# Date 2008-01-16 Time 02:55:47 PST -0800 (1200480947.30 s)
#phil __OFF__

Command line arguments: "../1027.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20478
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1027

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.93, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99103
Completeness in resolution range: 0.963504
Completeness with d_max=infinity: 0.960575

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9910

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99103
Completeness in resolution range: 0.963504
Completeness with d_max=infinity: 0.960575

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2607 [2133/2159]  1922   211   9.9%
  bin  2:  4.2607 -  3.3943 [2046/2065]  1840   206  10.1%
  bin  3:  3.3943 -  2.9690 [2030/2049]  1825   205  10.1%
  bin  4:  2.9690 -  2.6992 [2009/2039]  1809   200  10.0%
  bin  5:  2.6992 -  2.5066 [1993/2012]  1799   194   9.7%
  bin  6:  2.5066 -  2.3594 [1979/2004]  1775   204  10.3%
  bin  7:  2.3594 -  2.2417 [1968/1996]  1770   198  10.1%
  bin  8:  2.2417 -  2.1444 [1972/2008]  1777   195   9.9%
  bin  9:  2.1444 -  2.0620 [1970/2012]  1771   199  10.1%
  bin 10:  2.0620 -  1.9910 [1489/1987]  1342   147   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1027/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2191
        3.04 -     3.66: 4638
        3.66 -     4.28: 9013
        4.28 -     4.90: 12292
  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 "  1.967 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.209 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.282 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28140 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_1027/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1027/model_refine_001.geo

CPU time processing inputs: 9.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.93 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4264   r_free= 0.4147   ksol= 0.00   Bsol= 0.00   scale= 0.822    |
|                                                                             |
| 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: 6.219586                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7523 0.99   1386  155 0.3653 0.3490      6.5238      6.4541|
|  2:  4.7523 -  3.7915 0.99   1340  146 0.3209 0.3306      6.6308      6.6438|
|  3:  3.7915 -  3.3180 0.99   1305  144 0.3669 0.3285      6.5366      6.5521|
|  4:  3.3180 -  3.0173 0.99   1300  153 0.3984 0.3709       6.437      6.3528|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.4417 0.4611      6.3071      6.3417|
|  6:  2.8025 -  2.6381 0.99   1278  143 0.4490 0.4516      6.2188      6.2019|
|  7:  2.6381 -  2.5066 0.99   1289  136 0.4846 0.4874      6.2213      6.1991|
|  8:  2.5066 -  2.3980 0.98   1263  151 0.4724 0.4503      6.1336      6.1297|
|  9:  2.3980 -  2.3060 0.98   1265  142 0.4628 0.4725      6.0808      6.0699|
| 10:  2.3060 -  2.2267 0.99   1274  135 0.4816 0.4651      6.0832      6.0518|
| 11:  2.2267 -  2.1572 0.98   1277  141 0.4906 0.4356      6.0236       5.996|
| 12:  2.1572 -  2.0957 0.97   1236  144 0.4680 0.5135       5.952      6.0061|
| 13:  2.0957 -  2.0407 1.00   1277  135 0.5151 0.4960      5.8864      5.8386|
| 14:  2.0407 -  1.9910 0.65    843   95 0.4905 0.4358      5.8407      5.6984|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7523  1386   155  0.74  30.83   0.81     0.77      57632.38|
|  2:  4.7523 -  3.7915  1340   146  0.79  27.52   0.91     0.83      70045.64|
|  3:  3.7915 -  3.3180  1305   144  0.72  33.77   0.87     0.80      72923.42|
|  4:  3.3180 -  3.0173  1300   153  0.65  39.36   0.84     0.73      67964.47|
|  5:  3.0173 -  2.8025  1297   139  0.55  47.54   0.77     0.64      62022.06|
|  6:  2.8025 -  2.6381  1278   143  0.52  50.58   0.77     0.59      56764.29|
|  7:  2.6381 -  2.5066  1289   136  0.51  51.45   0.75     0.57      52450.69|
|  8:  2.5066 -  2.3980  1263   151  0.50  52.55   0.75     0.57      47438.72|
|  9:  2.3980 -  2.3060  1265   142  0.51  51.28   0.76     0.57      42002.09|
| 10:  2.3060 -  2.2267  1274   135  0.51  51.61   0.78     0.57      37830.92|
| 11:  2.2267 -  2.1572  1277   141  0.49  53.17   0.78     0.55      35521.94|
| 12:  2.1572 -  2.0957  1236   144  0.48  54.21   0.79     0.55      34673.58|
| 13:  2.0957 -  2.0407  1277   135  0.46  55.11   0.74     0.55      29479.22|
| 14:  2.0407 -  1.9910   843    95  0.56  47.68   0.73     0.60      21104.93|
|alpha:            min =        0.55 max =            0.83 mean =         0.64|
|beta:             min =    21104.93 max =        72923.42 mean =     50071.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.97 mean =        45.94|
|phase err.(test): min =        0.00 max =           89.96 mean =        46.02|
|-----------------------------------------------------------------------------|

============================== 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 = 8.006438              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.877   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.587396              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.562   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1502 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2615 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3908 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5024 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6553 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7666 |
|-----------------------------------------------------------------------------|
|-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 |       54.002 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.625 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    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 = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4348   r_free= 0.4245   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.224804                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4186   r_free= 0.4049   ksol= 0.34   Bsol= 20.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.95,7.90,7.85,0.00,0.00,0.00); trace/3= 8.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.214670                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.348660              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.938   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.600816              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.799   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4186      final r-factor (work) = 0.3097          |
| start r-factor (free) = 0.4049      final r-factor (free) = 0.3378          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.9021 = 7.35 * 0.50 * 6.2324 + 1.00 * 54.0024                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3578 = 7.35 * 0.50 * 6.0531 + 1.00 * 0.1166                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3097      final r-factor (work) = 0.2443          |
| start r-factor (free) = 0.3378      final r-factor (free) = 0.2819          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6515 = 0.60 * 1.00 * 6.0531 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5390 = 0.60 * 1.00 * 5.8716 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    51.37   9.91     None  None   None       |
|    all(noH): 2823   0      0.00    51.37   9.91     None  None   None       |
|    Sol.    : 438    0      0.00    51.37   26.02    None  None   None       |
|    Mac.    : 2385   0      0.00    48.39   6.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.137: 1186   |   5:    25.687 -  30.824:  122        |
|      1:     5.137 -  10.275:  765   |   6:    30.824 -  35.961:   77        |
|      2:    10.275 -  15.412:  314   |   7:    35.961 -  41.098:   65        |
|      3:    15.412 -  20.549:  141   |   8:    41.098 -  46.236:   26        |
