# Date 2008-01-16 Time 01:52:35 PST -0800 (1200477155.34 s)
#phil __OFF__

Command line arguments: "../607.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 = 4999
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 607

-------------------------------------------------------------------------------
  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: (70.25, 45.7567, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.95275
Completeness in resolution range: 0.956167
Completeness with d_max=infinity: 0.953329

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9320
                             d_min =   1.9527

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: (70.25, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.95275
Completeness in resolution range: 0.956167
Completeness with d_max=infinity: 0.953329

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9324 -  4.1792 [2148/2174]  1935   213   9.9%
  bin  2:  4.1792 -  3.3293 [2067/2087]  1858   209  10.1%
  bin  3:  3.3293 -  2.9120 [2045/2064]  1843   202   9.9%
  bin  4:  2.9120 -  2.6473 [2027/2057]  1821   206  10.2%
  bin  5:  2.6473 -  2.4585 [2015/2034]  1820   195   9.7%
  bin  6:  2.4585 -  2.3141 [1992/2017]  1783   209  10.5%
  bin  7:  2.3141 -  2.1986 [1996/2024]  1799   197   9.9%
  bin  8:  2.1986 -  2.1031 [1979/2015]  1782   197  10.0%
  bin  9:  2.1031 -  2.0224 [1963/2005]  1765   198  10.1%
  bin 10:  2.0224 -  1.9527 [1357/2010]  1224   133   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_607/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 31
        2.27 -     2.92: 1585
        2.92 -     3.58: 4610
        3.58 -     4.24: 9365
        4.24 -     4.90: 13313
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.607 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.780 3.040 -x+1/2,-y+1,z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28899 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_607/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_607/model_refine_001.geo

CPU time processing inputs: 9.46


============================ 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 = 70.25 45.75675 85.09415 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 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5012   r_free= 0.5021   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.303014                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.6617 0.99   1397  157 0.4370 0.4517      6.6495      6.7366|
|  2:  4.6617 -  3.7189 0.99   1344  148 0.4484 0.4163      6.8611      6.7852|
|  3:  3.7189 -  3.2544 0.99   1326  144 0.4711 0.4558      6.7234      6.7709|
|  4:  3.2544 -  2.9593 0.99   1313  153 0.4947 0.4660      6.5755      6.4946|
|  5:  2.9593 -  2.7486 0.99   1298  143 0.5225 0.5729      6.3853      6.4235|
|  6:  2.7486 -  2.5875 0.99   1303  141 0.5196 0.5628      6.2965      6.2274|
|  7:  2.5875 -  2.4585 0.99   1296  139 0.5323 0.4870      6.2639      6.2316|
|  8:  2.4585 -  2.3519 0.98   1257  146 0.5459 0.5126      6.1821      6.1621|
|  9:  2.3519 -  2.2617 0.98   1276  149 0.5257 0.5661      6.1301      6.2053|
| 10:  2.2617 -  2.1839 1.00   1299  140 0.5265 0.5415      6.1177      6.1004|
| 11:  2.1839 -  2.1158 0.98   1292  137 0.5213 0.5077      6.0432      6.0504|
| 12:  2.1158 -  2.0555 0.98   1243  144 0.5108 0.5721      5.9752      6.0198|
| 13:  2.0555 -  2.0015 0.99   1280  139 0.5552 0.5365      5.8888      5.8222|
| 14:  2.0015 -  1.9527 0.55    706   79 0.5614 0.4616      5.8633      5.8217|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.6617  1397   157  0.57  45.45   0.77     0.64     113347.79|
|  2:  4.6617 -  3.7189  1344   148  0.62  41.69   0.85     0.72     141944.17|
|  3:  3.7189 -  3.2544  1326   144  0.52  50.11   0.83     0.67     142587.20|
|  4:  3.2544 -  2.9593  1313   153  0.43  57.40   0.79     0.54     123605.04|
|  5:  2.9593 -  2.7486  1298   143  0.31  66.29   0.73     0.40      97879.26|
|  6:  2.7486 -  2.5875  1303   141  0.29  68.49   0.72     0.34      84378.57|
|  7:  2.5875 -  2.4585  1296   139  0.24  72.22   0.74     0.28      75057.33|
|  8:  2.4585 -  2.3519  1257   146  0.21  74.45   0.72     0.26      69995.73|
|  9:  2.3519 -  2.2617  1276   149  0.21  74.22   0.72     0.25      62340.36|
| 10:  2.2617 -  2.1839  1299   140  0.25  71.54   0.76     0.30      55156.35|
| 11:  2.1839 -  2.1158  1292   137  0.23  72.70   0.78     0.29      52673.58|
| 12:  2.1158 -  2.0555  1243   144  0.22  73.40   0.79     0.29      49143.03|
| 13:  2.0555 -  2.0015  1280   139  0.21  74.70   0.73     0.28      41817.00|
| 14:  2.0015 -  1.9527   706    79  0.31  67.18   0.72     0.34      29715.34|
|alpha:            min =        0.25 max =            0.72 mean =         0.41|
|beta:             min =    29715.34 max =       142587.20 mean =     83810.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.33|
|phase err.(work): min =        0.00 max =           89.99 mean =        64.64|
|phase err.(test): min =        0.00 max =           89.99 mean =        64.92|
|-----------------------------------------------------------------------------|

