# Date 2008-01-16 Time 01:22:55 PST -0800 (1200475375.21 s)
#phil __OFF__

Command line arguments: "../408.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23036
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 408

-------------------------------------------------------------------------------
  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: (69.5475, 46.6953, 84.6622, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8029 1.96114
Completeness in resolution range: 0.962888
Completeness with d_max=infinity: 0.959869

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8029
                             d_min =   1.9611

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: (69.5475, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8029 1.96114
Completeness in resolution range: 0.962888
Completeness with d_max=infinity: 0.959869

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8033 -  4.1961 [2129/2156]  1917   212  10.0%
  bin  2:  4.1961 -  3.3432 [2045/2061]  1839   206  10.1%
  bin  3:  3.3432 -  2.9243 [2033/2052]  1828   205  10.1%
  bin  4:  2.9243 -  2.6586 [2007/2037]  1809   198   9.9%
  bin  5:  2.6586 -  2.4690 [1996/2015]  1799   197   9.9%
  bin  6:  2.4690 -  2.3240 [1966/2002]  1772   194   9.9%
  bin  7:  2.3240 -  2.2080 [1974/2007]  1774   200  10.1%
  bin  8:  2.2080 -  2.1122 [1978/2012]  1777   201  10.2%
  bin  9:  2.1122 -  2.0311 [1958/1986]  1767   191   9.8%
  bin 10:  2.0311 -  1.9611 [1503/2016]  1348   155  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_408/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:
        1.55 -     2.22: 22
        2.22 -     2.89: 1352
        2.89 -     3.56: 4546
        3.56 -     4.23: 9359
        4.23 -     4.90: 13535
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.546 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.623 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.891 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.919 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28809 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_408/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_408/model_refine_001.geo

CPU time processing inputs: 8.68


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.69535 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4636   r_free= 0.4575   ksol= 0.00   Bsol= 0.00   scale= 0.816    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.261636                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8033 -  4.6799 0.99   1380  154 0.3834 0.3803      6.5597      6.5622|
|  2:  4.6799 -  3.7342 0.99   1346  146 0.3786 0.3612      6.7324      6.7394|
|  3:  3.7342 -  3.2680 0.99   1309  150 0.4150 0.3924      6.6379      6.7118|
|  4:  3.2680 -  2.9718 0.99   1297  142 0.4328 0.4468      6.4914      6.4684|
|  5:  2.9718 -  2.7603 0.99   1292  142 0.4826 0.4913      6.3594      6.3341|
|  6:  2.7603 -  2.5985 0.99   1285  145 0.4902 0.5579      6.2676      6.2777|
|  7:  2.5985 -  2.4690 0.99   1283  139 0.5015 0.4522      6.2402      6.1585|
|  8:  2.4690 -  2.3619 0.98   1273  148 0.5062 0.5180      6.1739      6.1522|
|  9:  2.3619 -  2.2714 0.98   1280  139 0.5127 0.4896        6.11      6.1156|
| 10:  2.2714 -  2.1932 0.98   1242  137 0.5206 0.5060      6.1124      6.0956|
| 11:  2.1932 -  2.1249 1.00   1284  143 0.5368 0.4996      6.0526      6.0269|
| 12:  2.1249 -  2.0643 0.97   1246  138 0.4987 0.4936      5.9776      6.0001|
| 13:  2.0643 -  2.0101 0.98   1257  144 0.5278 0.5301      5.8894      5.8578|
| 14:  2.0101 -  1.9611 0.66    856   92 0.5344 0.5089      5.8406      5.7595|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8033 -  4.6799  1380   154  0.68  35.86   0.81     0.72      74597.94|
|  2:  4.6799 -  3.7342  1346   146  0.71  34.27   0.90     0.79     101271.56|
|  3:  3.7342 -  3.2680  1309   150  0.62  41.93   0.87     0.75     105997.94|
|  4:  3.2680 -  2.9718  1297   142  0.56  47.44   0.84     0.66      93316.53|
|  5:  2.9718 -  2.7603  1292   142  0.46  54.89   0.75     0.56      77601.09|
|  6:  2.7603 -  2.5985  1285   145  0.43  57.43   0.75     0.51      68153.48|
|  7:  2.5985 -  2.4690  1283   139  0.42  58.47   0.74     0.48      61610.29|
|  8:  2.4690 -  2.3619  1273   148  0.42  58.50   0.75     0.49      55453.05|
|  9:  2.3619 -  2.2714  1280   139  0.43  57.78   0.75     0.51      48299.47|
| 10:  2.2714 -  2.1932  1242   137  0.45  56.37   0.77     0.53      42677.15|
| 11:  2.1932 -  2.1249  1284   143  0.42  58.49   0.78     0.52      40217.71|
| 12:  2.1249 -  2.0643  1246   138  0.40  59.73   0.78     0.50      39979.25|
| 13:  2.0643 -  2.0101  1257   144  0.33  65.52   0.76     0.42      36683.80|
| 14:  2.0101 -  1.9611   856    92  0.28  68.92   0.74     0.32      31120.06|
|alpha:            min =        0.32 max =            0.79 mean =         0.56|
|beta:             min =    31120.06 max =       105997.94 mean =     63842.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.38|
|phase err.(test): min =        0.00 max =           89.94 mean =        53.69|
|-----------------------------------------------------------------------------|

