# Date 2008-01-16 Time 02:21:48 PST -0800 (1200478908.01 s)
#phil __OFF__

Command line arguments: "../799.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18778
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 799

-------------------------------------------------------------------------------
  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: (70.6012, 47.1647, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0892
                             d_min =   2.0101

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: (70.6012, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0896 -  4.3003 [2096/2119]  1886   210  10.0%
  bin  2:  4.3003 -  3.4264 [2023/2043]  1821   202  10.0%
  bin  3:  3.4264 -  2.9972 [1990/2009]  1792   198   9.9%
  bin  4:  2.9972 -  2.7249 [1953/1983]  1757   196  10.0%
  bin  5:  2.7249 -  2.5306 [1970/1989]  1773   197  10.0%
  bin  6:  2.5306 -  2.3820 [1951/1976]  1754   197  10.1%
  bin  7:  2.3820 -  2.2631 [1925/1953]  1733   192  10.0%
  bin  8:  2.2631 -  2.1649 [1935/1971]  1741   194  10.0%
  bin  9:  2.1649 -  2.0818 [1920/1962]  1730   190   9.9%
  bin 10:  2.0818 -  2.0101 [1826/1956]  1643   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_799/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 12
        2.42 -     3.04: 2172
        3.04 -     3.66: 4594
        3.66 -     4.28: 8946
        4.28 -     4.90: 12272
  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 "  2.094 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.135 3.040 -x+1,y+1/2,-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
  ... (remaining 27991 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_799/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_799/model_refine_001.geo

CPU time processing inputs: 9.68


============================ 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 = 70.60125 47.16465 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4286   r_free= 0.4121   ksol= 0.00   Bsol= 0.00   scale= 0.818    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.219268                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7960 0.99   1371  152 0.3582 0.3319       6.522      6.4079|
|  2:  4.7960 -  3.8271 0.99   1299  146 0.3163 0.3295      6.6157      6.6915|
|  3:  3.8271 -  3.3494 0.99   1286  141 0.3709 0.3484      6.5585      6.5422|
|  4:  3.3494 -  3.0459 0.99   1280  142 0.4052 0.3648      6.4502      6.3527|
|  5:  3.0459 -  2.8291 0.99   1261  141 0.4394 0.4258      6.3076      6.3065|
|  6:  2.8291 -  2.6633 0.99   1268  141 0.4511 0.4780      6.2331      6.1988|
|  7:  2.6633 -  2.5306 0.99   1264  140 0.4762 0.4674      6.2009      6.1664|
|  8:  2.5306 -  2.4209 0.98   1249  137 0.4800 0.4377      6.1619      6.1147|
|  9:  2.4209 -  2.3280 0.98   1241  141 0.4783 0.4580      6.0843        6.08|
| 10:  2.3280 -  2.2480 1.00   1243  138 0.4916 0.4651      6.1063      6.0538|
| 11:  2.2480 -  2.1779 0.97   1249  138 0.4817 0.4599      6.0077      6.0199|
| 12:  2.1779 -  2.1158 0.98   1239  139 0.4973 0.4623      5.9767      5.9972|
| 13:  2.1158 -  2.0602 0.99   1248  137 0.4894 0.4899      5.8883      5.8761|
| 14:  2.0602 -  2.0101 0.91   1132  126 0.5031 0.4511      5.8569      5.7044|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7960  1371   152  0.76  29.30   0.81     0.77      52624.15|
|  2:  4.7960 -  3.8271  1299   146  0.79  27.42   0.91     0.82      69321.17|
|  3:  3.8271 -  3.3494  1286   141  0.72  33.36   0.87     0.79      72395.56|
|  4:  3.3494 -  3.0459  1280   142  0.67  38.44   0.84     0.71      65076.83|
|  5:  3.0459 -  2.8291  1261   141  0.58  45.67   0.77     0.64      57947.91|
|  6:  2.8291 -  2.6633  1268   141  0.55  48.20   0.76     0.60      54226.16|
|  7:  2.6633 -  2.5306  1264   140  0.52  50.71   0.75     0.58      50757.66|
|  8:  2.5306 -  2.4209  1249   137  0.51  51.17   0.77     0.58      45820.29|
|  9:  2.4209 -  2.3280  1241   141  0.53  49.90   0.74     0.59      40225.41|
| 10:  2.3280 -  2.2480  1243   138  0.54  49.29   0.76     0.60      36377.83|
| 11:  2.2480 -  2.1779  1249   138  0.51  51.21   0.76     0.58      34329.06|
| 12:  2.1779 -  2.1158  1239   139  0.48  53.56   0.78     0.57      33421.46|
| 13:  2.1158 -  2.0602  1248   137  0.49  52.82   0.75     0.56      28769.79|
| 14:  2.0602 -  2.0101  1132   126  0.55  48.39   0.73     0.58      21269.92|
|alpha:            min =        0.56 max =            0.82 mean =         0.64|
|beta:             min =    21269.92 max =        72395.56 mean =     47715.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.98 mean =        44.74|
|phase err.(test): min =        0.00 max =           89.93 mean =        44.85|
|-----------------------------------------------------------------------------|