============================== 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 = 23.541978             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.538   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.344821              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.260   (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:       36 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      179 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      734 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1540 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2690 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4020 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5171 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6651 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7920 |
|-----------------------------------------------------------------------------|
|-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 |       52.849 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.483 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.428)------------------------------------------|
|    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 = 11.428)------------------------------------------|
|    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 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5054   r_free= 0.5036   ksol= 0.00   Bsol= 0.00   scale= 0.756    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.303513                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4926   r_free= 0.4902   ksol= 0.38   Bsol= 0.00   scale= 0.970    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.41,9.52,7.95,0.00,0.00,0.00); trace/3= 7.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.297905                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.746474             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.323   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.107088              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.821   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4926      final r-factor (work) = 0.4380          |
| start r-factor (free) = 0.4902      final r-factor (free) = 0.4661          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 111.8946 = 18.75 * 0.50 * 6.2994 + 1.00 * 52.8488                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 58.7843 = 18.75 * 0.50 * 6.2561 + 1.00 * 0.1449                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4380      final r-factor (work) = 0.4005          |
| start r-factor (free) = 0.4661      final r-factor (free) = 0.4630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1964 = 2.11 * 1.00 * 6.2561 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1115 = 2.11 * 1.00 * 6.2112 + 1.00 * 0.0240                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.53  15.93    None  None   None       |
|    all(noH): 2823   0      0.00    107.53  15.93    None  None   None       |
|    Sol.    : 438    0      0.00    107.53  23.23    None  None   None       |
|    Mac.    : 2385   0      0.00    96.46   14.59    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 -  10.753: 1216   |   5:    53.764 -  64.517:   25        |
|      1:    10.753 -  21.506:  863   |   6:    64.517 -  75.269:    8        |
|      2:    21.506 -  32.258:  415   |   7:    75.269 -  86.022:    3        |
|      3:    32.258 -  43.011:  197   |   8:    86.022 -  96.775:    3        |
|      4:    43.011 -  53.764:   92   |   9:    96.775 - 107.528:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4005 r_free = 0.4630             target_work(ml) = 6.204         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4001 r_free = 0.4629             target_work(ml) = 6.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4001   r_free= 0.4629   ksol= 0.38   Bsol= 0.00   scale= 1.104    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.41,9.52,7.95,0.00,0.00,0.00); trace/3= 7.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.203995                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3980   r_free= 0.4592   ksol= 0.37   Bsol= 36.93   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,5.10,4.47,0.00,0.00,0.00); trace/3= 4.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.203902                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.153763             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.689  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.857657              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.362  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3980      final r-factor (work) = 0.3552          |
| start r-factor (free) = 0.4592      final r-factor (free) = 0.4256          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.7567 = 11.15 * 0.50 * 6.2063 + 1.00 * 0.1449                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.4367 = 11.15 * 0.50 * 6.1590 + 1.00 * 0.0889                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3552      final r-factor (work) = 0.3443          |
| start r-factor (free) = 0.4256      final r-factor (free) = 0.4173          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3069 = 0.86 * 1.00 * 6.1590 + 1.00 * 0.0246                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3525 = 0.86 * 1.00 * 6.1146 + 1.00 * 0.1083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.76  15.23    None  None   None       |
|    all(noH): 2823   0      0.00    110.76  15.23    None  None   None       |
|    Sol.    : 438    0      0.00    110.76  24.65    None  None   None       |
|    Mac.    : 2385   0      0.00    100.55  13.50    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 -  11.076: 1249   |   5:    55.378 -  66.453:   18        |
|      1:    11.076 -  22.151:  925   |   6:    66.453 -  77.529:    4        |
|      2:    22.151 -  33.227:  424   |   7:    77.529 -  88.604:    2        |
|      3:    33.227 -  44.302:  153   |   8:    88.604 -  99.680:    2        |
|      4:    44.302 -  55.378:   44   |   9:    99.680 - 110.755:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3443 r_free = 0.4173             target_work(ml) = 6.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3441 r_free = 0.4174             target_work(ml) = 6.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3441   r_free= 0.4174   ksol= 0.37   Bsol= 36.93   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,5.10,4.47,0.00,0.00,0.00); trace/3= 4.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.103778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3446   r_free= 0.4172   ksol= 0.37   Bsol= 59.76   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,3.34,3.18,0.00,0.00,0.00); trace/3= 2.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.105497                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.395004             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.120  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.457443              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.092   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3446      final r-factor (work) = 0.2856          |
| start r-factor (free) = 0.4172      final r-factor (free) = 0.3600          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.9248 = 11.40 * 0.50 * 6.1143 + 1.00 * 0.0886                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.5003 = 11.40 * 0.50 * 6.0363 + 1.00 * 0.1086                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2856      final r-factor (work) = 0.2563          |
| start r-factor (free) = 0.3600      final r-factor (free) = 0.3497          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 51.0676 = 8.46 * 1.00 * 6.0363 + 1.00 * 0.0162                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 50.0265 = 8.46 * 1.00 * 5.9117 + 1.00 * 0.0286                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    127.28  17.34    None  None   None       |
|    all(noH): 2823   0      0.00    127.28  17.34    None  None   None       |
|    Sol.    : 438    0      0.00    127.28  37.89    None  None   None       |
|    Mac.    : 2385   0      0.00    119.44  13.56    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 -  12.728: 1503   |   5:    63.642 -  76.370:   46        |
|      1:    12.728 -  25.457:  646   |   6:    76.370 -  89.098:   19        |
|      2:    25.457 -  38.185:  313   |   7:    89.098 - 101.826:    4        |
|      3:    38.185 -  50.913:  186   |   8:   101.826 - 114.555:    1        |
|      4:    50.913 -  63.642:  102   |   9:   114.555 - 127.283:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2563 r_free = 0.3497             target_work(ml) = 5.897         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2559 r_free = 0.3495             target_work(ml) = 5.896         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2559   r_free= 0.3495   ksol= 0.37   Bsol= 59.76   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,3.34,3.18,0.00,0.00,0.00); trace/3= 2.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.896173                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2559   r_free= 0.3475   ksol= 0.36   Bsol= 63.81   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,2.18,2.91,0.00,0.00,0.00); trace/3= 2.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.892561                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.590256              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.407  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.386266              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.241  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2559      final r-factor (work) = 0.2183          |
| start r-factor (free) = 0.3475      final r-factor (free) = 0.3004          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6284 = 5.59 * 0.50 * 5.9102 + 1.00 * 0.1086                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3809 = 5.59 * 0.50 * 5.8344 + 1.00 * 0.0729                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2183      final r-factor (work) = 0.2033          |
| start r-factor (free) = 0.3004      final r-factor (free) = 0.2668          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2824 = 0.39 * 1.00 * 5.8344 + 1.00 * 0.0288                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2223 = 0.39 * 1.00 * 5.7189 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    125.66  15.49    None  None   None       |