============================== 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 = 10.918744             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.757   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.955436              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.633   (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 |  0.953 -  1.348:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.348 -  1.742:       10 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.742 -  2.137:       75 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.137 -  2.532:      483 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.532 -  2.926:     1265 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.926 -  3.321:     2440 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.321 -  3.716:     3998 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.716 -  4.111:     5318 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.111 -  4.505:     6933 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.505 -  4.900:     8258 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.062 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  0.953 |       2.108 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.499)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.499)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4708   r_free= 0.4638   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.265007                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4543   r_free= 0.4461   ksol= 0.37   Bsol= 8.39   scale= 1.017    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.23,8.13,9.59,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.255865                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.396558              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.117   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.889639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.675   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4543      final r-factor (work) = 0.3684          |
| start r-factor (free) = 0.4461      final r-factor (free) = 0.3844          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.4942 = 9.40 * 0.50 * 6.2645 + 1.00 * 53.0617                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0558 = 9.40 * 0.50 * 6.1565 + 1.00 * 0.1307                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3684      final r-factor (work) = 0.3169          |
| start r-factor (free) = 0.3844      final r-factor (free) = 0.3607          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4914 = 0.89 * 1.00 * 6.1565 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3894 = 0.89 * 1.00 * 6.0420 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.499)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.37   12.32    None  None   None       |
|    all(noH): 2823   0      0.00    82.37   12.32    None  None   None       |
|    Sol.    : 438    0      0.00    73.76   27.07    None  None   None       |
|    Mac.    : 2385   0      0.00    82.37   9.61     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.237: 1326   |   5:    41.186 -  49.423:   55        |
|      1:     8.237 -  16.474:  762   |   6:    49.423 -  57.660:   21        |
|      2:    16.474 -  24.712:  359   |   7:    57.660 -  65.898:    8        |
|      3:    24.712 -  32.949:  182   |   8:    65.898 -  74.135:    5        |
|      4:    32.949 -  41.186:  104   |   9:    74.135 -  82.372:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3169 r_free = 0.3607             target_work(ml) = 6.017         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3163 r_free = 0.3612             target_work(ml) = 6.016         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3163   r_free= 0.3612   ksol= 0.37   Bsol= 8.39   scale= 1.111    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.23,8.13,9.59,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.016236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3112   r_free= 0.3569   ksol= 0.34   Bsol= 26.42   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.48,3.98,6.07,0.00,0.00,0.00); trace/3= 4.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.014522                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.324310              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.677   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.385702              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.941  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3112      final r-factor (work) = 0.2157          |
| start r-factor (free) = 0.3569      final r-factor (free) = 0.2666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2335 = 6.32 * 0.50 * 6.0411 + 1.00 * 0.1307                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.6138 = 6.32 * 0.50 * 5.8634 + 1.00 * 0.0729                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2157      final r-factor (work) = 0.1922          |
| start r-factor (free) = 0.2666      final r-factor (free) = 0.2396          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2757 = 0.39 * 1.00 * 5.8634 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1889 = 0.39 * 1.00 * 5.6495 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.499)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.88   12.27    None  None   None       |
|    all(noH): 2823   0      0.00    79.88   12.27    None  None   None       |
|    Sol.    : 438    0      1.66    65.77   32.08    None  None   None       |
|    Mac.    : 2385   0      0.00    79.88   8.63     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 -   7.988: 1478   |   5:    39.941 -  47.929:  103        |
|      1:     7.988 -  15.976:  691   |   6:    47.929 -  55.917:   33        |
|      2:    15.976 -  23.964:  219   |   7:    55.917 -  63.905:   14        |
|      3:    23.964 -  31.952:  142   |   8:    63.905 -  71.893:    4        |
|      4:    31.952 -  39.941:  137   |   9:    71.893 -  79.881:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1922 r_free = 0.2396             target_work(ml) = 5.597         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1918 r_free = 0.2396             target_work(ml) = 5.597         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1918   r_free= 0.2396   ksol= 0.34   Bsol= 26.42   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.48,3.98,6.07,0.00,0.00,0.00); trace/3= 4.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.596542                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1902   r_free= 0.2384   ksol= 0.33   Bsol= 33.12   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.57,3.75,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.594333                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.073430              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.847  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.297542              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.647  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1902      final r-factor (work) = 0.1469          |
| start r-factor (free) = 0.2384      final r-factor (free) = 0.1911          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9385 = 2.07 * 0.50 * 5.6578 + 1.00 * 0.0729                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7409 = 2.07 * 0.50 * 5.4839 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1469      final r-factor (work) = 0.1380          |
| start r-factor (free) = 0.1911      final r-factor (free) = 0.1820          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6414 = 0.30 * 1.00 * 5.4839 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5972 = 0.30 * 1.00 * 5.3356 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.499)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.90   12.44    None  None   None       |
|    all(noH): 2823   0      0.00    79.90   12.44    None  None   None       |
|    Sol.    : 438    0      2.65    63.82   34.40    None  None   None       |
|    Mac.    : 2385   0      0.00    79.90   8.41     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 -   7.990: 1563   |   5:    39.949 -  47.938:  108        |
|      1:     7.990 -  15.980:  638   |   6:    47.938 -  55.928:   59        |
|      2:    15.980 -  23.969:  181   |   7:    55.928 -  63.918:   27        |
|      3:    23.969 -  31.959:  118   |   8:    63.918 -  71.908:    2        |
|      4:    31.959 -  39.949:  125   |   9:    71.908 -  79.897:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1380 r_free = 0.1820             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1378 r_free = 0.1818             target_work(ml) = 5.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1378   r_free= 0.1818   ksol= 0.33   Bsol= 33.12   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.57,3.75,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.307438                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1811   ksol= 0.33   Bsol= 33.12   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.29,3.04,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.305334                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.507696              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.375  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.465608              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.925  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1376      final r-factor (work) = 0.1238          |