|      4:    20.549 -  25.687:  116   |   9:    46.236 -  51.373:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2443 r_free = 0.2819             target_work(ml) = 5.797         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2437 r_free = 0.2820             target_work(ml) = 5.796         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2437   r_free= 0.2820   ksol= 0.34   Bsol= 20.00   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.95,7.90,7.85,0.00,0.00,0.00); trace/3= 8.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.795834                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2391   r_free= 0.2759   ksol= 0.34   Bsol= 49.90   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.59,4.35,5.07,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.794019                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.546155              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.589   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.332667              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.967  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2391      final r-factor (work) = 0.1710          |
| start r-factor (free) = 0.2759      final r-factor (free) = 0.2127          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6024 = 2.55 * 0.50 * 5.8804 + 1.00 * 0.1162                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2409 = 2.55 * 0.50 * 5.6418 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1710      final r-factor (work) = 0.1615          |
| start r-factor (free) = 0.2127      final r-factor (free) = 0.2052          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9277 = 0.33 * 1.00 * 5.6418 + 1.00 * 0.0509                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9934 = 0.33 * 1.00 * 5.4647 + 1.00 * 0.1755                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.77   10.27    None  None   None       |
|    all(noH): 2823   0      0.00    77.77   10.27    None  None   None       |
|    Sol.    : 438    0      1.15    52.58   27.46    None  None   None       |
|    Mac.    : 2385   0      0.00    77.77   7.11     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 -   7.777: 1654   |   5:    38.883 -  46.659:   54        |
|      1:     7.777 -  15.553:  606   |   6:    46.659 -  54.436:   12        |
|      2:    15.553 -  23.330:  179   |   7:    54.436 -  62.213:    0        |
|      3:    23.330 -  31.106:  182   |   8:    62.213 -  69.989:    0        |
|      4:    31.106 -  38.883:  135   |   9:    69.989 -  77.766:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1615 r_free = 0.2052             target_work(ml) = 5.447         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1615 r_free = 0.2052             target_work(ml) = 5.446         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1615   r_free= 0.2052   ksol= 0.34   Bsol= 49.90   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.59,4.35,5.07,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.446327                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1606   r_free= 0.2037   ksol= 0.35   Bsol= 49.90   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.74,3.38,4.26,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.445898                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.926142              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.980  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.953755              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.098   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1606      final r-factor (work) = 0.1355          |
| start r-factor (free) = 0.2037      final r-factor (free) = 0.1822          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3274 = 1.93 * 0.50 * 5.4710 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2284 = 1.93 * 0.50 * 5.3673 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1355      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1822      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.2387 = 3.95 * 1.00 * 5.3673 + 1.00 * 0.0175                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.8500 = 3.95 * 1.00 * 5.2694 + 1.00 * 0.0161                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.70   11.82    None  None   None       |
|    all(noH): 2823   0      0.00    79.70   11.82    None  None   None       |
|    Sol.    : 438    0      0.46    79.70   35.32    None  None   None       |
|    Mac.    : 2385   0      0.00    70.94   7.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.970: 1674   |   5:    39.850 -  47.820:   86        |
|      1:     7.970 -  15.940:  553   |   6:    47.820 -  55.790:   75        |
|      2:    15.940 -  23.910:  170   |   7:    55.790 -  63.760:   43        |
|      3:    23.910 -  31.880:  102   |   8:    63.760 -  71.730:   15        |
|      4:    31.880 -  39.850:  101   |   9:    71.730 -  79.700:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1247 r_free = 0.1720             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1247 r_free = 0.1718             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1718   ksol= 0.35   Bsol= 49.90   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.74,3.38,4.26,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.238498                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1717   ksol= 0.33   Bsol= 49.90   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,3.22,4.09,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.238726                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.274308              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.480  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.236953              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.567   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1717      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6864 = 3.27 * 0.50 * 5.2696 + 1.00 * 0.0593                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5878 = 3.27 * 0.50 * 5.1990 + 1.00 * 0.0763                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2477 = 0.24 * 1.00 * 5.1990 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2456 = 0.24 * 1.00 * 5.1717 + 1.00 * 0.0201                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.10   11.34    None  None   None       |
|    all(noH): 2823   0      0.00    73.10   11.34    None  None   None       |
|    Sol.    : 438    0      0.91    73.10   33.06    None  None   None       |
|    Mac.    : 2385   0      0.00    71.86   7.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.310: 1623   |   5:    36.548 -  43.858:   78        |
|      1:     7.310 -  14.619:  590   |   6:    43.858 -  51.167:   76        |
|      2:    14.619 -  21.929:  173   |   7:    51.167 -  58.477:   42        |
|      3:    21.929 -  29.238:  104   |   8:    58.477 -  65.786:   14        |
|      4:    29.238 -  36.548:  113   |   9:    65.786 -  73.096:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1602             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1601             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1601   ksol= 0.33   Bsol= 49.90   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,3.22,4.09,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1600   ksol= 0.33   Bsol= 49.90   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,3.23,4.10,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160594                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.068370              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.333  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.495212              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.036   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4241 = 2.07 * 0.50 * 5.1710 + 1.00 * 0.0763                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4022 = 2.07 * 0.50 * 5.1621 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5681 = 0.50 * 1.00 * 5.1621 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5698 = 0.50 * 1.00 * 5.1561 + 1.00 * 0.0164                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.06   11.39    None  None   None       |
|    all(noH): 2823   0      0.00    76.06   11.39    None  None   None       |
|    Sol.    : 438    0      1.15    73.11   33.33    None  None   None       |
|    Mac.    : 2385   0      0.00    76.06   7.37     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 -   7.606: 1661   |   5:    38.031 -  45.637:   82        |
|      1:     7.606 -  15.212:  557   |   6:    45.637 -  53.243:   75        |
|      2:    15.212 -  22.818:  170   |   7:    53.243 -  60.849:   32        |