|    all(noH): 2823   0      0.00    125.66  15.49    None  None   None       |
|    Sol.    : 438    0      0.71    125.66  38.07    None  None   None       |
|    Mac.    : 2385   0      0.00    115.33  11.35    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 -  12.566: 1710   |   5:    62.832 -  75.398:   26        |
|      1:    12.566 -  25.133:  575   |   6:    75.398 -  87.964:   14        |
|      2:    25.133 -  37.699:  240   |   7:    87.964 - 100.531:    2        |
|      3:    37.699 -  50.265:  171   |   8:   100.531 - 113.097:    1        |
|      4:    50.265 -  62.832:   81   |   9:   113.097 - 125.663:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2033 r_free = 0.2668             target_work(ml) = 5.666         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2028 r_free = 0.2657             target_work(ml) = 5.663         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2028   r_free= 0.2657   ksol= 0.36   Bsol= 63.81   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,2.18,2.91,0.00,0.00,0.00); trace/3= 2.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.663343                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2029   r_free= 0.2640   ksol= 0.33   Bsol= 47.27   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.35,1.28,2.36,0.00,0.00,0.00); trace/3= 1.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.662084                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.525099              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.601   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.810205              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.172  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2029      final r-factor (work) = 0.1625          |
| start r-factor (free) = 0.2640      final r-factor (free) = 0.2165          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0101 = 4.53 * 0.50 * 5.7180 + 1.00 * 0.0729                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6683 = 4.53 * 0.50 * 5.5688 + 1.00 * 0.0686                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1625      final r-factor (work) = 0.1460          |
| start r-factor (free) = 0.2165      final r-factor (free) = 0.2032          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0938 = 1.81 * 1.00 * 5.5688 + 1.00 * 0.0131                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8253 = 1.81 * 1.00 * 5.4198 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    125.04  15.42    None  None   None       |
|    all(noH): 2823   0      0.00    125.04  15.42    None  None   None       |
|    Sol.    : 438    0      3.31    125.04  43.53    None  None   None       |
|    Mac.    : 2385   0      0.00    119.64  10.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.504: 1860   |   5:    62.519 -  75.023:   69        |
|      1:    12.504 -  25.008:  467   |   6:    75.023 -  87.527:   19        |
|      2:    25.008 -  37.512:  168   |   7:    87.527 - 100.031:    5        |
|      3:    37.512 -  50.016:  111   |   8:   100.031 - 112.535:    1        |
|      4:    50.016 -  62.519:  120   |   9:   112.535 - 125.039:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1460 r_free = 0.2032             target_work(ml) = 5.382         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1459 r_free = 0.2028             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.2028   ksol= 0.33   Bsol= 47.27   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.35,1.28,2.36,0.00,0.00,0.00); trace/3= 1.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.380326                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.6617 0.99   1397  157 0.1126 0.1469      5.5322      5.7269|
|  2:  4.6617 -  3.7189 0.99   1344  148 0.1058 0.1560      5.6473      5.9523|
|  3:  3.7189 -  3.2544 0.99   1326  144 0.1445 0.1807      5.7404      5.9957|
|  4:  3.2544 -  2.9593 0.99   1313  153 0.1606 0.2212      5.7112      5.8786|
|  5:  2.9593 -  2.7486 0.99   1298  143 0.1740 0.2391      5.5809       5.815|
|  6:  2.7486 -  2.5875 0.99   1303  141 0.1567 0.2350      5.4583      5.6589|
|  7:  2.5875 -  2.4585 0.99   1296  139 0.1630 0.2003      5.3952      5.5811|
|  8:  2.4585 -  2.3519 0.98   1257  146 0.1625 0.2345       5.326      5.5955|
|  9:  2.3519 -  2.2617 0.98   1276  149 0.1552 0.2218      5.2636      5.5183|
| 10:  2.2617 -  2.1839 1.00   1299  140 0.1455 0.2233      5.1964      5.4432|
| 11:  2.1839 -  2.1158 0.98   1292  137 0.1468 0.2263      5.1704      5.4488|
| 12:  2.1158 -  2.0555 0.98   1243  144 0.1445 0.2139      5.1023      5.4241|
| 13:  2.0555 -  2.0015 0.99   1280  139 0.1553 0.2249      5.0145      5.2396|
| 14:  2.0015 -  1.9527 0.55    706   79 0.1469 0.2039      4.9229      5.1837|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.6617  1397   157  0.92  11.94   0.98     0.96      10523.59|
|  2:  4.6617 -  3.7189  1344   148  0.93  11.67   1.05     1.02      14524.25|
|  3:  3.7189 -  3.2544  1326   144  0.89  16.67   1.07     1.05      18322.94|
|  4:  3.2544 -  2.9593  1313   153  0.87  19.35   1.04     0.99      17769.48|
|  5:  2.9593 -  2.7486  1298   143  0.84  22.17   1.02     0.97      14756.26|
|  6:  2.7486 -  2.5875  1303   141  0.85  21.90   1.01     0.95      12289.40|
|  7:  2.5875 -  2.4585  1296   139  0.84  22.20   1.03     0.99      10873.66|
|  8:  2.4585 -  2.3519  1257   146  0.85  21.71   1.02     0.98       9220.32|
|  9:  2.3519 -  2.2617  1276   149  0.86  20.69   1.02     0.98       8206.42|
| 10:  2.2617 -  2.1839  1299   140  0.85  21.36   1.02     0.96       7356.26|
| 11:  2.1839 -  2.1158  1292   137  0.85  21.38   1.05     0.99       7189.94|
| 12:  2.1158 -  2.0555  1243   144  0.86  21.07   1.05     1.02       6608.44|
| 13:  2.0555 -  2.0015  1280   139  0.85  21.95   1.04     1.00       5308.66|
| 14:  2.0015 -  1.9527   706    79  0.87  19.69   1.02     0.98       4177.71|
|alpha:            min =        0.95 max =            1.05 mean =         0.99|
|beta:             min =     4177.71 max =        18322.94 mean =     10775.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           90.00 mean =        19.47|
|phase err.(test): min =        0.00 max =           89.43 mean =        18.40|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1460   r_free= 0.2024   ksol= 0.32   Bsol= 43.93   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,-0.55,0.73,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.378495                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1460   r_free= 0.2024   ksol= 0.32   Bsol= 43.93   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,-0.55,0.73,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.378495                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.6617 0.99   1397  157 0.1121 0.1448      5.5155      5.7072|
|  2:  4.6617 -  3.7189 0.99   1344  148 0.1067 0.1547       5.644      5.9482|
|  3:  3.7189 -  3.2544 0.99   1326  144 0.1442 0.1795      5.7394      5.9952|
|  4:  3.2544 -  2.9593 0.99   1313  153 0.1607 0.2215      5.7111      5.8806|
|  5:  2.9593 -  2.7486 0.99   1298  143 0.1739 0.2394      5.5802      5.8168|
|  6:  2.7486 -  2.5875 0.99   1303  141 0.1566 0.2350      5.4585      5.6586|
|  7:  2.5875 -  2.4585 0.99   1296  139 0.1629 0.2003      5.3953       5.582|
|  8:  2.4585 -  2.3519 0.98   1257  146 0.1622 0.2347      5.3256      5.5961|
|  9:  2.3519 -  2.2617 0.98   1276  149 0.1548 0.2216       5.263       5.516|
| 10:  2.2617 -  2.1839 1.00   1299  140 0.1454 0.2246       5.196       5.446|
| 11:  2.1839 -  2.1158 0.98   1292  137 0.1469 0.2267      5.1709      5.4502|
| 12:  2.1158 -  2.0555 0.98   1243  144 0.1444 0.2142      5.1022      5.4241|
| 13:  2.0555 -  2.0015 0.99   1280  139 0.1552 0.2242      5.0143      5.2374|
| 14:  2.0015 -  1.9527 0.55    706   79 0.1469 0.2037      4.9214      5.1831|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.6617  1397   157  0.92  11.49   0.97     0.96       9899.49|
|  2:  4.6617 -  3.7189  1344   148  0.93  11.48   1.04     1.02      14138.81|
|  3:  3.7189 -  3.2544  1326   144  0.89  16.61   1.06     1.04      18269.39|
|  4:  3.2544 -  2.9593  1313   153  0.87  19.36   1.03     0.98      17779.86|
|  5:  2.9593 -  2.7486  1298   143  0.84  22.14   1.01     0.96      14744.02|
|  6:  2.7486 -  2.5875  1303   141  0.85  21.88   1.00     0.94      12294.17|
|  7:  2.5875 -  2.4585  1296   139  0.84  22.19   1.01     0.97      10877.08|
|  8:  2.4585 -  2.3519  1257   146  0.85  21.75   1.00     0.96       9236.15|
|  9:  2.3519 -  2.2617  1276   149  0.86  20.69   1.00     0.96       8211.92|
| 10:  2.2617 -  2.1839  1299   140  0.85  21.37   1.00     0.94       7363.89|
| 11:  2.1839 -  2.1158  1292   137  0.85  21.40   1.03     0.97       7205.84|
| 12:  2.1158 -  2.0555  1243   144  0.86  21.07   1.02     1.00       6608.75|
| 13:  2.0555 -  2.0015  1280   139  0.85  21.94   1.01     0.98       5304.27|
| 14:  2.0015 -  1.9527   706    79  0.87  19.63   0.99     0.95       4155.48|
|alpha:            min =        0.94 max =            1.04 mean =         0.97|
|beta:             min =     4155.48 max =        18269.39 mean =     10695.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.86 mean =        19.41|
|phase err.(test): min =        0.00 max =           89.34 mean =        18.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.428)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    126.25  16.63    None  None   None       |
|    all(noH): 2823   0      1.21    126.25  16.63    None  None   None       |
|    Sol.    : 438    0      4.52    126.25  44.74    None  None   None       |
|    Mac.    : 2385   0      1.21    120.85  11.47    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:     1.213 -  13.717: 1860   |   5:    63.733 -  76.237:   69        |
|      1:    13.717 -  26.221:  467   |   6:    76.237 -  88.741:   19        |
|      2:    26.221 -  38.725:  168   |   7:    88.741 - 101.244:    5        |
|      3:    38.725 -  51.229:  111   |   8:   101.244 - 113.748:    1        |
|      4:    51.229 -  63.733:  120   |   9:   113.748 - 126.252:    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)= 351         
Filter by distance & map next to the model:
   mapped sites are within: 0.506 - 5.843
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 346 from: 351
   mapped sites are within: 0.738 - 5.843

