# Date 2008-01-16 Time 02:39:34 PST -0800 (1200479974.90 s)
#phil __OFF__

Command line arguments: "../924.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27976
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 924

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.3993, 84.2302, 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: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95145
Completeness in resolution range: 0.921575
Completeness with d_max=infinity: 0.918852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95145
Completeness in resolution range: 0.921575
Completeness with d_max=infinity: 0.918852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1768 [2234/2263]  2012   222   9.9%
  bin  2:  4.1768 -  3.3272 [2138/2161]  1924   214  10.0%
  bin  3:  3.3272 -  2.9101 [2107/2132]  1892   215  10.2%
  bin  4:  2.9101 -  2.6456 [2093/2109]  1890   203   9.7%
  bin  5:  2.6456 -  2.4569 [2078/2122]  1870   208  10.0%
  bin  6:  2.4569 -  2.3126 [2079/2107]  1871   208  10.0%
  bin  7:  2.3126 -  2.1971 [2057/2093]  1848   209  10.2%
  bin  8:  2.1971 -  2.1017 [2045/2087]  1840   205  10.0%
  bin  9:  2.1017 -  2.0210 [2048/2094]  1847   201   9.8%
  bin 10:  2.0210 -  1.9514 [ 710/2088]   636    74  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_924/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.46 -     2.15: 19
        2.15 -     2.84: 1008
        2.84 -     3.52: 4443
        3.52 -     4.21: 9319
        4.21 -     4.90: 13638
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.461 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.528 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.792 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 396 "  1.829 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28422 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_924/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_924/model_refine_001.geo

CPU time processing inputs: 9.58


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.3993 84.23025 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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4822   r_free= 0.4821   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.285640                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6592 0.99   1451  164 0.3964 0.3876      6.6076      6.5863|
|  2:  4.6592 -  3.7167 0.99   1386  149 0.3981 0.4210      6.7919      6.8591|
|  3:  3.7167 -  3.2523 0.99   1370  155 0.4469 0.4143      6.6687      6.6736|
|  4:  3.2523 -  2.9575 0.99   1355  148 0.4615 0.4862      6.5075      6.5097|
|  5:  2.9575 -  2.7469 0.98   1344  147 0.5092 0.5325      6.3652      6.3662|
|  6:  2.7469 -  2.5858 0.99   1344  158 0.5060 0.5196      6.2721      6.2156|
|  7:  2.5858 -  2.4569 0.98   1338  141 0.5168 0.4376      6.2484      6.1589|
|  8:  2.4569 -  2.3503 0.99   1331  150 0.5395 0.5449      6.1575      6.1966|
|  9:  2.3503 -  2.2602 0.99   1335  151 0.5413 0.5275      6.1445      6.1136|
| 10:  2.2602 -  2.1824 0.98   1327  147 0.5253 0.5271      6.0702      6.1315|
| 11:  2.1824 -  2.1144 0.97   1303  136 0.5226 0.5327      6.0299      5.9963|
| 12:  2.1144 -  2.0541 0.99   1336  154 0.5520 0.5566      5.9421      5.9879|
| 13:  2.0541 -  2.0001 0.83   1109  130 0.5412 0.5408       5.876      5.8288|
| 14:  2.0001 -  1.9514 0.22    301   29 0.5534 0.5557      5.8139      5.8125|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6592  1451   164  0.70  34.18   0.80     0.73      70525.02|
|  2:  4.6592 -  3.7167  1386   149  0.69  36.27   0.88     0.76     109188.69|
|  3:  3.7167 -  3.2523  1370   155  0.56  46.79   0.82     0.69     123100.12|
|  4:  3.2523 -  2.9575  1355   148  0.46  55.33   0.80     0.57     112267.34|
|  5:  2.9575 -  2.7469  1344   147  0.37  62.30   0.73     0.47      91482.54|
|  6:  2.7469 -  2.5858  1344   158  0.39  60.89   0.74     0.46      72415.81|
|  7:  2.5858 -  2.4569  1338   141  0.40  59.94   0.74     0.45      61460.09|
|  8:  2.4569 -  2.3503  1331   150  0.37  62.15   0.71     0.44      56812.66|
|  9:  2.3503 -  2.2602  1335   151  0.31  66.55   0.74     0.38      56205.81|
| 10:  2.2602 -  2.1824  1327   147  0.26  70.37   0.74     0.32      55604.69|
| 11:  2.1824 -  2.1144  1303   136  0.22  73.55   0.78     0.28      52064.85|
| 12:  2.1144 -  2.0541  1336   154  0.18  76.32   0.73     0.25      48923.36|
| 13:  2.0541 -  2.0001  1109   130  0.17  77.12   0.72     0.23      42093.52|
| 14:  2.0001 -  1.9514   301    29  0.16  78.04   0.69     0.20      35932.58|
|alpha:            min =        0.20 max =            0.76 mean =         0.47|
|beta:             min =    35932.58 max =       123100.12 mean =     73289.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.98 mean =        59.92|
|phase err.(test): min =        0.00 max =           89.96 mean =        60.07|
|-----------------------------------------------------------------------------|

============================== 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 = 15.816715             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.568   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.431024              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.076   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       27 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      177 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      706 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1504 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2655 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3943 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5040 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6606 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7799 |
|-----------------------------------------------------------------------------|
|-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 |       53.533 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       2.053 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    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 = 11.830)------------------------------------------|
|    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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4869   r_free= 0.4884   ksol= 0.00   Bsol= 0.00   scale= 0.763    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.287191                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4733   r_free= 0.4727   ksol= 0.34   Bsol= 13.77   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.13,8.64,9.09,0.00,0.00,0.00); trace/3= 8.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 5.815916                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.593836             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.825   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.236265              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.765   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4733      final r-factor (work) = 0.4050          |
| start r-factor (free) = 0.4727      final r-factor (free) = 0.4351          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.0972 = 12.59 * 0.50 * 6.2831 + 1.00 * 53.5330                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2705 = 12.59 * 0.50 * 5.7371 + 1.00 * 0.1447                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4050      final r-factor (work) = 0.3684          |
| start r-factor (free) = 0.4351      final r-factor (free) = 0.4232          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1069 = 1.24 * 1.00 * 5.7371 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6181 = 1.24 * 1.00 * 6.1460 + 1.00 * 0.0200                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.08  12.49    None  None   None       |
|    all(noH): 2823   0      0.00    100.08  12.49    None  None   None       |
|    Sol.    : 438    0      0.00    54.37   21.71    None  None   None       |
|    Mac.    : 2385   0      0.00    100.08  10.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.008: 1295   |   5:    50.042 -  60.050:    3        |
|      1:    10.008 -  20.017: 1001   |   6:    60.050 -  70.059:    0        |
|      2:    20.017 -  30.025:  363   |   7:    70.059 -  80.067:    1        |
|      3:    30.025 -  40.034:  132   |   8:    80.067 -  90.075:    0        |