| start r-factor (free) = 0.1811      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0780 = 1.51 * 0.50 * 5.3357 + 1.00 * 0.0557                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0164 = 1.51 * 0.50 * 5.2584 + 1.00 * 0.0524                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1238      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4580 = 0.47 * 1.00 * 5.2584 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4324 = 0.47 * 1.00 * 5.2008 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.499)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.85   12.67    None  None   None       |
|    all(noH): 2823   0      0.00    83.85   12.67    None  None   None       |
|    Sol.    : 438    0      2.28    71.04   35.77    None  None   None       |
|    Mac.    : 2385   0      0.00    83.85   8.43     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.385: 1630   |   5:    41.926 -  50.312:   94        |
|      1:     8.385 -  16.771:  608   |   6:    50.312 -  58.697:   63        |
|      2:    16.771 -  25.156:  163   |   7:    58.697 -  67.082:   31        |
|      3:    25.156 -  33.541:  108   |   8:    67.082 -  75.467:    4        |
|      4:    33.541 -  41.926:  119   |   9:    75.467 -  83.853:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1639             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1639             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1639   ksol= 0.33   Bsol= 33.12   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.29,3.04,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.196088                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1639   ksol= 0.32   Bsol= 33.12   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.29,3.04,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.195682                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.290519              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.441  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.858440              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.915  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1639      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0083 = 2.29 * 0.50 * 5.2004 + 1.00 * 0.0524                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9727 = 2.29 * 0.50 * 5.1621 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4422 = 0.86 * 1.00 * 5.1621 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4216 = 0.86 * 1.00 * 5.1372 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.499)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.05   12.64    None  None   None       |
|    all(noH): 2823   0      0.00    88.05   12.64    None  None   None       |
|    Sol.    : 438    0      1.95    73.95   35.92    None  None   None       |
|    Mac.    : 2385   0      0.00    88.05   8.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.805: 1686   |   5:    44.023 -  52.827:   87        |
|      1:     8.805 -  17.609:  584   |   6:    52.827 -  61.632:   51        |
|      2:    17.609 -  26.414:  146   |   7:    61.632 -  70.436:   28        |
|      3:    26.414 -  35.218:  120   |   8:    70.436 -  79.241:    4        |
|      4:    35.218 -  44.023:  114   |   9:    79.241 -  88.045:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1108 r_free = 0.1593             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1592             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1592   ksol= 0.32   Bsol= 33.12   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,2.29,3.04,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139120                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8033 -  4.6799 0.99   1380  154 0.1013 0.1295      5.3956      5.5333|
|  2:  4.6799 -  3.7342 0.99   1346  146 0.0853 0.1110      5.4277      5.6167|
|  3:  3.7342 -  3.2680 0.99   1309  150 0.1047 0.1503      5.4602      5.8278|
|  4:  3.2680 -  2.9718 0.99   1297  142 0.1197 0.1648      5.4486      5.6278|
|  5:  2.9718 -  2.7603 0.99   1292  142 0.1256 0.1665      5.2955      5.4775|
|  6:  2.7603 -  2.5985 0.99   1285  145 0.1194 0.1818      5.1957      5.4455|
|  7:  2.5985 -  2.4690 0.99   1283  139 0.1217 0.1639      5.1493      5.3665|
|  8:  2.4690 -  2.3619 0.98   1273  148 0.1151 0.1790       5.078      5.3467|
|  9:  2.3619 -  2.2714 0.98   1280  139 0.1162 0.1852      5.0312      5.3251|
| 10:  2.2714 -  2.1932 0.98   1242  137 0.1105 0.1680      4.9595      5.1695|
| 11:  2.1932 -  2.1249 1.00   1284  143 0.1123 0.1813      4.9237      5.3175|
| 12:  2.1249 -  2.0643 0.97   1246  138 0.1091 0.1704      4.8795      5.1513|
| 13:  2.0643 -  2.0101 0.98   1257  144 0.1147 0.1808      4.8077      5.0794|
| 14:  2.0101 -  1.9611 0.66    856   92 0.1049 0.1691      4.6765      4.8973|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8033 -  4.6799  1380   154  0.94   9.10   0.99     0.97       7180.18|
|  2:  4.6799 -  3.7342  1346   146  0.96   7.65   1.03     1.01       8709.32|
|  3:  3.7342 -  3.2680  1309   150  0.93  11.32   1.04     1.03      10074.07|
|  4:  3.2680 -  2.9718  1297   142  0.92  13.31   1.02     1.01      10197.17|
|  5:  2.9718 -  2.7603  1292   142  0.90  15.40   1.00     0.97       7805.02|
|  6:  2.7603 -  2.5985  1285   145  0.90  15.59   0.99     0.95       6832.28|
|  7:  2.5985 -  2.4690  1283   139  0.91  15.46   0.99     0.97       6120.80|
|  8:  2.4690 -  2.3619  1273   148  0.91  15.53   1.00     0.97       5522.67|
|  9:  2.3619 -  2.2714  1280   139  0.91  15.46   1.01     1.00       5056.14|
| 10:  2.2714 -  2.1932  1242   137  0.91  15.32   1.01     0.98       4422.11|
| 11:  2.1932 -  2.1249  1284   143  0.90  16.29   1.01     0.97       4279.66|
| 12:  2.1249 -  2.0643  1246   138  0.91  15.12   1.02     1.00       4012.40|
| 13:  2.0643 -  2.0101  1257   144  0.90  16.44   1.02     1.01       3498.66|
| 14:  2.0101 -  1.9611   856    92  0.91  14.91   1.00     0.98       2641.85|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2641.85 max =        10197.17 mean =      6290.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.98|
|phase err.(test): min =        0.00 max =           89.46 mean =        13.51|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1591   ksol= 0.32   Bsol= 36.88   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.09,0.57,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140761                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1591   ksol= 0.32   Bsol= 36.88   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.09,0.57,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140761                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8033 -  4.6799 0.99   1380  154 0.1003 0.1310       5.403      5.5455|
|  2:  4.6799 -  3.7342 0.99   1346  146 0.0869 0.1120       5.445      5.6222|
|  3:  3.7342 -  3.2680 0.99   1309  150 0.1054 0.1495      5.4651      5.8205|
|  4:  3.2680 -  2.9718 0.99   1297  142 0.1201 0.1637      5.4494      5.6232|
|  5:  2.9718 -  2.7603 0.99   1292  142 0.1265 0.1667      5.2967      5.4807|
|  6:  2.7603 -  2.5985 0.99   1285  145 0.1191 0.1819      5.1942      5.4434|
|  7:  2.5985 -  2.4690 0.99   1283  139 0.1215 0.1639      5.1488      5.3683|
|  8:  2.4690 -  2.3619 0.98   1273  148 0.1154 0.1788      5.0773      5.3451|
|  9:  2.3619 -  2.2714 0.98   1280  139 0.1161 0.1847      5.0301      5.3235|
| 10:  2.2714 -  2.1932 0.98   1242  137 0.1101 0.1684      4.9572       5.169|
| 11:  2.1932 -  2.1249 1.00   1284  143 0.1118 0.1805      4.9231      5.3166|
| 12:  2.1249 -  2.0643 0.97   1246  138 0.1090 0.1708      4.8786       5.152|
| 13:  2.0643 -  2.0101 0.98   1257  144 0.1146 0.1803      4.8065      5.0767|
| 14:  2.0101 -  1.9611 0.66    856   92 0.1050 0.1687      4.6736      4.8958|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8033 -  4.6799  1380   154  0.94   9.22   0.98     0.96       7466.71|
|  2:  4.6799 -  3.7342  1346   146  0.95   7.78   1.03     1.01       8922.18|
|  3:  3.7342 -  3.2680  1309   150  0.93  11.31   1.04     1.03      10123.34|
|  4:  3.2680 -  2.9718  1297   142  0.92  13.30   1.02     1.01      10141.17|
|  5:  2.9718 -  2.7603  1292   142  0.90  15.42   1.00     0.97       7785.31|
|  6:  2.7603 -  2.5985  1285   145  0.90  15.60   0.99     0.95       6831.58|
|  7:  2.5985 -  2.4690  1283   139  0.91  15.43   1.00     0.97       6115.73|
|  8:  2.4690 -  2.3619  1273   148  0.91  15.51   1.00     0.97       5503.19|
|  9:  2.3619 -  2.2714  1280   139  0.91  15.45   1.02     1.00       5044.43|
| 10:  2.2714 -  2.1932  1242   137  0.91  15.33   1.01     0.98       4415.69|
| 11:  2.1932 -  2.1249  1284   143  0.90  16.30   1.01     0.98       4281.70|
| 12:  2.1249 -  2.0643  1246   138  0.91  15.11   1.02     1.00       4010.45|
| 13:  2.0643 -  2.0101  1257   144  0.90  16.39   1.02     1.01       3482.02|
| 14:  2.0101 -  1.9611   856    92  0.91  14.82   1.00     0.98       2617.50|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2617.50 max =        10141.17 mean =      6322.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.80 mean =        13.99|
|phase err.(test): min =        0.00 max =           88.53 mean =        13.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.499)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.42    90.46   15.06    None  None   None       |
|    all(noH): 2823   0      2.42    90.46   15.06    None  None   None       |
|    Sol.    : 438    0      4.37    76.36   38.33    None  None   None       |
|    Mac.    : 2385   0      2.42    90.46   10.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.417 -  11.222: 1686   |   5:    46.440 -  55.244:   87        |
|      1:    11.222 -  20.026:  584   |   6:    55.244 -  64.049:   51        |
|      2:    20.026 -  28.831:  146   |   7:    64.049 -  72.854:   28        |
|      3:    28.831 -  37.635:  120   |   8:    72.854 -  81.658:    4        |
|      4:    37.635 -  46.440:  114   |   9:    81.658 -  90.463:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.337 - 5.677
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 326 from: 328
   mapped sites are within: 0.717 - 5.677