============================== 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 = 7.082559              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.612   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.584280              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.530   (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:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1476 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2592 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3875 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5015 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6525 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7651 |
|-----------------------------------------------------------------------------|
|-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 |       54.206 |
| 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 |       1.631 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    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 = 12.142)------------------------------------------|
|    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: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4359   r_free= 0.4110   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.226969                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4200   r_free= 0.3953   ksol= 0.30   Bsol= 20.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.11,8.11,9.49,0.00,0.00,0.00); trace/3= 8.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.215199                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.617783              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.255   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.558126              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.286   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4200      final r-factor (work) = 0.3038          |
| start r-factor (free) = 0.3953      final r-factor (free) = 0.3246          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 74.8389 = 6.62 * 0.50 * 6.2357 + 1.00 * 54.2058                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0943 = 6.62 * 0.50 * 6.0375 + 1.00 * 0.1169                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3038      final r-factor (work) = 0.2388          |
| start r-factor (free) = 0.3246      final r-factor (free) = 0.2702          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3844 = 0.56 * 1.00 * 6.0375 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2705 = 0.56 * 1.00 * 5.8395 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.13   10.45    None  None   None       |
|    all(noH): 2823   0      0.00    73.13   10.45    None  None   None       |
|    Sol.    : 438    0      0.00    73.13   27.85    None  None   None       |
|    Mac.    : 2385   0      0.00    56.15   7.26     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 -   7.313: 1564   |   5:    36.566 -  43.879:   79        |
|      1:     7.313 -  14.627:  648   |   6:    43.879 -  51.193:   51        |
|      2:    14.627 -  21.940:  215   |   7:    51.193 -  58.506:   10        |
|      3:    21.940 -  29.253:  148   |   8:    58.506 -  65.819:    3        |
|      4:    29.253 -  36.566:  104   |   9:    65.819 -  73.132:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2388 r_free = 0.2702             target_work(ml) = 5.761         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2380 r_free = 0.2709             target_work(ml) = 5.759         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2380   r_free= 0.2709   ksol= 0.30   Bsol= 20.00   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.11,8.11,9.49,0.00,0.00,0.00); trace/3= 8.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.758848                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2330   r_free= 0.2646   ksol= 0.32   Bsol= 53.29   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.90,4.73,6.00,0.00,0.00,0.00); trace/3= 4.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.758585                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.273613              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.374   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.296736              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.629  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2330      final r-factor (work) = 0.1516          |
| start r-factor (free) = 0.2646      final r-factor (free) = 0.1888          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6164 = 4.27 * 0.50 * 5.8496 + 1.00 * 0.1169                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9573 = 4.27 * 0.50 * 5.5625 + 1.00 * 0.0713                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1516      final r-factor (work) = 0.1374          |
| start r-factor (free) = 0.1888      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6620 = 0.30 * 1.00 * 5.5625 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5913 = 0.30 * 1.00 * 5.3272 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.51   10.70    None  None   None       |
|    all(noH): 2823   0      0.00    71.51   10.70    None  None   None       |
|    Sol.    : 438    0      0.00    71.51   30.79    None  None   None       |
|    Mac.    : 2385   0      0.00    56.37   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 -   7.151: 1625   |   5:    35.757 -  42.908:  112        |
|      1:     7.151 -  14.303:  583   |   6:    42.908 -  50.060:   65        |
|      2:    14.303 -  21.454:  175   |   7:    50.060 -  57.211:   22        |
|      3:    21.454 -  28.606:  124   |   8:    57.211 -  64.363:    2        |
|      4:    28.606 -  35.757:  114   |   9:    64.363 -  71.514:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1374 r_free = 0.1774             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1374 r_free = 0.1775             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1374   r_free= 0.1775   ksol= 0.32   Bsol= 53.29   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.90,4.73,6.00,0.00,0.00,0.00); trace/3= 4.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.294300                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1772   ksol= 0.33   Bsol= 53.29   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,3.80,4.97,0.00,0.00,0.00); trace/3= 4.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.295302                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.568402              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.322  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.022480              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.303  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1372      final r-factor (work) = 0.1254          |
| start r-factor (free) = 0.1772      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2532 = 1.57 * 0.50 * 5.3325 + 1.00 * 0.0715                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1776 = 1.57 * 0.50 * 5.2528 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1254      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.8870 = 3.02 * 1.00 * 5.2528 + 1.00 * 0.0104                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.7268 = 3.02 * 1.00 * 5.1977 + 1.00 * 0.0170                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.90   11.66    None  None   None       |
|    all(noH): 2823   0      0.00    76.90   11.66    None  None   None       |
|    Sol.    : 438    0      0.00    75.24   35.57    None  None   None       |
|    Mac.    : 2385   0      0.00    76.90   7.27     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 -   7.690: 1680   |   5:    38.449 -  46.139:   73        |
|      1:     7.690 -  15.380:  541   |   6:    46.139 -  53.829:   90        |
|      2:    15.380 -  23.069:  157   |   7:    53.829 -  61.518:   44        |
|      3:    23.069 -  30.759:  109   |   8:    61.518 -  69.208:   28        |
|      4:    30.759 -  38.449:   94   |   9:    69.208 -  76.898:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1208 r_free = 0.1626             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1626             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1626   ksol= 0.33   Bsol= 53.29   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,3.80,4.97,0.00,0.00,0.00); trace/3= 4.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.198340                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1626   ksol= 0.33   Bsol= 53.29   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,3.80,4.97,0.00,0.00,0.00); trace/3= 4.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.198340                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.133399              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.951  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.412354              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.765   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2015 = 3.13 * 0.50 * 5.1976 + 1.00 * 0.0585                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1706 = 3.13 * 0.50 * 5.1634 + 1.00 * 0.0811                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1471 = 0.41 * 1.00 * 5.1634 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1580 = 0.41 * 1.00 * 5.1527 + 1.00 * 0.0332                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.70   11.36    None  None   None       |