peak=    9.478 closest distance to " CB  VAL A 296 " =    1.361
peak=    8.442 closest distance to " O   HOH Z 390 " =    1.714
peak=    7.786 closest distance to " CG2 VAL A 230 " =    1.356
peak=    6.859 closest distance to " O   HOH Z  15 " =    1.331
peak=    6.826 closest distance to " O   HOH Z 381 " =    1.242
peak=    6.636 closest distance to " O   HOH Z 289 " =    1.784
peak=    6.545 closest distance to " O   HOH Z 291 " =    1.466
peak=    6.536 closest distance to " O   HOH Z 415 " =    1.526
peak=    6.267 closest distance to " O   HOH Z 387 " =    1.750
peak=    6.085 closest distance to " O   HOH Z 130 " =    1.868
peak=    5.794 closest distance to " O   HOH Z 350 " =    1.393
peak=    5.644 closest distance to " CG  ARG A 138 " =    1.275
peak=    5.640 closest distance to " O   HOH Z 375 " =    1.373
peak=    5.612 closest distance to " O   HOH Z  46 " =    1.259
peak=    5.574 closest distance to " CD1AILE A 234 " =    1.068
peak=    5.567 closest distance to " O   HOH Z 268 " =    1.135
peak=    5.530 closest distance to " O   HOH Z  54 " =    1.305
peak=    5.522 closest distance to " O   HOH Z 120 " =    1.066
peak=    5.491 closest distance to " CG  LEU A   5 " =    1.621
peak=    5.418 closest distance to " NH2 ARG A  56 " =    2.164
peak=    5.349 closest distance to " O   HOH Z  61 " =    1.370
peak=    5.339 closest distance to " O   HOH Z 124 " =    1.865
peak=    5.310 closest distance to " O   HOH Z 222 " =    1.317
peak=    5.295 closest distance to " O   HOH Z  65 " =    1.890
peak=    5.263 closest distance to " O   HOH Z 428 " =    1.916
peak=    5.175 closest distance to " O   HOH Z   9 " =    1.725
peak=    5.093 closest distance to " O   PRO A 198 " =    1.445
peak=    5.032 closest distance to " O   HOH Z  28 " =    1.914
peak=    5.023 closest distance to " O   HOH Z   7 " =    2.034
peak=    5.022 closest distance to " O   HOH Z 214 " =    1.503
peak=    4.905 closest distance to " O   HOH Z 278 " =    1.428
peak=    4.868 closest distance to " O   HOH Z 142 " =    2.062
peak=    4.852 closest distance to " NE2 GLN A  11 " =    1.254
peak=    4.793 closest distance to " O   HOH Z  27 " =    1.098
peak=    4.786 closest distance to " CB  ARG A 275 " =    1.302
peak=    4.776 closest distance to " OE1 GLU A   2 " =    1.923
peak=    4.759 closest distance to " O   HOH Z 410 " =    1.422
peak=    4.747 closest distance to " O   HOH Z 139 " =    1.711
peak=    4.742 closest distance to " O   HOH Z 215 " =    1.529
peak=    4.742 closest distance to " O   HOH Z  57 " =    1.358
peak=    4.684 closest distance to " O   HOH Z 416 " =    1.502
peak=    4.650 closest distance to " O   HOH Z 427 " =    1.381
peak=    4.635 closest distance to " O   HOH Z 138 " =    0.918
peak=    4.623 closest distance to " NZ BLYS A 290 " =    1.145
peak=    4.612 closest distance to " O   HOH Z  59 " =    1.479
peak=    4.609 closest distance to " CB  PRO A  54 " =    1.117
peak=    4.602 closest distance to " O   HOH Z 363 " =    1.223
peak=    4.555 closest distance to " O   HOH Z 400 " =    0.910
peak=    4.528 closest distance to " CG1AVAL A 121 " =    0.999
peak=    4.526 closest distance to " O   HOH Z 250 " =    2.025
peak=    4.514 closest distance to " O   HOH Z  63 " =    1.954
peak=    4.511 closest distance to " O   HOH Z 358 " =    1.460
peak=    4.509 closest distance to " O   HOH Z 403 " =    1.745
peak=    4.440 closest distance to " NE1 TRP A 266 " =    1.998
peak=    4.417 closest distance to " O   HOH Z 417 " =    1.540
peak=    4.416 closest distance to " O   HOH Z 374 " =    1.135
peak=    4.378 closest distance to " OG ASER A 258 " =    3.131
peak=    4.344 closest distance to " O   HOH Z 344 " =    1.171
peak=    4.344 closest distance to " O   ASN A 285 " =    0.912
peak=    4.342 closest distance to " O   HOH Z 132 " =    1.302
peak=    4.338 closest distance to " O   HOH Z 361 " =    1.629
peak=    4.313 closest distance to " O   HOH Z 112 " =    1.337
peak=    4.304 closest distance to " CB  VAL A 230 " =    1.224
peak=    4.302 closest distance to " O   HOH Z 123 " =    1.453
peak=    4.293 closest distance to " O   HOH Z  69 " =    1.187
peak=    4.272 closest distance to " CB  SER A   3 " =    1.320
peak=    4.263 closest distance to " O   HOH Z 119 " =    1.483
peak=    4.262 closest distance to " O   HOH Z 347 " =    0.991
peak=    4.249 closest distance to " NH1 ARG A 138 " =    0.974
peak=    4.236 closest distance to " O   HOH Z 402 " =    1.495
peak=    4.223 closest distance to " OG  SER A 276 " =    0.954
peak=    4.188 closest distance to " O   HOH Z 426 " =    1.228
peak=    4.178 closest distance to " CD  ARG A 138 " =    0.793
peak=    4.160 closest distance to " NZ  LYS A 117 " =    1.234
peak=    4.150 closest distance to " O   HOH Z 414 " =    1.899
peak=    4.148 closest distance to " N   TYR A  15 " =    1.116
peak=    4.139 closest distance to " OD1 ASP A 286 " =    1.098
peak=    4.113 closest distance to " O   HOH Z  53 " =    2.217
peak=    4.104 closest distance to " CG2 THR A 279 " =    1.078
peak=    4.096 closest distance to " O   HOH Z 293 " =    1.405
peak=    4.095 closest distance to " CD2 LEU A 228 " =    1.201
peak=    4.079 closest distance to " O   HOH Z  24 " =    2.075
peak=    4.077 closest distance to " O   HOH Z 427 " =    2.370
peak=    4.064 closest distance to " O   HOH Z 259 " =    2.159
peak=    4.062 closest distance to " O   HOH Z 127 " =    1.133
peak=    4.056 closest distance to " CG  GLN A  88 " =    1.057
peak=    4.051 closest distance to " CE AMET A  47 " =    1.428
peak=    4.050 closest distance to " O   HOH Z 263 " =    1.594
peak=    4.044 closest distance to " NE1 TRP A 274 " =    1.094
peak=    4.031 closest distance to " OG ASER A 134 " =    1.304
peak=    4.021 closest distance to " O   HOH Z 418 " =    1.268
peak=    4.019 closest distance to " CE  MET A  93 " =    1.442
peak=    3.981 closest distance to " O   HOH Z 279 " =    1.068
peak=    3.969 closest distance to " CG  PRO A 213 " =    1.205
peak=    3.967 closest distance to " O   HOH Z 359 " =    1.631
peak=    3.963 closest distance to " O   HOH Z 232 " =    1.897
peak=    3.949 closest distance to " NE BARG A 275 " =    1.133
peak=    3.937 closest distance to " O   HOH Z 108 " =    1.662
peak=    3.928 closest distance to " O   HOH Z 130 " =    2.438
peak=    3.909 closest distance to " O   HOH Z 126 " =    1.721
peak=    3.904 closest distance to " O   HOH Z 239 " =    1.588
peak=    3.896 closest distance to " O   HOH Z  51 " =    1.325
peak=    3.883 closest distance to " OD1 ASP A  27 " =    0.871
peak=    3.878 closest distance to " O   HOH Z 247 " =    1.356
peak=    3.873 closest distance to " C   GLN A  73 " =    1.045
peak=    3.863 closest distance to " CB  SER A 216 " =    1.026
peak=    3.853 closest distance to " O   HOH Z 233 " =    1.445
peak=    3.853 closest distance to " CA  ASN A 127 " =    1.196
peak=    3.847 closest distance to " O   HOH Z 143 " =    1.441
peak=    3.845 closest distance to " NH2BARG A 145 " =    1.702
peak=    3.841 closest distance to " O   HOH Z 225 " =    1.488
peak=    3.819 closest distance to " CA  ILE A 234 " =    1.198
peak=    3.817 closest distance to " CB  ALA A   1 " =    1.154
peak=    3.815 closest distance to " NE2 GLN A  73 " =    1.485
peak=    3.811 closest distance to " O   HOH Z 133 " =    1.713