peak=   10.946 closest distance to " CB  VAL A 230 " =    1.408
peak=    9.630 closest distance to " CG2 VAL A 296 " =    1.371
peak=    6.136 closest distance to " NH2 ARG A  56 " =    2.151
peak=    6.013 closest distance to " CG  LEU A   5 " =    1.178
peak=    5.947 closest distance to " NE2 GLN A  11 " =    1.153
peak=    5.598 closest distance to " O   HOH Z 124 " =    1.516
peak=    5.592 closest distance to " O   HOH Z 278 " =    1.306
peak=    5.566 closest distance to " O   HOH Z 193 " =    1.663
peak=    5.483 closest distance to " CD2 LEU A   5 " =    1.263
peak=    5.283 closest distance to " O   HOH Z 142 " =    1.789
peak=    5.134 closest distance to " CG  PRO A  54 " =    1.232
peak=    5.130 closest distance to " O   HOH Z 126 " =    1.974
peak=    5.067 closest distance to " O   HOH Z 209 " =    2.290
peak=    4.966 closest distance to " CB  GLN A 183 " =    1.303
peak=    4.888 closest distance to " CB  ARG A 275 " =    0.929
peak=    4.822 closest distance to " CB  GLN A 223 " =    1.468
peak=    4.807 closest distance to " O   HOH Z 272 " =    1.885
peak=    4.794 closest distance to " CG  LEU A 228 " =    1.209
peak=    4.783 closest distance to " O   HOH Z 202 " =    1.214
peak=    4.687 closest distance to " O   HOH Z 236 " =    1.412
peak=    4.681 closest distance to " O   HOH Z 427 " =    2.767
peak=    4.647 closest distance to " CG  PRO A 213 " =    1.220
peak=    4.608 closest distance to " O   HOH Z 132 " =    1.038
peak=    4.579 closest distance to " CB  VAL A 230 " =    1.133
peak=    4.556 closest distance to " CB  SER A  63 " =    1.226
peak=    4.456 closest distance to " O   HOH Z 263 " =    1.456
peak=    4.438 closest distance to " O   HOH Z 232 " =    2.299
peak=    4.398 closest distance to " O   HOH Z 316 " =    2.876
peak=    4.386 closest distance to " CB  PRO A  54 " =    0.975
peak=    4.383 closest distance to " O   HOH Z 368 " =    2.148
peak=    4.369 closest distance to " O   HOH Z  59 " =    1.840
peak=    4.353 closest distance to " O   HOH Z 203 " =    1.513
peak=    4.340 closest distance to " O   HOH Z 298 " =    1.812
peak=    4.318 closest distance to " O   SER A  87 " =    2.357
peak=    4.302 closest distance to " OD1 ASN A  69 " =    2.654
peak=    4.297 closest distance to " O   HOH Z 403 " =    1.745
peak=    4.283 closest distance to " O   PRO A 198 " =    1.534
peak=    4.283 closest distance to " CB  TYR A 169 " =    0.920
peak=    4.280 closest distance to " O   HOH Z  85 " =    1.269
peak=    4.257 closest distance to " O   HOH Z 411 " =    3.732
peak=    4.249 closest distance to " CB  VAL A 296 " =    0.982
peak=    4.241 closest distance to " CG  PRO A 198 " =    1.179
peak=    4.236 closest distance to " CB  SER A   3 " =    1.328
peak=    4.235 closest distance to " O   HOH Z 234 " =    3.678
peak=    4.217 closest distance to " CB  GLU A 152 " =    1.194
peak=    4.203 closest distance to " O   HOH Z 369 " =    2.023
peak=    4.191 closest distance to " O   HOH Z   9 " =    2.179
peak=    4.177 closest distance to " O   HOH Z  78 " =    1.726
peak=    4.171 closest distance to " CB  VAL A 265 " =    1.240
peak=    4.155 closest distance to " O   HOH Z  97 " =    1.964
peak=    4.141 closest distance to " O   HOH Z  93 " =    2.331
peak=    4.106 closest distance to " CD2 LEU A 228 " =    1.190
peak=    4.077 closest distance to " O   HOH Z 260 " =    1.346
peak=    4.050 closest distance to " O   HOH Z  44 " =    1.866
peak=    4.046 closest distance to " CB  GLN A  88 " =    1.238
peak=    4.040 closest distance to " O   HOH Z 303 " =    2.138
peak=    4.022 closest distance to " O   HOH Z  66 " =    2.198
peak=    4.016 closest distance to " O   HOH Z 345 " =    3.174
peak=    4.006 closest distance to " CG1BVAL A  72 " =    1.456
peak=    4.005 closest distance to " O   HOH Z 346 " =    1.543
peak=    4.005 closest distance to " CB  TRP A 179 " =    1.273
peak=    4.003 closest distance to " O   HOH Z 299 " =    4.200
peak=    4.000 closest distance to " CD1AILE A 234 " =    0.898
peak=    3.986 closest distance to " O   HOH Z 371 " =    3.111
peak=    3.975 closest distance to " O   HOH Z  48 " =    1.524
peak=    3.973 closest distance to " CB  VAL A 202 " =    1.695
peak=    3.971 closest distance to " CB  ASN A 148 " =    1.363
peak=    3.953 closest distance to " CB  ARG A  79 " =    1.447
peak=    3.944 closest distance to " CB BVAL A  41 " =    1.171
peak=    3.924 closest distance to " NZ  LYS A 117 " =    3.015
peak=    3.912 closest distance to " O   HOH Z  50 " =    1.503
peak=    3.888 closest distance to " O   HOH Z 344 " =    2.684
peak=    3.888 closest distance to " O   HOH Z 425 " =    1.331
peak=    3.868 closest distance to " O   HOH Z 250 " =    1.313
peak=    3.859 closest distance to " O   HOH Z  61 " =    1.597
peak=    3.857 closest distance to " O   HOH Z  43 " =    2.082
peak=    3.852 closest distance to " O   HOH Z 344 " =    1.283
peak=    3.851 closest distance to " CG  ARG A  66 " =    2.926
peak=    3.843 closest distance to " OE1 GLU A   2 " =    2.141
peak=    3.841 closest distance to " O   HOH Z 261 " =    1.581
peak=    3.832 closest distance to " CA  ALA A  21 " =    1.108
peak=    3.827 closest distance to " O   HOH Z   3 " =    1.864
peak=    3.826 closest distance to " O   HOH Z 287 " =    1.754
peak=    3.825 closest distance to " O   HOH Z 284 " =    2.924
peak=    3.818 closest distance to " OD2 ASP A 286 " =    2.641
peak=    3.815 closest distance to " O   HOH Z 352 " =    1.345
peak=    3.815 closest distance to " O   HOH Z 322 " =    2.088
peak=    3.808 closest distance to " CB  GLU A 128 " =    1.083
peak=    3.803 closest distance to " O   HOH Z  54 " =    1.555
peak=    3.793 closest distance to " OG BSER A 164 " =    2.143
peak=    3.786 closest distance to " ND2 ASN A 187 " =    1.577
peak=    3.782 closest distance to " O   HOH Z 123 " =    1.068
peak=    3.767 closest distance to " O   HOH Z 423 " =    1.836
peak=    3.761 closest distance to " O   HOH Z 128 " =    1.978
peak=    3.758 closest distance to " CB  ARG A 139 " =    1.015
peak=    3.748 closest distance to " O   HOH Z 214 " =    2.368
peak=    3.743 closest distance to " O   HOH Z 192 " =    1.413
peak=    3.740 closest distance to " O   HOH Z 189 " =    2.531
peak=    3.740 closest distance to " O   HOH Z 108 " =    1.092
peak=    3.736 closest distance to " CB  GLU A 277 " =    3.487
peak=    3.728 closest distance to " O   HOH Z 118 " =    1.491
peak=    3.721 closest distance to " O   HOH Z 143 " =    0.918
peak=    3.721 closest distance to " O   HOH Z  48 " =    1.439
peak=    3.717 closest distance to " CA  VAL A  41 " =    0.857
peak=    3.714 closest distance to " CA  TYR A  30 " =    1.013
peak=    3.712 closest distance to " O   HOH Z 273 " =    2.781
peak=    3.692 closest distance to " CE1 TYR A 186 " =    1.266
peak=    3.691 closest distance to " O   HOH Z 392 " =    2.956
peak=    3.686 closest distance to " O   HOH Z 284 " =    1.578
