5.429041e+00
   3_occ:  0.1191 0.1637   5.195308e+00   5.428976e+00
   4_bss:  0.1191 0.1637   5.195015e+00   5.428822e+00
   4_xyz:  0.1124 0.1611   5.160303e+00   5.412522e+00
   4_adp:  0.1128 0.1589   5.155034e+00   5.400254e+00
   4_occ:  0.1127 0.1589   5.154723e+00   5.400256e+00
   5_bss:  0.1130 0.1586   5.154751e+00   5.398814e+00
   5_xyz:  0.1116 0.1583   5.148135e+00   5.396567e+00
   5_adp:  0.1116 0.1582   5.147583e+00   5.395218e+00
   5_occ:  0.1115 0.1582   5.147098e+00   5.395096e+00
   5_bss:  0.1115 0.1582   5.147143e+00   5.395146e+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:  0.335  20.001   8.124   7.929   8.707   0.000   0.000   0.000
   1_xyz:  0.335  20.001   8.124   7.929   8.707   0.000   0.000   0.000
   1_adp:  0.335  20.001   8.124   7.929   8.707   0.000   0.000   0.000
   1_occ:  0.335  20.001   8.124   7.929   8.707   0.000   0.000   0.000
   2_bss:  0.340  48.768   4.673   4.332   5.411   0.000   0.000   0.000
   2_xyz:  0.340  48.768   4.673   4.332   5.411   0.000   0.000   0.000
   2_adp:  0.340  48.768   4.673   4.332   5.411   0.000   0.000   0.000
   2_occ:  0.340  48.768   4.673   4.332   5.411   0.000   0.000   0.000
   3_bss:  0.329  48.768   3.677   3.635   4.799   0.000   0.000   0.000
   3_xyz:  0.329  48.768   3.677   3.635   4.799   0.000   0.000   0.000
   3_adp:  0.329  48.768   3.677   3.635   4.799   0.000   0.000   0.000
   3_occ:  0.329  48.768   3.677   3.635   4.799   0.000   0.000   0.000
   4_bss:  0.321  48.768   3.557   3.595   4.744   0.000   0.000   0.000
   4_xyz:  0.321  48.768   3.557   3.595   4.744   0.000   0.000   0.000
   4_adp:  0.321  48.768   3.557   3.595   4.744   0.000   0.000   0.000
   4_occ:  0.321  48.768   3.557   3.595   4.744   0.000   0.000   0.000
   5_bss:  0.324  48.768   3.557   3.595   4.744   0.000   0.000   0.000
   5_xyz:  0.324  48.768   3.557   3.595   4.744   0.000   0.000   0.000
   5_adp:  0.324  48.768   3.557   3.595   4.744   0.000   0.000   0.000
   5_occ:  0.324  48.768   3.557   3.595   4.744   0.000   0.000   0.000
   5_bss:  0.323  51.588  -0.409  -0.370   0.779   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.945 0.5969  0.6543    45885.418
   1_bss:  43.585 0.5997  0.8432    43671.470
   1_xyz:  33.522 0.7176  0.9764    26919.154
   1_adp:  24.755 0.8152  1.0614    16385.020
   1_occ:  24.779 0.8149  1.0608    16401.119
   2_bss:  24.514 0.8176  0.9389    16086.570
   2_xyz:  17.904 0.8816  0.9884     9155.751
   2_adp:  16.613 0.8937  0.9976     8327.638
   2_occ:  16.623 0.8936  0.9974     8323.512
   3_bss:  16.651 0.8933  0.9688     8360.525
   3_xyz:  14.920 0.9078  0.9757     7043.612
   3_adp:  14.704 0.9097  0.9752     6869.139
   3_occ:  14.702 0.9097  0.9752     6867.003
   4_bss:  14.697 0.9097  0.9725     6861.609
   4_xyz:  14.361 0.9124  0.9740     6645.486
   4_adp:  14.088 0.9147  0.9741     6491.507
   4_occ:  14.090 0.9146  0.9741     6490.485
   5_bss:  14.083 0.9146  0.9733     6456.514
   5_xyz:  14.014 0.9152  0.9730     6413.954
   5_adp:  13.978 0.9156  0.9708     6395.181
   5_occ:  13.977 0.9156  0.9706     6391.035
   5_bss:  13.977 0.9156  0.9706     6391.063
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4067e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4067e+01