|    all(noH): 2823   0      0.00    77.70   11.36    None  None   None       |
|    Sol.    : 438    0      0.51    72.63   34.31    None  None   None       |
|    Mac.    : 2385   0      0.00    77.70   7.14     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 -   7.770: 1723   |   5:    38.848 -  46.617:   86        |
|      1:     7.770 -  15.539:  521   |   6:    46.617 -  54.387:   72        |
|      2:    15.539 -  23.309:  154   |   7:    54.387 -  62.156:   37        |
|      3:    23.309 -  31.078:  105   |   8:    62.156 -  69.926:   20        |
|      4:    31.078 -  38.848:   99   |   9:    69.926 -  77.695:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1578             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1579             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1579   ksol= 0.33   Bsol= 53.29   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,3.80,4.97,0.00,0.00,0.00); trace/3= 4.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146484                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1576   ksol= 0.33   Bsol= 53.29   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.73,4.93,0.00,0.00,0.00); trace/3= 4.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.145947                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.783096              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.865  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.473607              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.954   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6746 = 1.78 * 0.50 * 5.1522 + 1.00 * 0.0811                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6604 = 1.78 * 0.50 * 5.1563 + 1.00 * 0.0633                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4766 = 0.47 * 1.00 * 5.1563 + 1.00 * 0.0345                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4571 = 0.47 * 1.00 * 5.1611 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.76   11.12    None  None   None       |
|    all(noH): 2823   0      0.00    79.76   11.12    None  None   None       |
|    Sol.    : 438    0      0.49    71.80   33.29    None  None   None       |
|    Mac.    : 2385   0      0.00    79.76   7.05     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 -   7.976: 1748   |   5:    39.880 -  47.856:   82        |
|      1:     7.976 -  15.952:  506   |   6:    47.856 -  55.832:   60        |
|      2:    15.952 -  23.928:  161   |   7:    55.832 -  63.808:   27        |
|      3:    23.928 -  31.904:  105   |   8:    63.808 -  71.784:   13        |
|      4:    31.904 -  39.880:  117   |   9:    71.784 -  79.760:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1143 r_free = 0.1585             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1586             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1586   ksol= 0.33   Bsol= 53.29   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.73,4.93,0.00,0.00,0.00); trace/3= 4.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162275                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7960 0.99   1371  152 0.1027 0.1295      5.4032       5.514|
|  2:  4.7960 -  3.8271 0.99   1299  146 0.0871 0.1096      5.4496      5.6336|
|  3:  3.8271 -  3.3494 0.99   1286  141 0.1068 0.1419      5.4887      5.8136|
|  4:  3.3494 -  3.0459 0.99   1280  142 0.1206 0.1601      5.4526      5.6383|
|  5:  3.0459 -  2.8291 0.99   1261  141 0.1334 0.1751      5.3461      5.5374|
|  6:  2.8291 -  2.6633 0.99   1268  141 0.1232 0.1889      5.2348       5.518|
|  7:  2.6633 -  2.5306 0.99   1264  140 0.1307 0.1644       5.199      5.3615|
|  8:  2.5306 -  2.4209 0.98   1249  137 0.1207 0.1823      5.1174      5.4114|
|  9:  2.4209 -  2.3280 0.98   1241  141 0.1203 0.1816      5.0702      5.2985|
| 10:  2.3280 -  2.2480 1.00   1243  138 0.1185 0.1751      5.0162      5.2921|
| 11:  2.2480 -  2.1779 0.97   1249  138 0.1190 0.1670      4.9726      5.2161|
| 12:  2.1779 -  2.1158 0.98   1239  139 0.1177 0.1797      4.9074      5.2791|
| 13:  2.1158 -  2.0602 0.99   1248  137 0.1151 0.1676      4.8213      5.0575|
| 14:  2.0602 -  2.0101 0.91   1132  126 0.1075 0.1829      4.6897      4.9778|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7960  1371   152  0.94   9.27   0.97     0.95       7267.40|
|  2:  4.7960 -  3.8271  1299   146  0.95   7.88   1.01     0.99       8966.91|
|  3:  3.8271 -  3.3494  1286   141  0.94  11.04   1.02     1.01      10383.38|
|  4:  3.3494 -  3.0459  1280   142  0.92  13.01   1.00     0.98       9940.88|
|  5:  3.0459 -  2.8291  1261   141  0.90  15.79   0.99     0.97       8560.36|
|  6:  2.8291 -  2.6633  1268   141  0.90  16.05   0.98     0.95       7274.14|
|  7:  2.6633 -  2.5306  1264   140  0.90  15.86   0.98     0.96       6471.98|
|  8:  2.5306 -  2.4209  1249   137  0.91  15.32   0.99     0.97       5771.72|
|  9:  2.4209 -  2.3280  1241   141  0.90  16.13   1.00     0.96       5439.55|
| 10:  2.3280 -  2.2480  1243   138  0.90  16.07   1.00     0.95       4715.41|
| 11:  2.2480 -  2.1779  1249   138  0.90  16.29   0.99     0.95       4602.72|
| 12:  2.1779 -  2.1158  1239   139  0.91  15.75   1.01     0.99       4065.94|
| 13:  2.1158 -  2.0602  1248   137  0.91  15.58   0.99     0.97       3470.34|
| 14:  2.0602 -  2.0101  1132   126  0.91  14.77   0.97     0.93       2619.23|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2619.23 max =        10383.38 mean =      6454.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.14|
|phase err.(test): min =        0.00 max =           89.90 mean =        13.64|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1586   ksol= 0.33   Bsol= 57.28   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,-0.26,0.93,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162275                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1586   ksol= 0.33   Bsol= 57.28   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,-0.26,0.93,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162275                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7960 0.99   1371  152 0.1027 0.1295      5.4032       5.514|
|  2:  4.7960 -  3.8271 0.99   1299  146 0.0871 0.1096      5.4496      5.6336|
|  3:  3.8271 -  3.3494 0.99   1286  141 0.1068 0.1419      5.4887      5.8136|
|  4:  3.3494 -  3.0459 0.99   1280  142 0.1206 0.1601      5.4526      5.6383|
|  5:  3.0459 -  2.8291 0.99   1261  141 0.1334 0.1751      5.3461      5.5374|
|  6:  2.8291 -  2.6633 0.99   1268  141 0.1232 0.1889      5.2348       5.518|
|  7:  2.6633 -  2.5306 0.99   1264  140 0.1307 0.1644       5.199      5.3615|
|  8:  2.5306 -  2.4209 0.98   1249  137 0.1207 0.1823      5.1174      5.4114|
|  9:  2.4209 -  2.3280 0.98   1241  141 0.1203 0.1816      5.0702      5.2985|
| 10:  2.3280 -  2.2480 1.00   1243  138 0.1185 0.1751      5.0162      5.2921|
| 11:  2.2480 -  2.1779 0.97   1249  138 0.1190 0.1670      4.9726      5.2161|
| 12:  2.1779 -  2.1158 0.98   1239  139 0.1177 0.1797      4.9074      5.2791|
| 13:  2.1158 -  2.0602 0.99   1248  137 0.1151 0.1676      4.8213      5.0575|
| 14:  2.0602 -  2.0101 0.91   1132  126 0.1075 0.1829      4.6897      4.9778|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7960  1371   152  0.94   9.27   0.97     0.95       7267.40|
|  2:  4.7960 -  3.8271  1299   146  0.95   7.88   1.01     0.99       8966.91|
|  3:  3.8271 -  3.3494  1286   141  0.94  11.04   1.02     1.01      10383.38|
|  4:  3.3494 -  3.0459  1280   142  0.92  13.01   1.00     0.98       9940.88|
|  5:  3.0459 -  2.8291  1261   141  0.90  15.79   0.99     0.97       8560.36|
|  6:  2.8291 -  2.6633  1268   141  0.90  16.05   0.98     0.95       7274.14|
|  7:  2.6633 -  2.5306  1264   140  0.90  15.86   0.98     0.96       6471.98|
|  8:  2.5306 -  2.4209  1249   137  0.91  15.32   0.99     0.97       5771.72|
|  9:  2.4209 -  2.3280  1241   141  0.90  16.13   1.00     0.96       5439.55|
| 10:  2.3280 -  2.2480  1243   138  0.90  16.07   1.00     0.95       4715.41|
| 11:  2.2480 -  2.1779  1249   138  0.90  16.29   0.99     0.95       4602.72|
| 12:  2.1779 -  2.1158  1239   139  0.91  15.75   1.01     0.99       4065.94|
| 13:  2.1158 -  2.0602  1248   137  0.91  15.58   0.99     0.97       3470.34|
| 14:  2.0602 -  2.0101  1132   126  0.91  14.77   0.97     0.93       2619.23|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2619.23 max =        10383.38 mean =      6454.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.14|
|phase err.(test): min =        0.00 max =           89.90 mean =        13.64|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      4.00    83.76   15.12    None  None   None       |
|    all(noH): 2823   0      4.00    83.76   15.12    None  None   None       |
|    Sol.    : 438    0      4.49    75.79   37.29    None  None   None       |
|    Mac.    : 2385   0      4.00    83.76   11.04    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:     3.996 -  11.972: 1748   |   5:    43.876 -  51.852:   82        |
|      1:    11.972 -  19.948:  506   |   6:    51.852 -  59.828:   60        |
|      2:    19.948 -  27.924:  161   |   7:    59.828 -  67.804:   27        |
|      3:    27.924 -  35.900:  105   |   8:    67.804 -  75.780:   13        |
|      4:    35.900 -  43.876:  117   |   9:    75.780 -  83.756:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.282 - 4.614
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 324
   mapped sites are within: 0.703 - 4.614