peak=    3.685 closest distance to " CA  PHE A 283 " =    1.302
peak=    3.681 closest distance to " O   HOH Z 402 " =    1.364
peak=    3.673 closest distance to " CB  TRP A 266 " =    1.078
peak=    3.673 closest distance to " O   HOH Z 108 " =    2.112
peak=    3.669 closest distance to " CG2 ILE A  20 " =    1.561
peak=    3.660 closest distance to " O   HOH Z 407 " =    2.371
peak=    3.657 closest distance to " CD BLYS A 290 " =    1.210
peak=    3.653 closest distance to " CD  ARG A 269 " =    1.072
peak=    3.650 closest distance to " O   LYS A 290 " =    2.365
peak=    3.638 closest distance to " N   ASN A  39 " =    1.174
peak=    3.636 closest distance to " CG AARG A 275 " =    1.027
peak=    3.635 closest distance to " CA  ARG A 275 " =    1.950
peak=    3.635 closest distance to " O   HOH Z 326 " =    1.336
peak=    3.632 closest distance to " C   LYS A 290 " =    1.304
peak=    3.632 closest distance to " O   HOH Z 213 " =    1.746
peak=    3.630 closest distance to " CG2 VAL A 257 " =    0.828
peak=    3.627 closest distance to " NH2BARG A 145 " =    2.081
peak=    3.624 closest distance to " CB  LEU A 255 " =    0.772
peak=    3.621 closest distance to " O   HOH Z 134 " =    1.344
peak=    3.621 closest distance to " O   HOH Z 227 " =    2.197
peak=    3.616 closest distance to " O   HOH Z 193 " =    1.974
peak=    3.610 closest distance to " CA  VAL A 126 " =    0.999
peak=    3.604 closest distance to " CD2 TRP A 179 " =    1.426
peak=    3.600 closest distance to " O   HOH Z 276 " =    1.309
peak=    3.600 closest distance to " CG  ARG A  66 " =    0.955
peak=    3.595 closest distance to " O   HOH Z 128 " =    2.001
peak=    3.582 closest distance to " O   HOH Z 366 " =    2.828
peak=    3.580 closest distance to " O   HOH Z 118 " =    1.426
peak=    3.576 closest distance to " O   HOH Z 193 " =    1.781
peak=    3.574 closest distance to " CZ AARG A 102 " =    1.707
peak=    3.573 closest distance to " O   HOH Z 151 " =    1.714
peak=    3.571 closest distance to " O   HOH Z  40 " =    1.360
peak=    3.570 closest distance to " O   HOH Z 144 " =    2.259
peak=    3.563 closest distance to " O   HOH Z 374 " =    2.425
peak=    3.560 closest distance to " O   HOH Z 248 " =    1.744
peak=    3.560 closest distance to " O   HOH Z 227 " =    1.812
peak=    3.548 closest distance to " O   HOH Z  61 " =    1.562
peak=    3.547 closest distance to " CB  SER A  26 " =    1.560
peak=    3.542 closest distance to " O   HOH Z 158 " =    2.945
peak=    3.538 closest distance to " O   HOH Z 280 " =    1.602
peak=    3.536 closest distance to " O   HOH Z 303 " =    1.667
peak=    3.530 closest distance to " CG  LEU A 167 " =    1.138
peak=    3.518 closest distance to " O   HOH Z 422 " =    2.585
peak=    3.517 closest distance to " CA  LYS A 117 " =    1.251
peak=    3.514 closest distance to " O   HOH Z 334 " =    1.375
peak=    3.507 closest distance to " O   HOH Z 426 " =    1.458
peak=    3.506 closest distance to " O   HOH Z 357 " =    1.864
peak=    3.506 closest distance to " O   HOH Z 173 " =    2.166
peak=    3.496 closest distance to " CG  GLN A  77 " =    2.357
peak=    3.492 closest distance to " O   HOH Z 180 " =    2.174
peak=    3.490 closest distance to " O   HOH Z 148 " =    3.295
peak=    3.489 closest distance to " CG1 ILE A  33 " =    1.335
peak=    3.483 closest distance to " O   HOH Z 265 " =    2.353
peak=    3.482 closest distance to " O   HOH Z  59 " =    2.104
peak=    3.479 closest distance to " C   ALA A 299 " =    0.967
peak=    3.454 closest distance to " NH1 ARG A 138 " =    1.222
peak=    3.446 closest distance to " CB  ASN A 148 " =    1.871
peak=    3.439 closest distance to " CA  ASN A 215 " =    1.114
peak=    3.434 closest distance to " NH1 ARG A  14 " =    1.018
peak=    3.433 closest distance to " O   MET A 105 " =    1.860
peak=    3.428 closest distance to " CG2 ILE A 120 " =    1.269
peak=    3.427 closest distance to " O   HOH Z  10 " =    1.768
peak=    3.426 closest distance to " CA  ALA A  51 " =    0.985
peak=    3.422 closest distance to " CB  ASN A  39 " =    0.852
peak=    3.419 closest distance to " O   HOH Z 172 " =    3.724
peak=    3.414 closest distance to " CG2 THR A 221 " =    1.173
peak=    3.409 closest distance to " O   HOH Z 329 " =    3.592
peak=    3.401 closest distance to " O   HOH Z 222 " =    2.332
peak=    3.395 closest distance to " CE  MET A  93 " =    1.409
peak=    3.394 closest distance to " CE AMET A  47 " =    1.522
peak=    3.393 closest distance to " CG  PRO A 243 " =    1.228
peak=    3.388 closest distance to " CD1 LEU A 228 " =    1.670
peak=    3.386 closest distance to " CB  ARG A 102 " =    0.717
peak=    3.382 closest distance to " CA  GLN A 194 " =    1.243
peak=    3.382 closest distance to " O   HOH Z 368 " =    3.696
peak=    3.380 closest distance to " CB  LEU A 143 " =    1.167
peak=    3.378 closest distance to " N   ARG A 156 " =    1.264
peak=    3.377 closest distance to " C   ALA A   1 " =    1.781
peak=    3.375 closest distance to " CD2 HIS A  81 " =    1.075
peak=    3.373 closest distance to " O   SER A  26 " =    1.528
peak=    3.372 closest distance to " CB  ARG A 190 " =    1.780
peak=    3.367 closest distance to " O   HOH Z 389 " =    1.209
peak=    3.364 closest distance to " CD1 ILE A  33 " =    1.654
peak=    3.364 closest distance to " O   HOH Z 425 " =    2.064
peak=    3.359 closest distance to " CE2 TRP A 179 " =    1.643
peak=    3.357 closest distance to " O   HOH Z 405 " =    1.059
peak=    3.353 closest distance to " O   HOH Z 133 " =    1.385
peak=    3.350 closest distance to " NH1BARG A 145 " =    1.364
peak=    3.349 closest distance to " O   HOH Z  43 " =    2.695
peak=    3.349 closest distance to " O   HOH Z 380 " =    1.692
peak=    3.346 closest distance to " CA  THR A 221 " =    0.931
peak=    3.346 closest distance to " O   HOH Z 249 " =    1.132
peak=    3.344 closest distance to " CB  VAL A 268 " =    0.836
peak=    3.342 closest distance to " CA  ALA A 248 " =    1.399
peak=    3.338 closest distance to " CB  THR A  31 " =    1.713
peak=    3.336 closest distance to " O   HOH Z 280 " =    2.448
peak=    3.335 closest distance to " O   HOH Z 383 " =    1.797
peak=    3.335 closest distance to " NE2 GLN A  58 " =    5.665
peak=    3.335 closest distance to " CA  ALA A 158 " =    1.179
peak=    3.334 closest distance to " OD1BASN A 224 " =    2.140
peak=    3.332 closest distance to " O   HOH Z  88 " =    3.009
peak=    3.330 closest distance to " N   SER A 135 " =    1.294
peak=    3.326 closest distance to " CB  ASN A 142 " =    1.047
peak=    3.320 closest distance to " O   HOH Z  30 " =    2.276
peak=    3.316 closest distance to " CA  THR A 264 " =    0.763
peak=    3.314 closest distance to " CD  LYS A 119 " =    1.556
peak=    3.312 closest distance to " CB  GLN A 278 " =    0.840
peak=    3.310 closest distance to " O   HOH Z 247 " =    1.218