   1_xyz:   1.444  0.011  0.098 17.945  0.005  4.125   1.0966e-01
   1_adp:   1.444  0.011  0.098 17.945  0.005  4.125   1.0966e-01
   1_occ:   1.444  0.011  0.098 17.945  0.005  4.125   1.0966e-01
   2_bss:   1.444  0.011  0.098 17.945  0.005  4.125   1.0966e-01
   2_xyz:   0.963  0.007  0.072 16.366  0.004  4.125   6.0171e-02
   2_adp:   0.963  0.007  0.072 16.366  0.004  4.125   6.0171e-02
   2_occ:   0.963  0.007  0.072 16.366  0.004  4.125   6.0171e-02
   3_bss:   0.963  0.007  0.072 16.366  0.004  4.125   6.0171e-02
   3_xyz:   1.017  0.007  0.082 16.168  0.003  4.135   6.3897e-02
   3_adp:   1.017  0.007  0.082 16.168  0.003  4.135   6.3897e-02
   3_occ:   1.017  0.007  0.082 16.168  0.003  4.135   6.3897e-02
   4_bss:   1.017  0.007  0.082 16.168  0.003  4.135   6.3897e-02
   4_xyz:   1.075  0.009  0.089 15.951  0.004  4.140   7.1853e-02
   4_adp:   1.075  0.009  0.089 15.951  0.004  4.140   7.1853e-02
   4_occ:   1.075  0.009  0.089 15.951  0.004  4.140   7.1853e-02
   5_bss:   1.075  0.009  0.089 15.951  0.004  4.140   7.1853e-02
   5_xyz:   1.054  0.009  0.087 15.751  0.004  4.143   6.9379e-02
   5_adp:   1.054  0.009  0.087 15.751  0.004  4.143   6.9379e-02
   5_occ:   1.054  0.009  0.087 15.751  0.004  4.143   6.9379e-02
   5_bss:   1.054  0.009  0.087 15.751  0.004  4.143   6.9379e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0108e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0108e+00
   1_xyz:  11.510  0.126  0.390 87.900  0.037  2.291   8.1154e-02
   1_adp:  11.510  0.126  0.390 87.900  0.037  2.291   8.1154e-02
   1_occ:  11.510  0.126  0.390 87.900  0.037  2.291   8.1154e-02
   2_bss:  11.510  0.126  0.390 87.900  0.037  2.291   8.1154e-02
   2_xyz:   6.740  0.057  0.321 85.262  0.037  2.387   4.4135e-02
   2_adp:   6.740  0.057  0.321 85.262  0.037  2.387   4.4135e-02
   2_occ:   6.740  0.057  0.321 85.262  0.037  2.387   4.4135e-02
   3_bss:   6.740  0.057  0.321 85.262  0.037  2.387   4.4135e-02
   3_xyz:   8.738  0.056  0.495 82.512  0.037  2.364   3.7691e-02
   3_adp:   8.738  0.056  0.495 82.512  0.037  2.364   3.7691e-02
   3_occ:   8.738  0.056  0.495 82.512  0.037  2.364   3.7691e-02
   4_bss:   8.738  0.056  0.495 82.512  0.037  2.364   3.7691e-02
   4_xyz:   7.481  0.042  0.627 83.329  0.038  2.317   5.0490e-02
   4_adp:   7.481  0.042  0.627 83.329  0.038  2.317   5.0490e-02
   4_occ:   7.481  0.042  0.627 83.329  0.038  2.317   5.0490e-02
   5_bss:   7.481  0.042  0.627 83.329  0.038  2.317   5.0490e-02
   5_xyz:   7.259  0.048  0.594 83.062  0.040  2.306   4.7202e-02
   5_adp:   7.259  0.048  0.594 83.062  0.040  2.306   4.7202e-02
   5_occ:   7.259  0.048  0.594 83.062  0.040  2.306   4.7202e-02
   5_bss:   7.259  0.048  0.594 83.062  0.040  2.306   4.7202e-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:  58.26   0.00  10.19  58.26   0.00   6.98  57.89   0.00  27.68
   1_occ:  58.26   0.00  10.19  58.26   0.00   6.98  57.89   0.00  27.68
   2_bss:  58.26   0.00  10.19  58.26   0.00   6.98  57.89   0.00  27.68
   2_xyz:  58.26   0.00  10.19  58.26   0.00   6.98  57.89   0.00  27.68
   2_adp:  58.79   0.00  10.55  57.45   0.00   6.93  58.79   0.00  30.24
   2_occ:  58.79   0.00  10.55  57.45   0.00   6.93  58.79   0.00  30.24
   3_bss:  58.79   0.00  10.55  57.45   0.00   6.93  58.79   0.00  30.24