|      4:    40.034 -  50.042:   27   |   9:    90.075 - 100.084:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3684 r_free = 0.4232             target_work(ml) = 6.132         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3680 r_free = 0.4244             target_work(ml) = 6.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3680   r_free= 0.4244   ksol= 0.34   Bsol= 13.77   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.13,8.64,9.09,0.00,0.00,0.00); trace/3= 8.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.132210                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3661   r_free= 0.4186   ksol= 0.33   Bsol= 41.01   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,5.08,6.08,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.132790                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.533596              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.337  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.747426              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.210  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3661      final r-factor (work) = 0.2900          |
| start r-factor (free) = 0.4186      final r-factor (free) = 0.3558          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.2849 = 7.53 * 0.50 * 6.1432 + 1.00 * 0.1447                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8474 = 7.53 * 0.50 * 6.0430 + 1.00 * 0.0846                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2900      final r-factor (work) = 0.2680          |
| start r-factor (free) = 0.3558      final r-factor (free) = 0.3337          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6526 = 0.75 * 1.00 * 6.0430 + 1.00 * 0.1359                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4442 = 0.75 * 1.00 * 5.9293 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.91   13.72    None  None   None       |
|    all(noH): 2823   0      0.00    72.91   13.72    None  None   None       |
|    Sol.    : 438    0      0.72    70.47   31.30    None  None   None       |
|    Mac.    : 2385   0      0.00    72.91   10.49    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 -   7.291: 1073   |   5:    36.454 -  43.745:   92        |
|      1:     7.291 -  14.582:  811   |   6:    43.745 -  51.036:   61        |
|      2:    14.582 -  21.873:  382   |   7:    51.036 -  58.327:   40        |
|      3:    21.873 -  29.163:  200   |   8:    58.327 -  65.618:   14        |
|      4:    29.163 -  36.454:  147   |   9:    65.618 -  72.909:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2680 r_free = 0.3337             target_work(ml) = 5.902         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2677 r_free = 0.3337             target_work(ml) = 5.901         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2677   r_free= 0.3337   ksol= 0.33   Bsol= 41.01   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,5.08,6.08,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.900960                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2659   r_free= 0.3312   ksol= 0.32   Bsol= 42.25   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,3.05,3.69,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.900064                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.370017              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.511  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.389077              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.330  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2659      final r-factor (work) = 0.1957          |
| start r-factor (free) = 0.3312      final r-factor (free) = 0.2532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0077 = 5.37 * 0.50 * 5.9304 + 1.00 * 0.0846                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6201 = 5.37 * 0.50 * 5.7893 + 1.00 * 0.0757                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1957      final r-factor (work) = 0.1720          |
| start r-factor (free) = 0.2532      final r-factor (free) = 0.2343          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.6329 = 3.39 * 1.00 * 5.7893 + 1.00 * 0.0124                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.9297 = 3.39 * 1.00 * 5.5804 + 1.00 * 0.0173                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.31   15.12    None  None   None       |
|    all(noH): 2823   0      0.00    97.31   15.12    None  None   None       |
|    Sol.    : 438    0      1.64    94.05   42.03    None  None   None       |
|    Mac.    : 2385   0      0.00    97.31   10.17    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 -   9.731: 1551   |   5:    48.656 -  58.387:   78        |
|      1:     9.731 -  19.462:  653   |   6:    58.387 -  68.118:   61        |
|      2:    19.462 -  29.194:  179   |   7:    68.118 -  77.850:   37        |
|      3:    29.194 -  38.925:  119   |   8:    77.850 -  87.581:   12        |
|      4:    38.925 -  48.656:  125   |   9:    87.581 -  97.312:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1720 r_free = 0.2343             target_work(ml) = 5.538         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1718 r_free = 0.2342             target_work(ml) = 5.537         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1718   r_free= 0.2342   ksol= 0.32   Bsol= 42.25   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,3.05,3.69,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.537226                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1716   r_free= 0.2339   ksol= 0.31   Bsol= 42.25   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,2.09,2.17,0.00,0.00,0.00); trace/3= 1.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.535360                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.090896              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.470  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.136348              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.704  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1716      final r-factor (work) = 0.1409          |
| start r-factor (free) = 0.2339      final r-factor (free) = 0.1976          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5004 = 4.09 * 0.50 * 5.5854 + 1.00 * 0.0757                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2388 = 4.09 * 0.50 * 5.4616 + 1.00 * 0.0675                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1409      final r-factor (work) = 0.1337          |
| start r-factor (free) = 0.1976      final r-factor (free) = 0.1867          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2235 = 1.14 * 1.00 * 5.4616 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0832 = 1.14 * 1.00 * 5.3403 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.58  14.67    None  None   None       |
|    all(noH): 2823   0      0.00    107.58  14.67    None  None   None       |
|    Sol.    : 438    0      2.95    92.01   41.67    None  None   None       |
|    Mac.    : 2385   0      0.00    107.58  9.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.758: 1746   |   5:    53.790 -  64.547:   63        |
|      1:    10.758 -  21.516:  546   |   6:    64.547 -  75.305:   52        |
|      2:    21.516 -  32.274:  154   |   7:    75.305 -  86.063:   18        |
|      3:    32.274 -  43.032:  108   |   8:    86.063 -  96.821:    8        |
|      4:    43.032 -  53.790:  125   |   9:    96.821 - 107.579:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1337 r_free = 0.1867             target_work(ml) = 5.309         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1334 r_free = 0.1864             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1864   ksol= 0.31   Bsol= 42.25   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,2.09,2.17,0.00,0.00,0.00); trace/3= 1.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.307828                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1339   r_free= 0.1877   ksol= 0.32   Bsol= 45.79   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.45,1.91,1.90,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.311735                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.783811              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.998  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.494688              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.324  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1339      final r-factor (work) = 0.1277          |
| start r-factor (free) = 0.1877      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8311 = 1.78 * 0.50 * 5.3410 + 1.00 * 0.0675                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7782 = 1.78 * 0.50 * 5.2969 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1734          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6350 = 0.49 * 1.00 * 5.2969 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6161 = 0.49 * 1.00 * 5.2628 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.15  14.18    None  None   None       |
|    all(noH): 2823   0      0.00    109.15  14.18    None  None   None       |