peak=    3.308 closest distance to " CG1BVAL A 121 " =    1.094
peak=    3.304 closest distance to " CD  GLN A 194 " =    1.420
peak=    3.303 closest distance to " O   HOH Z 435 " =    2.111
peak=    3.302 closest distance to " O   HOH Z 286 " =    2.320
peak=    3.301 closest distance to " O   HOH Z 327 " =    1.555
peak=    3.295 closest distance to " NZ  LYS A  76 " =    1.351
peak=    3.291 closest distance to " N   PHE A 130 " =    1.386
peak=    3.289 closest distance to " CG AARG A 275 " =    1.180
peak=    3.288 closest distance to " O   HOH Z 255 " =    1.614
peak=    3.287 closest distance to " CG  MET A 185 " =    1.072
peak=    3.283 closest distance to " O   HOH Z 313 " =    1.812
peak=    3.281 closest distance to " CG  MET A 185 " =    1.230
peak=    3.278 closest distance to " OD1 ASP A 286 " =    1.652
peak=    3.277 closest distance to " CB  ILE A  20 " =    1.432
peak=    3.277 closest distance to " O   HOH Z 214 " =    1.108
peak=    3.272 closest distance to " CA  LEU A 101 " =    1.533
peak=    3.271 closest distance to " CG  GLU A 277 " =    2.079
peak=    3.268 closest distance to " O   HOH Z 185 " =    1.548
peak=    3.266 closest distance to " O   HOH Z 145 " =    1.935
peak=    3.262 closest distance to " O   HOH Z  40 " =    2.368
peak=    3.262 closest distance to " CD1 ILE A 106 " =    1.206
peak=    3.261 closest distance to " NZ  LYS A 119 " =    1.479
peak=    3.261 closest distance to " CB  LEU A 228 " =    1.418
peak=    3.260 closest distance to " CZ2 TRP A 274 " =    1.735
peak=    3.260 closest distance to " O   HOH Z  40 " =    1.494
peak=    3.259 closest distance to " O   HOH Z 209 " =    2.331
peak=    3.258 closest distance to " O   HOH Z 406 " =    1.610
peak=    3.257 closest distance to " O   HOH Z   1 " =    1.759
peak=    3.254 closest distance to " CD2 LEU A 297 " =    0.993
peak=    3.254 closest distance to " O   HOH Z 271 " =    1.749
peak=    3.254 closest distance to " O   HOH Z  11 " =    1.433
peak=    3.247 closest distance to " CB  ALA A 248 " =    1.016
peak=    3.245 closest distance to " CE1 HIS A 108 " =    1.156
peak=    3.229 closest distance to " O   HOH Z 417 " =    1.925
peak=    3.228 closest distance to " CB  TYR A  30 " =    1.563
peak=    3.228 closest distance to " CB  ALA A   9 " =    1.582
peak=    3.227 closest distance to " OG  SER A  22 " =    2.738
peak=    3.226 closest distance to " CD  LYS A 166 " =    1.339
peak=    3.226 closest distance to " O   HOH Z 211 " =    2.365
peak=    3.222 closest distance to " O   HOH Z 112 " =    1.610
peak=    3.221 closest distance to " O   HOH Z 245 " =    1.347
peak=    3.220 closest distance to " CA  ASP A 140 " =    1.161
peak=    3.216 closest distance to " ND1 HIS A  81 " =    1.486
peak=    3.214 closest distance to " CA  ARG A  36 " =    0.999
peak=    3.213 closest distance to " CB  ALA A 291 " =    1.389
peak=    3.212 closest distance to " OG  SER A  62 " =    2.952
peak=    3.210 closest distance to " O   HOH Z 419 " =    1.609
peak=    3.208 closest distance to " O   HOH Z 189 " =    2.554
peak=    3.207 closest distance to " O   HOH Z 194 " =    1.919
peak=    3.202 closest distance to " O   HOH Z 359 " =    1.986
peak=    3.199 closest distance to " O   HOH Z 371 " =    3.383
peak=    3.198 closest distance to " CB  GLN A 205 " =    1.250
peak=    3.197 closest distance to " OD1 ASN A  45 " =    1.313
peak=    3.195 closest distance to " O   HOH Z 411 " =    1.731
peak=    3.189 closest distance to " O   HOH Z 132 " =    2.504
peak=    3.189 closest distance to " CG  GLN A  88 " =    1.029
peak=    3.188 closest distance to " O   HOH Z 258 " =    2.220
peak=    3.188 closest distance to " O   HOH Z 367 " =    3.521
peak=    3.188 closest distance to " O   HOH Z 244 " =    1.583
peak=    3.186 closest distance to " O   HOH Z 281 " =    4.509
peak=    3.184 closest distance to " O   ASN A 217 " =    1.230
peak=    3.183 closest distance to " CA  ASN A 176 " =    1.043
peak=    3.173 closest distance to " CB  ALA A   1 " =    1.150
peak=    3.173 closest distance to " O   THR A  31 " =    1.588
peak=    3.171 closest distance to " CB  SER A 216 " =    0.805
peak=    3.170 closest distance to " O   HOH Z 433 " =    1.790
peak=    3.170 closest distance to " O   HOH Z  68 " =    2.707
peak=    3.167 closest distance to " OE2 GLU A  53 " =    2.005
peak=    3.167 closest distance to " CB  ALA A  84 " =    1.601
peak=    3.161 closest distance to " CB  ALA A 295 " =    1.348
peak=    3.148 closest distance to " O   HOH Z  71 " =    1.302
peak=    3.148 closest distance to " O   HOH Z 251 " =    1.573
peak=    3.144 closest distance to " O   HOH Z 437 " =    2.145
peak=    3.143 closest distance to " CA  ASN A 127 " =    1.031
peak=    3.142 closest distance to " CG  MET A 188 " =    1.301
peak=    3.141 closest distance to " CG  LEU A 281 " =    0.974
peak=    3.134 closest distance to " O   ALA A 165 " =    1.300
peak=    3.133 closest distance to " CA  ASP A 191 " =    0.945
peak=    3.130 closest distance to " O   HOH Z  89 " =    1.646
peak=    3.130 closest distance to " CE  LYS A  48 " =    1.472
peak=    3.129 closest distance to " O   HOH Z 337 " =    3.535
peak=    3.117 closest distance to " CB  ASP A 140 " =    0.724
peak=    3.109 closest distance to " O   HOH Z 189 " =    2.560
peak=    3.105 closest distance to " O   HOH Z 109 " =    2.553
peak=    3.101 closest distance to " CG1 ILE A 120 " =    1.256
peak=    3.100 closest distance to " NH2BARG A 190 " =    1.756
peak=    3.100 closest distance to " O   HOH Z 191 " =    1.384
peak=    3.096 closest distance to " O   HOH Z 171 " =    2.360
peak=    3.094 closest distance to " O   HOH Z 430 " =    5.677
peak=    3.094 closest distance to " CD2 TYR A  30 " =    0.971
peak=    3.094 closest distance to " CZ3 TRP A 274 " =    2.374
peak=    3.088 closest distance to " CB  ASN A 110 " =    1.177
peak=    3.087 closest distance to " CA  ALA A 295 " =    1.061
peak=    3.087 closest distance to " O   HOH Z 438 " =    2.222
peak=    3.081 closest distance to " CG2 THR A 294 " =    1.561
peak=    3.080 closest distance to " NH1BARG A 145 " =    2.000
peak=    3.079 closest distance to " O   HOH Z 389 " =    1.624
peak=    3.072 closest distance to " CA  LEU A 282 " =    1.163
peak=    3.071 closest distance to " O   HOH Z 423 " =    2.816
peak=    3.067 closest distance to " O   GLY A  91 " =    1.608
peak=    3.063 closest distance to " O   SER A 164 " =    1.325
peak=    3.060 closest distance to " O   HOH Z  59 " =    1.945
peak=    3.049 closest distance to " O   HOH Z 409 " =    3.474
peak=    3.048 closest distance to " CD  LYS A  76 " =    1.901
peak=    3.043 closest distance to " O   HOH Z 233 " =    1.531
peak=    3.039 closest distance to " CA  LEU A 300 " =    1.111
peak=    3.026 closest distance to " O   HOH Z 148 " =    2.204
peak=    3.025 closest distance to " O   HOH Z 289 " =    1.475
peak=    3.024 closest distance to " O   HOH Z   4 " =    1.490