peak=   10.520 closest distance to " CG2 VAL A 230 " =    1.390
peak=    6.335 closest distance to " NH2 ARG A  56 " =    2.287
peak=    6.120 closest distance to " CG  LEU A   5 " =    1.262
peak=    5.695 closest distance to " CG  LEU A 228 " =    1.200
peak=    5.601 closest distance to " CB  GLN A 223 " =    1.451
peak=    5.526 closest distance to " CG2 VAL A 296 " =    1.026
peak=    5.431 closest distance to " CD2 LEU A   5 " =    1.177
peak=    5.234 closest distance to " CB  VAL A 296 " =    1.100
peak=    4.913 closest distance to " CB  VAL A 230 " =    1.228
peak=    4.911 closest distance to " CB  GLN A 183 " =    1.244
peak=    4.844 closest distance to " CG1 VAL A 296 " =    1.165
peak=    4.772 closest distance to " CZ  PHE A 218 " =    1.114
peak=    4.641 closest distance to " NE2 GLN A  11 " =    1.105
peak=    4.638 closest distance to " CG  PRO A 198 " =    1.245
peak=    4.613 closest distance to " O   HOH Z 142 " =    1.682
peak=    4.594 closest distance to " CB  ARG A 275 " =    0.915
peak=    4.557 closest distance to " CG  PRO A 213 " =    1.197
peak=    4.507 closest distance to " O   HOH Z 126 " =    1.935
peak=    4.503 closest distance to " CG  PRO A 243 " =    1.124
peak=    4.472 closest distance to " CB  SER A  63 " =    1.279
peak=    4.438 closest distance to " O   HOH Z 232 " =    2.361
peak=    4.427 closest distance to " O   HOH Z 369 " =    2.124
peak=    4.374 closest distance to " O   HOH Z 272 " =    1.916
peak=    4.355 closest distance to " C   PRO A 198 " =    1.532
peak=    4.352 closest distance to " O   HOH Z 368 " =    2.249
peak=    4.256 closest distance to " O   SER A  87 " =    2.289
peak=    4.250 closest distance to " O   HOH Z 236 " =    1.994
peak=    4.249 closest distance to " O   HOH Z 265 " =    2.304
peak=    4.247 closest distance to " O   HOH Z 427 " =    3.041
peak=    4.237 closest distance to " ND2 ASN A 187 " =    1.475
peak=    4.215 closest distance to " O   HOH Z 298 " =    1.839
peak=    4.192 closest distance to " CB  ASN A 148 " =    1.410
peak=    4.189 closest distance to " CB  ARG A 190 " =    1.588
peak=    4.162 closest distance to " CB  GLU A 128 " =    1.077
peak=    4.142 closest distance to " CB  ASP A 124 " =    0.703
peak=    4.139 closest distance to " O   HOH Z  44 " =    2.225
peak=    4.104 closest distance to " CB  ARG A  79 " =    1.466
peak=    4.097 closest distance to " CA  TYR A  30 " =    0.960
peak=    4.091 closest distance to " O   HOH Z  61 " =    1.667
peak=    4.085 closest distance to " O   HOH Z  43 " =    2.008
peak=    4.073 closest distance to " O   HOH Z 234 " =    3.734
peak=    4.070 closest distance to " O   HOH Z  78 " =    1.657
peak=    4.065 closest distance to " O   HOH Z 189 " =    2.952
peak=    4.040 closest distance to " CB  TRP A 266 " =    0.951
peak=    4.036 closest distance to " CB  ASN A  39 " =    0.895
peak=    4.034 closest distance to " CB  ASP A 140 " =    0.991
peak=    4.027 closest distance to " O   HOH Z 261 " =    1.849
peak=    4.022 closest distance to " N   ASN A  39 " =    1.234
peak=    4.003 closest distance to " O   HOH Z 423 " =    1.772
peak=    3.986 closest distance to " O   HOH Z 316 " =    3.135
peak=    3.983 closest distance to " OD1 ASN A  69 " =    2.596
peak=    3.982 closest distance to " CA  ARG A 195 " =    1.221
peak=    3.960 closest distance to " O   HOH Z 158 " =    3.194
peak=    3.957 closest distance to " CB  GLU A 152 " =    1.160
peak=    3.949 closest distance to " O   HOH Z  63 " =    2.014
peak=    3.949 closest distance to " CB  VAL A 265 " =    1.282
peak=    3.946 closest distance to " CB  VAL A 202 " =    1.584
peak=    3.943 closest distance to " O   HOH Z  40 " =    1.726
peak=    3.928 closest distance to " NH1AARG A 145 " =    1.196
peak=    3.920 closest distance to " O   HOH Z 303 " =    2.106
peak=    3.910 closest distance to " O   HOH Z 402 " =    1.458
peak=    3.903 closest distance to " O   HOH Z  68 " =    2.202
peak=    3.891 closest distance to " O   HOH Z 346 " =    1.595
peak=    3.878 closest distance to " CD2 LEU A 228 " =    1.118
peak=    3.859 closest distance to " O   HOH Z 214 " =    2.153
peak=    3.850 closest distance to " CB  GLU A 277 " =    3.676
peak=    3.849 closest distance to " O   HOH Z 203 " =    1.797
peak=    3.844 closest distance to " CB  ASN A 187 " =    1.306
peak=    3.839 closest distance to " CB  PRO A  54 " =    0.821
peak=    3.824 closest distance to " O   HOH Z 248 " =    1.586
peak=    3.815 closest distance to " CA  ALA A  51 " =    0.949
peak=    3.775 closest distance to " O   HOH Z 128 " =    2.120
peak=    3.772 closest distance to " O   HOH Z 126 " =    1.602
peak=    3.767 closest distance to " CB  ASN A 142 " =    1.090
peak=    3.762 closest distance to " CG2 VAL A 257 " =    0.866
peak=    3.762 closest distance to " O   HOH Z 411 " =    3.816
peak=    3.755 closest distance to " O   HOH Z  19 " =    2.280
peak=    3.755 closest distance to " CD  LYS A 166 " =    1.310
peak=    3.753 closest distance to " CD BLYS A 290 " =    1.042
peak=    3.750 closest distance to " CB  GLU A  46 " =    0.973
peak=    3.745 closest distance to " CB  ALA A   9 " =    1.611
peak=    3.743 closest distance to " CG1 VAL A 153 " =    0.973
peak=    3.739 closest distance to " O   HOH Z 280 " =    2.975
peak=    3.735 closest distance to " CD1 LEU A 300 " =    1.171
peak=    3.732 closest distance to " ND2 ASN A 249 " =    1.892
peak=    3.727 closest distance to " CA  THR A 264 " =    0.764
peak=    3.726 closest distance to " O   HOH Z 193 " =    1.862
peak=    3.702 closest distance to " O   HOH Z  80 " =    1.699
peak=    3.696 closest distance to " O   HOH Z 422 " =    2.726
peak=    3.693 closest distance to " CB  SER A   3 " =    1.275
peak=    3.690 closest distance to " CG1BVAL A  72 " =    1.759
peak=    3.680 closest distance to " OG BSER A 164 " =    2.297
peak=    3.679 closest distance to " O   HOH Z 403 " =    1.592
peak=    3.665 closest distance to " O   HOH Z 285 " =    2.704
peak=    3.662 closest distance to " CG  MET A 185 " =    1.241
peak=    3.657 closest distance to " CD  ARG A 159 " =    0.737
peak=    3.650 closest distance to " CB  THR A  31 " =    1.608
peak=    3.642 closest distance to " O   HOH Z 128 " =    2.159
peak=    3.641 closest distance to " O   HOH Z 403 " =    1.466
peak=    3.639 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.634 closest distance to " O   HOH Z   9 " =    2.212
peak=    3.634 closest distance to " NH2 ARG A 156 " =    1.124
peak=    3.633 closest distance to " CA  ASN A 215 " =    1.168
peak=    3.625 closest distance to " O   HOH Z 273 " =    2.798
peak=    3.622 closest distance to " CE  LYS A  76 " =    0.860
peak=    3.614 closest distance to " O   HOH Z 425 " =    1.376
peak=    3.611 closest distance to " CB  SER A 212 " =    1.197
peak=    3.610 closest distance to " O   HOH Z 172 " =    3.671
peak=    3.609 closest distance to " CZ  PHE A 192 " =    0.975
peak=    3.609 closest distance to " CB  LEU A 143 " =    1.179
peak=    3.594 closest distance to " CD  ARG A  66 " =    2.623
peak=    3.592 closest distance to " CA  ARG A  36 " =    1.084
peak=    3.581 closest distance to " CA  SER A  87 " =    0.999
peak=    3.581 closest distance to " CB  ALA A 291 " =    1.295
peak=    3.568 closest distance to " CG  LEU A 167 " =    1.181
peak=    3.567 closest distance to " CA  ALA A 291 " =    0.868
peak=    3.562 closest distance to " O   HOH Z 313 " =    1.791
peak=    3.554 closest distance to " CA  ALA A 295 " =    1.081
peak=    3.549 closest distance to " O   HOH Z 437 " =    1.775
peak=    3.545 closest distance to " CG1 ILE A  49 " =    1.540
peak=    3.545 closest distance to " CB  ALA A 104 " =    0.732
peak=    3.540 closest distance to " CB  ARG A  79 " =    0.918
peak=    3.539 closest distance to " O   HOH Z 193 " =    2.053
peak=    3.533 closest distance to " CB  ALA A 248 " =    1.404
peak=    3.522 closest distance to " CG2 THR A 221 " =    1.229
peak=    3.515 closest distance to " CE1 TYR A 186 " =    1.300
peak=    3.514 closest distance to " O   HOH Z 193 " =    1.701
peak=    3.513 closest distance to " N   PHE A 130 " =    1.211
peak=    3.510 closest distance to " NE2 GLN A  77 " =    3.365
peak=    3.509 closest distance to " CD1 LEU A   5 " =    1.360
peak=    3.506 closest distance to " O  BHOH Z 338 " =    2.444
peak=    3.498 closest distance to " CA  TYR A  30 " =    1.071
peak=    3.498 closest distance to " CA  ALA A  21 " =    1.126
peak=    3.497 closest distance to " O   TRP A 274 " =    1.815
peak=    3.492 closest distance to " O   HOH Z  21 " =    1.743
peak=    3.491 closest distance to " O   HOH Z 251 " =    1.501
peak=    3.476 closest distance to " O   HOH Z 147 " =    1.816
peak=    3.473 closest distance to " CZ  PHE A  38 " =    1.153
peak=    3.472 closest distance to " O   MET A 105 " =    1.839
peak=    3.466 closest distance to " O   HOH Z 353 " =    2.614
peak=    3.462 closest distance to " CD2 TRP A 179 " =    1.363
peak=    3.461 closest distance to " O   ASP A 124 " =    0.982
peak=    3.460 closest distance to " O   HOH Z 258 " =    2.135
peak=    3.459 closest distance to " CB  ALA A 242 " =    0.793
peak=    3.458 closest distance to " O   HOH Z 406 " =    1.517
peak=    3.457 closest distance to " CA  ALA A 154 " =    0.966
peak=    3.455 closest distance to " CB  GLN A  89 " =    1.190
peak=    3.444 closest distance to " O   HOH Z 171 " =    3.894
peak=    3.443 closest distance to " O   HOH Z 261 " =    1.626
peak=    3.441 closest distance to " O   HOH Z 180 " =    2.168
peak=    3.438 closest distance to " O   HOH Z  97 " =    2.073
peak=    3.432 closest distance to " O   HOH Z 145 " =    2.186
peak=    3.430 closest distance to " CA  THR A 221 " =    0.898
peak=    3.426 closest distance to " CB  GLN A  88 " =    1.187
peak=    3.423 closest distance to " CA  LYS A 117 " =    1.238
peak=    3.413 closest distance to " CB  LYS A 117 " =    1.255