peak=    3.798 closest distance to " O   HOH Z 357 " =    1.852
peak=    3.796 closest distance to " O   HOH Z 326 " =    1.490
peak=    3.796 closest distance to " O   HOH Z 272 " =    1.848
peak=    3.795 closest distance to " CG  PRO A 198 " =    1.400
peak=    3.792 closest distance to " O   HOH Z 158 " =    1.333
peak=    3.781 closest distance to " O   HOH Z 227 " =    1.911
peak=    3.775 closest distance to " O   HOH Z 423 " =    1.727
peak=    3.772 closest distance to " CB  TRP A 179 " =    1.411
peak=    3.769 closest distance to " CD2 TRP A 179 " =    2.305
peak=    3.768 closest distance to " O   HOH Z 226 " =    1.121
peak=    3.764 closest distance to " O   HOH Z 240 " =    1.973
peak=    3.763 closest distance to " O   HOH Z   1 " =    1.894
peak=    3.760 closest distance to " OG BSER A  12 " =    0.883
peak=    3.758 closest distance to " O   HOH Z 431 " =    0.892
peak=    3.756 closest distance to " CG  LYS A 119 " =    1.016
peak=    3.749 closest distance to " CE AMET A  47 " =    1.297
peak=    3.739 closest distance to " CA  LEU A 282 " =    1.027
peak=    3.737 closest distance to " CE  LYS A  48 " =    0.923
peak=    3.736 closest distance to " O   HOH Z 179 " =    0.812
peak=    3.725 closest distance to " ND2 ASN A 301 " =    1.219
peak=    3.717 closest distance to " OG BSER A 258 " =    1.068
peak=    3.716 closest distance to " NE2 GLN A  58 " =    5.203
peak=    3.705 closest distance to " OD1 ASN A  45 " =    1.065
peak=    3.694 closest distance to " OE2 GLU A  53 " =    2.048
peak=    3.692 closest distance to " O   HOH Z 353 " =    1.869
peak=    3.688 closest distance to " OE1 GLN A  77 " =    0.830
peak=    3.686 closest distance to " CE2 PHE A  16 " =    0.854
peak=    3.684 closest distance to " O   HOH Z 389 " =    1.361
peak=    3.683 closest distance to " O   HOH Z 296 " =    1.592
peak=    3.678 closest distance to " O   HOH Z 368 " =    1.119
peak=    3.675 closest distance to " OG BSER A 212 " =    2.811
peak=    3.673 closest distance to " O   HOH Z 248 " =    2.206
peak=    3.671 closest distance to " CA  ALA A 295 " =    0.910
peak=    3.668 closest distance to " O   HOH Z 108 " =    1.827
peak=    3.666 closest distance to " CG2 THR A 294 " =    1.165
peak=    3.651 closest distance to " O   HOH Z 176 " =    1.642
peak=    3.649 closest distance to " O   HOH Z 161 " =    0.973
peak=    3.642 closest distance to " CB  GLU A 277 " =    3.597
peak=    3.622 closest distance to " O   HOH Z 284 " =    1.563
peak=    3.622 closest distance to " CZ  PHE A  16 " =    0.896
peak=    3.620 closest distance to " CG  GLN A  11 " =    2.013
peak=    3.616 closest distance to " O   VAL A  72 " =    0.876
peak=    3.611 closest distance to " O   HOH Z 193 " =    1.465
peak=    3.610 closest distance to " O   HOH Z 158 " =    2.290
peak=    3.603 closest distance to " CB  ALA A  10 " =    0.982
peak=    3.595 closest distance to " O   HOH Z 128 " =    1.900
peak=    3.593 closest distance to " O   HOH Z 147 " =    1.714
peak=    3.588 closest distance to " N   GLN A 278 " =    0.894
peak=    3.587 closest distance to " O   HOH Z  22 " =    1.926
peak=    3.586 closest distance to " O   HOH Z 302 " =    1.757
peak=    3.583 closest distance to " O   HOH Z 151 " =    1.763
peak=    3.581 closest distance to " O   HOH Z  30 " =    1.471
peak=    3.579 closest distance to " O   HOH Z 368 " =    2.822
peak=    3.577 closest distance to " N   GLU A   2 " =    1.528
peak=    3.573 closest distance to " CB  ASN A 148 " =    1.340
peak=    3.573 closest distance to " ND2BASN A 224 " =    0.751
peak=    3.566 closest distance to " O   HOH Z 366 " =    2.654
peak=    3.562 closest distance to " CA  ALA A  21 " =    1.185
peak=    3.562 closest distance to " CB  ALA A 233 " =    1.188
peak=    3.554 closest distance to " O   GLY A 302 " =    2.223
peak=    3.546 closest distance to " O   HOH Z 363 " =    2.529
peak=    3.542 closest distance to " O   HOH Z  57 " =    2.162
peak=    3.539 closest distance to " O   HOH Z 371 " =    3.169
peak=    3.536 closest distance to " CA  TRP A  92 " =    1.274
peak=    3.523 closest distance to " O   HOH Z 205 " =    0.916
peak=    3.522 closest distance to " O   SER A  87 " =    2.242
peak=    3.518 closest distance to " O   HOH Z 105 " =    1.211
peak=    3.515 closest distance to " O   HOH Z 423 " =    1.705
peak=    3.506 closest distance to " CG  LEU A   5 " =    1.168
peak=    3.501 closest distance to " O   HOH Z 180 " =    2.221
peak=    3.500 closest distance to " CB  ASP A 132 " =    3.698
peak=    3.500 closest distance to " O   HOH Z 191 " =    4.542
peak=    3.500 closest distance to " O   HOH Z 193 " =    1.783
peak=    3.497 closest distance to " CG  LEU A 228 " =    1.095
peak=    3.492 closest distance to " O   HOH Z 117 " =    1.121
peak=    3.491 closest distance to " O   HOH Z 217 " =    1.663
peak=    3.489 closest distance to " O   HOH Z 192 " =    1.225
peak=    3.456 closest distance to " O   HOH Z 425 " =    2.190
peak=    3.453 closest distance to " CB  ASP A 200 " =    0.889
peak=    3.447 closest distance to " O   HOH Z 422 " =    0.928
peak=    3.445 closest distance to " O   HOH Z 258 " =    2.239
peak=    3.445 closest distance to " CG1 VAL A 265 " =    0.841
peak=    3.442 closest distance to " O   HOH Z 287 " =    2.025
peak=    3.438 closest distance to " ND2 ASN A 284 " =    0.869
peak=    3.434 closest distance to " CG  PRO A 243 " =    1.031
peak=    3.432 closest distance to " NH1AARG A 275 " =    1.130
peak=    3.431 closest distance to " CA  ASP A  50 " =    1.173
peak=    3.427 closest distance to " CG1BVAL A 121 " =    1.992
peak=    3.422 closest distance to " NH2 ARG A 269 " =    0.738
peak=    3.421 closest distance to " O   HOH Z   6 " =    2.065
peak=    3.420 closest distance to " CA  TYR A  30 " =    1.103
peak=    3.418 closest distance to " O   HOH Z 334 " =    2.403
peak=    3.415 closest distance to " CG2 ILE A 151 " =    0.938
peak=    3.413 closest distance to " O   HOH Z  88 " =    2.929
peak=    3.411 closest distance to " CG  ASN A  60 " =    1.329
peak=    3.411 closest distance to " O   HOH Z   1 " =    1.885
peak=    3.409 closest distance to " CZ BARG A 145 " =    2.245
peak=    3.408 closest distance to " CZ3 TRP A 274 " =    1.416
peak=    3.407 closest distance to " O   HOH Z 217 " =    2.842
peak=    3.404 closest distance to " O   HOH Z  48 " =    1.658
peak=    3.400 closest distance to " O   HOH Z  69 " =    2.021
peak=    3.399 closest distance to " O   HOH Z 356 " =    1.714
peak=    3.395 closest distance to " OD2 ASP A  65 " =    2.073
peak=    3.394 closest distance to " CG  ASP A 238 " =    0.792
peak=    3.393 closest distance to " O   HOH Z  97 " =    1.820
peak=    3.386 closest distance to " CD1 LEU A   5 " =    1.516
peak=    3.384 closest distance to " CB  VAL A 202 " =    1.821
peak=    3.383 closest distance to " CA  GLY A 267 " =    1.243
peak=    3.381 closest distance to " O   HOH Z 245 " =    1.415
peak=    3.381 closest distance to " CG2 THR A 246 " =    1.820
peak=    3.380 closest distance to " CA  ARG A  36 " =    1.355
peak=    3.380 closest distance to " CB  ALA A 104 " =    1.107
peak=    3.375 closest distance to " O   HOH Z 207 " =    2.518
peak=    3.372 closest distance to " CB  LEU A 300 " =    0.858
peak=    3.364 closest distance to " OD2 ASP A 286 " =    2.340
peak=    3.363 closest distance to " CG  LEU A 281 " =    0.942