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.621 - 5.963
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 187 from: 188
   mapped sites are within: 0.793 - 5.963

peak=   -4.849 closest distance to " CG2 VAL A 230 " =    0.805
peak=   -4.841 closest distance to " CD  ARG A 156 " =    2.082
peak=   -4.737 closest distance to " O   VAL A  67 " =    2.695
peak=   -4.668 closest distance to " SG  CYS A 254 " =    3.191
peak=   -4.392 closest distance to " O   HOH Z 266 " =    4.513
peak=   -4.337 closest distance to " CB  ALA A 161 " =    2.537
peak=   -4.198 closest distance to " O   PRO A 163 " =    1.990
peak=   -4.179 closest distance to " OXT GLY A 302 " =    2.800
peak=   -4.175 closest distance to " C   HIS A 108 " =    1.152
peak=   -4.045 closest distance to " O   HOH Z  43 " =    1.987
peak=   -4.042 closest distance to " N   ALA A 248 " =    1.632
peak=   -4.005 closest distance to " CD1 LEU A 255 " =    2.748
peak=   -4.002 closest distance to " N   GLN A  58 " =    1.755
peak=   -3.997 closest distance to " CE2 TYR A  30 " =    2.851
peak=   -3.963 closest distance to " O   HOH Z 290 " =    1.074
peak=   -3.939 closest distance to " O   VAL A  67 " =    2.855
peak=   -3.939 closest distance to " CG2 VAL A 296 " =    1.680
peak=   -3.933 closest distance to " CB  ALA A 248 " =    1.961
peak=   -3.933 closest distance to " OG BSER A 134 " =    1.167
peak=   -3.924 closest distance to " OD1 ASN A  39 " =    2.097
peak=   -3.895 closest distance to " CG  GLN A 223 " =    2.210
peak=   -3.875 closest distance to " O   HOH Z  11 " =    1.880
peak=   -3.863 closest distance to " O   HOH Z 362 " =    5.963
peak=   -3.862 closest distance to " O   HOH Z 231 " =    1.820
peak=   -3.834 closest distance to " O   PRO A 198 " =    1.278
peak=   -3.832 closest distance to " CG  LYS A 193 " =    2.214
peak=   -3.821 closest distance to " O   HOH Z  98 " =    1.897
peak=   -3.817 closest distance to " O   HOH Z 102 " =    1.739
peak=   -3.814 closest distance to " CD1 LEU A 101 " =    2.430
peak=   -3.783 closest distance to " NH2 ARG A  79 " =    1.919
peak=   -3.773 closest distance to " O   HOH Z 166 " =    2.044
peak=   -3.767 closest distance to " O   HOH Z 165 " =    1.977
peak=   -3.759 closest distance to " O   ALA A   8 " =    1.826
peak=   -3.751 closest distance to " CB  ASP A 132 " =    2.285
peak=   -3.736 closest distance to " N   SER A 276 " =    1.175
peak=   -3.730 closest distance to " O   HOH Z 389 " =    4.620
peak=   -3.725 closest distance to " O   ALA A 161 " =    1.630
peak=   -3.710 closest distance to " CB  ASN A  39 " =    2.110
peak=   -3.705 closest distance to " CG  PHE A 283 " =    2.595
peak=   -3.694 closest distance to " O   HOH Z 166 " =    1.525
peak=   -3.685 closest distance to " N   HIS A 115 " =    1.932
peak=   -3.673 closest distance to " ND2 ASN A  45 " =    1.072
peak=   -3.671 closest distance to " OD2 ASP A  50 " =    1.502
peak=   -3.671 closest distance to " O   HOH Z 198 " =    2.167
peak=   -3.669 closest distance to " O   ASN A 187 " =    1.453
peak=   -3.649 closest distance to " CZ  TYR A 169 " =    1.708
peak=   -3.645 closest distance to " C   ASN A 187 " =    1.861
peak=   -3.640 closest distance to " CB  PRO A 280 " =    2.037
peak=   -3.617 closest distance to " CB  PRO A 243 " =    2.581
peak=   -3.610 closest distance to " ND2 ASN A 187 " =    1.663
peak=   -3.608 closest distance to " CE2 PHE A 218 " =    2.595
peak=   -3.602 closest distance to " CG  ASP A  50 " =    2.310
peak=   -3.602 closest distance to " CG  LEU A 228 " =    1.049
peak=   -3.602 closest distance to " CB  ALA A  51 " =    1.821
peak=   -3.589 closest distance to " CD1 LEU A 228 " =    2.081
peak=   -3.588 closest distance to " O   HOH Z 191 " =    5.112
peak=   -3.581 closest distance to " O   HOH Z 193 " =    1.647
peak=   -3.572 closest distance to " C   ASN A 285 " =    2.257
peak=   -3.572 closest distance to " O   ALA A  51 " =    1.292
peak=   -3.553 closest distance to " CD2 LEU A 300 " =    2.820
peak=   -3.552 closest distance to " CD  GLN A  88 " =    1.000
peak=   -3.551 closest distance to " O   HOH Z  13 " =    1.419
peak=   -3.551 closest distance to " CD1 PHE A  59 " =    1.888
peak=   -3.548 closest distance to " CB  PHE A 192 " =    1.760
peak=   -3.547 closest distance to " O   HOH Z  11 " =    1.914
peak=   -3.534 closest distance to " O   HOH Z  63 " =    1.106
peak=   -3.515 closest distance to " O   HOH Z 103 " =    1.793
peak=   -3.509 closest distance to " O   HOH Z  19 " =    2.260
peak=   -3.509 closest distance to " O   HOH Z 423 " =    2.233
peak=   -3.503 closest distance to " CA  ASP A 298 " =    1.033
peak=   -3.497 closest distance to " O   HOH Z 134 " =    2.694
peak=   -3.491 closest distance to " C   ALA A 158 " =    1.231
peak=   -3.486 closest distance to " O   MET A  40 " =    2.574
peak=   -3.485 closest distance to " O   HOH Z 385 " =    1.915
peak=   -3.482 closest distance to " O   HOH Z 350 " =    2.029
peak=   -3.479 closest distance to " C   GLN A 205 " =    1.920
peak=   -3.477 closest distance to " O   HOH Z 388 " =    2.052
peak=   -3.468 closest distance to " O   HOH Z 234 " =    4.051
peak=   -3.464 closest distance to " OG  SER A 206 " =    1.525
peak=   -3.448 closest distance to " O   HOH Z 132 " =    0.793
peak=   -3.447 closest distance to " O   HOH Z 339 " =    1.812
peak=   -3.447 closest distance to " O   HOH Z  47 " =    1.497
peak=   -3.439 closest distance to " O   HOH Z 114 " =    2.655
peak=   -3.429 closest distance to " OG ASER A 134 " =    1.161
peak=   -3.425 closest distance to " CB  ASP A 132 " =    2.163
peak=   -3.423 closest distance to " O   HOH Z 407 " =    3.013
peak=   -3.419 closest distance to " CG  ARG A 219 " =    2.760
peak=   -3.417 closest distance to " CG  ASP A 231 " =    0.808
peak=   -3.415 closest distance to " OXT GLY A 302 " =    3.656
peak=   -3.408 closest distance to " CD  LYS A 289 " =    2.537
peak=   -3.408 closest distance to " N   ALA A  43 " =    2.736
peak=   -3.393 closest distance to " OD1 ASP A 200 " =    1.279
peak=   -3.393 closest distance to " O   TRP A  92 " =    1.678
peak=   -3.392 closest distance to " CA  ASP A  27 " =    2.379
peak=   -3.389 closest distance to " CG2 VAL A 189 " =    1.987
peak=   -3.389 closest distance to " C   LEU A 143 " =    1.068
peak=   -3.385 closest distance to " CZ  PHE A  59 " =    1.446
peak=   -3.383 closest distance to " O   HOH Z 211 " =    1.522
peak=   -3.379 closest distance to " CG1 VAL A 112 " =    2.746
peak=   -3.374 closest distance to " O   HOH Z 423 " =    1.100
peak=   -3.374 closest distance to " CB  ALA A 291 " =    2.411
peak=   -3.371 closest distance to " OG  SER A   3 " =    1.381
peak=   -3.352 closest distance to " O   HOH Z 389 " =    1.861
peak=   -3.347 closest distance to " O   HOH Z 427 " =    1.558
peak=   -3.347 closest distance to " O   HOH Z  97 " =    1.464
peak=   -3.342 closest distance to " C   ASP A 231 " =    2.561
peak=   -3.340 closest distance to " O   HOH Z 148 " =    1.893
peak=   -3.340 closest distance to " N   THR A 157 " =    1.392
peak=   -3.337 closest distance to " O   SER A  22 " =    2.310
peak=   -3.333 closest distance to " OD2 ASP A 191 " =    1.467
peak=   -3.320 closest distance to " O   HOH Z 250 " =    1.408
peak=   -3.315 closest distance to " O   VAL A 197 " =    1.225
peak=   -3.312 closest distance to " OG  SER A  97 " =    2.068
peak=   -3.308 closest distance to " N   ALA A 226 " =    1.930
peak=   -3.306 closest distance to " O   SER A 135 " =    1.584
peak=   -3.306 closest distance to " O   HOH Z 385 " =    2.089
peak=   -3.303 closest distance to " OG BSER A 134 " =    1.601
peak=   -3.299 closest distance to " CA  GLY A 133 " =    1.882
peak=   -3.296 closest distance to " CG2 VAL A 296 " =    1.043
peak=   -3.292 closest distance to " CG  GLU A   2 " =    2.044
peak=   -3.289 closest distance to " CB  PRO A 163 " =    2.619
peak=   -3.285 closest distance to " O   HOH Z 351 " =    1.525
peak=   -3.284 closest distance to " O   HOH Z  93 " =    1.236
peak=   -3.281 closest distance to " CG  GLU A 152 " =    2.382
peak=   -3.269 closest distance to " O   PRO A 198 " =    1.305
peak=   -3.269 closest distance to " OE1 GLN A  88 " =    1.094
peak=   -3.268 closest distance to " CD  ARG A 139 " =    1.694
peak=   -3.268 closest distance to " O   HOH Z 281 " =    2.947
peak=   -3.266 closest distance to " NH2AARG A 275 " =    5.037
peak=   -3.264 closest distance to " OG  SER A  62 " =    1.565
peak=   -3.261 closest distance to " OH  TYR A 214 " =    1.313
peak=   -3.259 closest distance to " CD  GLN A  58 " =    1.239
peak=   -3.259 closest distance to " O   HOH Z 198 " =    1.436
peak=   -3.248 closest distance to " ND2 ASN A 142 " =    1.928
peak=   -3.245 closest distance to " CG  MET A 105 " =    0.928
peak=   -3.243 closest distance to " CA  GLY A 203 " =    2.241
peak=   -3.239 closest distance to " CD1 TYR A 247 " =    2.372
peak=   -3.239 closest distance to " CB  ILE A  33 " =    2.869
peak=   -3.237 closest distance to " O   HOH Z 394 " =    1.576
peak=   -3.231 closest distance to " ND2 ASN A  60 " =    1.382
peak=   -3.231 closest distance to " CG  TRP A 266 " =    1.888
peak=   -3.229 closest distance to " CE1 PHE A 208 " =    2.243
peak=   -3.220 closest distance to " O   HOH Z 313 " =    1.780
peak=   -3.210 closest distance to " OD1 ASN A 249 " =    1.126
peak=   -3.208 closest distance to " O   HOH Z 431 " =    1.637
peak=   -3.206 closest distance to " O   HOH Z 310 " =    1.663
peak=   -3.202 closest distance to " O   HOH Z 436 " =    1.481
peak=   -3.201 closest distance to " O   HOH Z 344 " =    2.412
peak=   -3.200 closest distance to " O   HOH Z 140 " =    1.680
peak=   -3.199 closest distance to " OG1 THR A  82 " =    1.375
peak=   -3.199 closest distance to " CG2 ILE A 263 " =    2.221
peak=   -3.196 closest distance to " CE  MET A 105 " =    2.012
peak=   -3.195 closest distance to " O   HOH Z 139 " =    3.048
peak=   -3.194 closest distance to " O   HOH Z 210 " =    1.166
peak=   -3.174 closest distance to " ND2 ASN A  45 " =    1.130
peak=   -3.173 closest distance to " O   HOH Z 377 " =    0.931
peak=   -3.164 closest distance to " CA  ASN A 127 " =    1.105
peak=   -3.164 closest distance to " ND2 ASN A  39 " =    1.313
peak=   -3.164 closest distance to " CA  GLY A  35 " =    2.012
peak=   -3.158 closest distance to " OE1 GLN A  77 " =    1.692
peak=   -3.155 closest distance to " O   TRP A  70 " =    1.499
peak=   -3.154 closest distance to " O   GLY A  80 " =    2.524
peak=   -3.153 closest distance to " O   HOH Z  44 " =    2.091
peak=   -3.149 closest distance to " O   HOH Z 211 " =    1.359
peak=   -3.147 closest distance to " CD1 ILE A 239 " =    2.573
peak=   -3.141 closest distance to " O   HOH Z 150 " =    1.742
peak=   -3.141 closest distance to " OD1 ASP A 191 " =    1.483
peak=   -3.139 closest distance to " CE3 TRP A 274 " =    2.349
peak=   -3.138 closest distance to " OG1 THR A 178 " =    1.140
peak=   -3.136 closest distance to " O   HOH Z 166 " =    2.113
peak=   -3.118 closest distance to " CE2 TRP A 179 " =    1.369
peak=   -3.116 closest distance to " CE BMET A  47 " =    1.317
peak=   -3.116 closest distance to " OD1 ASN A 301 " =    1.964
peak=   -3.113 closest distance to " O   HOH Z 222 " =    1.501
peak=   -3.098 closest distance to " O   HOH Z 137 " =    1.598
peak=   -3.097 closest distance to " O   SER A 146 " =    0.898
peak=   -3.095 closest distance to " CD2 LEU A 237 " =    2.833
peak=   -3.093 closest distance to " CG2BVAL A  72 " =    2.040
peak=   -3.086 closest distance to " CG  PRO A 163 " =    2.668
peak=   -3.086 closest distance to " CG  ASN A  45 " =    1.875
peak=   -3.082 closest distance to " CD2 LEU A 237 " =    2.712
peak=   -3.072 closest distance to " O   VAL A 174 " =    1.911
peak=   -3.065 closest distance to " O   HOH Z 353 " =    2.177
peak=   -3.051 closest distance to " N   GLN A  77 " =    1.577
peak=   -3.046 closest distance to " CB  LEU A  25 " =    2.347
peak=   -3.046 closest distance to " O   HOH Z 175 " =    4.335
peak=   -3.039 closest distance to " O   HOH Z 407 " =    3.435