|      3:    22.818 -  30.425:  114   |   8:    60.849 -  68.455:   10        |
|      4:    30.425 -  38.031:  113   |   9:    68.455 -  76.061:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1129 r_free = 0.1599             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1129 r_free = 0.1599             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1599   ksol= 0.33   Bsol= 49.90   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,3.23,4.10,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158643                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7523 0.99   1386  155 0.1004 0.1355      5.3946      5.5402|
|  2:  4.7523 -  3.7915 0.99   1340  146 0.0887 0.1118       5.461      5.6451|
|  3:  3.7915 -  3.3180 0.99   1305  144 0.1056 0.1576      5.4814       5.895|
|  4:  3.3180 -  3.0173 0.99   1300  153 0.1208 0.1497      5.4619       5.566|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.1341 0.1830      5.3422      5.5878|
|  6:  2.8025 -  2.6381 0.99   1278  143 0.1210 0.1855      5.2165      5.4897|
|  7:  2.6381 -  2.5066 0.99   1289  136 0.1279 0.1610       5.189      5.3599|
|  8:  2.5066 -  2.3980 0.98   1263  151 0.1185 0.1762      5.0814      5.3685|
|  9:  2.3980 -  2.3060 0.98   1265  142 0.1199 0.1860      5.0669      5.3629|
| 10:  2.3060 -  2.2267 0.99   1274  135 0.1143 0.1703      4.9801      5.2053|
| 11:  2.2267 -  2.1572 0.98   1277  141 0.1165 0.1774       4.964      5.2985|
| 12:  2.1572 -  2.0957 0.97   1236  144 0.1114 0.1659      4.8923       5.125|
| 13:  2.0957 -  2.0407 1.00   1277  135 0.1175 0.1795      4.8072      5.1235|
| 14:  2.0407 -  1.9910 0.65    843   95 0.1012 0.1743      4.6473      4.9042|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7523  1386   155  0.94   9.17   0.98     0.95       7345.60|
|  2:  4.7523 -  3.7915  1340   146  0.95   8.13   1.01     1.00       9358.04|
|  3:  3.7915 -  3.3180  1305   144  0.93  11.43   1.02     1.01      10676.72|
|  4:  3.3180 -  3.0173  1300   153  0.92  13.83   1.00     0.98      10485.44|
|  5:  3.0173 -  2.8025  1297   139  0.90  16.17   0.99     0.96       8489.59|
|  6:  2.8025 -  2.6381  1278   143  0.90  15.96   0.98     0.96       7311.67|
|  7:  2.6381 -  2.5066  1289   136  0.90  15.69   0.99     0.96       6406.35|
|  8:  2.5066 -  2.3980  1263   151  0.90  15.65   0.99     0.96       5528.97|
|  9:  2.3980 -  2.3060  1265   142  0.90  15.90   1.00     0.98       5349.29|
| 10:  2.3060 -  2.2267  1274   135  0.90  15.79   1.00     0.96       4511.48|
| 11:  2.2267 -  2.1572  1277   141  0.90  16.70   1.00     0.96       4574.31|
| 12:  2.1572 -  2.0957  1236   144  0.92  14.92   1.00     0.99       4067.25|
| 13:  2.0957 -  2.0407  1277   135  0.90  16.73   1.00     0.99       3502.10|
| 14:  2.0407 -  1.9910   843    95  0.92  14.52   0.98     0.95       2500.34|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2500.34 max =        10676.72 mean =      6570.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.71 mean =        14.26|
|phase err.(test): min =        0.00 max =           87.87 mean =        13.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1599   ksol= 0.33   Bsol= 53.45   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,-0.33,0.56,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158655                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1599   ksol= 0.33   Bsol= 53.45   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,-0.33,0.56,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158655                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7523 0.99   1386  155 0.1004 0.1355      5.3946      5.5402|
|  2:  4.7523 -  3.7915 0.99   1340  146 0.0887 0.1117       5.461       5.645|
|  3:  3.7915 -  3.3180 0.99   1305  144 0.1055 0.1575      5.4813      5.8948|
|  4:  3.3180 -  3.0173 0.99   1300  153 0.1208 0.1497      5.4619       5.566|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.1341 0.1830      5.3423      5.5879|
|  6:  2.8025 -  2.6381 0.99   1278  143 0.1210 0.1854      5.2166      5.4894|
|  7:  2.6381 -  2.5066 0.99   1289  136 0.1279 0.1610      5.1889      5.3597|
|  8:  2.5066 -  2.3980 0.98   1263  151 0.1185 0.1762      5.0813      5.3686|
|  9:  2.3980 -  2.3060 0.98   1265  142 0.1199 0.1859      5.0669      5.3628|
| 10:  2.3060 -  2.2267 0.99   1274  135 0.1143 0.1703      4.9801      5.2055|
| 11:  2.2267 -  2.1572 0.98   1277  141 0.1165 0.1775      4.9641      5.2987|
| 12:  2.1572 -  2.0957 0.97   1236  144 0.1114 0.1658      4.8925      5.1252|
| 13:  2.0957 -  2.0407 1.00   1277  135 0.1175 0.1796      4.8072      5.1238|
| 14:  2.0407 -  1.9910 0.65    843   95 0.1012 0.1743      4.6472       4.904|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7523  1386   155  0.94   9.17   0.98     0.95       7344.80|
|  2:  4.7523 -  3.7915  1340   146  0.95   8.13   1.01     1.00       9356.09|
|  3:  3.7915 -  3.3180  1305   144  0.93  11.43   1.02     1.01      10673.68|
|  4:  3.3180 -  3.0173  1300   153  0.92  13.83   1.00     0.98      10486.31|
|  5:  3.0173 -  2.8025  1297   139  0.90  16.17   0.99     0.96       8488.91|
|  6:  2.8025 -  2.6381  1278   143  0.90  15.96   0.98     0.96       7311.95|
|  7:  2.6381 -  2.5066  1289   136  0.90  15.69   0.99     0.96       6404.58|
|  8:  2.5066 -  2.3980  1263   151  0.90  15.65   0.99     0.96       5528.29|
|  9:  2.3980 -  2.3060  1265   142  0.90  15.90   1.00     0.98       5348.20|
| 10:  2.3060 -  2.2267  1274   135  0.90  15.80   1.00     0.96       4512.59|
| 11:  2.2267 -  2.1572  1277   141  0.90  16.70   1.00     0.96       4575.66|
| 12:  2.1572 -  2.0957  1236   144  0.92  14.92   1.00     0.99       4069.96|
| 13:  2.0957 -  2.0407  1277   135  0.90  16.73   1.00     0.99       3502.66|
| 14:  2.0407 -  1.9910   843    95  0.92  14.52   0.98     0.95       2499.77|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2499.77 max =        10673.68 mean =      6570.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.71 mean =        14.26|
|phase err.(test): min =        0.00 max =           87.87 mean =        13.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.55    79.61   14.95    None  None   None       |
|    all(noH): 2823   0      3.55    79.61   14.95    None  None   None       |
|    Sol.    : 438    0      4.70    76.66   36.88    None  None   None       |
|    Mac.    : 2385   0      3.55    79.61   10.92    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:     3.553 -  11.159: 1661   |   5:    41.583 -  49.189:   82        |
|      1:    11.159 -  18.765:  557   |   6:    49.189 -  56.795:   75        |
|      2:    18.765 -  26.371:  170   |   7:    56.795 -  64.402:   32        |
|      3:    26.371 -  33.977:  114   |   8:    64.402 -  72.008:   10        |
|      4:    33.977 -  41.583:  113   |   9:    72.008 -  79.614:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.356 - 5.853
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 308
   mapped sites are within: 0.703 - 5.853

peak=   10.517 closest distance to " CG2 VAL A 230 " =    1.374
peak=    7.054 closest distance to " CG2 VAL A 296 " =    1.116
peak=    6.150 closest distance to " CG  LEU A   5 " =    1.238
peak=    5.865 closest distance to " NH2 ARG A  56 " =    2.255
peak=    5.656 closest distance to " CD2 LEU A   5 " =    1.189
peak=    5.608 closest distance to " CB  GLN A 223 " =    1.440
peak=    5.603 closest distance to " CG  LEU A 228 " =    1.172
peak=    4.985 closest distance to " O   HOH Z 232 " =    2.282
peak=    4.909 closest distance to " CB  SER A  63 " =    1.324
peak=    4.882 closest distance to " CB  VAL A 230 " =    1.183
peak=    4.830 closest distance to " CB  VAL A 296 " =    1.085
peak=    4.823 closest distance to " CB  GLN A 183 " =    1.264
peak=    4.718 closest distance to " CG  PRO A 213 " =    1.201
peak=    4.683 closest distance to " O   HOH Z 126 " =    1.906
peak=    4.628 closest distance to " NE2 GLN A  11 " =    1.114
peak=    4.546 closest distance to " O   HOH Z 142 " =    1.672
peak=    4.516 closest distance to " CG  PRO A 243 " =    1.139
peak=    4.514 closest distance to " O   HOH Z 316 " =    3.041
peak=    4.498 closest distance to " CB  GLU A 152 " =    1.168
peak=    4.493 closest distance to " O   HOH Z 298 " =    1.797
peak=    4.475 closest distance to " OD1 ASN A  69 " =    2.662