peak=    3.412 closest distance to " CA  LYS A 181 " =    1.051
peak=    3.412 closest distance to " O   HOH Z 371 " =    3.025
peak=    3.408 closest distance to " CB  LEU A 228 " =    1.247
peak=    3.408 closest distance to " O   HOH Z  48 " =    1.615
peak=    3.407 closest distance to " CB  MET A  40 " =    0.775
peak=    3.407 closest distance to " O   HOH Z 263 " =    1.674
peak=    3.406 closest distance to " O   HOH Z 133 " =    2.443
peak=    3.401 closest distance to " O   HOH Z 365 " =    2.905
peak=    3.399 closest distance to " O   HOH Z 247 " =    1.385
peak=    3.392 closest distance to " CB  TRP A 179 " =    1.420
peak=    3.389 closest distance to " O   HOH Z 227 " =    1.678
peak=    3.388 closest distance to " O   HOH Z 368 " =    3.544
peak=    3.384 closest distance to " O   HOH Z  97 " =    2.415
peak=    3.382 closest distance to " CB  ALA A 114 " =    1.151
peak=    3.382 closest distance to " O   HOH Z 344 " =    3.038
peak=    3.381 closest distance to " O   HOH Z 380 " =    1.863
peak=    3.379 closest distance to " CA  ALA A 158 " =    1.183
peak=    3.375 closest distance to " NZ  LYS A 117 " =    3.281
peak=    3.372 closest distance to " O   ALA A 165 " =    1.511
peak=    3.372 closest distance to " O   HOH Z 294 " =    1.602
peak=    3.371 closest distance to " CB  GLN A 205 " =    1.046
peak=    3.369 closest distance to " O   HOH Z 187 " =    2.323
peak=    3.369 closest distance to " O   HOH Z  59 " =    2.218
peak=    3.366 closest distance to " O   HOH Z 102 " =    1.285
peak=    3.365 closest distance to " O   HOH Z 290 " =    1.128
peak=    3.365 closest distance to " O   PRO A 213 " =    1.548
peak=    3.365 closest distance to " OG  SER A 276 " =    1.267
peak=    3.362 closest distance to " NZ  LYS A  48 " =    1.320
peak=    3.361 closest distance to " CG  MET A 185 " =    1.040
peak=    3.360 closest distance to " N   SER A 135 " =    1.419
peak=    3.360 closest distance to " O   HOH Z  88 " =    3.135
peak=    3.356 closest distance to " CD2 LEU A   5 " =    0.715
peak=    3.353 closest distance to " O   HOH Z  66 " =    2.219
peak=    3.353 closest distance to " CA  LEU A 282 " =    1.061
peak=    3.352 closest distance to " CB  HIS A 108 " =    0.784
peak=    3.350 closest distance to " CB  ILE A 120 " =    1.300
peak=    3.349 closest distance to " O   HOH Z 325 " =    2.203
peak=    3.345 closest distance to " CA  TYR A 116 " =    1.477
peak=    3.345 closest distance to " CG1 ILE A 151 " =    1.034
peak=    3.342 closest distance to " O   HOH Z 305 " =    3.717
peak=    3.339 closest distance to " CB  MET A  47 " =    1.047
peak=    3.332 closest distance to " CD2 LEU A 297 " =    0.909
peak=    3.329 closest distance to " N   ASP A 162 " =    1.254
peak=    3.325 closest distance to " CA  PHE A 283 " =    1.182
peak=    3.322 closest distance to " CA  ASP A 162 " =    1.000
peak=    3.318 closest distance to " O   HOH Z 417 " =    3.060
peak=    3.316 closest distance to " O   HOH Z 383 " =    1.943
peak=    3.312 closest distance to " O   HOH Z 197 " =    3.016
peak=    3.311 closest distance to " O   HOH Z 141 " =    1.616
peak=    3.309 closest distance to " CB  SER A  26 " =    1.794
peak=    3.307 closest distance to " CB  ASN A 110 " =    1.111
peak=    3.298 closest distance to " O   HOH Z 250 " =    1.375
peak=    3.298 closest distance to " O   HOH Z 291 " =    1.603
peak=    3.297 closest distance to " O   HOH Z 245 " =    1.396
peak=    3.297 closest distance to " CB  PRO A 243 " =    1.534
peak=    3.296 closest distance to " CA  MET A 105 " =    0.946
peak=    3.294 closest distance to " CB  SER A 216 " =    0.807
peak=    3.292 closest distance to " N   VAL A 126 " =    1.364
peak=    3.291 closest distance to " CG  GLN A 205 " =    0.863
peak=    3.281 closest distance to " N   ARG A 156 " =    1.421
peak=    3.280 closest distance to " ND1 HIS A  81 " =    1.646
peak=    3.280 closest distance to " CB  SER A 210 " =    0.824
peak=    3.278 closest distance to " OG1 THR A 294 " =    2.423
peak=    3.275 closest distance to " CB  TRP A 150 " =    1.403
peak=    3.273 closest distance to " O   HOH Z 407 " =    2.497
peak=    3.273 closest distance to " ND2 ASN A 249 " =    0.886
peak=    3.272 closest distance to " CA  ASN A 127 " =    1.057
peak=    3.271 closest distance to " CD1 ILE A  33 " =    1.697
peak=    3.271 closest distance to " CB  ALA A 248 " =    1.111
peak=    3.269 closest distance to " CG1 ILE A  33 " =    1.319
peak=    3.266 closest distance to " OE1 GLN A  11 " =    1.836
peak=    3.261 closest distance to " CB  ALA A 295 " =    1.237
peak=    3.260 closest distance to " CA  ASP A 140 " =    1.272
peak=    3.260 closest distance to " CG  GLN A  88 " =    1.068
peak=    3.257 closest distance to " CB  ARG A 139 " =    0.833
peak=    3.248 closest distance to " CA  ASN A 217 " =    1.226
peak=    3.247 closest distance to " CG2 ILE A 120 " =    1.088
peak=    3.245 closest distance to " O   HOH Z 435 " =    2.007
peak=    3.244 closest distance to " CE2 TYR A  30 " =    0.747
peak=    3.239 closest distance to " CZ3 TRP A 266 " =    1.150
peak=    3.236 closest distance to " O   HOH Z 313 " =    1.668
peak=    3.232 closest distance to " CB  SER A 273 " =    0.890
peak=    3.231 closest distance to " CA  ILE A 106 " =    0.740
peak=    3.230 closest distance to " CG  PHE A 204 " =    0.926
peak=    3.230 closest distance to " N   ARG A 190 " =    1.001
peak=    3.226 closest distance to " O   HOH Z 234 " =    1.806
peak=    3.226 closest distance to " CA  ASP A 191 " =    1.075
peak=    3.225 closest distance to " O   HOH Z 350 " =    1.623
peak=    3.225 closest distance to " CB  ALA A  34 " =    0.809
peak=    3.225 closest distance to " CB  ASN A 215 " =    1.168
peak=    3.222 closest distance to " O   HOH Z 133 " =    1.606
peak=    3.221 closest distance to " O   HOH Z 299 " =    4.297
peak=    3.216 closest distance to " CA  GLY A 211 " =    1.354
peak=    3.216 closest distance to " CZ3 TRP A  85 " =    1.061
peak=    3.215 closest distance to " O   HOH Z 327 " =    1.883
peak=    3.215 closest distance to " CB  GLN A 278 " =    0.836
peak=    3.210 closest distance to " O   ARG A  56 " =    2.913
peak=    3.207 closest distance to " O   ASN A  74 " =    1.561
peak=    3.204 closest distance to " O   HOH Z 148 " =    3.297
peak=    3.204 closest distance to " CB  THR A 157 " =    1.177
peak=    3.203 closest distance to " CG2 THR A 220 " =    0.844
peak=    3.200 closest distance to " ND1 HIS A  86 " =    1.670
peak=    3.199 closest distance to " O   HOH Z 171 " =    2.436
peak=    3.198 closest distance to " O   ALA A 292 " =    1.599
peak=    3.195 closest distance to " CA  SER A 146 " =    1.719
peak=    3.195 closest distance to " O   HOH Z 112 " =    1.682
peak=    3.194 closest distance to " CG2 ILE A  20 " =    1.443
peak=    3.193 closest distance to " O   HOH Z 250 " =    1.323
peak=    3.189 closest distance to " O   HOH Z 128 " =    1.826
peak=    3.187 closest distance to " CD  LYS A 119 " =    1.819
peak=    3.187 closest distance to " O   HOH Z 359 " =    1.433
peak=    3.186 closest distance to " O   HOH Z 293 " =    1.778
peak=    3.184 closest distance to " NE2 HIS A 207 " =    1.254
peak=    3.181 closest distance to " CA  ALA A 233 " =    1.389
peak=    3.179 closest distance to " O   TYR A 116 " =    1.327
peak=    3.175 closest distance to " CB  TYR A 116 " =    0.851
peak=    3.171 closest distance to " O   HOH Z 421 " =    3.054
peak=    3.169 closest distance to " OG  SER A  22 " =    2.797
peak=    3.169 closest distance to " CB  GLN A 103 " =    0.951
peak=    3.167 closest distance to " O   HOH Z 329 " =    4.032
peak=    3.167 closest distance to " CE1 HIS A 108 " =    1.172
peak=    3.163 closest distance to " OH  TYR A 214 " =    1.218
peak=    3.160 closest distance to " CB  PRO A  90 " =    1.187
peak=    3.157 closest distance to " O   HOH Z 302 " =    1.932
peak=    3.156 closest distance to " CB  ALA A 100 " =    1.221
peak=    3.155 closest distance to " CG BARG A 102 " =    1.794
peak=    3.151 closest distance to " O   HOH Z 417 " =    2.105
peak=    3.151 closest distance to " CB  ASN A 173 " =    1.057
peak=    3.149 closest distance to " CD1 ILE A 199 " =    0.828
peak=    3.149 closest distance to " CB  VAL A 268 " =    0.839
peak=    3.147 closest distance to " CG  GLN A  77 " =    2.238
peak=    3.145 closest distance to " CZ3 TRP A 274 " =    4.614
peak=    3.144 closest distance to " OG BSER A 134 " =    2.840
peak=    3.144 closest distance to " CB  ASN A 224 " =    1.000
peak=    3.141 closest distance to " CG2 ILE A 234 " =    0.837
peak=    3.138 closest distance to " O   HOH Z  90 " =    2.315
peak=    3.127 closest distance to " CD1 LEU A 261 " =    1.247
peak=    3.124 closest distance to " CD1 LEU A 228 " =    2.075
peak=    3.123 closest distance to " CA  ILE A 234 " =    0.836
peak=    3.122 closest distance to " CB  ARG A 145 " =    0.747
peak=    3.118 closest distance to " CG2 VAL A 197 " =    1.047
peak=    3.114 closest distance to " O   HOH Z 425 " =    1.986
peak=    3.112 closest distance to " CB  PHE A 204 " =    0.823
peak=    3.107 closest distance to " C   ASN A  39 " =    1.052
peak=    3.107 closest distance to " O   HOH Z 213 " =    1.820
peak=    3.098 closest distance to " CG2 VAL A 202 " =    1.099
peak=    3.096 closest distance to " O   HOH Z 337 " =    3.572
peak=    3.083 closest distance to " N   ASN A 127 " =    1.184
peak=    3.080 closest distance to " CA  ASN A 176 " =    1.111
peak=    3.076 closest distance to " CG2 ILE A 263 " =    0.866
peak=    3.074 closest distance to " O   ALA A 158 " =    1.382
peak=    3.065 closest distance to " O   HOH Z   1 " =    2.169
peak=    3.053 closest distance to " O   HOH Z 420 " =    1.815
peak=    3.045 closest distance to " CB  ALA A  43 " =    0.856
peak=    3.038 closest distance to " CG  ARG A 269 " =    1.804
peak=    3.021 closest distance to " N   GLY A 133 " =    3.740