peak=    3.362 closest distance to " CB  ARG A  79 " =    0.802
peak=    3.362 closest distance to " O   HOH Z 130 " =    1.596
peak=    3.360 closest distance to " O   HOH Z  48 " =    1.653
peak=    3.358 closest distance to " O   HOH Z 238 " =    1.186
peak=    3.356 closest distance to " O   HOH Z 244 " =    1.400
peak=    3.351 closest distance to " CB  ASP A 124 " =    0.988
peak=    3.350 closest distance to " CB  ALA A 248 " =    1.405
peak=    3.342 closest distance to " CA  ALA A 299 " =    0.932
peak=    3.341 closest distance to " CB  GLN A 223 " =    1.451
peak=    3.339 closest distance to " CB  ASN A  60 " =    0.886
peak=    3.337 closest distance to " CB  ALA A 137 " =    0.915
peak=    3.337 closest distance to " O   HOH Z  49 " =    2.844
peak=    3.334 closest distance to " CB  SER A 210 " =    1.075
peak=    3.332 closest distance to " O   HOH Z 276 " =    1.435
peak=    3.331 closest distance to " O   HOH Z 178 " =    1.197
peak=    3.330 closest distance to " CG1 ILE A 120 " =    1.584
peak=    3.330 closest distance to " CB  ASN A 187 " =    1.124
peak=    3.329 closest distance to " O   HOH Z  97 " =    1.226
peak=    3.329 closest distance to " CB  GLN A 183 " =    1.149
peak=    3.320 closest distance to " CB  SER A  62 " =    1.303
peak=    3.317 closest distance to " O   HOH Z 167 " =    1.538
peak=    3.310 closest distance to " OG  SER A  22 " =    2.767
peak=    3.305 closest distance to " OD1 ASN A 170 " =    1.227
peak=    3.302 closest distance to " CG  LYS A 166 " =    1.425
peak=    3.299 closest distance to " CB  TRP A 266 " =    0.956
peak=    3.295 closest distance to " CB  PHE A 204 " =    0.895
peak=    3.294 closest distance to " NH2 ARG A 219 " =    1.698
peak=    3.292 closest distance to " O   HOH Z 185 " =    1.356
peak=    3.284 closest distance to " O   HOH Z 124 " =    1.998
peak=    3.284 closest distance to " CG  PRO A 280 " =    0.904
peak=    3.283 closest distance to " NH2 ARG A 138 " =    1.620
peak=    3.280 closest distance to " O   HOH Z 392 " =    1.737
peak=    3.278 closest distance to " O   HOH Z 380 " =    2.144
peak=    3.275 closest distance to " NE AARG A 275 " =    1.541
peak=    3.273 closest distance to " CD  LYS A 119 " =    2.315
peak=    3.272 closest distance to " N   ALA A 154 " =    0.761
peak=    3.270 closest distance to " O   HOH Z 428 " =    1.163
peak=    3.268 closest distance to " CD BARG A 275 " =    1.040
peak=    3.268 closest distance to " O   HOH Z  65 " =    1.145
peak=    3.267 closest distance to " O   HOH Z  89 " =    2.205
peak=    3.262 closest distance to " O   HOH Z 378 " =    1.153
peak=    3.262 closest distance to " O   HOH Z  28 " =    2.313
peak=    3.262 closest distance to " O   HOH Z 128 " =    2.277
peak=    3.261 closest distance to " O   HOH Z 172 " =    1.400
peak=    3.258 closest distance to " O   HOH Z 334 " =    1.925
peak=    3.254 closest distance to " OD2 ASP A 140 " =    0.995
peak=    3.254 closest distance to " O   HOH Z 422 " =    2.618
peak=    3.249 closest distance to " O   HOH Z 209 " =    2.220
peak=    3.246 closest distance to " CB  GLU A 277 " =    1.190
peak=    3.244 closest distance to " O   HOH Z 287 " =    1.611
peak=    3.238 closest distance to " CG2 ILE A 239 " =    1.695
peak=    3.237 closest distance to " CD2 LEU A 297 " =    0.931
peak=    3.237 closest distance to " O   HOH Z 279 " =    2.476
peak=    3.234 closest distance to " O   HOH Z  50 " =    1.869
peak=    3.234 closest distance to " O   HOH Z 384 " =    1.897
peak=    3.232 closest distance to " CB  LEU A 228 " =    1.405
peak=    3.229 closest distance to " CB  SER A  63 " =    1.333
peak=    3.228 closest distance to " N   GLN A  73 " =    1.330
peak=    3.224 closest distance to " O   HOH Z   7 " =    2.908
peak=    3.220 closest distance to " CB  PHE A 225 " =    1.511
peak=    3.220 closest distance to " O   HOH Z 383 " =    1.002
peak=    3.218 closest distance to " O   HOH Z 106 " =    2.601
peak=    3.216 closest distance to " O   HOH Z 406 " =    1.836
peak=    3.215 closest distance to " O   HOH Z 271 " =    2.405
peak=    3.212 closest distance to " CB  MET A 105 " =    1.265
peak=    3.211 closest distance to " O   HOH Z  89 " =    1.557
peak=    3.208 closest distance to " O   HOH Z  32 " =    1.591
peak=    3.208 closest distance to " OG BSER A 164 " =    1.256
peak=    3.203 closest distance to " O   THR A 251 " =    0.967
peak=    3.200 closest distance to " CB  GLU A 152 " =    1.260
peak=    3.196 closest distance to " CD2 LEU A  25 " =    1.098
peak=    3.196 closest distance to " CD BLYS A 290 " =    1.101
peak=    3.196 closest distance to " O   HOH Z 133 " =    2.302
peak=    3.195 closest distance to " CG2 ILE A 234 " =    0.748
peak=    3.194 closest distance to " O   HOH Z 371 " =    1.618
peak=    3.191 closest distance to " O   HOH Z 204 " =    1.572
peak=    3.189 closest distance to " O   HOH Z 331 " =    1.149
peak=    3.189 closest distance to " ND2 ASN A 285 " =    0.775
peak=    3.187 closest distance to " C   GLY A 111 " =    1.532
peak=    3.183 closest distance to " CA  ARG A 195 " =    1.303
peak=    3.180 closest distance to " CA  ASN A 284 " =    1.037
peak=    3.176 closest distance to " NH1AARG A 145 " =    1.112
peak=    3.176 closest distance to " O   HOH Z 434 " =    5.843
peak=    3.174 closest distance to " O   THR A  52 " =    1.936
peak=    3.171 closest distance to " O   HOH Z  44 " =    2.878
peak=    3.163 closest distance to " O   HOH Z 112 " =    2.344
peak=    3.162 closest distance to " CB  MET A  40 " =    0.795
peak=    3.161 closest distance to " CB  ASP A 140 " =    0.905
peak=    3.158 closest distance to " OE1 GLN A 240 " =    1.724
peak=    3.151 closest distance to " O   HOH Z 364 " =    1.299
peak=    3.150 closest distance to " O   HOH Z 410 " =    3.256
peak=    3.140 closest distance to " CA  ASN A  74 " =    1.197
peak=    3.134 closest distance to " CB  PRO A 163 " =    3.841
peak=    3.129 closest distance to " O   HOH Z 222 " =    2.238
peak=    3.125 closest distance to " O   HOH Z 375 " =    2.006
peak=    3.115 closest distance to " CG2 THR A 251 " =    1.827
peak=    3.114 closest distance to " O   HOH Z  61 " =    1.915
peak=    3.106 closest distance to " O   HOH Z 116 " =    5.521
peak=    3.094 closest distance to " CG  MET A 188 " =    1.075
peak=    3.091 closest distance to " N   GLY A 287 " =    0.945
peak=    3.090 closest distance to " CE  LYS A 166 " =    1.857
peak=    3.086 closest distance to " OG1 THR A 157 " =    1.054
peak=    3.085 closest distance to " CA  ALA A 158 " =    1.034
peak=    3.082 closest distance to " CZ3 TRP A 177 " =    1.070
peak=    3.073 closest distance to " N   ARG A 275 " =    0.893
peak=    3.064 closest distance to " O   HOH Z 424 " =    2.147
peak=    3.061 closest distance to " CG2 ILE A  20 " =    1.255
peak=    3.059 closest distance to " O   HOH Z  59 " =    2.147
peak=    3.050 closest distance to " CG  LEU A 297 " =    0.880
peak=    3.040 closest distance to " NH2BARG A 190 " =    1.442
peak=    3.034 closest distance to " O   HOH Z 164 " =    1.682
peak=    3.033 closest distance to " O   HOH Z 277 " =    2.878
peak=    3.029 closest distance to " O   HOH Z 133 " =    1.293
peak=    3.028 closest distance to " CB  PHE A  61 " =    1.424
peak=    3.026 closest distance to " CA  ALA A  43 " =    1.153