|    Sol.    : 438    0      2.11    93.67   39.99    None  None   None       |
|    Mac.    : 2385   0      0.00    109.15  9.45     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.915: 1806   |   5:    54.573 -  65.487:   69        |
|      1:    10.915 -  21.829:  518   |   6:    65.487 -  76.402:   33        |
|      2:    21.829 -  32.744:  150   |   7:    76.402 -  87.316:   17        |
|      3:    32.744 -  43.658:  117   |   8:    87.316 -  98.231:    3        |
|      4:    43.658 -  54.573:  107   |   9:    98.231 - 109.145:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1260 r_free = 0.1734             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1258 r_free = 0.1732             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1258   r_free= 0.1732   ksol= 0.32   Bsol= 45.79   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.45,1.91,1.90,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252720                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6592 0.99   1451  164 0.1004 0.1302      5.3971      5.5721|
|  2:  4.6592 -  3.7167 0.99   1386  149 0.0942 0.1227      5.4973      5.7366|
|  3:  3.7167 -  3.2523 0.99   1370  155 0.1177 0.1740      5.5658      5.9117|
|  4:  3.2523 -  2.9575 0.99   1355  148 0.1426 0.1598       5.545      5.6647|
|  5:  2.9575 -  2.7469 0.98   1344  147 0.1507 0.1866      5.4233      5.5789|
|  6:  2.7469 -  2.5858 0.99   1344  158 0.1421 0.2234      5.3337      5.6019|
|  7:  2.5858 -  2.4569 0.98   1338  141 0.1428 0.1810       5.292      5.4655|
|  8:  2.4569 -  2.3503 0.99   1331  150 0.1334 0.1888      5.1667      5.3862|
|  9:  2.3503 -  2.2602 0.99   1335  151 0.1292 0.2043      5.1084      5.3688|
| 10:  2.2602 -  2.1824 0.98   1327  147 0.1274 0.1881      5.0702      5.3682|
| 11:  2.1824 -  2.1144 0.97   1303  136 0.1322 0.2007      5.0296      5.2881|
| 12:  2.1144 -  2.0541 0.99   1336  154 0.1318 0.1829      4.9741      5.1632|
| 13:  2.0541 -  2.0001 0.83   1109  130 0.1307 0.2109      4.8806      5.1385|
| 14:  2.0001 -  1.9514 0.22    301   29 0.1263 0.1748      4.7909      5.0879|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6592  1451   164  0.94   9.16   0.97     0.96       7391.67|
|  2:  4.6592 -  3.7167  1386   149  0.95   8.68   1.01     0.99       9735.88|
|  3:  3.7167 -  3.2523  1370   155  0.92  13.08   1.03     1.04      12604.21|
|  4:  3.2523 -  2.9575  1355   148  0.90  15.88   1.02     0.99      12046.25|
|  5:  2.9575 -  2.7469  1344   147  0.88  18.58   0.99     0.97      10298.29|
|  6:  2.7469 -  2.5858  1344   158  0.88  18.35   0.99     0.97       9158.35|
|  7:  2.5858 -  2.4569  1338   141  0.88  18.09   0.99     0.96       8121.56|
|  8:  2.4569 -  2.3503  1331   150  0.88  18.32   1.00     0.95       6683.87|
|  9:  2.3503 -  2.2602  1335   151  0.89  17.86   1.01     0.98       5971.12|
| 10:  2.2602 -  2.1824  1327   147  0.89  17.14   1.00     0.97       5556.20|
| 11:  2.1824 -  2.1144  1303   136  0.88  18.37   0.99     0.96       5191.52|
| 12:  2.1144 -  2.0541  1336   154  0.89  18.18   1.00     0.99       4852.63|
| 13:  2.0541 -  2.0001  1109   130  0.88  18.77   1.00     0.97       4094.69|
| 14:  2.0001 -  1.9514   301    29  0.87  19.38   0.99     0.96       3547.09|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3547.09 max =        12604.21 mean =      7823.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.13|
|phase err.(test): min =        0.00 max =           87.83 mean =        15.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1258   r_free= 0.1731   ksol= 0.32   Bsol= 45.62   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.31,0.16,0.15,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252707                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1258   r_free= 0.1731   ksol= 0.32   Bsol= 45.62   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.31,0.16,0.15,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252707                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6592 0.99   1451  164 0.1004 0.1299      5.3967      5.5706|
|  2:  4.6592 -  3.7167 0.99   1386  149 0.0940 0.1224       5.496      5.7344|
|  3:  3.7167 -  3.2523 0.99   1370  155 0.1176 0.1739       5.565      5.9113|
|  4:  3.2523 -  2.9575 0.99   1355  148 0.1426 0.1599      5.5449      5.6646|
|  5:  2.9575 -  2.7469 0.98   1344  147 0.1507 0.1866      5.4235      5.5793|
|  6:  2.7469 -  2.5858 0.99   1344  158 0.1422 0.2234       5.334       5.602|
|  7:  2.5858 -  2.4569 0.98   1338  141 0.1429 0.1809      5.2923      5.4655|
|  8:  2.4569 -  2.3503 0.99   1331  150 0.1335 0.1889       5.167      5.3868|
|  9:  2.3503 -  2.2602 0.99   1335  151 0.1292 0.2042      5.1087       5.369|
| 10:  2.2602 -  2.1824 0.98   1327  147 0.1274 0.1881      5.0705      5.3685|
| 11:  2.1824 -  2.1144 0.97   1303  136 0.1323 0.2008      5.0298      5.2883|
| 12:  2.1144 -  2.0541 0.99   1336  154 0.1318 0.1830      4.9743      5.1634|
| 13:  2.0541 -  2.0001 0.83   1109  130 0.1307 0.2111      4.8809      5.1388|
| 14:  2.0001 -  1.9514 0.22    301   29 0.1263 0.1748      4.7912      5.0881|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6592  1451   164  0.94   9.15   0.97     0.96       7373.55|
|  2:  4.6592 -  3.7167  1386   149  0.95   8.66   1.01     0.99       9707.92|
|  3:  3.7167 -  3.2523  1370   155  0.92  13.05   1.03     1.04      12570.38|
|  4:  3.2523 -  2.9575  1355   148  0.90  15.88   1.02     0.99      12038.27|
|  5:  2.9575 -  2.7469  1344   147  0.88  18.58   0.99     0.97      10298.37|
|  6:  2.7469 -  2.5858  1344   158  0.88  18.35   0.99     0.97       9161.73|
|  7:  2.5858 -  2.4569  1338   141  0.88  18.09   0.99     0.96       8125.03|
|  8:  2.4569 -  2.3503  1331   150  0.88  18.32   1.00     0.95       6687.74|
|  9:  2.3503 -  2.2602  1335   151  0.88  17.87   1.01     0.98       5975.49|
| 10:  2.2602 -  2.1824  1327   147  0.89  17.15   1.00     0.96       5560.06|
| 11:  2.1824 -  2.1144  1303   136  0.88  18.38   0.99     0.96       5194.75|
| 12:  2.1144 -  2.0541  1336   154  0.89  18.19   1.00     0.99       4855.09|
| 13:  2.0541 -  2.0001  1109   130  0.88  18.78   1.00     0.97       4097.67|
| 14:  2.0001 -  1.9514   301    29  0.87  19.39   0.99     0.96       3550.44|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3550.44 max =        12570.38 mean =      7818.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        16.13|
|phase err.(test): min =        0.00 max =           87.88 mean =        15.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.75    110.90  15.94    None  None   None       |
|    all(noH): 2823   0      1.75    110.90  15.94    None  None   None       |
|    Sol.    : 438    0      3.86    95.42   41.74    None  None   None       |
|    Mac.    : 2385   0      1.75    110.90  11.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.751 -  12.665: 1806   |   5:    56.323 -  67.238:   69        |
|      1:    12.665 -  23.580:  518   |   6:    67.238 -  78.153:   33        |
|      2:    23.580 -  34.494:  150   |   7:    78.153 -  89.067:   17        |
|      3:    34.494 -  45.409:  117   |   8:    89.067 -  99.982:    3        |
|      4:    45.409 -  56.323:  107   |   9:    99.982 - 110.896:    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)= 344         
Filter by distance & map next to the model:
   mapped sites are within: 0.649 - 5.769
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 340 from: 344
   mapped sites are within: 0.701 - 5.769

peak=    9.494 closest distance to " CB  VAL A 230 " =    1.436
peak=    8.882 closest distance to " CG2 VAL A 296 " =    1.316
peak=    7.126 closest distance to " O   HOH Z  37 " =    1.551
peak=    6.971 closest distance to " O   HOH Z 279 " =    1.364
peak=    6.415 closest distance to " CG  ARG A 138 " =    1.131
peak=    6.204 closest distance to " O   HOH Z 120 " =    1.183
peak=    6.108 closest distance to " NH2 ARG A  56 " =    2.246
peak=    6.101 closest distance to " O   HOH Z 277 " =    1.308
peak=    6.013 closest distance to " O   HOH Z 278 " =    1.477
peak=    5.652 closest distance to " CG  LEU A   5 " =    1.375
peak=    5.605 closest distance to " O   HOH Z 247 " =    1.493
peak=    5.594 closest distance to " CD2 LEU A   5 " =    1.259
peak=    5.571 closest distance to " NH2BARG A 102 " =    1.008
peak=    5.384 closest distance to " O   HOH Z 132 " =    1.666
peak=    5.366 closest distance to " CG  PRO A 198 " =    1.364
peak=    5.366 closest distance to " CB  GLN A 223 " =    1.470
peak=    5.356 closest distance to " O   HOH Z  48 " =    1.956
peak=    5.192 closest distance to " O   HOH Z 124 " =    1.544
peak=    5.129 closest distance to " O   HOH Z 138 " =    1.008
peak=    5.094 closest distance to " CD1AILE A 234 " =    1.087
peak=    5.064 closest distance to " O   HOH Z 199 " =    1.113