peak=    4.434 closest distance to " O   HOH Z 369 " =    2.116
peak=    4.413 closest distance to " C   PRO A 198 " =    1.537
peak=    4.384 closest distance to " CB  ASN A 148 " =    1.377
peak=    4.381 closest distance to " CB  ARG A 275 " =    0.853
peak=    4.340 closest distance to " O   HOH Z 427 " =    3.098
peak=    4.329 closest distance to " CG  PRO A 198 " =    1.231
peak=    4.318 closest distance to " CD2 LEU A 228 " =    1.170
peak=    4.313 closest distance to " CB  GLU A 128 " =    1.069
peak=    4.287 closest distance to " CB  TYR A 169 " =    0.703
peak=    4.280 closest distance to " O   HOH Z 368 " =    2.181
peak=    4.270 closest distance to " O   HOH Z  54 " =    2.461
peak=    4.218 closest distance to " CB  TRP A 266 " =    0.982
peak=    4.208 closest distance to " O   HOH Z 403 " =    1.731
peak=    4.197 closest distance to " CB  ASP A 124 " =    0.717
peak=    4.190 closest distance to " O   HOH Z 272 " =    1.867
peak=    4.124 closest distance to " O   HOH Z 236 " =    1.885
peak=    4.123 closest distance to " O   HOH Z 425 " =    1.397
peak=    4.122 closest distance to " O   HOH Z 303 " =    2.092
peak=    4.115 closest distance to " CB  VAL A 265 " =    1.274
peak=    4.101 closest distance to " O   HOH Z 158 " =    3.052
peak=    4.096 closest distance to " CB  SER A   3 " =    1.369
peak=    4.086 closest distance to " ND2 ASN A 187 " =    1.468
peak=    4.065 closest distance to " CZ  PHE A 218 " =    1.062
peak=    4.061 closest distance to " CB  ASP A 140 " =    0.901
peak=    4.055 closest distance to " O   HOH Z  78 " =    1.697
peak=    4.019 closest distance to " CB  GLU A 277 " =    3.637
peak=    4.012 closest distance to " CD  ARG A  66 " =    2.548
peak=    4.011 closest distance to " NH1AARG A 145 " =    1.151
peak=    3.998 closest distance to " CB  ARG A  79 " =    1.440
peak=    3.997 closest distance to " O   HOH Z 411 " =    3.690
peak=    3.987 closest distance to " O   HOH Z  61 " =    1.678
peak=    3.983 closest distance to " CB  SER A 216 " =    0.846
peak=    3.969 closest distance to " O   SER A  87 " =    2.301
peak=    3.948 closest distance to " CB  ASN A 187 " =    1.111
peak=    3.945 closest distance to " CA  TYR A  30 " =    0.956
peak=    3.942 closest distance to " O   HOH Z 261 " =    2.076
peak=    3.938 closest distance to " O   HOH Z 346 " =    1.599
peak=    3.933 closest distance to " O   HOH Z 193 " =    1.890
peak=    3.924 closest distance to " O   HOH Z 280 " =    2.945
peak=    3.921 closest distance to " ND2 ASN A 249 " =    1.913
peak=    3.919 closest distance to " CA  ALA A  51 " =    1.037
peak=    3.915 closest distance to " CD  ARG A 159 " =    0.773
peak=    3.897 closest distance to " O   HOH Z 203 " =    1.749
peak=    3.884 closest distance to " O   HOH Z 193 " =    1.716
peak=    3.881 closest distance to " CB  PRO A  54 " =    0.794
peak=    3.846 closest distance to " CB  ASN A  39 " =    0.909
peak=    3.842 closest distance to " CB  SER A 212 " =    1.215
peak=    3.837 closest distance to " CA  ASN A 215 " =    1.213
peak=    3.828 closest distance to " CB  LEU A 143 " =    1.166
peak=    3.827 closest distance to " O   HOH Z  44 " =    2.256
peak=    3.827 closest distance to " OD2 ASP A 286 " =    2.880
peak=    3.827 closest distance to " CA  THR A 264 " =    0.754
peak=    3.818 closest distance to " O   HOH Z 112 " =    1.654
peak=    3.812 closest distance to " CZ  PHE A 192 " =    0.945
peak=    3.807 closest distance to " CB  LEU A 228 " =    1.237
peak=    3.804 closest distance to " NH2 ARG A 156 " =    1.126
peak=    3.796 closest distance to " CB  ALA A   9 " =    1.596
peak=    3.787 closest distance to " O   HOH Z 234 " =    3.702
peak=    3.768 closest distance to " O   HOH Z  15 " =    2.114
peak=    3.764 closest distance to " O   HOH Z  43 " =    1.860
peak=    3.758 closest distance to " O   HOH Z 193 " =    2.020
peak=    3.756 closest distance to " CD1 LEU A 300 " =    1.142
peak=    3.753 closest distance to " O   HOH Z  88 " =    3.289
peak=    3.747 closest distance to " O   HOH Z 189 " =    2.776
peak=    3.747 closest distance to " O   MET A 105 " =    1.793
peak=    3.744 closest distance to " O   HOH Z  68 " =    2.109
peak=    3.737 closest distance to " CG1BVAL A  72 " =    1.597
peak=    3.718 closest distance to " CG2 THR A 221 " =    1.153
peak=    3.709 closest distance to " O   HOH Z 247 " =    1.342
peak=    3.706 closest distance to " O   HOH Z 263 " =    1.626
peak=    3.705 closest distance to " O   HOH Z 197 " =    3.122
peak=    3.700 closest distance to " CG  LEU A 167 " =    1.186
peak=    3.698 closest distance to " CD BLYS A 290 " =    1.025
peak=    3.693 closest distance to " CA  SER A  87 " =    0.961
peak=    3.681 closest distance to " CG1 ILE A  33 " =    1.300
peak=    3.681 closest distance to " CB  ARG A 190 " =    1.651
peak=    3.675 closest distance to " CD  ARG A 269 " =    0.992
peak=    3.670 closest distance to " O   HOH Z 423 " =    1.673
peak=    3.670 closest distance to " CG2 VAL A 257 " =    0.911
peak=    3.663 closest distance to " CA  THR A 221 " =    0.913
peak=    3.656 closest distance to " O   HOH Z 126 " =    2.050
peak=    3.653 closest distance to " CA  ALA A  21 " =    1.181
peak=    3.650 closest distance to " O   TRP A 274 " =    1.877
peak=    3.646 closest distance to " CB  TRP A 179 " =    1.440
peak=    3.643 closest distance to " O   HOH Z 344 " =    2.975
peak=    3.639 closest distance to " CA  LYS A 117 " =    1.212
peak=    3.635 closest distance to " O   HOH Z 437 " =    1.863
peak=    3.635 closest distance to " CG1 VAL A 153 " =    0.909
peak=    3.623 closest distance to " O   GLN A 278 " =    1.352
peak=    3.621 closest distance to " O   HOH Z  40 " =    2.396
peak=    3.620 closest distance to " ND1 HIS A  81 " =    1.709
peak=    3.619 closest distance to " O   HOH Z 371 " =    3.150
peak=    3.619 closest distance to " CG  GLN A  88 " =    1.041
peak=    3.611 closest distance to " O   HOH Z  97 " =    2.057
peak=    3.608 closest distance to " N   VAL A 126 " =    1.343
peak=    3.608 closest distance to " CG  MET A 185 " =    1.191
peak=    3.591 closest distance to " CG BARG A 275 " =    1.528
peak=    3.586 closest distance to " CB  ALA A 248 " =    1.436
peak=    3.581 closest distance to " CA  ALA A 158 " =    1.160
peak=    3.579 closest distance to " O   HOH Z 132 " =    2.652
peak=    3.578 closest distance to " CB  MET A  40 " =    0.806
peak=    3.574 closest distance to " O   HOH Z 273 " =    2.639
peak=    3.567 closest distance to " O   HOH Z 133 " =    1.696
peak=    3.560 closest distance to " O   HOH Z 135 " =    1.846
peak=    3.545 closest distance to " O   HOH Z  59 " =    2.111
peak=    3.544 closest distance to " O   HOH Z 147 " =    1.731
peak=    3.535 closest distance to " CB  ALA A 291 " =    1.383
peak=    3.535 closest distance to " O   HOH Z 425 " =    2.046
peak=    3.533 closest distance to " O   HOH Z 368 " =    3.564
peak=    3.532 closest distance to " N   SER A 135 " =    1.373
peak=    3.532 closest distance to " O   HOH Z 128 " =    2.087
peak=    3.528 closest distance to " CB AVAL A  41 " =    1.251
peak=    3.527 closest distance to " CD  LYS A 166 " =    1.318
peak=    3.525 closest distance to " CA  MET A  40 " =    1.125
peak=    3.521 closest distance to " N   PHE A 130 " =    1.261
peak=    3.521 closest distance to " N   ASN A  39 " =    1.207
peak=    3.513 closest distance to " O   HOH Z 245 " =    1.406
peak=    3.510 closest distance to " O   ALA A 158 " =    1.408
peak=    3.507 closest distance to " NZ  LYS A 117 " =    3.301
peak=    3.507 closest distance to " CD2 LEU A 255 " =    1.632
peak=    3.501 closest distance to " CB  VAL A 202 " =    1.595
peak=    3.500 closest distance to " OG BSER A 164 " =    2.177
peak=    3.500 closest distance to " O   HOH Z 359 " =    3.853
peak=    3.497 closest distance to " CA  GLY A 267 " =    0.778
peak=    3.496 closest distance to " CA  ALA A 295 " =    1.060
peak=    3.496 closest distance to " CG1 VAL A 296 " =    1.212
peak=    3.494 closest distance to " O   HOH Z 214 " =    2.076
peak=    3.494 closest distance to " CE1 TYR A 186 " =    1.317
peak=    3.491 closest distance to " O   HOH Z 402 " =    1.486
peak=    3.490 closest distance to " CB  GLN A  88 " =    1.255
peak=    3.487 closest distance to " CB  ARG A 139 " =    0.897
peak=    3.481 closest distance to " OG  SER A  22 " =    2.864