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.767 - 5.482
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.767 - 5.482

peak=   -5.329 closest distance to " CG2 VAL A 230 " =    0.783
peak=   -4.634 closest distance to " CD  ARG A 156 " =    2.033
peak=   -4.452 closest distance to " CD  GLN A  58 " =    1.045
peak=   -4.392 closest distance to " CG1 VAL A 296 " =    1.147
peak=   -4.356 closest distance to " SG  CYS A 254 " =    3.348
peak=   -4.315 closest distance to " CB  PRO A 243 " =    2.695
peak=   -4.297 closest distance to " O   VAL A  67 " =    2.685
peak=   -4.219 closest distance to " O   HOH Z 196 " =    2.136
peak=   -4.157 closest distance to " O   HOH Z 266 " =    5.390
peak=   -4.053 closest distance to " O   ILE A 109 " =    2.573
peak=   -4.016 closest distance to " CG  GLN A 223 " =    2.124
peak=   -4.014 closest distance to " C   HIS A 108 " =    1.186
peak=   -4.002 closest distance to " CE2 TYR A  30 " =    2.754
peak=   -3.901 closest distance to " CZ2 TRP A  92 " =    2.851
peak=   -3.900 closest distance to " O   HOH Z 114 " =    3.052
peak=   -3.882 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.881 closest distance to " O   HOH Z 231 " =    2.154
peak=   -3.853 closest distance to " N   ALA A 226 " =    2.126
peak=   -3.841 closest distance to " O   HOH Z 351 " =    1.556
peak=   -3.837 closest distance to " CG1 VAL A 250 " =    2.778
peak=   -3.831 closest distance to " O   HOH Z 166 " =    1.955
peak=   -3.828 closest distance to " OG BSER A 134 " =    1.222
peak=   -3.791 closest distance to " CZ3 TRP A 179 " =    1.206
peak=   -3.780 closest distance to " O   VAL A  67 " =    2.794
peak=   -3.774 closest distance to " OG  SER A  97 " =    2.365
peak=   -3.772 closest distance to " CG  ASP A 231 " =    0.767
peak=   -3.771 closest distance to " OXT GLY A 302 " =    2.906
peak=   -3.771 closest distance to " O   HOH Z 290 " =    1.202
peak=   -3.765 closest distance to " CD2 PHE A 192 " =    2.042
peak=   -3.748 closest distance to " C   ALA A 158 " =    1.313
peak=   -3.746 closest distance to " CE3 TRP A 150 " =    2.224
peak=   -3.733 closest distance to " CG2 ILE A 263 " =    2.401
peak=   -3.729 closest distance to " O   HOH Z 185 " =    2.387
peak=   -3.716 closest distance to " O   PRO A 163 " =    2.231
peak=   -3.711 closest distance to " O   HOH Z 394 " =    1.549
peak=   -3.689 closest distance to " CG1 VAL A 112 " =    2.647
peak=   -3.685 closest distance to " CG1 VAL A 112 " =    2.830
peak=   -3.679 closest distance to " CA  GLY A 241 " =    3.135
peak=   -3.674 closest distance to " O   HOH Z  11 " =    1.955
peak=   -3.669 closest distance to " OD1 ASN A 148 " =    1.443
peak=   -3.651 closest distance to " ND2 ASN A  45 " =    1.134
peak=   -3.634 closest distance to " CE  MET A 105 " =    2.198
peak=   -3.633 closest distance to " CG2 VAL A 296 " =    1.344
peak=   -3.625 closest distance to " O   HOH Z  73 " =    2.217
peak=   -3.622 closest distance to " O   HOH Z 211 " =    1.542
peak=   -3.612 closest distance to " O   HOH Z  37 " =    1.914
peak=   -3.607 closest distance to " CD2 TYR A 293 " =    1.981
peak=   -3.602 closest distance to " C   MET A 188 " =    1.411
peak=   -3.596 closest distance to " CD2 LEU A 300 " =    2.750
peak=   -3.590 closest distance to " O   PRO A 198 " =    1.253
peak=   -3.587 closest distance to " O   HOH Z 435 " =    2.773
peak=   -3.566 closest distance to " CD1 LEU A 101 " =    2.432
peak=   -3.558 closest distance to " O   HOH Z  52 " =    1.601
peak=   -3.550 closest distance to " O   HOH Z 377 " =    2.127
peak=   -3.544 closest distance to " ND2 ASN A  45 " =    1.829
peak=   -3.542 closest distance to " NH2 ARG A  79 " =    1.580
peak=   -3.542 closest distance to " C   LEU A 143 " =    1.058
peak=   -3.535 closest distance to " N   ALA A  43 " =    2.546
peak=   -3.530 closest distance to " CB  ALA A  43 " =    2.605
peak=   -3.519 closest distance to " NE2 GLN A  88 " =    2.001
peak=   -3.510 closest distance to " CB  ALA A 248 " =    2.386
peak=   -3.508 closest distance to " CG  TRP A 266 " =    1.830
peak=   -3.501 closest distance to " NH2AARG A 275 " =    5.200
peak=   -3.501 closest distance to " CZ  TYR A 169 " =    1.717
peak=   -3.500 closest distance to " NE2 GLN A 103 " =    1.791
peak=   -3.499 closest distance to " CG  HIS A  86 " =    1.132
peak=   -3.497 closest distance to " O   HOH Z  10 " =    1.531
peak=   -3.496 closest distance to " CA  GLY A 241 " =    2.355
peak=   -3.482 closest distance to " O   HOH Z 222 " =    1.466
peak=   -3.472 closest distance to " CG  ARG A 269 " =    2.400
peak=   -3.471 closest distance to " O   HOH Z  44 " =    2.253
peak=   -3.455 closest distance to " N   THR A 157 " =    1.556
peak=   -3.454 closest distance to " ND2 ASN A 249 " =    2.460
peak=   -3.453 closest distance to " CG  GLU A 277 " =    1.137
peak=   -3.445 closest distance to " CD2 LEU A 167 " =    1.836
peak=   -3.442 closest distance to " O   VAL A 189 " =    2.582
peak=   -3.425 closest distance to " O   HOH Z 102 " =    1.692
peak=   -3.421 closest distance to " CD2 PHE A  61 " =    2.575
peak=   -3.417 closest distance to " O   HOH Z  63 " =    1.238
peak=   -3.416 closest distance to " CB  ASP A 132 " =    2.329
peak=   -3.416 closest distance to " CD1 LEU A 228 " =    2.304
peak=   -3.413 closest distance to " O   HOH Z 426 " =    1.695
peak=   -3.396 closest distance to " O   HOH Z 429 " =    2.043
peak=   -3.394 closest distance to " CE BMET A  47 " =    1.817
peak=   -3.389 closest distance to " O   SER A 271 " =    2.247
peak=   -3.386 closest distance to " O   SER A  95 " =    1.717
peak=   -3.384 closest distance to " NH2 ARG A  79 " =    2.051
peak=   -3.381 closest distance to " N   THR A  18 " =    1.311
peak=   -3.379 closest distance to " N   ALA A 248 " =    2.410
peak=   -3.378 closest distance to " O   HOH Z 359 " =    3.101
peak=   -3.377 closest distance to " O   HOH Z 389 " =    2.007
peak=   -3.369 closest distance to " O   HOH Z 241 " =    1.253
peak=   -3.368 closest distance to " CD1 PHE A  59 " =    1.971
peak=   -3.365 closest distance to " N   THR A  52 " =    1.660
peak=   -3.361 closest distance to " N   ALA A 248 " =    1.925
peak=   -3.349 closest distance to " O   HOH Z 128 " =    2.637
peak=   -3.348 closest distance to " CB  ASN A  39 " =    2.289