peak=    4.936 closest distance to " CG  PRO A  54 " =    1.257
peak=    4.835 closest distance to " O   HOH Z  97 " =    1.844
peak=    4.797 closest distance to " NH1 ARG A 138 " =    1.034
peak=    4.789 closest distance to " O   HOH Z  11 " =    1.300
peak=    4.787 closest distance to " O   HOH Z 142 " =    1.605
peak=    4.742 closest distance to " O   HOH Z 411 " =    3.481
peak=    4.737 closest distance to " O   HOH Z 126 " =    1.670
peak=    4.686 closest distance to " O   HOH Z 202 " =    1.406
peak=    4.657 closest distance to " CB  PRO A  54 " =    0.838
peak=    4.657 closest distance to " O   HOH Z 316 " =    0.966
peak=    4.624 closest distance to " O   HOH Z 221 " =    1.342
peak=    4.622 closest distance to " CG  PRO A 213 " =    1.287
peak=    4.579 closest distance to " O   HOH Z 192 " =    1.340
peak=    4.515 closest distance to " O   HOH Z 291 " =    1.315
peak=    4.500 closest distance to " CA  ALA A  21 " =    1.277
peak=    4.496 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.466 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.455 closest distance to " O   HOH Z 389 " =    1.850
peak=    4.452 closest distance to " CB  SER A  63 " =    1.381
peak=    4.435 closest distance to " CG  PRO A 280 " =    0.812
peak=    4.426 closest distance to " O   HOH Z 205 " =    1.070
peak=    4.421 closest distance to " O   HOH Z 263 " =    1.402
peak=    4.416 closest distance to " CD  ARG A 138 " =    1.209
peak=    4.408 closest distance to " O   HOH Z 272 " =    1.929
peak=    4.379 closest distance to " CB  VAL A 230 " =    1.273
peak=    4.371 closest distance to " O   HOH Z 128 " =    1.951
peak=    4.344 closest distance to " CG  LEU A 228 " =    1.338
peak=    4.332 closest distance to " CD  ARG A 269 " =    0.897
peak=    4.316 closest distance to " CB  SER A   3 " =    1.433
peak=    4.304 closest distance to " C   PRO A 198 " =    1.498
peak=    4.281 closest distance to " O   HOH Z 371 " =    3.320
peak=    4.264 closest distance to " O   HOH Z 134 " =    1.616
peak=    4.261 closest distance to " CB  LEU A 228 " =    1.337
peak=    4.218 closest distance to " CB  TYR A 169 " =    0.900
peak=    4.212 closest distance to " O   HOH Z  78 " =    2.048
peak=    4.210 closest distance to " CA  VAL A  41 " =    0.843
peak=    4.192 closest distance to " O   HOH Z  61 " =    1.398
peak=    4.192 closest distance to " CG2 THR A 221 " =    1.021
peak=    4.179 closest distance to " O   HOH Z 131 " =    2.364
peak=    4.176 closest distance to " O   HOH Z  92 " =    1.144
peak=    4.159 closest distance to " CD  LYS A 119 " =    1.301
peak=    4.153 closest distance to " CB  ASN A 148 " =    1.269
peak=    4.142 closest distance to " O   HOH Z 394 " =    1.547
peak=    4.122 closest distance to " O   HOH Z 260 " =    1.311
peak=    4.102 closest distance to " NH1 ARG A  14 " =    1.122
peak=    4.097 closest distance to " CG1 VAL A 153 " =    1.039
peak=    4.086 closest distance to " CD2 LEU A 228 " =    1.225
peak=    4.079 closest distance to " O   HOH Z  43 " =    1.426
peak=    4.073 closest distance to " O   HOH Z 193 " =    1.781
peak=    4.066 closest distance to " CB  GLU A 152 " =    1.128
peak=    4.057 closest distance to " OE1 GLN A  58 " =    5.769
peak=    4.052 closest distance to " O   HOH Z 427 " =    3.087
peak=    4.006 closest distance to " O   HOH Z 112 " =    1.497
peak=    3.996 closest distance to " O   HOH Z 276 " =    1.464
peak=    3.994 closest distance to " O   HOH Z 155 " =    1.699
peak=    3.989 closest distance to " CG  PRO A 243 " =    1.255
peak=    3.959 closest distance to " OD2 ASP A 286 " =    2.812
peak=    3.951 closest distance to " CA  ASP A 191 " =    0.919
peak=    3.921 closest distance to " O   HOH Z 180 " =    2.061
peak=    3.904 closest distance to " CB  TRP A 179 " =    1.349
peak=    3.903 closest distance to " O   HOH Z  15 " =    2.225
peak=    3.903 closest distance to " CB  VAL A 202 " =    1.582
peak=    3.893 closest distance to " O   HOH Z 331 " =    1.341
peak=    3.892 closest distance to " O   HOH Z 136 " =    1.438
peak=    3.886 closest distance to " CB  GLU A 128 " =    1.162
peak=    3.884 closest distance to " O   HOH Z  80 " =    1.900
peak=    3.884 closest distance to " O   HOH Z 344 " =    2.688
peak=    3.884 closest distance to " CD2 LEU A 255 " =    1.274
peak=    3.879 closest distance to " O   SER A  87 " =    2.313
peak=    3.876 closest distance to " O   HOH Z  30 " =    1.561
peak=    3.859 closest distance to " O   HOH Z 236 " =    1.767
peak=    3.859 closest distance to " CG1BVAL A  72 " =    1.645
peak=    3.858 closest distance to " O   HOH Z   4 " =    1.689
peak=    3.855 closest distance to " O   HOH Z 215 " =    1.463
peak=    3.854 closest distance to " CA  THR A 221 " =    0.915
peak=    3.851 closest distance to " O   HOH Z 377 " =    1.265
peak=    3.850 closest distance to " NE2 GLN A  11 " =    1.139
peak=    3.843 closest distance to " O   HOH Z 326 " =    1.442
peak=    3.832 closest distance to " CA  LEU A 101 " =    1.665
peak=    3.831 closest distance to " O   HOH Z 316 " =    2.244
peak=    3.830 closest distance to " O   HOH Z 232 " =    2.121
peak=    3.830 closest distance to " O   HOH Z 303 " =    2.159
peak=    3.826 closest distance to " O   ASP A 132 " =    3.779
peak=    3.826 closest distance to " CB  VAL A 265 " =    1.198
peak=    3.824 closest distance to " O   HOH Z 386 " =    2.147
peak=    3.799 closest distance to " O   HOH Z 334 " =    3.047
peak=    3.798 closest distance to " O   MET A 105 " =    1.835
peak=    3.796 closest distance to " CB  PRO A 198 " =    1.036
peak=    3.792 closest distance to " O   HOH Z 214 " =    0.910
peak=    3.780 closest distance to " CA  ALA A 295 " =    1.113
peak=    3.778 closest distance to " O   HOH Z 189 " =    2.486
peak=    3.772 closest distance to " O   HOH Z 374 " =    3.004
peak=    3.770 closest distance to " NZ  LYS A 117 " =    3.152
peak=    3.768 closest distance to " O   HOH Z 133 " =    2.010
peak=    3.767 closest distance to " O   HOH Z 227 " =    1.915
peak=    3.765 closest distance to " O   HOH Z 163 " =    1.554
peak=    3.759 closest distance to " O   HOH Z 346 " =    1.529
peak=    3.753 closest distance to " OD1 ASN A 217 " =    1.740
peak=    3.742 closest distance to " O   HOH Z 243 " =    1.070
peak=    3.741 closest distance to " CA  ALA A 160 " =    0.844
peak=    3.740 closest distance to " CB  ASP A 124 " =    0.811
peak=    3.740 closest distance to " O   HOH Z 108 " =    1.553
peak=    3.736 closest distance to " CB  ILE A 199 " =    1.058
peak=    3.731 closest distance to " O   HOH Z 126 " =    1.693
peak=    3.716 closest distance to " O   HOH Z  48 " =    2.002
peak=    3.716 closest distance to " O   HOH Z 403 " =    1.774
peak=    3.715 closest distance to " O   HOH Z 295 " =    1.587
peak=    3.710 closest distance to " CA  TYR A  30 " =    1.011
peak=    3.709 closest distance to " O   HOH Z 217 " =    1.778
peak=    3.706 closest distance to " O   HOH Z  88 " =    3.233
peak=    3.701 closest distance to " CA  LEU A 282 " =    1.014
peak=    3.697 closest distance to " C   SER A  32 " =    1.123
peak=    3.696 closest distance to " O   HOH Z  63 " =    1.461
peak=    3.694 closest distance to " OG  SER A  22 " =    2.907
peak=    3.694 closest distance to " O   HOH Z 130 " =    2.831
peak=    3.692 closest distance to " O   HOH Z  58 " =    1.447
peak=    3.689 closest distance to " O   HOH Z  67 " =    1.863
peak=    3.687 closest distance to " CA  ASN A  74 " =    1.319
peak=    3.680 closest distance to " OE1 GLN A  11 " =    1.763
peak=    3.678 closest distance to " O   HOH Z  40 " =    1.581
peak=    3.676 closest distance to " O   HOH Z 298 " =    1.945
peak=    3.667 closest distance to " NH1 ARG A  56 " =    1.067
peak=    3.667 closest distance to " O   HOH Z 352 " =    1.267
peak=    3.662 closest distance to " O   HOH Z 426 " =    1.466
peak=    3.660 closest distance to " O   HOH Z  93 " =    2.614
peak=    3.655 closest distance to " O   HOH Z 426 " =    3.072
peak=    3.651 closest distance to " O   HOH Z 423 " =    1.954
peak=    3.648 closest distance to " CA  GLY A 211 " =    1.160
peak=    3.635 closest distance to " O   HOH Z 154 " =    1.314
peak=    3.629 closest distance to " CG1 ILE A  33 " =    1.392
peak=    3.628 closest distance to " CG AARG A 275 " =    0.996
peak=    3.623 closest distance to " CD1 LEU A 300 " =    1.155
peak=    3.610 closest distance to " O   HOH Z 366 " =    2.919
peak=    3.608 closest distance to " O   HOH Z 369 " =    2.117
peak=    3.605 closest distance to " N   ASN A  39 " =    1.296
peak=    3.604 closest distance to " O   HOH Z  78 " =    1.878
peak=    3.604 closest distance to " CD BLYS A 290 " =    1.000
peak=    3.603 closest distance to " CB  SER A 273 " =    0.879