   3_xyz:  58.79   0.00  10.55  57.45   0.00   6.93  58.79   0.00  30.24
   3_adp:  76.46   0.00  11.60  73.27   0.00   7.25  76.46   0.00  35.24
   3_occ:  76.46   0.00  11.60  73.27   0.00   7.25  76.46   0.00  35.24
   4_bss:  76.46   0.00  11.60  73.27   0.00   7.25  76.46   0.00  35.24
   4_xyz:  76.46   0.00  11.60  73.27   0.00   7.25  76.46   0.00  35.24
   4_adp:  75.09   0.00  11.09  75.09   0.00   7.06  72.95   0.54  33.03
   4_occ:  75.09   0.00  11.09  75.09   0.00   7.06  72.95   0.54  33.03
   5_bss:  75.09   0.00  11.09  75.09   0.00   7.06  72.95   0.54  33.03
   5_xyz:  75.09   0.00  11.09  75.09   0.00   7.06  72.95   0.54  33.03
   5_adp:  75.59   0.00  11.01  75.59   0.00   7.01  72.40   0.70  32.76
   5_occ:  75.59   0.00  11.01  75.59   0.00   7.01  72.40   0.70  32.76
   5_bss:  79.55   3.97  14.97  79.55   3.97  10.98  76.37   4.66  36.72
------------------------------------------------------------------------
 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:    1.173    0.010    0.397
   1_adp:    1.173    0.010    0.397
   1_occ:    1.173    0.010    0.397
   2_bss:    1.173    0.010    0.397
   2_xyz:    1.457    0.021    0.469
   2_adp:    1.457    0.021    0.469
   2_occ:    1.457    0.021    0.469
   3_bss:    1.457    0.021    0.469
   3_xyz:    1.452    0.025    0.495
   3_adp:    1.452    0.025    0.495
   3_occ:    1.452    0.025    0.495
   4_bss:    1.452    0.025    0.495
   4_xyz:    1.504    0.029    0.510
   4_adp:    1.504    0.029    0.510
   4_occ:    1.504    0.029    0.510
   5_bss:    1.504    0.029    0.510
   5_xyz:    1.469    0.041    0.521
   5_adp:    1.469    0.041    0.521
   5_occ:    1.469    0.041    0.521
   5_bss:    1.469    0.041    0.521
------------------------------------------------------------------------

CPU time actual refinement: 327.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_908/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_908/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_908/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_908/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_908/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.43 
  Macro-tasks:
    bulk solvent and scale       = 42.90  
    individual site refinement   = 134.30 
    weights calculation          = 31.85  
    collect and process          = 6.62   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 215.82 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 98.34  
    alpha_beta                      = 8.25   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 110.10 
    fmodel                         = 7.51   
    r_factors                      = 0.23   
    phase_errors                   = 11.03  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 238.65 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.580 micro seconds
Total CPU time: 5.68 minutes
from_scatterers_fft:    647 calls, 97.99 s
gradients_fft:          592 calls, 96.42 s

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

# Date 2008-01-16 Time 02:43:27 PST -0800 (1200480207.46 s)
Start R-work = 0.4171, R-free = 0.4021 (no bulk solvent and anisotropic scale)
Final R-work = 0.1288, R-free = 0.1742 (no bulk solvent and anisotropic scale)

Start R-work = 0.4101, R-free = 0.3879
Final R-work = 0.1115, R-free = 0.1582