peak=   -3.347 closest distance to " OG  SER A  87 " =    1.502
peak=   -3.338 closest distance to " O   HOH Z 292 " =    4.661
peak=   -3.337 closest distance to " O   HOH Z  60 " =    2.103
peak=   -3.336 closest distance to " N   THR A 235 " =    1.286
peak=   -3.334 closest distance to " O   HOH Z 216 " =    1.547
peak=   -3.329 closest distance to " N   SER A 212 " =    1.909
peak=   -3.327 closest distance to " CB  PRO A 163 " =    2.537
peak=   -3.324 closest distance to " O   HOH Z  19 " =    2.389
peak=   -3.317 closest distance to " OE1 GLN A  88 " =    1.002
peak=   -3.314 closest distance to " NE2 GLN A 194 " =    1.814
peak=   -3.314 closest distance to " CB  ALA A 291 " =    2.219
peak=   -3.309 closest distance to " C   PHE A  59 " =    1.320
peak=   -3.308 closest distance to " CB  VAL A 230 " =    1.077
peak=   -3.307 closest distance to " ND2 ASN A 187 " =    1.593
peak=   -3.306 closest distance to " O   MET A  40 " =    2.795
peak=   -3.304 closest distance to " NE2 GLN A 278 " =    1.950
peak=   -3.300 closest distance to " OD2 ASP A  50 " =    2.363
peak=   -3.297 closest distance to " CE3 TRP A  70 " =    1.813
peak=   -3.289 closest distance to " O   HOH Z 313 " =    1.142
peak=   -3.285 closest distance to " CD1 ILE A 239 " =    2.140
peak=   -3.284 closest distance to " O   ARG A  24 " =    2.091
peak=   -3.280 closest distance to " CD  LYS A 289 " =    2.529
peak=   -3.277 closest distance to " O   HOH Z  43 " =    1.791
peak=   -3.276 closest distance to " O   HOH Z 176 " =    0.830
peak=   -3.275 closest distance to " CB  VAL A 296 " =    1.241
peak=   -3.275 closest distance to " O   HOH Z 353 " =    2.131
peak=   -3.270 closest distance to " O   HOH Z  22 " =    2.411
peak=   -3.268 closest distance to " CB  ASP A 171 " =    2.316
peak=   -3.267 closest distance to " OG  SER A 206 " =    1.739
peak=   -3.265 closest distance to " O   GLY A 203 " =    2.360
peak=   -3.260 closest distance to " O   HOH Z 198 " =    2.397
peak=   -3.258 closest distance to " NH2 ARG A 159 " =    2.305
peak=   -3.258 closest distance to " O   GLY A 196 " =    1.264
peak=   -3.257 closest distance to " O   TYR A 247 " =    2.892
peak=   -3.257 closest distance to " NE2 GLN A  88 " =    1.017
peak=   -3.254 closest distance to " O   HOH Z 326 " =    5.104
peak=   -3.252 closest distance to " O   HOH Z 123 " =    2.555
peak=   -3.251 closest distance to " O   HOH Z 191 " =    5.482
peak=   -3.245 closest distance to " OG BSER A 134 " =    1.873
peak=   -3.242 closest distance to " O   ALA A  10 " =    1.715
peak=   -3.241 closest distance to " ND2 ASN A  69 " =    1.872
peak=   -3.240 closest distance to " CD1 LEU A 101 " =    2.709
peak=   -3.237 closest distance to " CB  ALA A 291 " =    2.202
peak=   -3.231 closest distance to " O   HOH Z  13 " =    1.524
peak=   -3.222 closest distance to " O   HOH Z 133 " =    1.371
peak=   -3.221 closest distance to " CD  PRO A 243 " =    2.065
peak=   -3.213 closest distance to " O   HOH Z 262 " =    2.860
peak=   -3.208 closest distance to " CA  VAL A 296 " =    1.013
peak=   -3.207 closest distance to " N   SER A   3 " =    1.964
peak=   -3.199 closest distance to " CG1 VAL A 125 " =    1.970
peak=   -3.198 closest distance to " O   HOH Z 407 " =    3.123
peak=   -3.196 closest distance to " O   HOH Z 434 " =    1.740
peak=   -3.192 closest distance to " CB  ASN A  69 " =    1.252
peak=   -3.186 closest distance to " O   HOH Z  38 " =    1.617
peak=   -3.185 closest distance to " C   ASN A 187 " =    1.896
peak=   -3.185 closest distance to " O   HOH Z 165 " =    1.871
peak=   -3.181 closest distance to " O   HOH Z 275 " =    1.485
peak=   -3.179 closest distance to " O   GLY A  80 " =    2.552
peak=   -3.177 closest distance to " CG1 VAL A 112 " =    2.885
peak=   -3.173 closest distance to " CD2 TYR A 247 " =    2.266
peak=   -3.172 closest distance to " CG1 VAL A  67 " =    3.026
peak=   -3.162 closest distance to " ND2 ASN A  60 " =    1.281
peak=   -3.161 closest distance to " CG  MET A 105 " =    0.922
peak=   -3.159 closest distance to " O   HOH Z 251 " =    5.015
peak=   -3.158 closest distance to " O   HOH Z 139 " =    3.147
peak=   -3.157 closest distance to " O   HOH Z 252 " =    4.046
peak=   -3.153 closest distance to " CD  PRO A 213 " =    2.118
peak=   -3.151 closest distance to " CG2 VAL A 189 " =    2.026
peak=   -3.146 closest distance to " C   LEU A 222 " =    0.893
peak=   -3.145 closest distance to " CG2 THR A 178 " =    2.247
peak=   -3.133 closest distance to " O   HOH Z 175 " =    4.226
peak=   -3.130 closest distance to " ND2 ASN A 252 " =    1.905
peak=   -3.120 closest distance to " O   HOH Z 369 " =    2.279
peak=   -3.116 closest distance to " CA  GLY A 203 " =    2.474
peak=   -3.116 closest distance to " O   HOH Z 113 " =    2.078
peak=   -3.116 closest distance to " CD  ARG A 139 " =    1.686
peak=   -3.116 closest distance to " O   HOH Z 421 " =    3.180
peak=   -3.113 closest distance to " CA  GLY A 133 " =    2.308
peak=   -3.112 closest distance to " O   PRO A 198 " =    1.358
peak=   -3.112 closest distance to " OD1 ASN A 187 " =    1.571
peak=   -3.111 closest distance to " O   HOH Z 106 " =    1.873
peak=   -3.106 closest distance to " C   ASP A 270 " =    1.196
peak=   -3.103 closest distance to " O   HOH Z 210 " =    1.117
peak=   -3.103 closest distance to " CG1AVAL A  41 " =    3.003
peak=   -3.101 closest distance to " OG  SER A  63 " =    1.266
peak=   -3.100 closest distance to " CD1 ILE A 151 " =    2.403
peak=   -3.099 closest distance to " O   HOH Z 166 " =    1.671
peak=   -3.094 closest distance to " O   HOH Z 396 " =    1.814
peak=   -3.092 closest distance to " CD1 TYR A 247 " =    2.379
peak=   -3.072 closest distance to " O   HOH Z 111 " =    2.164
peak=   -3.066 closest distance to " CD2 HIS A 207 " =    2.419
peak=   -3.065 closest distance to " O   HOH Z 313 " =    1.615
peak=   -3.063 closest distance to " O   HOH Z  90 " =    1.667
peak=   -3.057 closest distance to " SD BMET A  47 " =    1.078
peak=   -3.057 closest distance to " CE1 TYR A 247 " =    2.639
peak=   -3.053 closest distance to " CG1 VAL A 197 " =    2.252
peak=   -3.051 closest distance to " CB  ASP A 132 " =    2.398
peak=   -3.047 closest distance to " O   HOH Z   6 " =    1.636
peak=   -3.046 closest distance to " NH2 ARG A  66 " =    1.943