peak=    3.599 closest distance to " OD1 ASN A  69 " =    2.598
peak=    3.592 closest distance to " O   HOH Z 128 " =    2.160
peak=    3.586 closest distance to " CG  GLN A  77 " =    0.918
peak=    3.578 closest distance to " NE2 HIS A 115 " =    0.937
peak=    3.577 closest distance to " O   HOH Z 133 " =    1.587
peak=    3.575 closest distance to " CG  GLN A  88 " =    1.000
peak=    3.575 closest distance to " CB  ALA A 291 " =    1.309
peak=    3.575 closest distance to " O   HOH Z 344 " =    1.396
peak=    3.569 closest distance to " O   HOH Z 184 " =    1.244
peak=    3.563 closest distance to " NH1 ARG A 269 " =    0.903
peak=    3.556 closest distance to " O   HOH Z 143 " =    1.296
peak=    3.551 closest distance to " O   SER A 164 " =    0.978
peak=    3.546 closest distance to " CB  ALA A 256 " =    1.020
peak=    3.540 closest distance to " O   TRP A 274 " =    1.756
peak=    3.537 closest distance to " O   HOH Z 214 " =    1.956
peak=    3.535 closest distance to " CA  VAL A 296 " =    1.017
peak=    3.535 closest distance to " O   HOH Z 280 " =    1.632
peak=    3.526 closest distance to " OE1 GLU A   2 " =    2.043
peak=    3.520 closest distance to " CG2 VAL A 174 " =    1.281
peak=    3.520 closest distance to " CB  GLU A 277 " =    3.601
peak=    3.518 closest distance to " NZ  LYS A  76 " =    1.255
peak=    3.517 closest distance to " CE  LYS A 119 " =    1.141
peak=    3.515 closest distance to " O   HOH Z 215 " =    1.408
peak=    3.514 closest distance to " O   HOH Z 132 " =    3.348
peak=    3.513 closest distance to " O   HOH Z 327 " =    2.577
peak=    3.508 closest distance to " O   HOH Z 332 " =    1.595
peak=    3.498 closest distance to " O   HOH Z 236 " =    1.703
peak=    3.483 closest distance to " O   HOH Z  13 " =    1.439
peak=    3.480 closest distance to " O   HOH Z 203 " =    1.630
peak=    3.476 closest distance to " O   HOH Z 284 " =    1.310
peak=    3.466 closest distance to " NH2 ARG A 156 " =    1.087
peak=    3.459 closest distance to " CB  ALA A 100 " =    1.394
peak=    3.458 closest distance to " O   HOH Z 186 " =    1.075
peak=    3.457 closest distance to " CG  LEU A 167 " =    1.102
peak=    3.456 closest distance to " O   HOH Z  21 " =    2.017
peak=    3.454 closest distance to " O   HOH Z 118 " =    1.698
peak=    3.454 closest distance to " C   GLY A  80 " =    1.208
peak=    3.450 closest distance to " OD1 ASP A 238 " =    0.902
peak=    3.442 closest distance to " O   THR A  31 " =    1.536
peak=    3.440 closest distance to " O   HOH Z 197 " =    2.162
peak=    3.435 closest distance to " O   HOH Z 395 " =    1.407
peak=    3.431 closest distance to " O   HOH Z 145 " =    2.269
peak=    3.428 closest distance to " O   HOH Z 261 " =    1.777
peak=    3.425 closest distance to " O   HOH Z 207 " =    2.380
peak=    3.421 closest distance to " CA  LYS A 117 " =    1.297
peak=    3.421 closest distance to " O   HOH Z 166 " =    1.590
peak=    3.415 closest distance to " O   HOH Z  44 " =    2.453
peak=    3.413 closest distance to " CA  VAL A 126 " =    1.107
peak=    3.413 closest distance to " CZ  PHE A 192 " =    1.126
peak=    3.413 closest distance to " CD2 HIS A  81 " =    1.187
peak=    3.411 closest distance to " CB  GLN A  88 " =    1.242
peak=    3.410 closest distance to " O   HOH Z 345 " =    3.247
peak=    3.398 closest distance to " O   HOH Z 151 " =    1.730
peak=    3.395 closest distance to " O   HOH Z  63 " =    1.977
peak=    3.395 closest distance to " O   GLN A 278 " =    1.297
peak=    3.393 closest distance to " O   HOH Z 102 " =    1.280
peak=    3.389 closest distance to " CB BVAL A  41 " =    1.179
peak=    3.384 closest distance to " O   HOH Z  49 " =    1.883
peak=    3.380 closest distance to " CB  LYS A 193 " =    1.131
peak=    3.372 closest distance to " CB  LEU A 255 " =    0.912
peak=    3.371 closest distance to " CB  TRP A 266 " =    0.918
peak=    3.370 closest distance to " O   HOH Z  19 " =    1.640
peak=    3.370 closest distance to " O   HOH Z 290 " =    1.155
peak=    3.362 closest distance to " CB  ALA A 161 " =    0.956
peak=    3.354 closest distance to " CG  MET A 188 " =    1.390
peak=    3.353 closest distance to " O   HOH Z  71 " =    1.297
peak=    3.352 closest distance to " O   HOH Z 355 " =    1.886
peak=    3.349 closest distance to " CD1 ILE A 199 " =    1.035
peak=    3.349 closest distance to " O   HOH Z 422 " =    2.649
peak=    3.347 closest distance to " N   LYS A 166 " =    0.933
peak=    3.343 closest distance to " CA  THR A 246 " =    1.226
peak=    3.340 closest distance to " CG BARG A 102 " =    1.918
peak=    3.338 closest distance to " CD  ARG A 159 " =    0.787
peak=    3.334 closest distance to " O   HOH Z 211 " =    1.126
peak=    3.334 closest distance to " O   HOH Z  99 " =    1.687
peak=    3.334 closest distance to " O   HOH Z 271 " =    1.932
peak=    3.333 closest distance to " CG2 THR A  82 " =    1.005
peak=    3.329 closest distance to " NE1 TRP A 274 " =    0.900
peak=    3.327 closest distance to " O   HOH Z 156 " =    2.497
peak=    3.324 closest distance to " CB  MET A  40 " =    0.701
peak=    3.324 closest distance to " CD2 HIS A 115 " =    0.825
peak=    3.323 closest distance to " O   GLY A  91 " =    1.226
peak=    3.321 closest distance to " NH2BARG A 145 " =    2.225
peak=    3.317 closest distance to " CA  ASP A 140 " =    1.240
peak=    3.315 closest distance to " OG ASER A 134 " =    1.373
peak=    3.309 closest distance to " CA  ALA A 248 " =    1.150
peak=    3.308 closest distance to " O   HOH Z  50 " =    1.837
peak=    3.306 closest distance to " NH1AARG A 145 " =    0.972
peak=    3.302 closest distance to " O   HOH Z 185 " =    1.696
peak=    3.297 closest distance to " O   ASN A 217 " =    1.376
peak=    3.296 closest distance to " O   HOH Z  54 " =    1.525
peak=    3.294 closest distance to " O   HOH Z 329 " =    3.448
peak=    3.294 closest distance to " NE  ARG A 156 " =    1.048
peak=    3.288 closest distance to " O   HOH Z 139 " =    5.248
peak=    3.287 closest distance to " O   HOH Z 393 " =    3.566
peak=    3.286 closest distance to " CB  MET A  47 " =    1.051
peak=    3.286 closest distance to " CB  GLN A  58 " =    0.824
peak=    3.286 closest distance to " CB  PHE A  16 " =    1.004
peak=    3.281 closest distance to " O   HOH Z 279 " =    2.380
peak=    3.277 closest distance to " C   ALA A 299 " =    0.928
peak=    3.277 closest distance to " CG1 ILE A 120 " =    1.120
peak=    3.276 closest distance to " CB  LEU A 143 " =    1.120
peak=    3.271 closest distance to " O   HOH Z 149 " =    1.323
peak=    3.270 closest distance to " O   HOH Z 104 " =    3.343
peak=    3.268 closest distance to " O   GLY A  57 " =    2.323
peak=    3.265 closest distance to " CE1 TYR A 186 " =    1.326
peak=    3.264 closest distance to " CD  LYS A 166 " =    1.487
peak=    3.264 closest distance to " CB  ARG A 102 " =    0.848
peak=    3.263 closest distance to " CA  ALA A 158 " =    1.052
peak=    3.262 closest distance to " CG2 THR A 294 " =    1.672
peak=    3.257 closest distance to " CB  SER A  62 " =    1.292
peak=    3.253 closest distance to " O   HOH Z 209 " =    2.226
peak=    3.252 closest distance to " CB  ARG A 259 " =    1.909
peak=    3.245 closest distance to " O   HOH Z 407 " =    3.717
peak=    3.244 closest distance to " ND1 HIS A  81 " =    1.613
peak=    3.241 closest distance to " O   ALA A 158 " =    1.296
peak=    3.238 closest distance to " CA  ARG A  36 " =    1.056
peak=    3.236 closest distance to " CA  GLN A 194 " =    1.070
peak=    3.232 closest distance to " O   HOH Z  48 " =    2.008
peak=    3.231 closest distance to " O   HOH Z 211 " =    1.970
peak=    3.230 closest distance to " O   HOH Z  37 " =    2.628
peak=    3.230 closest distance to " CA  MET A  40 " =    0.997
peak=    3.229 closest distance to " CD1 TRP A 266 " =    1.181
peak=    3.219 closest distance to " O   HOH Z 374 " =    2.426
peak=    3.215 closest distance to " O   HOH Z 149 " =    2.077
peak=    3.213 closest distance to " O   HOH Z 406 " =    1.758
peak=    3.209 closest distance to " O   HOH Z  85 " =    2.030
peak=    3.209 closest distance to " CA  ALA A 154 " =    1.283
peak=    3.208 closest distance to " N   THR A  52 " =    1.083
peak=    3.201 closest distance to " O   HOH Z 270 " =    1.798
peak=    3.193 closest distance to " CB  SER A 141 " =    1.044
peak=    3.187 closest distance to " O   HOH Z 106 " =    2.372
peak=    3.187 closest distance to " O   HOH Z 287 " =    1.860
peak=    3.185 closest distance to " CB  ALA A 248 " =    1.276
peak=    3.184 closest distance to " CB  GLN A 194 " =    0.958
peak=    3.183 closest distance to " CG2 VAL A 257 " =    0.799
peak=    3.183 closest distance to " CE1 PHE A 208 " =    1.089
peak=    3.183 closest distance to " CD1 ILE A  33 " =    1.603
peak=    3.179 closest distance to " CB  ALA A  34 " =    0.877