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.741 - 5.250
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 198
   mapped sites are within: 0.741 - 5.250

peak=   -4.575 closest distance to " CD  ARG A 138 " =    1.177
peak=   -4.451 closest distance to " OG ASER A 134 " =    0.951
peak=   -4.447 closest distance to " O   PRO A 198 " =    1.162
peak=   -4.376 closest distance to " OE1 GLU A 277 " =    2.456
peak=   -4.173 closest distance to " O   SER A 135 " =    1.615
peak=   -4.131 closest distance to " CD  ARG A  14 " =    2.940
peak=   -4.117 closest distance to " CG2 VAL A 230 " =    1.014
peak=   -4.047 closest distance to " CG1 VAL A 296 " =    0.803
peak=   -4.047 closest distance to " OG  SER A  97 " =    2.307
peak=   -4.022 closest distance to " O   GLN A  11 " =    1.639
peak=   -4.001 closest distance to " O   HOH Z  56 " =    0.907
peak=   -3.978 closest distance to " O   HOH Z 404 " =    1.034
peak=   -3.976 closest distance to " O   HOH Z 163 " =    1.439
peak=   -3.960 closest distance to " NE1 TRP A 179 " =    1.154
peak=   -3.950 closest distance to " O   HOH Z 381 " =    0.892
peak=   -3.947 closest distance to " CG  PRO A 163 " =    2.666
peak=   -3.928 closest distance to " CE2 PHE A 218 " =    2.599
peak=   -3.886 closest distance to " CD1 LEU A  96 " =    2.312
peak=   -3.847 closest distance to " O   HOH Z  68 " =    1.155
peak=   -3.834 closest distance to " O   ASN A 301 " =    1.541
peak=   -3.825 closest distance to " O   HOH Z 426 " =    1.441
peak=   -3.822 closest distance to " OG  SER A   3 " =    0.923
peak=   -3.815 closest distance to " CA  GLY A  35 " =    1.853
peak=   -3.790 closest distance to " O   HOH Z 264 " =    1.015
peak=   -3.767 closest distance to " CB  ARG A  79 " =    2.559
peak=   -3.766 closest distance to " O   HOH Z 385 " =    0.922
peak=   -3.745 closest distance to " CA  GLY A 133 " =    2.015
peak=   -3.744 closest distance to " CD2 LEU A   5 " =    1.046
peak=   -3.737 closest distance to " CA  GLY A  98 " =    2.102
peak=   -3.729 closest distance to " OE1 GLN A 223 " =    2.343
peak=   -3.722 closest distance to " O   ILE A  49 " =    1.544
peak=   -3.706 closest distance to " O   HOH Z 336 " =    4.803
peak=   -3.682 closest distance to " O   HOH Z  95 " =    0.932
peak=   -3.673 closest distance to " O   HOH Z 235 " =    0.835
peak=   -3.672 closest distance to " N   VAL A 125 " =    1.055
peak=   -3.656 closest distance to " O   HOH Z 354 " =    2.551
peak=   -3.654 closest distance to " CA  ILE A 106 " =    2.212
peak=   -3.653 closest distance to " CD2 TRP A 150 " =    1.430
peak=   -3.646 closest distance to " O   HOH Z 313 " =    1.074
peak=   -3.641 closest distance to " O   HOH Z 359 " =    2.431
peak=   -3.638 closest distance to " OG1 THR A 178 " =    1.000
peak=   -3.637 closest distance to " CG  GLN A  88 " =    0.798
peak=   -3.621 closest distance to " O   HOH Z 431 " =    1.028
peak=   -3.615 closest distance to " CB  ASP A  27 " =    2.457
peak=   -3.608 closest distance to " O   HOH Z  24 " =    1.121
peak=   -3.608 closest distance to " O   HOH Z 268 " =    1.157
peak=   -3.593 closest distance to " N   VAL A  72 " =    2.068
peak=   -3.581 closest distance to " N   ARG A 275 " =    0.867
peak=   -3.576 closest distance to " O   ALA A  51 " =    1.428
peak=   -3.576 closest distance to " CB  ALA A 100 " =    2.022
peak=   -3.557 closest distance to " O   HOH Z 111 " =    0.963
peak=   -3.549 closest distance to " C   PHE A 155 " =    0.942
peak=   -3.547 closest distance to " O   HOH Z 393 " =    3.357
peak=   -3.541 closest distance to " OD2 ASP A 140 " =    0.984
peak=   -3.536 closest distance to " O   HOH Z  60 " =    1.643
peak=   -3.532 closest distance to " O   GLY A 118 " =    1.340
peak=   -3.520 closest distance to " CA  TYR A  68 " =    1.132
peak=   -3.517 closest distance to " CG1 ILE A 234 " =    1.990
peak=   -3.517 closest distance to " O   HOH Z  52 " =    1.045
peak=   -3.511 closest distance to " O   GLY A  57 " =    1.366
peak=   -3.502 closest distance to " CA  GLY A  98 " =    1.860
peak=   -3.500 closest distance to " O   THR A 220 " =    1.520
peak=   -3.498 closest distance to " N   GLN A  58 " =    1.206
peak=   -3.497 closest distance to " O   HOH Z 125 " =    3.214
peak=   -3.494 closest distance to " OG  SER A  87 " =    1.546
peak=   -3.492 closest distance to " O   HOH Z 286 " =    1.503
peak=   -3.492 closest distance to " CD  ARG A 139 " =    1.391
peak=   -3.483 closest distance to " O   TRP A 179 " =    1.801
peak=   -3.474 closest distance to " O   GLU A  44 " =    1.861
peak=   -3.470 closest distance to " O   HOH Z 131 " =    3.960
peak=   -3.465 closest distance to " N   SER A 276 " =    1.046
peak=   -3.464 closest distance to " O   SER A 146 " =    1.365
peak=   -3.464 closest distance to " O   HOH Z 337 " =    1.992
peak=   -3.462 closest distance to " O   HOH Z 407 " =    3.104
peak=   -3.455 closest distance to " ND2 ASN A 173 " =    1.654
peak=   -3.447 closest distance to " O   GLY A 136 " =    1.583
peak=   -3.440 closest distance to " O   HOH Z  69 " =    1.776
peak=   -3.438 closest distance to " O   HOH Z 258 " =    4.732
peak=   -3.422 closest distance to " O   HOH Z 376 " =    2.376
peak=   -3.420 closest distance to " CG  TRP A 266 " =    1.625
peak=   -3.418 closest distance to " O   HOH Z 409 " =    1.651
peak=   -3.413 closest distance to " CG  MET A 105 " =    0.841
peak=   -3.410 closest distance to " O   HOH Z 222 " =    4.712
peak=   -3.397 closest distance to " NH2AARG A 275 " =    5.250
peak=   -3.394 closest distance to " O   HOH Z  77 " =    1.427
peak=   -3.390 closest distance to " O   GLY A 211 " =    1.121
peak=   -3.390 closest distance to " O   HOH Z 166 " =    2.113
peak=   -3.386 closest distance to " CG  ASN A 284 " =    1.260
peak=   -3.381 closest distance to " O   HOH Z 413 " =    4.364
peak=   -3.373 closest distance to " CG  GLN A  11 " =    1.011
peak=   -3.358 closest distance to " O   HOH Z 416 " =    0.970
peak=   -3.357 closest distance to " O   HOH Z 165 " =    2.202
peak=   -3.357 closest distance to " O   SER A  22 " =    1.199
peak=   -3.356 closest distance to " O   HOH Z 251 " =    1.710
peak=   -3.351 closest distance to " O   HOH Z  71 " =    1.033
peak=   -3.350 closest distance to " NH2 ARG A  79 " =    1.949
peak=   -3.348 closest distance to " O   GLN A  77 " =    1.732
peak=   -3.347 closest distance to " ND2 ASN A 285 " =    1.973
peak=   -3.347 closest distance to " O   HOH Z 236 " =    2.032
peak=   -3.341 closest distance to " CD  LYS A 289 " =    2.248
peak=   -3.338 closest distance to " CB  ALA A 248 " =    2.022
peak=   -3.335 closest distance to " CB  TYR A  15 " =    2.103
peak=   -3.333 closest distance to " ND2 ASN A 209 " =    1.628
peak=   -3.332 closest distance to " CG  GLN A  11 " =    2.188
peak=   -3.331 closest distance to " O   HOH Z 350 " =    1.751
peak=   -3.331 closest distance to " O   HOH Z  93 " =    1.787
peak=   -3.326 closest distance to " O   HOH Z 378 " =    2.070
peak=   -3.326 closest distance to " O   HOH Z 210 " =    2.192
peak=   -3.320 closest distance to " OD2 ASP A 286 " =    1.228
peak=   -3.320 closest distance to " O   HOH Z 377 " =    1.419
peak=   -3.316 closest distance to " OG  SER A   3 " =    0.956
peak=   -3.309 closest distance to " CD2 PHE A  61 " =    2.417
peak=   -3.307 closest distance to " CG  ARG A 138 " =    1.160
peak=   -3.304 closest distance to " O   HOH Z  54 " =    0.761
peak=   -3.303 closest distance to " CD2 LEU A 297 " =    1.140
peak=   -3.294 closest distance to " O   HOH Z 290 " =    1.083
peak=   -3.288 closest distance to " CD  LYS A 166 " =    2.691
peak=   -3.285 closest distance to " O   HOH Z 435 " =    2.313
peak=   -3.281 closest distance to " CD2 LEU A 237 " =    2.513
peak=   -3.280 closest distance to " CD1 TRP A 274 " =    1.188
peak=   -3.280 closest distance to " CA  ARG A  56 " =    1.296
peak=   -3.274 closest distance to " CD  ARG A 219 " =    2.522
peak=   -3.273 closest distance to " O   LYS A 119 " =    0.861
peak=   -3.272 closest distance to " O   HOH Z 179 " =    1.363
peak=   -3.267 closest distance to " O   HOH Z 124 " =    3.828
peak=   -3.266 closest distance to " CA  TYR A  68 " =    2.778
peak=   -3.265 closest distance to " CA  GLY A 203 " =    2.340
peak=   -3.262 closest distance to " OG1 THR A 157 " =    1.679
peak=   -3.260 closest distance to " O   HOH Z 401 " =    0.979
peak=   -3.259 closest distance to " O   HOH Z 300 " =    1.143
peak=   -3.259 closest distance to " O   VAL A 189 " =    2.511
peak=   -3.256 closest distance to " O   HOH Z 411 " =    4.649
peak=   -3.256 closest distance to " O   SER A 216 " =    2.068
peak=   -3.253 closest distance to " O   TRP A  92 " =    1.474
peak=   -3.237 closest distance to " O   HOH Z 347 " =    0.941
peak=   -3.236 closest distance to " O   HOH Z 100 " =    1.567
peak=   -3.233 closest distance to " O   HOH Z 231 " =    1.711
peak=   -3.232 closest distance to " O   HOH Z 298 " =    0.741
peak=   -3.232 closest distance to " O   HOH Z 186 " =    1.426
peak=   -3.231 closest distance to " CE1 PHE A  59 " =    1.512
peak=   -3.230 closest distance to " CE  MET A 185 " =    2.673
peak=   -3.226 closest distance to " C   SER A 206 " =    1.558
peak=   -3.225 closest distance to " O   HOH Z  76 " =    1.303
peak=   -3.221 closest distance to " O   ASP A 286 " =    1.128
peak=   -3.220 closest distance to " CD1 LEU A   5 " =    2.657
peak=   -3.220 closest distance to " CE BMET A  47 " =    1.437
peak=   -3.218 closest distance to " C   ASP A 231 " =    1.961
peak=   -3.218 closest distance to " O   HOH Z 135 " =    0.896
peak=   -3.215 closest distance to " CA  GLY A  57 " =    2.000
peak=   -3.211 closest distance to " O   PRO A 243 " =    2.468
peak=   -3.206 closest distance to " CD1 ILE A  33 " =    2.041
peak=   -3.195 closest distance to " O   VAL A  72 " =    0.918
peak=   -3.192 closest distance to " N   PRO A 163 " =    1.380
peak=   -3.192 closest distance to " O   HOH Z 276 " =    1.534
peak=   -3.191 closest distance to " O   HOH Z 389 " =    2.031
peak=   -3.189 closest distance to " CG2 ILE A 120 " =    1.621
peak=   -3.187 closest distance to " O   ALA A   1 " =    1.327
peak=   -3.186 closest distance to " CD1 PHE A  59 " =    1.559
peak=   -3.185 closest distance to " CD1 ILE A 151 " =    2.379
peak=   -3.183 closest distance to " O   HOH Z  60 " =    1.509
peak=   -3.183 closest distance to " O   HOH Z 374 " =    2.836
peak=   -3.180 closest distance to " OG  SER A 276 " =    1.010
peak=   -3.166 closest distance to " O   HOH Z   1 " =    3.286
peak=   -3.164 closest distance to " CD  PRO A 198 " =    1.595
peak=   -3.161 closest distance to " O   HOH Z 198 " =    2.507
peak=   -3.160 closest distance to " CG  PRO A 243 " =    1.703
peak=   -3.159 closest distance to " O   HOH Z 120 " =    1.140
peak=   -3.158 closest distance to " C   ALA A 158 " =    1.381
peak=   -3.152 closest distance to " O   HOH Z  30 " =    1.150
peak=   -3.150 closest distance to " CG2BVAL A 121 " =    0.914
peak=   -3.145 closest distance to " OD2 ASP A 191 " =    1.481
peak=   -3.142 closest distance to " O   HOH Z  95 " =    1.567
peak=   -3.138 closest distance to " C   ILE A 239 " =    1.958
peak=   -3.136 closest distance to " CA  GLN A  55 " =    1.117
peak=   -3.135 closest distance to " N   GLN A  55 " =    1.610
peak=   -3.133 closest distance to " O   ALA A  10 " =    1.665
peak=   -3.129 closest distance to " O   HOH Z 156 " =    1.687
peak=   -3.129 closest distance to " O   HOH Z 217 " =    1.694
peak=   -3.125 closest distance to " OG BSER A 134 " =    1.571
peak=   -3.123 closest distance to " NH1 ARG A  56 " =    2.481
peak=   -3.119 closest distance to " C   SER A  63 " =    1.106
peak=   -3.118 closest distance to " OE2 GLU A 152 " =    1.045
peak=   -3.116 closest distance to " OG  SER A 245 " =    1.707
peak=   -3.106 closest distance to " O   HOH Z 368 " =    1.613
peak=   -3.105 closest distance to " C   MET A 188 " =    1.534
peak=   -3.102 closest distance to " CG1BVAL A  72 " =    4.595
peak=   -3.098 closest distance to " O   HOH Z  88 " =    1.590
peak=   -3.091 closest distance to " OD2 ASP A 171 " =    1.539
peak=   -3.090 closest distance to " O   HOH Z 205 " =    1.171
peak=   -3.089 closest distance to " CB  ASN A 285 " =    2.209
peak=   -3.089 closest distance to " O   HOH Z 252 " =    3.344
peak=   -3.087 closest distance to " O   HOH Z 426 " =    2.068
peak=   -3.061 closest distance to " O   HOH Z 373 " =    1.073
peak=   -3.060 closest distance to " C   ALA A 299 " =    1.147
peak=   -3.060 closest distance to " O   HOH Z 193 " =    1.860
peak=   -3.042 closest distance to " O   GLY A 136 " =    1.650
peak=   -3.038 closest distance to " O  BHOH Z  74 " =    2.295
peak=   -3.029 closest distance to " O   LEU A 143 " =    1.346