================= 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    :  0.4286 0.4121   6.219268e+00   6.187148e+00
   1_bss:  0.4200 0.3953   6.215199e+00   6.170926e+00
   1_xyz:  0.3038 0.3246   5.979664e+00   6.019003e+00
   1_adp:  0.2388 0.2702   5.760524e+00   5.868823e+00
   1_occ:  0.2380 0.2709   5.758848e+00   5.870509e+00
   2_bss:  0.2330 0.2646   5.758585e+00   5.865875e+00
   2_xyz:  0.1516 0.1888   5.377059e+00   5.558579e+00
   2_adp:  0.1374 0.1774   5.294953e+00   5.495038e+00
   2_occ:  0.1374 0.1775   5.294300e+00   5.494742e+00
   3_bss:  0.1372 0.1772   5.295302e+00   5.494509e+00
   3_xyz:  0.1254 0.1637   5.216975e+00   5.426431e+00
   3_adp:  0.1208 0.1626   5.198500e+00   5.423219e+00
   3_occ:  0.1208 0.1626   5.198340e+00   5.423042e+00
   4_bss:  0.1208 0.1626   5.198340e+00   5.423042e+00
   4_xyz:  0.1119 0.1596   5.152079e+00   5.403556e+00
   4_adp:  0.1118 0.1578   5.146643e+00   5.394018e+00
   4_occ:  0.1117 0.1579   5.146484e+00   5.394313e+00
   5_bss:  0.1118 0.1576   5.145947e+00   5.392314e+00
   5_xyz:  0.1142 0.1587   5.161108e+00   5.400951e+00
   5_adp:  0.1143 0.1585   5.162318e+00   5.402060e+00
   5_occ:  0.1143 0.1586   5.162275e+00   5.402174e+00
   5_bss:  0.1143 0.1586   5.162275e+00   5.402174e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   7.114   8.112   9.489   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.114   8.112   9.489   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.114   8.112   9.489   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.114   8.112   9.489   0.000   0.000   0.000
   2_bss:  0.324  53.287   3.902   4.732   6.000   0.000   0.000   0.000
   2_xyz:  0.324  53.287   3.902   4.732   6.000   0.000   0.000   0.000
   2_adp:  0.324  53.287   3.902   4.732   6.000   0.000   0.000   0.000
   2_occ:  0.324  53.287   3.902   4.732   6.000   0.000   0.000   0.000
   3_bss:  0.330  53.287   3.230   3.804   4.966   0.000   0.000   0.000
   3_xyz:  0.330  53.287   3.230   3.804   4.966   0.000   0.000   0.000
   3_adp:  0.330  53.287   3.230   3.804   4.966   0.000   0.000   0.000
   3_occ:  0.330  53.287   3.230   3.804   4.966   0.000   0.000   0.000
   4_bss:  0.330  53.287   3.230   3.804   4.966   0.000   0.000   0.000
   4_xyz:  0.330  53.287   3.230   3.804   4.966   0.000   0.000   0.000
   4_adp:  0.330  53.287   3.230   3.804   4.966   0.000   0.000   0.000
   4_occ:  0.330  53.287   3.230   3.804   4.966   0.000   0.000   0.000
   5_bss:  0.330  53.287   3.323   3.734   4.930   0.000   0.000   0.000
   5_xyz:  0.330  53.287   3.323   3.734   4.930   0.000   0.000   0.000
   5_adp:  0.330  53.287   3.323   3.734   4.930   0.000   0.000   0.000
   5_occ:  0.330  53.287   3.323   3.734   4.930   0.000   0.000   0.000
   5_bss:  0.330  57.283  -0.673  -0.261   0.934   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.754 0.5874  0.6430    47714.732
   1_bss:  43.743 0.5986  0.8398    45124.744
   1_xyz:  34.485 0.7066  0.9572    28273.994
   1_adp:  26.515 0.7964  1.0410    18271.927
   1_occ:  26.539 0.7961  1.0403    18323.361
   2_bss:  26.341 0.7982  0.9241    18090.196
   2_xyz:  17.827 0.8819  0.9912     8989.531
   2_adp:  16.190 0.8969  1.0008     7940.875
   2_occ:  16.178 0.8969  1.0008     7933.000
   3_bss:  16.167 0.8970  0.9690     7935.751
   3_xyz:  14.583 0.9107  0.9726     6818.803
   3_adp:  14.529 0.9112  0.9694     6744.137
   3_occ:  14.526 0.9113  0.9693     6742.669
   4_bss:  14.526 0.9113  0.9693     6742.669
   4_xyz:  14.186 0.9138  0.9726     6532.614
   4_adp:  13.967 0.9156  0.9718     6397.862
   4_occ:  13.975 0.9156  0.9716     6403.338
   5_bss:  13.948 0.9157  0.9709     6362.499
   5_xyz:  14.068 0.9149  0.9692     6441.227
   5_adp:  14.085 0.9148  0.9664     6453.238
   5_occ:  14.089 0.9148  0.9662     6454.301
   5_bss:  14.089 0.9148  0.9662     6454.301
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4206e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4206e+01
   1_xyz:   1.508  0.011  0.102 17.937  0.006  4.127   1.1691e-01
   1_adp:   1.508  0.011  0.102 17.937  0.006  4.127   1.1691e-01
   1_occ:   1.508  0.011  0.102 17.937  0.006  4.127   1.1691e-01
   2_bss:   1.508  0.011  0.102 17.937  0.006  4.127   1.1691e-01
   2_xyz:   1.066  0.009  0.078 16.334  0.004  4.130   7.1301e-02
   2_adp:   1.066  0.009  0.078 16.334  0.004  4.130   7.1301e-02
   2_occ:   1.066  0.009  0.078 16.334  0.004  4.130   7.1301e-02
   3_bss:   1.066  0.009  0.078 16.334  0.004  4.130   7.1301e-02
   3_xyz:   0.954  0.007  0.076 15.875  0.003  4.128   5.8315e-02
   3_adp:   0.954  0.007  0.076 15.875  0.003  4.128   5.8315e-02
   3_occ:   0.954  0.007  0.076 15.875  0.003  4.128   5.8315e-02
   4_bss:   0.954  0.007  0.076 15.875  0.003  4.128   5.8315e-02
   4_xyz:   1.142  0.011  0.094 15.983  0.004  4.127   8.1121e-02
   4_adp:   1.142  0.011  0.094 15.983  0.004  4.127   8.1121e-02
   4_occ:   1.142  0.011  0.094 15.983  0.004  4.127   8.1121e-02
   5_bss:   1.142  0.011  0.094 15.983  0.004  4.127   8.1121e-02
   5_xyz:   0.998  0.008  0.080 15.638  0.004  4.126   6.3334e-02
   5_adp:   0.998  0.008  0.080 15.638  0.004  4.126   6.3334e-02
   5_occ:   0.998  0.008  0.080 15.638  0.004  4.126   6.3334e-02
   5_bss:   0.998  0.008  0.080 15.638  0.004  4.126   6.3334e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0286e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0286e+00
   1_xyz:  12.557  0.134  0.403 88.134  0.036  2.257   8.8215e-02
   1_adp:  12.557  0.134  0.403 88.134  0.036  2.257   8.8215e-02
   1_occ:  12.557  0.134  0.403 88.134  0.036  2.257   8.8215e-02
   2_bss:  12.557  0.134  0.403 88.134  0.036  2.257   8.8215e-02
   2_xyz:   6.913  0.074  0.295 83.874  0.036  2.314   6.1125e-02
   2_adp:   6.913  0.074  0.295 83.874  0.036  2.314   6.1125e-02
   2_occ:   6.913  0.074  0.295 83.874  0.036  2.314   6.1125e-02
   3_bss:   6.913  0.074  0.295 83.874  0.036  2.314   6.1125e-02
   3_xyz:   6.606  0.040  0.372 82.708  0.039  2.405   3.1951e-02
   3_adp:   6.606  0.040  0.372 82.708  0.039  2.405   3.1951e-02
   3_occ:   6.606  0.040  0.372 82.708  0.039  2.405   3.1951e-02
   4_bss:   6.606  0.040  0.372 82.708  0.039  2.405   3.1951e-02
   4_xyz:   7.557  0.054  0.569 82.722  0.041  2.312   6.1518e-02
   4_adp:   7.557  0.054  0.569 82.722  0.041  2.312   6.1518e-02
   4_occ:   7.557  0.054  0.569 82.722  0.041  2.312   6.1518e-02
   5_bss:   7.557  0.054  0.569 82.722  0.041  2.312   6.1518e-02
   5_xyz:   7.037  0.048  0.411 81.950  0.039  2.395   4.3237e-02
   5_adp:   7.037  0.048  0.411 81.950  0.039  2.395   4.3237e-02
   5_occ:   7.037  0.048  0.411 81.950  0.039  2.395   4.3237e-02
   5_bss:   7.037  0.048  0.411 81.950  0.039  2.395   4.3237e-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:  73.13   0.00  10.45  56.15   0.00   7.26  73.13   0.00  27.85
   1_occ:  73.13   0.00  10.45  56.15   0.00   7.26  73.13   0.00  27.85
   2_bss:  73.13   0.00  10.45  56.15   0.00   7.26  73.13   0.00  27.85
   2_xyz:  73.13   0.00  10.45  56.15   0.00   7.26  73.13   0.00  27.85
   2_adp:  71.51   0.00  10.70  56.37   0.00   7.01  71.51   0.00  30.79
   2_occ:  71.51   0.00  10.70  56.37   0.00   7.01  71.51   0.00  30.79
   3_bss:  71.51   0.00  10.70  56.37   0.00   7.01  71.51   0.00  30.79
   3_xyz:  71.51   0.00  10.70  56.37   0.00   7.01  71.51   0.00  30.79
   3_adp:  76.90   0.00  11.66  76.90   0.00   7.27  75.24   0.00  35.57
   3_occ:  76.90   0.00  11.66  76.90   0.00   7.27  75.24   0.00  35.57
   4_bss:  76.90   0.00  11.66  76.90   0.00   7.27  75.24   0.00  35.57
   4_xyz:  76.90   0.00  11.66  76.90   0.00   7.27  75.24   0.00  35.57
   4_adp:  77.70   0.00  11.36  77.70   0.00   7.14  72.63   0.51  34.31
   4_occ:  77.70   0.00  11.36  77.70   0.00   7.14  72.63   0.51  34.31
   5_bss:  77.70   0.00  11.36  77.70   0.00   7.14  72.63   0.51  34.31
   5_xyz:  77.70   0.00  11.36  77.70   0.00   7.14  72.63   0.51  34.31
   5_adp:  79.76   0.00  11.12  79.76   0.00   7.05  71.80   0.49  33.29
   5_occ:  79.76   0.00  11.12  79.76   0.00   7.05  71.80   0.49  33.29
   5_bss:  83.76   4.00  15.12  83.76   4.00  11.04  75.79   4.49  37.29
------------------------------------------------------------------------
 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:    1.204    0.012    0.402
   1_adp:    1.204    0.012    0.402
   1_occ:    1.204    0.012    0.402
   2_bss:    1.204    0.012    0.402
   2_xyz:    1.477    0.019    0.502
   2_adp:    1.477    0.019    0.502
   2_occ:    1.477    0.019    0.502
   3_bss:    1.477    0.019    0.502
   3_xyz:    1.512    0.049    0.520
   3_adp:    1.512    0.049    0.520
   3_occ:    1.512    0.049    0.520
   4_bss:    1.512    0.049    0.520
   4_xyz:    1.512    0.053    0.537
   4_adp:    1.512    0.053    0.537
   4_occ:    1.512    0.053    0.537
   5_bss:    1.512    0.053    0.537
   5_xyz:    1.581    0.053    0.543
   5_adp:    1.581    0.053    0.543
   5_occ:    1.581    0.053    0.543
   5_bss:    1.581    0.053    0.543
------------------------------------------------------------------------

CPU time actual refinement: 323.49


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_799/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_799/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_799/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_799/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_799/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.34 
  Macro-tasks:
    bulk solvent and scale       = 43.32  
    individual site refinement   = 130.58 
    weights calculation          = 32.13  
    collect and process          = 6.55   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 212.69 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 96.94  
    alpha_beta                      = 8.06   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 107.84 
    fmodel                         = 7.14   
    r_factors                      = 0.33   
    phase_errors                   = 10.81  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 234.32 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.539 micro seconds
Total CPU time: 5.62 minutes
from_scatterers_fft:    650 calls, 96.62 s
gradients_fft:          594 calls, 94.48 s

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

# Date 2008-01-16 Time 02:27:23 PST -0800 (1200479243.60 s)
Start R-work = 0.4286, R-free = 0.4121 (no bulk solvent and anisotropic scale)
Final R-work = 0.1315, R-free = 0.1750 (no bulk solvent and anisotropic scale)

Start R-work = 0.4200, R-free = 0.3953
Final R-work = 0.1143, R-free = 0.1586