peak=    3.178 closest distance to " CD2 LEU A 297 " =    0.861
peak=    3.171 closest distance to " CE  MET A  93 " =    1.513
peak=    3.168 closest distance to " CG  ARG A 219 " =    1.205
peak=    3.167 closest distance to " O   HOH Z 114 " =    1.399
peak=    3.162 closest distance to " CG2 VAL A 268 " =    0.956
peak=    3.157 closest distance to " CA  ARG A 195 " =    1.217
peak=    3.153 closest distance to " CA  ALA A   9 " =    1.164
peak=    3.152 closest distance to " O   HOH Z 227 " =    1.922
peak=    3.152 closest distance to " O   HOH Z 417 " =    3.264
peak=    3.147 closest distance to " CA  ILE A  33 " =    1.419
peak=    3.146 closest distance to " O   HOH Z 227 " =    1.588
peak=    3.146 closest distance to " CG2 ILE A 120 " =    1.248
peak=    3.144 closest distance to " CB  TRP A 123 " =    1.025
peak=    3.142 closest distance to " O   HOH Z 292 " =    3.145
peak=    3.137 closest distance to " O   HOH Z  85 " =    1.256
peak=    3.130 closest distance to " O   HOH Z 410 " =    1.408
peak=    3.129 closest distance to " O   HOH Z 345 " =    1.799
peak=    3.127 closest distance to " CZ3 TRP A  92 " =    1.070
peak=    3.126 closest distance to " CA  ALA A 100 " =    1.122
peak=    3.122 closest distance to " CB  GLU A 152 " =    1.534
peak=    3.113 closest distance to " N   GLN A 278 " =    1.012
peak=    3.109 closest distance to " CD  GLU A 152 " =    0.812
peak=    3.105 closest distance to " CG  GLN A  77 " =    2.120
peak=    3.100 closest distance to " O   HOH Z 271 " =    2.261
peak=    3.097 closest distance to " CB  ASN A 148 " =    1.939
peak=    3.095 closest distance to " OD2 ASP A 286 " =    2.341
peak=    3.092 closest distance to " O   HOH Z  20 " =    1.950
peak=    3.086 closest distance to " O   HOH Z 374 " =    1.006
peak=    3.086 closest distance to " O   HOH Z   8 " =    1.243
peak=    3.082 closest distance to " O   HOH Z 365 " =    5.724
peak=    3.077 closest distance to " CD  ARG A  14 " =    1.261
peak=    3.073 closest distance to " CG2 VAL A 202 " =    1.247
peak=    3.065 closest distance to " OG BSER A 164 " =    2.076
peak=    3.062 closest distance to " CH2 TRP A 274 " =    2.120
peak=    3.053 closest distance to " CB  ASN A 215 " =    1.104
peak=    3.052 closest distance to " CB  ARG A 139 " =    0.817
peak=    3.044 closest distance to " CB  GLN A  89 " =    1.042
peak=    3.039 closest distance to " N   THR A 264 " =    1.212
peak=    3.037 closest distance to " O   HOH Z 368 " =    4.065
peak=    3.022 closest distance to " O   SER A 164 " =    1.450
peak=    3.015 closest distance to " O   HOH Z 209 " =    1.087
peak=    3.014 closest distance to " CB  ASN A 187 " =    1.465

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.565 - 5.534
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 205
   mapped sites are within: 0.715 - 5.534

peak=   -4.979 closest distance to " CG2 VAL A 230 " =    0.880
peak=   -4.787 closest distance to " CG  ARG A 138 " =    0.952
peak=   -4.769 closest distance to " NE  ARG A 138 " =    1.389
peak=   -4.690 closest distance to " OG ASER A 134 " =    1.168
peak=   -4.333 closest distance to " O   HOH Z  13 " =    1.047
peak=   -4.193 closest distance to " O   HOH Z 266 " =    4.768
peak=   -4.126 closest distance to " O   HOH Z 166 " =    1.752
peak=   -4.085 closest distance to " NH2 ARG A  66 " =    1.479
peak=   -4.045 closest distance to " O   HOH Z  52 " =    1.944
peak=   -4.041 closest distance to " C   ASN A 187 " =    1.872
peak=   -4.007 closest distance to " O   HOH Z  19 " =    2.090
peak=   -3.983 closest distance to " O   HOH Z 198 " =    2.425
peak=   -3.973 closest distance to " C   ALA A 158 " =    1.184
peak=   -3.966 closest distance to " O   HOH Z 274 " =    2.609
peak=   -3.957 closest distance to " CG  ASP A 231 " =    0.857
peak=   -3.938 closest distance to " O   HOH Z  11 " =    1.577
peak=   -3.934 closest distance to " OG1 THR A   4 " =    1.811
peak=   -3.930 closest distance to " N   ALA A 226 " =    2.052
peak=   -3.922 closest distance to " O   HOH Z 407 " =    3.236
peak=   -3.918 closest distance to " OD1 ASN A  39 " =    2.249
peak=   -3.913 closest distance to " O   HOH Z 266 " =    4.330
peak=   -3.911 closest distance to " O   HOH Z 221 " =    1.166
peak=   -3.910 closest distance to " CB  ALA A 161 " =    2.682
peak=   -3.856 closest distance to " O   HOH Z  92 " =    1.232
peak=   -3.852 closest distance to " O   HOH Z 151 " =    1.278
peak=   -3.826 closest distance to " NH2AARG A 275 " =    5.233
peak=   -3.808 closest distance to " O   HOH Z 210 " =    0.715
peak=   -3.803 closest distance to " C   ASN A 285 " =    2.481
peak=   -3.801 closest distance to " O   HOH Z 231 " =    1.411
peak=   -3.772 closest distance to " O   HOH Z 423 " =    2.201
peak=   -3.763 closest distance to " OE2 GLU A   2 " =    1.539
peak=   -3.757 closest distance to " CD  ARG A 156 " =    2.103
peak=   -3.756 closest distance to " CD1 PHE A  59 " =    1.780
peak=   -3.733 closest distance to " N   GLN A  58 " =    1.807
peak=   -3.725 closest distance to " CE2 TYR A  30 " =    2.809
peak=   -3.722 closest distance to " O   HOH Z 103 " =    1.808
peak=   -3.696 closest distance to " O   HOH Z  71 " =    0.856
peak=   -3.696 closest distance to " O   HOH Z 290 " =    1.025
peak=   -3.695 closest distance to " CD  GLN A  88 " =    2.349
peak=   -3.685 closest distance to " CG1 VAL A 296 " =    1.342
peak=   -3.676 closest distance to " CD2 LEU A 167 " =    1.763
peak=   -3.672 closest distance to " O   HOH Z 388 " =    1.809
peak=   -3.663 closest distance to " O   HOH Z 292 " =    4.394
peak=   -3.658 closest distance to " O   HOH Z  17 " =    1.292
peak=   -3.656 closest distance to " O   HOH Z 138 " =    0.984
peak=   -3.652 closest distance to " OE1 GLN A 223 " =    2.413
peak=   -3.651 closest distance to " CA  SER A 164 " =    1.862
peak=   -3.650 closest distance to " CG  MET A 105 " =    0.861
peak=   -3.636 closest distance to " CG2 VAL A 112 " =    2.620
peak=   -3.625 closest distance to " CD  ARG A 139 " =    1.665
peak=   -3.595 closest distance to " CD2 LEU A 300 " =    2.772
peak=   -3.590 closest distance to " CA  GLY A 133 " =    1.809
peak=   -3.586 closest distance to " O   HOH Z 243 " =    1.564
peak=   -3.575 closest distance to " O   HOH Z  98 " =    1.638
peak=   -3.574 closest distance to " CE3 TRP A 150 " =    2.226
peak=   -3.564 closest distance to " CG  GLU A  53 " =    1.485
peak=   -3.561 closest distance to " N   SER A 276 " =    1.393
peak=   -3.557 closest distance to " CZ  TYR A 169 " =    1.813
peak=   -3.556 closest distance to " O   ALA A 161 " =    1.302
peak=   -3.551 closest distance to " O   ASN A 187 " =    1.407
peak=   -3.543 closest distance to " CB  CYS A 254 " =    2.414
peak=   -3.539 closest distance to " OG  SER A  32 " =    1.011
peak=   -3.520 closest distance to " O   HOH Z 184 " =    1.177
peak=   -3.520 closest distance to " CD  LYS A 289 " =    2.498
peak=   -3.508 closest distance to " NH1BARG A 190 " =    2.136
peak=   -3.507 closest distance to " O   HOH Z 177 " =    1.184
peak=   -3.504 closest distance to " CB  ALA A 227 " =    2.377
peak=   -3.502 closest distance to " O   HOH Z 241 " =    1.231
peak=   -3.496 closest distance to " OG1 THR A  82 " =    1.329
peak=   -3.484 closest distance to " N   GLN A 122 " =    1.736
peak=   -3.483 closest distance to " O   HOH Z 377 " =    1.077
peak=   -3.483 closest distance to " O   HOH Z  37 " =    1.652
peak=   -3.480 closest distance to " O   HOH Z  10 " =    1.482
peak=   -3.469 closest distance to " O   HOH Z 265 " =    1.517
peak=   -3.464 closest distance to " O   HOH Z 113 " =    1.775
peak=   -3.462 closest distance to " O   ALA A   7 " =    1.657
peak=   -3.458 closest distance to " O   VAL A  67 " =    2.727
peak=   -3.456 closest distance to " CD1 LEU A 228 " =    2.481
peak=   -3.454 closest distance to " O   GLY A 118 " =    2.017
peak=   -3.453 closest distance to " CB  ALA A 248 " =    1.914
peak=   -3.453 closest distance to " O   HOH Z 352 " =    0.977
peak=   -3.448 closest distance to " O   HOH Z 100 " =    0.967
peak=   -3.440 closest distance to " O   HOH Z 125 " =    2.898
peak=   -3.439 closest distance to " O   HOH Z 275 " =    1.513
peak=   -3.439 closest distance to " ND2 ASN A  45 " =    1.066
peak=   -3.436 closest distance to " CD1 LEU A 101 " =    2.680
peak=   -3.431 closest distance to " O   GLY A 196 " =    1.099
peak=   -3.430 closest distance to " O   HOH Z  93 " =    1.561
peak=   -3.427 closest distance to " O   HOH Z 420 " =    5.534
peak=   -3.422 closest distance to " OG  SER A  87 " =    1.321
peak=   -3.415 closest distance to " O   ASP A 191 " =    1.384
peak=   -3.413 closest distance to " O   HOH Z 165 " =    2.081
peak=   -3.410 closest distance to " CG  ASP A  50 " =    2.216