peak=    3.480 closest distance to " CB  ASN A 142 " =    1.018
peak=    3.478 closest distance to " O   HOH Z 248 " =    1.758
peak=    3.472 closest distance to " CA  ARG A 195 " =    1.247
peak=    3.469 closest distance to " O   HOH Z 305 " =    3.541
peak=    3.468 closest distance to " CB  HIS A 108 " =    0.811
peak=    3.458 closest distance to " CD1 LEU A  96 " =    0.709
peak=    3.458 closest distance to " CE  LYS A  76 " =    0.876
peak=    3.456 closest distance to " CG1 ILE A 151 " =    1.025
peak=    3.456 closest distance to " CD1 LEU A   5 " =    1.333
peak=    3.456 closest distance to " CG2 THR A 220 " =    0.937
peak=    3.452 closest distance to " OG BSER A 134 " =    2.967
peak=    3.449 closest distance to " CA  LEU A 282 " =    1.014
peak=    3.445 closest distance to " O   HOH Z 290 " =    1.117
peak=    3.431 closest distance to " ND2 ASN A 110 " =    1.731
peak=    3.429 closest distance to " O   ASP A 124 " =    1.008
peak=    3.426 closest distance to " CB  VAL A 268 " =    0.871
peak=    3.422 closest distance to " O   HOH Z 426 " =    1.558
peak=    3.421 closest distance to " O   HOH Z  97 " =    2.666
peak=    3.414 closest distance to " CG  ARG A 138 " =    1.080
peak=    3.412 closest distance to " ND1 HIS A  86 " =    1.684
peak=    3.411 closest distance to " O   HOH Z 250 " =    1.323
peak=    3.411 closest distance to " CB  ALA A 242 " =    0.856
peak=    3.409 closest distance to " O   HOH Z 345 " =    3.498
peak=    3.402 closest distance to " CA  VAL A  41 " =    0.896
peak=    3.401 closest distance to " O   HOH Z 227 " =    1.635
peak=    3.400 closest distance to " O   HOH Z  10 " =    1.819
peak=    3.400 closest distance to " CB  THR A  82 " =    1.391
peak=    3.398 closest distance to " CB  LYS A 117 " =    1.175
peak=    3.397 closest distance to " CG  MET A 185 " =    1.064
peak=    3.392 closest distance to " O   HOH Z 171 " =    2.411
peak=    3.390 closest distance to " CB  ASN A 110 " =    1.230
peak=    3.389 closest distance to " O   HOH Z 329 " =    3.852
peak=    3.389 closest distance to " O   HOH Z 132 " =    3.103
peak=    3.385 closest distance to " O   HOH Z 383 " =    2.124
peak=    3.375 closest distance to " CB  THR A  31 " =    1.684
peak=    3.370 closest distance to " CA  ASP A 140 " =    1.237
peak=    3.367 closest distance to " O   HOH Z 145 " =    1.839
peak=    3.366 closest distance to " O   HOH Z 302 " =    1.927
peak=    3.365 closest distance to " CB  THR A 157 " =    1.133
peak=    3.364 closest distance to " CD1 ILE A  33 " =    1.616
peak=    3.360 closest distance to " O   HOH Z  21 " =    1.669
peak=    3.353 closest distance to " N   ARG A 156 " =    1.343
peak=    3.350 closest distance to " NE2 HIS A 207 " =    1.393
peak=    3.349 closest distance to " CB  ALA A  34 " =    0.798
peak=    3.348 closest distance to " O   HOH Z 126 " =    1.596
peak=    3.346 closest distance to " CB  TRP A 150 " =    1.392
peak=    3.346 closest distance to " O   HOH Z 172 " =    3.766
peak=    3.345 closest distance to " CB  ALA A 161 " =    0.896
peak=    3.344 closest distance to " O   HOH Z 180 " =    2.102
peak=    3.344 closest distance to " CA  ALA A 291 " =    0.952
peak=    3.337 closest distance to " O   HOH Z   1 " =    1.955
peak=    3.327 closest distance to " O   HOH Z 409 " =    3.176
peak=    3.324 closest distance to " CD1 ILE A 106 " =    0.994
peak=    3.319 closest distance to " O   HOH Z 313 " =    1.792
peak=    3.312 closest distance to " O   HOH Z 213 " =    1.767
peak=    3.308 closest distance to " CG1 ILE A  49 " =    1.442
peak=    3.307 closest distance to " CB  MET A  47 " =    1.111
peak=    3.307 closest distance to " CB  ILE A 120 " =    1.317
peak=    3.306 closest distance to " CA  ALA A 233 " =    1.393
peak=    3.305 closest distance to " O   HOH Z 313 " =    1.789
peak=    3.297 closest distance to " NH1 ARG A  56 " =    0.979
peak=    3.293 closest distance to " CA  ALA A 154 " =    1.032
peak=    3.292 closest distance to " CB  ALA A 137 " =    1.068
peak=    3.291 closest distance to " NH1 ARG A  14 " =    0.934
peak=    3.288 closest distance to " O   HOH Z 350 " =    1.606
peak=    3.283 closest distance to " OG  SER A 206 " =    1.200
peak=    3.280 closest distance to " CD2 TRP A 179 " =    1.386
peak=    3.279 closest distance to " CB  ALA A   1 " =    4.715
peak=    3.278 closest distance to " CB  ALA A 104 " =    0.727
peak=    3.277 closest distance to " CA  LYS A 290 " =    1.334
peak=    3.272 closest distance to " O   HOH Z 295 " =    1.474
peak=    3.269 closest distance to " CA  ASP A 191 " =    0.714
peak=    3.266 closest distance to " CA  ARG A  36 " =    1.119
peak=    3.266 closest distance to " CA  GLY A 211 " =    1.274
peak=    3.261 closest distance to " O   HOH Z 423 " =    2.836
peak=    3.261 closest distance to " CB  LEU A 237 " =    0.771
peak=    3.259 closest distance to " NH2 ARG A 219 " =    1.769
peak=    3.257 closest distance to " CG BARG A 102 " =    1.824
peak=    3.255 closest distance to " O   HOH Z 271 " =    2.553
peak=    3.254 closest distance to " O   HOH Z  19 " =    2.581
peak=    3.252 closest distance to " CD  ARG A 219 " =    1.078
peak=    3.252 closest distance to " O   HOH Z  58 " =    1.441
peak=    3.250 closest distance to " CG  LEU A   5 " =    0.766
peak=    3.249 closest distance to " N   GLN A 278 " =    1.015
peak=    3.248 closest distance to " CB  GLN A 278 " =    0.908
peak=    3.246 closest distance to " C   SER A  32 " =    1.005
peak=    3.243 closest distance to " O   HOH Z 285 " =    3.073
peak=    3.242 closest distance to " CG2AVAL A 121 " =    2.395
peak=    3.237 closest distance to " CD  LYS A 119 " =    1.540
peak=    3.237 closest distance to " CB  ALA A 248 " =    1.072
peak=    3.235 closest distance to " CB  TYR A  30 " =    1.484
peak=    3.234 closest distance to " CA  ILE A 106 " =    0.775
peak=    3.232 closest distance to " O   HOH Z 271 " =    2.048
peak=    3.232 closest distance to " O   HOH Z  20 " =    1.710
peak=    3.231 closest distance to " OH  TYR A 214 " =    1.189
peak=    3.229 closest distance to " O   HOH Z 291 " =    1.576
peak=    3.229 closest distance to " O   HOH Z 175 " =    2.179
peak=    3.228 closest distance to " CD2 HIS A  81 " =    1.070
peak=    3.225 closest distance to " CA  ALA A 299 " =    0.968
peak=    3.223 closest distance to " O   HOH Z 145 " =    3.591
peak=    3.222 closest distance to " CB  GLU A  46 " =    1.026
peak=    3.222 closest distance to " N   ASN A 127 " =    1.230
peak=    3.220 closest distance to " O   HOH Z 184 " =    1.427
peak=    3.219 closest distance to " O   HOH Z 128 " =    2.203
peak=    3.218 closest distance to " O   HOH Z 116 " =    1.756
peak=    3.214 closest distance to " CB  ALA A 114 " =    1.243
peak=    3.210 closest distance to " CG2 ILE A 120 " =    1.263
peak=    3.208 closest distance to " CB  LEU A 255 " =    0.805
peak=    3.206 closest distance to " O   HOH Z 303 " =    1.763
peak=    3.204 closest distance to " O   HOH Z  62 " =    2.184
peak=    3.204 closest distance to " CA  TYR A 116 " =    1.445
peak=    3.203 closest distance to " O   HOH Z 163 " =    1.542
peak=    3.194 closest distance to " O   HOH Z 227 " =    2.056
peak=    3.193 closest distance to " O   HOH Z 216 " =    2.733
peak=    3.190 closest distance to " O   HOH Z 355 " =    1.762
peak=    3.190 closest distance to " O   HOH Z 148 " =    3.318
peak=    3.187 closest distance to " O   HOH Z  80 " =    1.605
peak=    3.181 closest distance to " O   HOH Z 109 " =    2.596
peak=    3.177 closest distance to " N   TYR A  15 " =    0.795
peak=    3.177 closest distance to " O   HOH Z 133 " =    2.479
peak=    3.176 closest distance to " O   HOH Z 353 " =    2.724
peak=    3.176 closest distance to " CB  ASN A 224 " =    1.028
peak=    3.175 closest distance to " CB  GLN A  89 " =    1.145
peak=    3.167 closest distance to " O   ALA A   1 " =    1.605
peak=    3.167 closest distance to " OD1 ASN A 217 " =    1.638
peak=    3.166 closest distance to " O   HOH Z  48 " =    1.795
peak=    3.166 closest distance to " O   HOH Z  49 " =    2.725
peak=    3.158 closest distance to " O   HOH Z 187 " =    2.297
peak=    3.157 closest distance to " N   SER A 146 " =    1.732
peak=    3.154 closest distance to " O   HOH Z 294 " =    1.611
peak=    3.153 closest distance to " CE2 TYR A 186 " =    0.886