================= 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    :  0.4636 0.4575   6.261636e+00   6.250390e+00
   1_bss:  0.4543 0.4461   6.255865e+00   6.236752e+00
   1_xyz:  0.3684 0.3844   6.124640e+00   6.151596e+00
   1_adp:  0.3169 0.3607   6.016879e+00   6.109395e+00
   1_occ:  0.3163 0.3612   6.016236e+00   6.110099e+00
   2_bss:  0.3112 0.3569   6.014522e+00   6.106515e+00
   2_xyz:  0.2157 0.2666   5.702716e+00   5.871010e+00
   2_adp:  0.1922 0.2396   5.597269e+00   5.776101e+00
   2_occ:  0.1918 0.2396   5.596542e+00   5.775708e+00
   3_bss:  0.1902 0.2384   5.594333e+00   5.773445e+00
   3_xyz:  0.1469 0.1911   5.364875e+00   5.570794e+00
   3_adp:  0.1380 0.1820   5.307899e+00   5.518329e+00
   3_occ:  0.1378 0.1818   5.307438e+00   5.517811e+00
   4_bss:  0.1376 0.1811   5.305334e+00   5.514369e+00
   4_xyz:  0.1238 0.1645   5.211951e+00   5.428226e+00
   4_adp:  0.1209 0.1639   5.196343e+00   5.417806e+00
   4_occ:  0.1208 0.1639   5.196088e+00   5.417493e+00
   5_bss:  0.1208 0.1639   5.195682e+00   5.417152e+00
   5_xyz:  0.1120 0.1586   5.142275e+00   5.384298e+00
   5_adp:  0.1108 0.1593   5.139546e+00   5.386852e+00
   5_occ:  0.1108 0.1592   5.139120e+00   5.386328e+00
   5_bss:  0.1110 0.1591   5.140761e+00   5.386448e+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:  0.369   8.389   7.227   8.131   9.595   0.000   0.000   0.000
   1_xyz:  0.369   8.389   7.227   8.131   9.595   0.000   0.000   0.000
   1_adp:  0.369   8.389   7.227   8.131   9.595   0.000   0.000   0.000
   1_occ:  0.369   8.389   7.227   8.131   9.595   0.000   0.000   0.000
   2_bss:  0.340  26.423   3.484   3.982   6.073   0.000   0.000   0.000
   2_xyz:  0.340  26.423   3.484   3.982   6.073   0.000   0.000   0.000
   2_adp:  0.340  26.423   3.484   3.982   6.073   0.000   0.000   0.000
   2_occ:  0.340  26.423   3.484   3.982   6.073   0.000   0.000   0.000
   3_bss:  0.328  33.121   2.135   2.572   3.754   0.000   0.000   0.000
   3_xyz:  0.328  33.121   2.135   2.572   3.754   0.000   0.000   0.000
   3_adp:  0.328  33.121   2.135   2.572   3.754   0.000   0.000   0.000
   3_occ:  0.328  33.121   2.135   2.572   3.754   0.000   0.000   0.000
   4_bss:  0.328  33.121   1.871   2.289   3.038   0.000   0.000   0.000
   4_xyz:  0.328  33.121   1.871   2.289   3.038   0.000   0.000   0.000
   4_adp:  0.328  33.121   1.871   2.289   3.038   0.000   0.000   0.000
   4_occ:  0.328  33.121   1.871   2.289   3.038   0.000   0.000   0.000
   5_bss:  0.320  33.121   1.871   2.289   3.038   0.000   0.000   0.000
   5_xyz:  0.320  33.121   1.871   2.289   3.038   0.000   0.000   0.000
   5_adp:  0.320  33.121   1.871   2.289   3.038   0.000   0.000   0.000
   5_occ:  0.320  33.121   1.871   2.289   3.038   0.000   0.000   0.000
   5_bss:  0.319  36.882  -0.481  -0.088   0.569   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.409 0.4790  0.5607    63842.894
   1_bss:  53.601 0.4739  0.7034    60268.084
   1_xyz:  43.102 0.6045  0.8830    42352.759
   1_adp:  39.126 0.6530  0.9760    36895.027
   1_occ:  39.178 0.6524  0.9747    36905.213
   2_bss:  38.801 0.6567  0.8564    36324.903
   2_xyz:  27.354 0.7857  0.9935    18623.155
   2_adp:  23.478 0.8276  1.0300    14832.616
   2_occ:  23.457 0.8278  1.0298    14807.114
   3_bss:  23.298 0.8292  0.9687    14635.632
   3_xyz:  18.043 0.8801  0.9939     9307.457
   3_adp:  16.727 0.8923  0.9975     8408.962
   3_occ:  16.716 0.8924  0.9973     8395.385
   4_bss:  16.653 0.8929  0.9820     8325.221
   4_xyz:  14.845 0.9080  0.9901     6881.603
   4_adp:  14.575 0.9105  0.9897     6741.703
   4_occ:  14.570 0.9106  0.9896     6735.746
   5_bss:  14.561 0.9106  0.9896     6726.346
   5_xyz:  13.904 0.9158  0.9914     6266.056
   5_adp:  13.943 0.9156  0.9876     6297.542
   5_occ:  13.934 0.9156  0.9876     6290.962
   5_bss:  13.944 0.9157  0.9878     6322.235
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3062e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3062e+01
   1_xyz:   1.617  0.012  0.104 18.138  0.006  4.108   1.3073e-01
   1_adp:   1.617  0.012  0.104 18.138  0.006  4.108   1.3073e-01
   1_occ:   1.617  0.012  0.104 18.138  0.006  4.108   1.3073e-01
   2_bss:   1.617  0.012  0.104 18.138  0.006  4.108   1.3073e-01
   2_xyz:   1.081  0.008  0.079 16.117  0.004  4.117   7.2949e-02
   2_adp:   1.081  0.008  0.079 16.117  0.004  4.117   7.2949e-02
   2_occ:   1.081  0.008  0.079 16.117  0.004  4.117   7.2949e-02
   3_bss:   1.081  0.008  0.079 16.117  0.004  4.117   7.2949e-02
   3_xyz:   0.944  0.005  0.070 15.623  0.003  4.109   5.5651e-02
   3_adp:   0.944  0.005  0.070 15.623  0.003  4.109   5.5651e-02
   3_occ:   0.944  0.005  0.070 15.623  0.003  4.109   5.5651e-02
   4_bss:   0.944  0.005  0.070 15.623  0.003  4.109   5.5651e-02
   4_xyz:   0.906  0.005  0.070 15.556  0.003  4.109   5.2436e-02
   4_adp:   0.906  0.005  0.070 15.556  0.003  4.109   5.2436e-02
   4_occ:   0.906  0.005  0.070 15.556  0.003  4.109   5.2436e-02
   5_bss:   0.906  0.005  0.070 15.556  0.003  4.109   5.2436e-02
   5_xyz:   1.002  0.006  0.077 15.595  0.004  4.110   6.0786e-02
   5_adp:   1.002  0.006  0.077 15.595  0.004  4.110   6.0786e-02
   5_occ:   1.002  0.006  0.077 15.595  0.004  4.110   6.0786e-02
   5_bss:   1.002  0.006  0.077 15.595  0.004  4.110   6.0786e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.953   6.8767e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.953   6.8767e+00
   1_xyz:  13.242  0.163  0.447 85.578  0.048  2.254   9.2546e-02
   1_adp:  13.242  0.163  0.447 85.578  0.048  2.254   9.2546e-02
   1_occ:  13.242  0.163  0.447 85.578  0.048  2.254   9.2546e-02
   2_bss:  13.242  0.163  0.447 85.578  0.048  2.254   9.2546e-02
   2_xyz:   7.060  0.077  0.326 85.349  0.039  2.268   6.0073e-02
   2_adp:   7.060  0.077  0.326 85.349  0.039  2.268   6.0073e-02
   2_occ:   7.060  0.077  0.326 85.349  0.039  2.268   6.0073e-02
   3_bss:   7.060  0.077  0.326 85.349  0.039  2.268   6.0073e-02
   3_xyz:   6.395  0.042  0.365 89.941  0.022  2.349   5.3478e-02
   3_adp:   6.395  0.042  0.365 89.941  0.022  2.349   5.3478e-02
   3_occ:   6.395  0.042  0.365 89.941  0.022  2.349   5.3478e-02
   4_bss:   6.395  0.042  0.365 89.941  0.022  2.349   5.3478e-02
   4_xyz:   6.281  0.037  0.386 83.871  0.026  2.365   2.7976e-02
   4_adp:   6.281  0.037  0.386 83.871  0.026  2.365   2.7976e-02
   4_occ:   6.281  0.037  0.386 83.871  0.026  2.365   2.7976e-02
   5_bss:   6.281  0.037  0.386 83.871  0.026  2.365   2.7976e-02
   5_xyz:   6.185  0.039  0.470 83.587  0.030  2.288   4.2169e-02
   5_adp:   6.185  0.039  0.470 83.587  0.030  2.288   4.2169e-02
   5_occ:   6.185  0.039  0.470 83.587  0.030  2.288   4.2169e-02
   5_bss:   6.185  0.039  0.470 83.587  0.030  2.288   4.2169e-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:  82.37   0.00  12.32  82.37   0.00   9.61  73.76   0.00  27.07
   1_occ:  82.37   0.00  12.32  82.37   0.00   9.61  73.76   0.00  27.07
   2_bss:  82.37   0.00  12.32  82.37   0.00   9.61  73.76   0.00  27.07
   2_xyz:  82.37   0.00  12.32  82.37   0.00   9.61  73.76   0.00  27.07
   2_adp:  79.88   0.00  12.27  79.88   0.00   8.63  65.77   1.66  32.08
   2_occ:  79.88   0.00  12.27  79.88   0.00   8.63  65.77   1.66  32.08
   3_bss:  79.88   0.00  12.27  79.88   0.00   8.63  65.77   1.66  32.08
   3_xyz:  79.88   0.00  12.27  79.88   0.00   8.63  65.77   1.66  32.08
   3_adp:  79.90   0.00  12.44  79.90   0.00   8.41  63.82   2.65  34.40
   3_occ:  79.90   0.00  12.44  79.90   0.00   8.41  63.82   2.65  34.40
   4_bss:  79.90   0.00  12.44  79.90   0.00   8.41  63.82   2.65  34.40
   4_xyz:  79.90   0.00  12.44  79.90   0.00   8.41  63.82   2.65  34.40
   4_adp:  83.85   0.00  12.67  83.85   0.00   8.43  71.04   2.28  35.77
   4_occ:  83.85   0.00  12.67  83.85   0.00   8.43  71.04   2.28  35.77
   5_bss:  83.85   0.00  12.67  83.85   0.00   8.43  71.04   2.28  35.77
   5_xyz:  83.85   0.00  12.67  83.85   0.00   8.43  71.04   2.28  35.77
   5_adp:  88.05   0.00  12.64  88.05   0.00   8.36  73.95   1.95  35.92
   5_occ:  88.05   0.00  12.64  88.05   0.00   8.36  73.95   1.95  35.92
   5_bss:  90.46   2.42  15.06  90.46   2.42  10.78  76.36   4.37  38.33
------------------------------------------------------------------------
 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:    1.217    0.014    0.406
   1_adp:    1.217    0.014    0.406
   1_occ:    1.217    0.014    0.406
   2_bss:    1.217    0.014    0.406
   2_xyz:    1.435    0.055    0.560
   2_adp:    1.435    0.055    0.560
   2_occ:    1.435    0.055    0.560
   3_bss:    1.435    0.055    0.560
   3_xyz:    1.417    0.043    0.608
   3_adp:    1.417    0.043    0.608
   3_occ:    1.417    0.043    0.608
   4_bss:    1.417    0.043    0.608
   4_xyz:    1.543    0.039    0.634
   4_adp:    1.543    0.039    0.634
   4_occ:    1.543    0.039    0.634
   5_bss:    1.543    0.039    0.634
   5_xyz:    1.571    0.050    0.653
   5_adp:    1.571    0.050    0.653
   5_occ:    1.571    0.050    0.653
   5_bss:    1.571    0.050    0.653
------------------------------------------------------------------------

CPU time actual refinement: 325.18


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_408/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_408/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_408/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_408/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_408/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.03 
  Macro-tasks:
    bulk solvent and scale       = 44.19  
    individual site refinement   = 132.87 
    weights calculation          = 30.50  
    collect and process          = 6.50   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 214.16 
  Micro-tasks:
    mask                            = 2.22   
    f_calc                          = 99.64  
    alpha_beta                      = 8.41   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 105.58 
    fmodel                         = 6.95   
    r_factors                      = 0.18   
    phase_errors                   = 11.40  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 235.81 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.573 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    636 calls, 99.26 s
gradients_fft:          581 calls, 94.09 s

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

# Date 2008-01-16 Time 01:28:34 PST -0800 (1200475714.59 s)
Start R-work = 0.4636, R-free = 0.4575 (no bulk solvent and anisotropic scale)
Final R-work = 0.1283, R-free = 0.1753 (no bulk solvent and anisotropic scale)

Start R-work = 0.4543, R-free = 0.4461
Final R-work = 0.1110, R-free = 0.1591