peak=   -3.404 closest distance to " ND2 ASN A  60 " =    1.551
peak=   -3.403 closest distance to " CG  ASN A  45 " =    1.668
peak=   -3.402 closest distance to " O   HOH Z 166 " =    1.785
peak=   -3.402 closest distance to " CD2 LEU A 237 " =    2.557
peak=   -3.401 closest distance to " CA  ASP A 298 " =    1.075
peak=   -3.400 closest distance to " O   HOH Z 185 " =    2.076
peak=   -3.399 closest distance to " O   ASN A 301 " =    1.762
peak=   -3.394 closest distance to " O   HOH Z 189 " =    1.988
peak=   -3.392 closest distance to " O   HOH Z  43 " =    1.640
peak=   -3.382 closest distance to " OD1 ASN A 249 " =    1.219
peak=   -3.379 closest distance to " O   HOH Z 341 " =    1.206
peak=   -3.377 closest distance to " O   HOH Z  55 " =    2.560
peak=   -3.375 closest distance to " O   HOH Z 208 " =    1.318
peak=   -3.361 closest distance to " NH2 ARG A 159 " =    2.337
peak=   -3.355 closest distance to " O   HOH Z 377 " =    2.093
peak=   -3.354 closest distance to " O   ALA A 256 " =    1.263
peak=   -3.352 closest distance to " C   GLY A  91 " =    1.468
peak=   -3.348 closest distance to " NH2 ARG A  79 " =    1.892
peak=   -3.345 closest distance to " O   HOH Z 430 " =    1.493
peak=   -3.344 closest distance to " CG  GLU A 277 " =    1.318
peak=   -3.341 closest distance to " O   HOH Z 108 " =    2.298
peak=   -3.340 closest distance to " C   HIS A 108 " =    1.045
peak=   -3.337 closest distance to " O   VAL A  67 " =    2.468
peak=   -3.337 closest distance to " N   GLN A  55 " =    1.532
peak=   -3.328 closest distance to " O   HOH Z 396 " =    1.404
peak=   -3.325 closest distance to " CD1 TRP A 179 " =    1.077
peak=   -3.318 closest distance to " O   GLY A 211 " =    1.398
peak=   -3.317 closest distance to " O   HOH Z  60 " =    2.202
peak=   -3.311 closest distance to " NE1 TRP A  85 " =    1.136
peak=   -3.306 closest distance to " OD2 ASP A 171 " =    1.791
peak=   -3.303 closest distance to " O   LEU A 228 " =    2.336
peak=   -3.302 closest distance to " CA  TYR A  30 " =    1.013
peak=   -3.300 closest distance to " O   ASP A 270 " =    1.907
peak=   -3.296 closest distance to " CD  GLN A  88 " =    0.834
peak=   -3.294 closest distance to " O   HOH Z 418 " =    1.740
peak=   -3.293 closest distance to " CD2 PHE A  61 " =    1.745
peak=   -3.285 closest distance to " O   ALA A 161 " =    2.774
peak=   -3.283 closest distance to " CG  TRP A 266 " =    1.777
peak=   -3.279 closest distance to " CD2 TYR A 293 " =    2.239
peak=   -3.278 closest distance to " NE2 HIS A  86 " =    1.060
peak=   -3.274 closest distance to " OG BSER A 134 " =    1.192
peak=   -3.273 closest distance to " O   HOH Z 222 " =    1.089
peak=   -3.271 closest distance to " CD  ARG A  14 " =    3.159
peak=   -3.268 closest distance to " CZ3 TRP A  92 " =    1.123
peak=   -3.262 closest distance to " CE  MET A  93 " =    1.384
peak=   -3.258 closest distance to " O   HOH Z   9 " =    2.073
peak=   -3.255 closest distance to " O   HOH Z 427 " =    1.465
peak=   -3.255 closest distance to " O   HOH Z  38 " =    1.565
peak=   -3.249 closest distance to " OD1 ASP A 200 " =    1.236
peak=   -3.248 closest distance to " CA  SER A 271 " =    2.308
peak=   -3.247 closest distance to " O   HOH Z  97 " =    1.957
peak=   -3.244 closest distance to " CB  ASP A 124 " =    2.135
peak=   -3.239 closest distance to " CZ  TYR A 172 " =    1.713
peak=   -3.237 closest distance to " C   LEU A 101 " =    0.933
peak=   -3.235 closest distance to " O   PRO A 198 " =    1.272
peak=   -3.234 closest distance to " CB  PRO A 243 " =    2.774
peak=   -3.230 closest distance to " O   HOH Z 147 " =    2.144
peak=   -3.226 closest distance to " O   GLN A  11 " =    1.264
peak=   -3.222 closest distance to " CD1 LEU A   5 " =    2.412
peak=   -3.222 closest distance to " ND2BASN A 224 " =    1.784
peak=   -3.221 closest distance to " CG  LYS A 193 " =    2.467
peak=   -3.212 closest distance to " N   GLY A  17 " =    1.472
peak=   -3.207 closest distance to " O   HOH Z 353 " =    2.378
peak=   -3.203 closest distance to " OG  SER A  62 " =    1.548
peak=   -3.199 closest distance to " O   HOH Z 435 " =    2.634
peak=   -3.191 closest distance to " CB  ALA A 100 " =    1.938
peak=   -3.191 closest distance to " CB  ALA A  43 " =    2.553
peak=   -3.190 closest distance to " O   HOH Z 117 " =    4.358
peak=   -3.189 closest distance to " CA  ASN A 127 " =    1.029
peak=   -3.188 closest distance to " N   THR A 235 " =    1.186
peak=   -3.187 closest distance to " O   HOH Z 292 " =    2.997
peak=   -3.183 closest distance to " CG1 ILE A 234 " =    1.904
peak=   -3.176 closest distance to " N   THR A 157 " =    1.623
peak=   -3.176 closest distance to " CG  TYR A 169 " =    1.906
peak=   -3.173 closest distance to " O   HOH Z 221 " =    1.716
peak=   -3.158 closest distance to " N   ALA A  43 " =    2.503
peak=   -3.157 closest distance to " O   HOH Z 317 " =    2.368
peak=   -3.155 closest distance to " NH2 ARG A  66 " =    4.791
peak=   -3.155 closest distance to " O   HOH Z 291 " =    1.101
peak=   -3.154 closest distance to " O   HOH Z 227 " =    1.076
peak=   -3.153 closest distance to " N   ASP A 191 " =    1.246
peak=   -3.152 closest distance to " O   ALA A  51 " =    1.607
peak=   -3.151 closest distance to " O   LEU A 143 " =    1.394
peak=   -3.150 closest distance to " CG  GLN A  58 " =    1.236
peak=   -3.146 closest distance to " O   HOH Z 360 " =    2.468
peak=   -3.146 closest distance to " NE2 GLN A  73 " =    1.600
peak=   -3.143 closest distance to " CA  GLY A 133 " =    2.300
peak=   -3.141 closest distance to " O   HOH Z 105 " =    1.991
peak=   -3.130 closest distance to " O   HOH Z 234 " =    4.296
peak=   -3.128 closest distance to " CA  VAL A 296 " =    0.973
peak=   -3.126 closest distance to " NH1 ARG A  56 " =    2.507
peak=   -3.125 closest distance to " N   SER A 258 " =    1.191
peak=   -3.121 closest distance to " CA  VAL A 197 " =    1.074
peak=   -3.113 closest distance to " CD1 PHE A  59 " =    2.294
peak=   -3.107 closest distance to " CD  PRO A 198 " =    1.212
peak=   -3.103 closest distance to " OXT GLY A 302 " =    3.283
peak=   -3.089 closest distance to " OH  TYR A 169 " =    0.974
peak=   -3.087 closest distance to " CD2 LEU A   5 " =    1.041
peak=   -3.084 closest distance to " O   HOH Z  40 " =    3.595
peak=   -3.083 closest distance to " O   MET A  40 " =    2.684
peak=   -3.079 closest distance to " OG BSER A 134 " =    1.774
peak=   -3.078 closest distance to " CG  PRO A 243 " =    1.576
peak=   -3.067 closest distance to " CZ3 TRP A 266 " =    1.590
peak=   -3.062 closest distance to " CZ  TYR A  68 " =    1.236
peak=   -3.052 closest distance to " O   HOH Z 426 " =    2.215
peak=   -3.051 closest distance to " CE  MET A 105 " =    2.100
peak=   -3.043 closest distance to " O   LEU A 255 " =    1.641
peak=   -3.040 closest distance to " O   HOH Z 399 " =    2.301
peak=   -3.039 closest distance to " CG1 VAL A 296 " =    1.574
peak=   -3.021 closest distance to " N   ALA A 248 " =    1.849

================= 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    :  0.4822 0.4821   6.285640e+00   6.280853e+00
   1_bss:  0.4733 0.4727   5.815916e+00   5.800848e+00
   1_xyz:  0.4050 0.4351   6.189056e+00   6.228782e+00
   1_adp:  0.3684 0.4232   6.132399e+00   6.212556e+00
   1_occ:  0.3680 0.4244   6.132210e+00   6.212716e+00
   2_bss:  0.3661 0.4186   6.132790e+00   6.210372e+00
   2_xyz:  0.2900 0.3558   5.962373e+00   6.104222e+00
   2_adp:  0.2680 0.3337   5.901824e+00   6.058991e+00
   2_occ:  0.2677 0.3337   5.900960e+00   6.058599e+00
   3_bss:  0.2659 0.3312   5.900064e+00   6.056322e+00
   3_xyz:  0.1957 0.2532   5.634335e+00   5.839198e+00
   3_adp:  0.1720 0.2343   5.537769e+00   5.764683e+00
   3_occ:  0.1718 0.2342   5.537226e+00   5.764160e+00
   4_bss:  0.1716 0.2339   5.535360e+00   5.761742e+00
   4_xyz:  0.1409 0.1976   5.359561e+00   5.601553e+00
   4_adp:  0.1337 0.1867   5.309078e+00   5.547490e+00
   4_occ:  0.1334 0.1864   5.307828e+00   5.546462e+00
   5_bss:  0.1339 0.1877   5.311735e+00   5.550411e+00
   5_xyz:  0.1277 0.1758   5.267287e+00   5.496630e+00
   5_adp:  0.1260 0.1734   5.253548e+00   5.481226e+00
   5_occ:  0.1258 0.1732   5.252720e+00   5.480710e+00
   5_bss:  0.1258 0.1731   5.252707e+00   5.480551e+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:  0.337  13.772   7.134   8.635   9.087   0.000   0.000   0.000
   1_xyz:  0.337  13.772   7.134   8.635   9.087   0.000   0.000   0.000
   1_adp:  0.337  13.772   7.134   8.635   9.087   0.000   0.000   0.000
   1_occ:  0.337  13.772   7.134   8.635   9.087   0.000   0.000   0.000
   2_bss:  0.328  41.008   3.676   5.080   6.084   0.000   0.000   0.000
   2_xyz:  0.328  41.008   3.676   5.080   6.084   0.000   0.000   0.000
   2_adp:  0.328  41.008   3.676   5.080   6.084   0.000   0.000   0.000