peak=    3.152 closest distance to " CB  TYR A 116 " =    0.875
peak=    3.150 closest distance to " O   HOH Z 435 " =    2.052
peak=    3.143 closest distance to " CG1 VAL A 174 " =    1.094
peak=    3.139 closest distance to " O   HOH Z 410 " =    1.438
peak=    3.137 closest distance to " CA  VAL A 126 " =    0.870
peak=    3.135 closest distance to " O   HOH Z 141 " =    1.655
peak=    3.122 closest distance to " O   HOH Z 329 " =    2.730
peak=    3.121 closest distance to " NE2 GLN A  58 " =    5.853
peak=    3.094 closest distance to " O   HOH Z  61 " =    1.570
peak=    3.093 closest distance to " CA  GLN A 194 " =    1.259
peak=    3.076 closest distance to " CG  LEU A  25 " =    1.939
peak=    3.074 closest distance to " CG  GLU A  37 " =    0.810
peak=    3.066 closest distance to " CA  ASN A 176 " =    1.112
peak=    3.055 closest distance to " O   HOH Z 156 " =    3.012
peak=    3.052 closest distance to " CB  ASN A 215 " =    1.150
peak=    3.041 closest distance to " O   HOH Z 201 " =    3.225
peak=    3.034 closest distance to " CB  ILE A  20 " =    1.443
peak=    3.029 closest distance to " CG  GLN A 278 " =    1.340
peak=    3.023 closest distance to " O   HOH Z 392 " =    1.948

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.522 - 5.498
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 210
   mapped sites are within: 0.764 - 5.498

peak=   -5.234 closest distance to " CG2 VAL A 230 " =    0.835
peak=   -4.397 closest distance to " CD  ARG A 156 " =    1.983
peak=   -4.153 closest distance to " CG  GLN A 223 " =    2.052
peak=   -4.139 closest distance to " O   ILE A 109 " =    2.608
peak=   -4.120 closest distance to " SG  CYS A 254 " =    3.317
peak=   -4.081 closest distance to " O   HOH Z 290 " =    1.185
peak=   -4.067 closest distance to " O   HOH Z 266 " =    5.058
peak=   -4.015 closest distance to " CE2 TYR A  30 " =    2.826
peak=   -4.010 closest distance to " CB  PRO A 243 " =    2.633
peak=   -3.990 closest distance to " O   HOH Z 231 " =    1.723
peak=   -3.987 closest distance to " N   ALA A  43 " =    2.437
peak=   -3.925 closest distance to " O   HOH Z  52 " =    1.615
peak=   -3.896 closest distance to " O   HOH Z 389 " =    1.924
peak=   -3.859 closest distance to " O   HOH Z 118 " =    3.095
peak=   -3.858 closest distance to " CZ3 TRP A 179 " =    1.180
peak=   -3.846 closest distance to " O   HOH Z 351 " =    1.489
peak=   -3.845 closest distance to " CG  ASP A 231 " =    0.764
peak=   -3.839 closest distance to " O   PRO A 163 " =    2.050
peak=   -3.833 closest distance to " CG2 VAL A 296 " =    1.422
peak=   -3.831 closest distance to " OG BSER A 134 " =    1.204
peak=   -3.831 closest distance to " CG1 VAL A 296 " =    1.385
peak=   -3.802 closest distance to " C   HIS A 108 " =    1.163
peak=   -3.787 closest distance to " CG2BVAL A  41 " =    2.631
peak=   -3.776 closest distance to " CB  PRO A 163 " =    2.562
peak=   -3.766 closest distance to " NH2AARG A 275 " =    5.358
peak=   -3.753 closest distance to " CD1 LEU A 228 " =    2.356
peak=   -3.733 closest distance to " CB  ALA A  43 " =    2.527
peak=   -3.729 closest distance to " OD1 ASN A 148 " =    1.477
peak=   -3.721 closest distance to " CD2 LEU A 300 " =    2.846
peak=   -3.717 closest distance to " O   HOH Z 435 " =    2.804
peak=   -3.693 closest distance to " N   ALA A 226 " =    2.153
peak=   -3.691 closest distance to " C   ALA A 158 " =    1.326
peak=   -3.684 closest distance to " O   HOH Z 103 " =    1.838
peak=   -3.673 closest distance to " CG  ARG A 269 " =    2.346
peak=   -3.664 closest distance to " OG  SER A  87 " =    1.506
peak=   -3.661 closest distance to " O   HOH Z 211 " =    1.537
peak=   -3.653 closest distance to " CG1 VAL A 250 " =    2.741
peak=   -3.652 closest distance to " O   SER A 271 " =    2.286
peak=   -3.647 closest distance to " CD1 LEU A 101 " =    2.511
peak=   -3.643 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -3.642 closest distance to " O   HOH Z 166 " =    1.969
peak=   -3.633 closest distance to " CG  LEU A 101 " =    2.491
peak=   -3.631 closest distance to " O   HOH Z 394 " =    1.525
peak=   -3.627 closest distance to " CD  GLN A  58 " =    1.063
peak=   -3.624 closest distance to " CG1 VAL A 112 " =    2.977
peak=   -3.614 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.612 closest distance to " O   HOH Z 377 " =    2.032
peak=   -3.605 closest distance to " OG  SER A  97 " =    2.227
peak=   -3.603 closest distance to " O   HOH Z  11 " =    1.953
peak=   -3.601 closest distance to " N   THR A 157 " =    1.514
peak=   -3.595 closest distance to " O   HOH Z 241 " =    1.183
peak=   -3.576 closest distance to " O   PRO A 198 " =    1.222
peak=   -3.570 closest distance to " O   HOH Z 275 " =    1.481
peak=   -3.562 closest distance to " O   HOH Z 185 " =    2.301
peak=   -3.550 closest distance to " CG  MET A 105 " =    0.970
peak=   -3.549 closest distance to " CG  PHE A 283 " =    2.845
peak=   -3.547 closest distance to " O   HOH Z 196 " =    2.200
peak=   -3.542 closest distance to " ND2 ASN A  45 " =    1.191
peak=   -3.540 closest distance to " O   HOH Z  43 " =    1.706
peak=   -3.539 closest distance to " O   GLY A 203 " =    2.374
peak=   -3.538 closest distance to " CA  ASP A  27 " =    2.472
peak=   -3.531 closest distance to " CA  GLY A 241 " =    3.020
peak=   -3.527 closest distance to " O   GLY A 196 " =    1.200
peak=   -3.525 closest distance to " CD1 TYR A 247 " =    2.864
peak=   -3.522 closest distance to " O   HOH Z 426 " =    1.656
peak=   -3.520 closest distance to " CG2 ILE A 263 " =    2.422
peak=   -3.510 closest distance to " CG1 VAL A 197 " =    2.302
peak=   -3.490 closest distance to " CG  TRP A 266 " =    1.783
peak=   -3.484 closest distance to " OD1 ASN A 187 " =    1.587
peak=   -3.483 closest distance to " OXT GLY A 302 " =    2.982
peak=   -3.475 closest distance to " CB  ALA A 291 " =    2.158
peak=   -3.471 closest distance to " O   VAL A 189 " =    2.594
peak=   -3.453 closest distance to " O   HOH Z  38 " =    1.630
peak=   -3.451 closest distance to " CB  PHE A 192 " =    1.849
peak=   -3.450 closest distance to " O   GLY A 211 " =    1.416
peak=   -3.450 closest distance to " CE  MET A 105 " =    2.149
peak=   -3.448 closest distance to " O   VAL A  67 " =    2.655
peak=   -3.446 closest distance to " N   GLN A  58 " =    1.817
peak=   -3.441 closest distance to " CE3 TRP A 150 " =    2.054
peak=   -3.435 closest distance to " CD  ARG A 139 " =    1.619
peak=   -3.432 closest distance to " C   ASN A 187 " =    1.790
peak=   -3.426 closest distance to " CD  LYS A 289 " =    2.553
peak=   -3.420 closest distance to " CD2 TYR A 293 " =    2.087
peak=   -3.420 closest distance to " CA  GLY A 203 " =    2.375
peak=   -3.419 closest distance to " CE BMET A  47 " =    1.706
peak=   -3.417 closest distance to " CB  ALA A 248 " =    2.088
peak=   -3.417 closest distance to " O   HOH Z  10 " =    1.517
peak=   -3.410 closest distance to " CE2 PHE A 218 " =    2.560
peak=   -3.410 closest distance to " O   HOH Z  60 " =    2.214
peak=   -3.408 closest distance to " CA  GLY A 241 " =    2.263
peak=   -3.407 closest distance to " NE2 GLN A  88 " =    2.172
peak=   -3.403 closest distance to " O   HOH Z 231 " =    1.237
peak=   -3.400 closest distance to " O   HOH Z 311 " =    3.808
peak=   -3.394 closest distance to " O   HOH Z 353 " =    2.156
peak=   -3.393 closest distance to " O   HOH Z  13 " =    1.370
peak=   -3.388 closest distance to " CD1 LEU A 101 " =    2.607
peak=   -3.388 closest distance to " O   HOH Z 407 " =    3.151
peak=   -3.384 closest distance to " OE1 GLN A  88 " =    1.102
peak=   -3.383 closest distance to " NZ  LYS A 119 " =    3.506
peak=   -3.382 closest distance to " NH2 ARG A  79 " =    2.000
peak=   -3.377 closest distance to " O   HOH Z 102 " =    1.659
peak=   -3.375 closest distance to " OG BSER A 134 " =    1.735
peak=   -3.373 closest distance to " O   GLY A  80 " =    2.514
peak=   -3.373 closest distance to " O   HOH Z 417 " =    2.850
peak=   -3.371 closest distance to " CG2 VAL A 112 " =    2.563
peak=   -3.370 closest distance to " O   HOH Z  44 " =    2.185
peak=   -3.368 closest distance to " O   HOH Z 372 " =    2.347
peak=   -3.360 closest distance to " OG  SER A  62 " =    1.668
peak=   -3.360 closest distance to " OD2 ASP A  50 " =    2.382
peak=   -3.359 closest distance to " NH2 ARG A  66 " =    1.995
peak=   -3.356 closest distance to " O   HOH Z 166 " =    1.550