================= 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    :  0.5012 0.5021   6.303014e+00   6.297403e+00
   1_bss:  0.4926 0.4902   6.297905e+00   6.289310e+00
   1_xyz:  0.4380 0.4661   6.243558e+00   6.267614e+00
   1_adp:  0.4005 0.4630   6.204314e+00   6.264450e+00
   1_occ:  0.4001 0.4629   6.203995e+00   6.264784e+00
   2_bss:  0.3980 0.4592   6.203902e+00   6.263262e+00
   2_xyz:  0.3552 0.4256   6.119339e+00   6.224409e+00
   2_adp:  0.3443 0.4173   6.103983e+00   6.211699e+00
   2_occ:  0.3441 0.4174   6.103778e+00   6.211698e+00
   3_bss:  0.3446 0.4172   6.105497e+00   6.212106e+00
   3_xyz:  0.2856 0.3600   5.955723e+00   6.105752e+00
   3_adp:  0.2563 0.3497   5.896535e+00   6.085724e+00
   3_occ:  0.2559 0.3495   5.896173e+00   6.085815e+00
   4_bss:  0.2559 0.3475   5.892561e+00   6.081999e+00
   4_xyz:  0.2183 0.3004   5.744309e+00   5.956346e+00
   4_adp:  0.2033 0.2668   5.665828e+00   5.865775e+00
   4_occ:  0.2028 0.2657   5.663343e+00   5.863043e+00
   5_bss:  0.2029 0.2640   5.662084e+00   5.860286e+00
   5_xyz:  0.1625 0.2165   5.464253e+00   5.691948e+00
   5_adp:  0.1460 0.2032   5.381786e+00   5.624800e+00
   5_occ:  0.1459 0.2028   5.380326e+00   5.622609e+00
   5_bss:  0.1460 0.2024   5.378495e+00   5.621009e+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:  0.378   0.000   6.409   9.518   7.949   0.000   0.000   0.000
   1_xyz:  0.378   0.000   6.409   9.518   7.949   0.000   0.000   0.000
   1_adp:  0.378   0.000   6.409   9.518   7.949   0.000   0.000   0.000
   1_occ:  0.378   0.000   6.409   9.518   7.949   0.000   0.000   0.000
   2_bss:  0.374  36.931   2.976   5.101   4.473   0.000   0.000   0.000
   2_xyz:  0.374  36.931   2.976   5.101   4.473   0.000   0.000   0.000
   2_adp:  0.374  36.931   2.976   5.101   4.473   0.000   0.000   0.000
   2_occ:  0.374  36.931   2.976   5.101   4.473   0.000   0.000   0.000
   3_bss:  0.371  59.762   2.002   3.339   3.176   0.000   0.000   0.000
   3_xyz:  0.371  59.762   2.002   3.339   3.176   0.000   0.000   0.000
   3_adp:  0.371  59.762   2.002   3.339   3.176   0.000   0.000   0.000
   3_occ:  0.371  59.762   2.002   3.339   3.176   0.000   0.000   0.000
   4_bss:  0.360  63.811   1.950   2.183   2.913   0.000   0.000   0.000
   4_xyz:  0.360  63.811   1.950   2.183   2.913   0.000   0.000   0.000
   4_adp:  0.360  63.811   1.950   2.183   2.913   0.000   0.000   0.000
   4_occ:  0.360  63.811   1.950   2.183   2.913   0.000   0.000   0.000
   5_bss:  0.333  47.275   1.350   1.277   2.359   0.000   0.000   0.000
   5_xyz:  0.333  47.275   1.350   1.277   2.359   0.000   0.000   0.000
   5_adp:  0.333  47.275   1.350   1.277   2.359   0.000   0.000   0.000
   5_occ:  0.333  47.275   1.350   1.277   2.359   0.000   0.000   0.000
   5_bss:  0.317  43.933  -0.180  -0.546   0.726   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.670 0.3337  0.4060    83813.930
   1_bss:  63.491 0.3482  0.5283    80590.211
   1_xyz:  57.503 0.4249  0.6325    69774.670
   1_adp:  56.604 0.4363  0.7090    68805.614
   1_occ:  56.597 0.4366  0.7087    69094.968
   2_bss:  56.048 0.4435  0.6401    68402.945
   2_xyz:  49.752 0.5224  0.7514    55897.512
   2_adp:  47.717 0.5485  0.7998    53354.258
   2_occ:  47.699 0.5487  0.8000    53349.695
   3_bss:  47.602 0.5499  0.7646    53285.169
   3_xyz:  38.906 0.6551  0.8946    36878.522
   3_adp:  36.979 0.6783  0.9048    34706.304
   3_occ:  36.995 0.6781  0.9037    34711.139
   4_bss:  36.791 0.6802  0.8907    34215.797
   4_xyz:  30.468 0.7522  0.9587    23749.072
   4_adp:  26.396 0.7974  0.9840    18767.504
   4_occ:  26.296 0.7984  0.9844    18587.063
   5_bss:  26.234 0.7989  0.9599    18429.055
   5_xyz:  21.166 0.8504  0.9936    12399.407
   5_adp:  19.409 0.8676  0.9896    10843.035
   5_occ:  19.361 0.8680  0.9898    10775.982
   5_bss:  19.305 0.8684  0.9736    10695.642
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.2849e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.2849e+01
   1_xyz:   1.697  0.013  0.106 18.384  0.006  4.106   1.4489e-01
   1_adp:   1.697  0.013  0.106 18.384  0.006  4.106   1.4489e-01
   1_occ:   1.697  0.013  0.106 18.384  0.006  4.106   1.4489e-01
   2_bss:   1.697  0.013  0.106 18.384  0.006  4.106   1.4489e-01
   2_xyz:   1.175  0.008  0.077 16.322  0.005  4.117   8.8871e-02
   2_adp:   1.175  0.008  0.077 16.322  0.005  4.117   8.8871e-02
   2_occ:   1.175  0.008  0.077 16.322  0.005  4.117   8.8871e-02
   3_bss:   1.175  0.008  0.077 16.322  0.005  4.117   8.8871e-02
   3_xyz:   1.355  0.010  0.098 16.845  0.005  4.101   1.0864e-01
   3_adp:   1.355  0.010  0.098 16.845  0.005  4.101   1.0864e-01
   3_occ:   1.355  0.010  0.098 16.845  0.005  4.101   1.0864e-01
   4_bss:   1.355  0.010  0.098 16.845  0.005  4.101   1.0864e-01
   4_xyz:   1.003  0.007  0.071 15.585  0.004  4.111   7.2917e-02
   4_adp:   1.003  0.007  0.071 15.585  0.004  4.111   7.2917e-02
   4_occ:   1.003  0.007  0.071 15.585  0.004  4.111   7.2917e-02
   5_bss:   1.003  0.007  0.071 15.585  0.004  4.111   7.2917e-02
   5_xyz:   1.067  0.007  0.073 15.687  0.004  4.107   6.8607e-02
   5_adp:   1.067  0.007  0.073 15.687  0.004  4.107   6.8607e-02
   5_occ:   1.067  0.007  0.073 15.687  0.004  4.107   6.8607e-02
   5_bss:   1.067  0.007  0.073 15.687  0.004  4.107   6.8607e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8463e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8463e+00
   1_xyz:  13.048  0.191  0.413 87.183  0.050  2.163   9.6677e-02
   1_adp:  13.048  0.191  0.413 87.183  0.050  2.163   9.6677e-02
   1_occ:  13.048  0.191  0.413 87.183  0.050  2.163   9.6677e-02
   2_bss:  13.048  0.191  0.413 87.183  0.050  2.163   9.6677e-02
   2_xyz:   7.201  0.086  0.284 78.629  0.047  2.126   5.1433e-02
   2_adp:   7.201  0.086  0.284 78.629  0.047  2.126   5.1433e-02
   2_occ:   7.201  0.086  0.284 78.629  0.047  2.126   5.1433e-02
   3_bss:   7.201  0.086  0.284 78.629  0.047  2.126   5.1433e-02
   3_xyz:   9.820  0.058  0.331 74.058  0.031  2.069   8.7952e-02
   3_adp:   9.820  0.058  0.331 74.058  0.031  2.069   8.7952e-02
   3_occ:   9.820  0.058  0.331 74.058  0.031  2.069   8.7952e-02
   4_bss:   9.820  0.058  0.331 74.058  0.031  2.069   8.7952e-02
   4_xyz:   6.680  0.056  0.279 77.193  0.033  2.299   1.7700e-01
   4_adp:   6.680  0.056  0.279 77.193  0.033  2.299   1.7700e-01
   4_occ:   6.680  0.056  0.279 77.193  0.033  2.299   1.7700e-01
   5_bss:   6.680  0.056  0.279 77.193  0.033  2.299   1.7700e-01
   5_xyz:   7.251  0.070  0.257 82.679  0.028  2.270   5.3662e-02
   5_adp:   7.251  0.070  0.257 82.679  0.028  2.270   5.3662e-02
   5_occ:   7.251  0.070  0.257 82.679  0.028  2.270   5.3662e-02
   5_bss:   7.251  0.070  0.257 82.679  0.028  2.270   5.3662e-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: 107.53   0.00  15.93  96.46   0.00  14.59 107.53   0.00  23.23
   1_occ: 107.53   0.00  15.93  96.46   0.00  14.59 107.53   0.00  23.23
   2_bss: 107.53   0.00  15.93  96.46   0.00  14.59 107.53   0.00  23.23
   2_xyz: 107.53   0.00  15.93  96.46   0.00  14.59 107.53   0.00  23.23
   2_adp: 110.76   0.00  15.23 100.55   0.00  13.50 110.76   0.00  24.65
   2_occ: 110.76   0.00  15.23 100.55   0.00  13.50 110.76   0.00  24.65
   3_bss: 110.76   0.00  15.23 100.55   0.00  13.50 110.76   0.00  24.65
   3_xyz: 110.76   0.00  15.23 100.55   0.00  13.50 110.76   0.00  24.65
   3_adp: 127.28   0.00  17.34 119.44   0.00  13.56 127.28   0.00  37.89
   3_occ: 127.28   0.00  17.34 119.44   0.00  13.56 127.28   0.00  37.89
   4_bss: 127.28   0.00  17.34 119.44   0.00  13.56 127.28   0.00  37.89
   4_xyz: 127.28   0.00  17.34 119.44   0.00  13.56 127.28   0.00  37.89
   4_adp: 125.66   0.00  15.49 115.33   0.00  11.35 125.66   0.71  38.07
   4_occ: 125.66   0.00  15.49 115.33   0.00  11.35 125.66   0.71  38.07
   5_bss: 125.66   0.00  15.49 115.33   0.00  11.35 125.66   0.71  38.07
   5_xyz: 125.66   0.00  15.49 115.33   0.00  11.35 125.66   0.71  38.07
   5_adp: 125.04   0.00  15.42 119.64   0.00  10.25 125.04   3.31  43.53
   5_occ: 125.04   0.00  15.42 119.64   0.00  10.25 125.04   3.31  43.53
   5_bss: 126.25   1.21  16.63 120.85   1.21  11.47 126.25   4.52  44.74
------------------------------------------------------------------------
 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:    1.264    0.012    0.409
   1_adp:    1.264    0.012    0.409
   1_occ:    1.264    0.012    0.409
   2_bss:    1.264    0.012    0.409
   2_xyz:    1.659    0.034    0.539
   2_adp:    1.659    0.034    0.539
   2_occ:    1.659    0.034    0.539
   3_bss:    1.659    0.034    0.539
   3_xyz:    1.669    0.024    0.727
   3_adp:    1.669    0.024    0.727
   3_occ:    1.669    0.024    0.727
   4_bss:    1.669    0.024    0.727
   4_xyz:    1.958    0.045    0.805
   4_adp:    1.958    0.045    0.805
   4_occ:    1.958    0.045    0.805
   5_bss:    1.958    0.045    0.805
   5_xyz:    2.113    0.049    0.891
   5_adp:    2.113    0.049    0.891
   5_occ:    2.113    0.049    0.891
   5_bss:    2.113    0.049    0.891
------------------------------------------------------------------------

CPU time actual refinement: 352.08


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_607/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_607/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_607/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_607/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_607/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.93 
  Macro-tasks:
    bulk solvent and scale       = 42.24  
    individual site refinement   = 151.68 
    weights calculation          = 32.51  
    collect and process          = 6.25   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 232.81 
  Micro-tasks:
    mask                            = 3.15   
    f_calc                          = 111.13 
    alpha_beta                      = 8.22   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 121.30 
    fmodel                         = 7.23   
    r_factors                      = 0.21   
    phase_errors                   = 9.63   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 262.20 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.928 micro seconds
Total CPU time: 6.10 minutes
from_scatterers_fft:    642 calls, 110.87 s
gradients_fft:          586 calls, 108.03 s

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

# Date 2008-01-16 Time 01:58:41 PST -0800 (1200477521.88 s)
Start R-work = 0.5012, R-free = 0.5021 (no bulk solvent and anisotropic scale)
Final R-work = 0.1601, R-free = 0.2159 (no bulk solvent and anisotropic scale)

Start R-work = 0.4926, R-free = 0.4902
Final R-work = 0.1460, R-free = 0.2024