   2_occ:  0.328  41.008   3.676   5.080   6.084   0.000   0.000   0.000
   3_bss:  0.322  42.252   2.244   3.048   3.690   0.000   0.000   0.000
   3_xyz:  0.322  42.252   2.244   3.048   3.690   0.000   0.000   0.000
   3_adp:  0.322  42.252   2.244   3.048   3.690   0.000   0.000   0.000
   3_occ:  0.322  42.252   2.244   3.048   3.690   0.000   0.000   0.000
   4_bss:  0.314  42.252   1.516   2.088   2.171   0.000   0.000   0.000
   4_xyz:  0.314  42.252   1.516   2.088   2.171   0.000   0.000   0.000
   4_adp:  0.314  42.252   1.516   2.088   2.171   0.000   0.000   0.000
   4_occ:  0.314  42.252   1.516   2.088   2.171   0.000   0.000   0.000
   5_bss:  0.318  45.786   1.445   1.909   1.898   0.000   0.000   0.000
   5_xyz:  0.318  45.786   1.445   1.909   1.898   0.000   0.000   0.000
   5_adp:  0.318  45.786   1.445   1.909   1.898   0.000   0.000   0.000
   5_occ:  0.318  45.786   1.445   1.909   1.898   0.000   0.000   0.000
   5_bss:  0.316  45.625  -0.305   0.158   0.148   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.939 0.3938  0.4660    73280.310
   1_bss:  60.938 0.3779  0.5545    70813.226
   1_xyz:  53.871 0.4677  0.6804    57647.843
   1_adp:  50.524 0.5108  0.7922    53207.303
   1_occ:  50.585 0.5101  0.7916    53460.354
   2_bss:  50.161 0.5153  0.7175    52891.041
   2_xyz:  39.110 0.6522  0.9035    36201.531
   2_adp:  35.918 0.6899  0.9523    31417.274
   2_occ:  35.890 0.6902  0.9520    31333.436
   3_bss:  35.709 0.6922  0.8908    31090.583
   3_xyz:  25.936 0.8007  0.9826    17167.660
   3_adp:  23.405 0.8275  0.9887    14521.786
   3_occ:  23.403 0.8275  0.9883    14501.636
   4_bss:  23.292 0.8285  0.9520    14404.389
   4_xyz:  19.180 0.8686  0.9767    10124.776
   4_adp:  17.718 0.8828  0.9783     9048.062
   4_occ:  17.682 0.8832  0.9783     9024.206
   5_bss:  17.772 0.8825  0.9719     9163.934
   5_xyz:  16.519 0.8937  0.9767     8101.374
   5_adp:  16.094 0.8977  0.9760     7831.505
   5_occ:  16.078 0.8978  0.9759     7822.657
   5_bss:  16.078 0.8978  0.9758     7817.838
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3533e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3533e+01
   1_xyz:   1.716  0.013  0.108 18.205  0.007  4.109   1.4473e-01
   1_adp:   1.716  0.013  0.108 18.205  0.007  4.109   1.4473e-01
   1_occ:   1.716  0.013  0.108 18.205  0.007  4.109   1.4473e-01
   2_bss:   1.716  0.013  0.108 18.205  0.007  4.109   1.4473e-01
   2_xyz:   1.167  0.008  0.077 16.315  0.005  4.111   8.4571e-02
   2_adp:   1.167  0.008  0.077 16.315  0.005  4.111   8.4571e-02
   2_occ:   1.167  0.008  0.077 16.315  0.005  4.111   8.4571e-02
   3_bss:   1.167  0.008  0.077 16.315  0.005  4.111   8.4571e-02
   3_xyz:   1.162  0.008  0.084 15.586  0.005  4.114   7.5715e-02
   3_adp:   1.162  0.008  0.084 15.586  0.005  4.114   7.5715e-02
   3_occ:   1.162  0.008  0.084 15.586  0.005  4.114   7.5715e-02
   4_bss:   1.162  0.008  0.084 15.586  0.005  4.114   7.5715e-02
   4_xyz:   1.073  0.007  0.079 15.549  0.004  4.119   6.7458e-02
   4_adp:   1.073  0.007  0.079 15.549  0.004  4.119   6.7458e-02
   4_occ:   1.073  0.007  0.079 15.549  0.004  4.119   6.7458e-02
   5_bss:   1.073  0.007  0.079 15.549  0.004  4.119   6.7458e-02
   5_xyz:   0.930  0.005  0.069 15.199  0.003  4.122   5.3890e-02
   5_adp:   0.930  0.005  0.069 15.199  0.003  4.122   5.3890e-02
   5_occ:   0.930  0.005  0.069 15.199  0.003  4.122   5.3890e-02
   5_bss:   0.930  0.005  0.069 15.199  0.003  4.122   5.3890e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9381e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9381e+00
   1_xyz:  14.905  0.172  0.472 85.595  0.054  2.198   9.9997e-02
   1_adp:  14.905  0.172  0.472 85.595  0.054  2.198   9.9997e-02
   1_occ:  14.905  0.172  0.472 85.595  0.054  2.198   9.9997e-02
   2_bss:  14.905  0.172  0.472 85.595  0.054  2.198   9.9997e-02
   2_xyz:   7.620  0.079  0.275 81.359  0.034  2.133   6.0402e-02
   2_adp:   7.620  0.079  0.275 81.359  0.034  2.133   6.0402e-02
   2_occ:   7.620  0.079  0.275 81.359  0.034  2.133   6.0402e-02
   3_bss:   7.620  0.079  0.275 81.359  0.034  2.133   6.0402e-02
   3_xyz:   7.283  0.067  0.372 81.950  0.047  2.281   5.7089e-02
   3_adp:   7.283  0.067  0.372 81.950  0.047  2.281   5.7089e-02
   3_occ:   7.283  0.067  0.372 81.950  0.047  2.281   5.7089e-02
   4_bss:   7.283  0.067  0.372 81.950  0.047  2.281   5.7089e-02
   4_xyz:   7.252  0.046  0.446 84.212  0.034  2.359   4.5076e-02
   4_adp:   7.252  0.046  0.446 84.212  0.034  2.359   4.5076e-02
   4_occ:   7.252  0.046  0.446 84.212  0.034  2.359   4.5076e-02
   5_bss:   7.252  0.046  0.446 84.212  0.034  2.359   4.5076e-02
   5_xyz:   7.305  0.043  0.360 80.044  0.032  2.405   3.4950e-02
   5_adp:   7.305  0.043  0.360 80.044  0.032  2.405   3.4950e-02
   5_occ:   7.305  0.043  0.360 80.044  0.032  2.405   3.4950e-02
   5_bss:   7.305  0.043  0.360 80.044  0.032  2.405   3.4950e-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: 100.08   0.00  12.49 100.08   0.00  10.79  54.37   0.00  21.71
   1_occ: 100.08   0.00  12.49 100.08   0.00  10.79  54.37   0.00  21.71
   2_bss: 100.08   0.00  12.49 100.08   0.00  10.79  54.37   0.00  21.71
   2_xyz: 100.08   0.00  12.49 100.08   0.00  10.79  54.37   0.00  21.71
   2_adp:  72.91   0.00  13.72  72.91   0.00  10.49  70.47   0.72  31.30
   2_occ:  72.91   0.00  13.72  72.91   0.00  10.49  70.47   0.72  31.30
   3_bss:  72.91   0.00  13.72  72.91   0.00  10.49  70.47   0.72  31.30
   3_xyz:  72.91   0.00  13.72  72.91   0.00  10.49  70.47   0.72  31.30
   3_adp:  97.31   0.00  15.12  97.31   0.00  10.17  94.05   1.64  42.03
   3_occ:  97.31   0.00  15.12  97.31   0.00  10.17  94.05   1.64  42.03
   4_bss:  97.31   0.00  15.12  97.31   0.00  10.17  94.05   1.64  42.03
   4_xyz:  97.31   0.00  15.12  97.31   0.00  10.17  94.05   1.64  42.03
   4_adp: 107.58   0.00  14.67 107.58   0.00   9.71  92.01   2.95  41.67
   4_occ: 107.58   0.00  14.67 107.58   0.00   9.71  92.01   2.95  41.67
   5_bss: 107.58   0.00  14.67 107.58   0.00   9.71  92.01   2.95  41.67
   5_xyz: 107.58   0.00  14.67 107.58   0.00   9.71  92.01   2.95  41.67
   5_adp: 109.15   0.00  14.18 109.15   0.00   9.45  93.67   2.11  39.99
   5_occ: 109.15   0.00  14.18 109.15   0.00   9.45  93.67   2.11  39.99
   5_bss: 110.90   1.75  15.94 110.90   1.75  11.20  95.42   3.86  41.74
------------------------------------------------------------------------
 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:    1.210    0.024    0.412
   1_adp:    1.210    0.024    0.412
   1_occ:    1.210    0.024    0.412
   2_bss:    1.210    0.024    0.412
   2_xyz:    1.852    0.058    0.574
   2_adp:    1.852    0.058    0.574
   2_occ:    1.852    0.058    0.574
   3_bss:    1.852    0.058    0.574
   3_xyz:    1.756    0.036    0.685
   3_adp:    1.756    0.036    0.685
   3_occ:    1.756    0.036    0.685
   4_bss:    1.756    0.036    0.685
   4_xyz:    1.737    0.040    0.737
   4_adp:    1.737    0.040    0.737
   4_occ:    1.737    0.040    0.737
   5_bss:    1.737    0.040    0.737
   5_xyz:    1.791    0.065    0.758
   5_adp:    1.791    0.065    0.758
   5_occ:    1.791    0.065    0.758
   5_bss:    1.791    0.065    0.758
------------------------------------------------------------------------

CPU time actual refinement: 362.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_924/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_924/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_924/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_924/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_924/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 361.94 
  Macro-tasks:
    bulk solvent and scale       = 40.62  
    individual site refinement   = 152.51 
    weights calculation          = 33.03  
    collect and process          = 6.47   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 232.76 
  Micro-tasks:
    mask                            = 2.68   
    f_calc                          = 116.46 
    alpha_beta                      = 8.48   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 126.53 
    fmodel                         = 7.38   
    r_factors                      = 0.24   
    phase_errors                   = 10.09  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 273.33 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.121 micro seconds
Total CPU time: 6.27 minutes
from_scatterers_fft:    640 calls, 116.06 s
gradients_fft:          585 calls, 113.39 s

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

# Date 2008-01-16 Time 02:45:49 PST -0800 (1200480349.79 s)
Start R-work = 0.4822, R-free = 0.4821 (no bulk solvent and anisotropic scale)
Final R-work = 0.1418, R-free = 0.1908 (no bulk solvent and anisotropic scale)

Start R-work = 0.4733, R-free = 0.4727
Final R-work = 0.1258, R-free = 0.1731