peak=   -3.350 closest distance to " O   HOH Z  73 " =    2.211
peak=   -3.350 closest distance to " C   ASN A 285 " =    2.475
peak=   -3.349 closest distance to " O   HOH Z 222 " =    1.478
peak=   -3.345 closest distance to " OG  SER A  26 " =    1.309
peak=   -3.339 closest distance to " CB  ASP A 132 " =    2.314
peak=   -3.337 closest distance to " N   THR A  18 " =    1.345
peak=   -3.337 closest distance to " ND2 ASN A  60 " =    1.427
peak=   -3.335 closest distance to " CG  GLU A 277 " =    1.127
peak=   -3.332 closest distance to " N   THR A 235 " =    1.283
peak=   -3.330 closest distance to " CD2 LEU A 167 " =    1.775
peak=   -3.324 closest distance to " O   HOH Z 388 " =    2.088
peak=   -3.322 closest distance to " CG  HIS A  86 " =    0.944
peak=   -3.320 closest distance to " CB  TYR A  15 " =    2.215
peak=   -3.311 closest distance to " C   LEU A 222 " =    0.851
peak=   -3.311 closest distance to " O   HOH Z 184 " =    1.610
peak=   -3.306 closest distance to " N   SER A 212 " =    1.916
peak=   -3.304 closest distance to " O   HOH Z 436 " =    1.552
peak=   -3.296 closest distance to " OG  SER A 206 " =    1.752
peak=   -3.295 closest distance to " CE1 TYR A 169 " =    2.470
peak=   -3.294 closest distance to " O   HOH Z 292 " =    4.612
peak=   -3.294 closest distance to " CB  ALA A 291 " =    2.263
peak=   -3.294 closest distance to " CG  LEU A 228 " =    0.989
peak=   -3.284 closest distance to " C   MET A 188 " =    1.448
peak=   -3.283 closest distance to " O   HOH Z 198 " =    1.495
peak=   -3.282 closest distance to " N   PHE A  59 " =    2.189
peak=   -3.279 closest distance to " CD1 ILE A 199 " =    2.607
peak=   -3.276 closest distance to " O   HOH Z  98 " =    2.059
peak=   -3.270 closest distance to " C   ASP A 231 " =    2.602
peak=   -3.265 closest distance to " O   HOH Z 368 " =    1.664
peak=   -3.265 closest distance to " CB  VAL A 230 " =    1.037
peak=   -3.264 closest distance to " O   HOH Z 191 " =    5.498
peak=   -3.257 closest distance to " O   HOH Z 350 " =    1.739
peak=   -3.257 closest distance to " CD1 ILE A 239 " =    2.082
peak=   -3.256 closest distance to " O   HOH Z 174 " =    2.556
peak=   -3.251 closest distance to " CD2 PHE A  61 " =    2.385
peak=   -3.250 closest distance to " CZ  PHE A  59 " =    1.555
peak=   -3.249 closest distance to " CB  ASP A 132 " =    2.290
peak=   -3.242 closest distance to " O   PRO A 198 " =    1.321
peak=   -3.238 closest distance to " CG  PRO A 163 " =    2.479
peak=   -3.233 closest distance to " O   HOH Z 111 " =    2.341
peak=   -3.226 closest distance to " NE2 GLN A 194 " =    1.822
peak=   -3.226 closest distance to " CD  GLN A  88 " =    0.856
peak=   -3.222 closest distance to " CD  PRO A 213 " =    2.185
peak=   -3.220 closest distance to " NH1 ARG A 195 " =    2.574
peak=   -3.215 closest distance to " O   ALA A 161 " =    1.628
peak=   -3.214 closest distance to " CB  VAL A 296 " =    1.247
peak=   -3.214 closest distance to " C   LEU A 143 " =    1.140
peak=   -3.207 closest distance to " CB  ASN A  39 " =    2.183
peak=   -3.204 closest distance to " CZ2 TRP A  92 " =    2.829
peak=   -3.200 closest distance to " O   HOH Z 262 " =    2.827
peak=   -3.192 closest distance to " CD1 LEU A 297 " =    2.444
peak=   -3.191 closest distance to " N   ALA A 248 " =    1.683
peak=   -3.189 closest distance to " O   HOH Z 310 " =    2.048
peak=   -3.187 closest distance to " O   HOH Z 377 " =    1.622
peak=   -3.185 closest distance to " N   SER A 276 " =    1.333
peak=   -3.181 closest distance to " CB  TRP A  85 " =    2.456
peak=   -3.180 closest distance to " O   HOH Z 295 " =    1.440
peak=   -3.177 closest distance to " O   MET A  40 " =    2.694
peak=   -3.176 closest distance to " CB  ASN A  69 " =    1.180
peak=   -3.174 closest distance to " CD1 PHE A  59 " =    1.904
peak=   -3.174 closest distance to " OG ASER A 134 " =    1.477
peak=   -3.174 closest distance to " CB  ALA A 248 " =    2.442
peak=   -3.169 closest distance to " OD2 ASP A 171 " =    1.836
peak=   -3.167 closest distance to " CD2 LEU A   5 " =    1.259
peak=   -3.165 closest distance to " N   MET A 105 " =    2.678
peak=   -3.161 closest distance to " O   HOH Z 176 " =    0.954
peak=   -3.157 closest distance to " O   HOH Z 128 " =    2.452
peak=   -3.152 closest distance to " CD1 TYR A 247 " =    2.343
peak=   -3.151 closest distance to " CD1 ILE A 151 " =    2.363
peak=   -3.151 closest distance to " CA  SER A 135 " =    1.339
peak=   -3.148 closest distance to " OG1 THR A 246 " =    1.446
peak=   -3.143 closest distance to " CA  ASN A 127 " =    1.103
peak=   -3.136 closest distance to " O   HOH Z 140 " =    1.604
peak=   -3.134 closest distance to " NE2 GLN A  88 " =    0.991
peak=   -3.124 closest distance to " N   ALA A 248 " =    2.536
peak=   -3.123 closest distance to " CD  ARG A 195 " =    5.118
peak=   -3.119 closest distance to " O   HOH Z 234 " =    4.321
peak=   -3.117 closest distance to " CZ  TYR A 169 " =    1.672
peak=   -3.114 closest distance to " C   PHE A  59 " =    1.317
peak=   -3.109 closest distance to " O   HOH Z 396 " =    1.762
peak=   -3.108 closest distance to " O   HOH Z 308 " =    1.750
peak=   -3.105 closest distance to " CA  GLY A 133 " =    2.242
peak=   -3.099 closest distance to " O   HOH Z 123 " =    2.386
peak=   -3.099 closest distance to " O   VAL A 125 " =    2.318
peak=   -3.097 closest distance to " O   HOH Z  37 " =    2.207
peak=   -3.075 closest distance to " O   HOH Z 148 " =    1.734
peak=   -3.074 closest distance to " O   SER A  22 " =    2.202
peak=   -3.070 closest distance to " O   HOH Z 128 " =    4.237
peak=   -3.066 closest distance to " O   HOH Z 139 " =    2.999
peak=   -3.065 closest distance to " O   HOH Z  51 " =    1.309
peak=   -3.062 closest distance to " O   HOH Z   6 " =    1.851
peak=   -3.061 closest distance to " O   TRP A  70 " =    1.501
peak=   -3.049 closest distance to " ND2 ASN A  60 " =    1.781
peak=   -3.031 closest distance to " ND2 ASN A 249 " =    2.371
peak=   -3.015 closest distance to " O   HOH Z 313 " =    1.620
peak=   -2.999 closest distance to " O   HOH Z 417 " =    2.714

================= 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    :  0.4264 0.4147   6.219586e+00   6.197893e+00
   1_bss:  0.4186 0.4049   6.214670e+00   6.187235e+00
   1_xyz:  0.3097 0.3378   5.994080e+00   6.058289e+00
   1_adp:  0.2443 0.2819   5.796957e+00   5.925859e+00
   1_occ:  0.2437 0.2820   5.795834e+00   5.927278e+00
   2_bss:  0.2391 0.2759   5.794019e+00   5.922484e+00
   2_xyz:  0.1710 0.2127   5.496466e+00   5.674394e+00
   2_adp:  0.1615 0.2052   5.446509e+00   5.637726e+00
   2_occ:  0.1615 0.2052   5.446327e+00   5.638103e+00
   3_bss:  0.1606 0.2037   5.445898e+00   5.636537e+00
   3_xyz:  0.1355 0.1822   5.307338e+00   5.526906e+00
   3_adp:  0.1247 0.1720   5.238989e+00   5.472768e+00
   3_occ:  0.1247 0.1718   5.238498e+00   5.472164e+00
   4_bss:  0.1251 0.1717   5.238726e+00   5.471418e+00
   4_xyz:  0.1138 0.1630   5.168780e+00   5.421776e+00
   4_adp:  0.1139 0.1602   5.160804e+00   5.405550e+00
   4_occ:  0.1138 0.1601   5.160600e+00   5.405651e+00
   5_bss:  0.1138 0.1600   5.160594e+00   5.405607e+00
   5_xyz:  0.1138 0.1598   5.160397e+00   5.403736e+00
   5_adp:  0.1129 0.1599   5.158589e+00   5.406518e+00
   5_occ:  0.1129 0.1599   5.158643e+00   5.406657e+00
   5_bss:  0.1129 0.1599   5.158655e+00   5.406657e+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:  0.338  20.000   8.947   7.900   7.848   0.000   0.000   0.000
   1_xyz:  0.338  20.000   8.947   7.900   7.848   0.000   0.000   0.000
   1_adp:  0.338  20.000   8.947   7.900   7.848   0.000   0.000   0.000
   1_occ:  0.338  20.000   8.947   7.900   7.848   0.000   0.000   0.000
   2_bss:  0.343  49.900   5.591   4.349   5.067   0.000   0.000   0.000
   2_xyz:  0.343  49.900   5.591   4.349   5.067   0.000   0.000   0.000
   2_adp:  0.343  49.900   5.591   4.349   5.067   0.000   0.000   0.000
   2_occ:  0.343  49.900   5.591   4.349   5.067   0.000   0.000   0.000
   3_bss:  0.347  49.900   3.740   3.381   4.259   0.000   0.000   0.000
   3_xyz:  0.347  49.900   3.740   3.381   4.259   0.000   0.000   0.000
   3_adp:  0.347  49.900   3.740   3.381   4.259   0.000   0.000   0.000
   3_occ:  0.347  49.900   3.740   3.381   4.259   0.000   0.000   0.000
   4_bss:  0.328  49.900   3.436   3.223   4.094   0.000   0.000   0.000
   4_xyz:  0.328  49.900   3.436   3.223   4.094   0.000   0.000   0.000
   4_adp:  0.328  49.900   3.436   3.223   4.094   0.000   0.000   0.000
   4_occ:  0.328  49.900   3.436   3.223   4.094   0.000   0.000   0.000
   5_bss:  0.328  49.900   3.344   3.229   4.099   0.000   0.000   0.000
   5_xyz:  0.328  49.900   3.344   3.229   4.099   0.000   0.000   0.000
   5_adp:  0.328  49.900   3.344   3.229   4.099   0.000   0.000   0.000
   5_occ:  0.328  49.900   3.344   3.229   4.099   0.000   0.000   0.000
   5_bss:  0.328  53.452  -0.233  -0.328   0.561   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.948 0.5726  0.6383    50074.301
   1_bss:  46.074 0.5688  0.8124    47942.647
   1_xyz:  36.475 0.6832  0.9472    31381.832
   1_adp:  28.682 0.7730  1.0358    21246.649
   1_occ:  28.700 0.7727  1.0352    21279.014
   2_bss:  28.433 0.7755  0.9248    20947.152
   2_xyz:  20.411 0.8578  0.9904    11500.897
   2_adp:  19.318 0.8688  1.0075    10701.293
   2_occ:  19.323 0.8687  1.0074    10706.231
   3_bss:  19.286 0.8692  0.9640    10676.765
   3_xyz:  16.834 0.8914  0.9756     8502.127
   3_adp:  15.664 0.9016  0.9782     7571.491
   3_occ:  15.651 0.9017  0.9782     7561.647
   4_bss:  15.644 0.9017  0.9703     7546.929
   4_xyz:  14.640 0.9099  0.9744     6805.496
   4_adp:  14.239 0.9133  0.9761     6608.603
   4_occ:  14.248 0.9132  0.9758     6606.796
   5_bss:  14.248 0.9132  0.9748     6605.601
   5_xyz:  14.143 0.9142  0.9742     6549.568
   5_adp:  14.210 0.9137  0.9726     6571.244
   5_occ:  14.211 0.9137  0.9724     6571.651
   5_bss:  14.211 0.9137  0.9723     6571.375
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4002e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4002e+01
   1_xyz:   1.501  0.011  0.100 17.921  0.006  4.124   1.1661e-01
   1_adp:   1.501  0.011  0.100 17.921  0.006  4.124   1.1661e-01
   1_occ:   1.501  0.011  0.100 17.921  0.006  4.124   1.1661e-01
   2_bss:   1.501  0.011  0.100 17.921  0.006  4.124   1.1661e-01
   2_xyz:   0.936  0.006  0.069 16.197  0.004  4.125   5.8418e-02
   2_adp:   0.936  0.006  0.069 16.197  0.004  4.125   5.8418e-02
   2_occ:   0.936  0.006  0.069 16.197  0.004  4.125   5.8418e-02
   3_bss:   0.936  0.006  0.069 16.197  0.004  4.125   5.8418e-02
   3_xyz:   0.980  0.006  0.076 15.933  0.003  4.133   5.9309e-02
   3_adp:   0.980  0.006  0.076 15.933  0.003  4.133   5.9309e-02
   3_occ:   0.980  0.006  0.076 15.933  0.003  4.133   5.9309e-02
   4_bss:   0.980  0.006  0.076 15.933  0.003  4.133   5.9309e-02
   4_xyz:   1.117  0.009  0.091 16.108  0.004  4.114   7.6267e-02
   4_adp:   1.117  0.009  0.091 16.108  0.004  4.114   7.6267e-02
   4_occ:   1.117  0.009  0.091 16.108  0.004  4.114   7.6267e-02
   5_bss:   1.117  0.009  0.091 16.108  0.004  4.114   7.6267e-02
   5_xyz:   1.006  0.008  0.082 15.742  0.004  4.114   6.3668e-02
   5_adp:   1.006  0.008  0.082 15.742  0.004  4.114   6.3668e-02
   5_occ:   1.006  0.008  0.082 15.742  0.004  4.114   6.3668e-02
   5_bss:   1.006  0.008  0.082 15.742  0.004  4.114   6.3668e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0023e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0023e+00
   1_xyz:  12.801  0.137  0.414 88.177  0.040  2.272   8.7569e-02
   1_adp:  12.801  0.137  0.414 88.177  0.040  2.272   8.7569e-02
   1_occ:  12.801  0.137  0.414 88.177  0.040  2.272   8.7569e-02
   2_bss:  12.801  0.137  0.414 88.177  0.040  2.272   8.7569e-02
   2_xyz:   6.577  0.054  0.237 83.628  0.039  2.369   4.0669e-02
   2_adp:   6.577  0.054  0.237 83.628  0.039  2.369   4.0669e-02
   2_occ:   6.577  0.054  0.237 83.628  0.039  2.369   4.0669e-02
   3_bss:   6.577  0.054  0.237 83.628  0.039  2.369   4.0669e-02
   3_xyz:   7.942  0.054  0.416 82.126  0.034  2.405   3.7976e-02
   3_adp:   7.942  0.054  0.416 82.126  0.034  2.405   3.7976e-02
   3_occ:   7.942  0.054  0.416 82.126  0.034  2.405   3.7976e-02
   4_bss:   7.942  0.054  0.416 82.126  0.034  2.405   3.7976e-02
   4_xyz:   7.847  0.072  0.621 83.636  0.039  2.310   5.5100e-02
   4_adp:   7.847  0.072  0.621 83.636  0.039  2.310   5.5100e-02
   4_occ:   7.847  0.072  0.621 83.636  0.039  2.310   5.5100e-02
   5_bss:   7.847  0.072  0.621 83.636  0.039  2.310   5.5100e-02
   5_xyz:   7.707  0.043  0.541 83.767  0.038  2.354   3.9285e-02
   5_adp:   7.707  0.043  0.541 83.767  0.038  2.354   3.9285e-02
   5_occ:   7.707  0.043  0.541 83.767  0.038  2.354   3.9285e-02
   5_bss:   7.707  0.043  0.541 83.767  0.038  2.354   3.9285e-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:  51.37   0.00   9.91  48.39   0.00   6.95  51.37   0.00  26.02
   1_occ:  51.37   0.00   9.91  48.39   0.00   6.95  51.37   0.00  26.02
   2_bss:  51.37   0.00   9.91  48.39   0.00   6.95  51.37   0.00  26.02
   2_xyz:  51.37   0.00   9.91  48.39   0.00   6.95  51.37   0.00  26.02
   2_adp:  77.77   0.00  10.27  77.77   0.00   7.11  52.58   1.15  27.46
   2_occ:  77.77   0.00  10.27  77.77   0.00   7.11  52.58   1.15  27.46
   3_bss:  77.77   0.00  10.27  77.77   0.00   7.11  52.58   1.15  27.46
   3_xyz:  77.77   0.00  10.27  77.77   0.00   7.11  52.58   1.15  27.46
   3_adp:  79.70   0.00  11.82  70.94   0.00   7.51  79.70   0.46  35.32
   3_occ:  79.70   0.00  11.82  70.94   0.00   7.51  79.70   0.46  35.32
   4_bss:  79.70   0.00  11.82  70.94   0.00   7.51  79.70   0.46  35.32
   4_xyz:  79.70   0.00  11.82  70.94   0.00   7.51  79.70   0.46  35.32
   4_adp:  73.10   0.00  11.34  71.86   0.00   7.36  73.10   0.91  33.06
   4_occ:  73.10   0.00  11.34  71.86   0.00   7.36  73.10   0.91  33.06
   5_bss:  73.10   0.00  11.34  71.86   0.00   7.36  73.10   0.91  33.06
   5_xyz:  73.10   0.00  11.34  71.86   0.00   7.36  73.10   0.91  33.06
   5_adp:  76.06   0.00  11.39  76.06   0.00   7.37  73.11   1.15  33.33
   5_occ:  76.06   0.00  11.39  76.06   0.00   7.37  73.11   1.15  33.33
   5_bss:  79.61   3.55  14.95  79.61   3.55  10.92  76.66   4.70  36.88
------------------------------------------------------------------------
 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:    1.167    0.023    0.403
   1_adp:    1.167    0.023    0.403
   1_occ:    1.167    0.023    0.403
   2_bss:    1.167    0.023    0.403
   2_xyz:    1.448    0.038    0.492
   2_adp:    1.448    0.038    0.492
   2_occ:    1.448    0.038    0.492
   3_bss:    1.448    0.038    0.492
   3_xyz:    1.398    0.030    0.522
   3_adp:    1.398    0.030    0.522
   3_occ:    1.398    0.030    0.522
   4_bss:    1.398    0.030    0.522
   4_xyz:    1.579    0.041    0.547
   4_adp:    1.579    0.041    0.547
   4_occ:    1.579    0.041    0.547
   5_bss:    1.579    0.041    0.547
   5_xyz:    1.649    0.037    0.552
   5_adp:    1.649    0.037    0.552
   5_occ:    1.649    0.037    0.552
   5_bss:    1.649    0.037    0.552
------------------------------------------------------------------------

CPU time actual refinement: 330.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1027/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_1027/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1027/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1027/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1027/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.49 
  Macro-tasks:
    bulk solvent and scale       = 43.26  
    individual site refinement   = 137.60 
    weights calculation          = 32.14  
    collect and process          = 6.66   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 219.77 
  Micro-tasks:
    mask                            = 1.71   
    f_calc                          = 98.92  
    alpha_beta                      = 8.19   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 110.87 
    fmodel                         = 7.52   
    r_factors                      = 0.27   
    phase_errors                   = 11.04  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 239.98 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.596 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    652 calls, 98.57 s
gradients_fft:          597 calls, 96.95 s

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

# Date 2008-01-16 Time 03:01:31 PST -0800 (1200481291.07 s)
Start R-work = 0.4264, R-free = 0.4147 (no bulk solvent and anisotropic scale)
Final R-work = 0.1298, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.4186, R-free = 0.4049
Final R-work = 0.1129, R-free = 0.1599