# Date 2008-01-16 Time 02:28:09 PST -0800 (1200479289.96 s)
#phil __OFF__

Command line arguments: "../849.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 = 22586
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 849

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.95275
Completeness in resolution range: 0.945643
Completeness with d_max=infinity: 0.942912

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0395
                             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: (70.9525, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.95275
Completeness in resolution range: 0.945643
Completeness with d_max=infinity: 0.942912

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0399 -  4.1798 [2171/2198]  1956   215   9.9%
  bin  2:  4.1798 -  3.3295 [2089/2109]  1878   211  10.1%
  bin  3:  3.3295 -  2.9121 [2060/2079]  1855   205  10.0%
  bin  4:  2.9121 -  2.6474 [2038/2068]  1832   206  10.1%
  bin  5:  2.6474 -  2.4585 [2044/2063]  1848   196   9.6%
  bin  6:  2.4585 -  2.3141 [2009/2034]  1795   214  10.7%
  bin  7:  2.3141 -  2.1986 [2028/2056]  1828   200   9.9%
  bin  8:  2.1986 -  2.1032 [1979/2015]  1784   195   9.9%
  bin  9:  2.1032 -  2.0224 [2006/2048]  1810   196   9.8%
  bin 10:  2.0224 -  1.9527 [1165/2045]  1044   121  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_849/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:
        1.44 -     2.13: 25
        2.13 -     2.82: 956
        2.82 -     3.52: 4526
        3.52 -     4.21: 9459
        4.21 -     4.90: 13775
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.442 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 201 " - " O   HOH Z 349 "  1.702 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28736 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_849/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_849/model_refine_001.geo

CPU time processing inputs: 9.68


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 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 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5070   r_free= 0.5031   ksol= 0.00   Bsol= 0.00   scale= 0.779    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.306069                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.6626 0.99   1413  159 0.4403 0.4629      6.6526      6.7314|
|  2:  4.6626 -  3.7193 0.99   1354  150 0.4511 0.4163      6.8715       6.817|
|  3:  3.7193 -  3.2546 0.99   1325  142 0.4743 0.4601      6.7232      6.7541|
|  4:  3.2546 -  2.9595 0.99   1334  156 0.5060 0.4905      6.5719      6.5071|
|  5:  2.9595 -  2.7487 0.99   1319  147 0.5251 0.5563      6.3894      6.4068|
|  6:  2.7487 -  2.5875 0.99   1316  144 0.5355 0.5459      6.2998      6.2352|
|  7:  2.5875 -  2.4585 0.99   1308  135 0.5395 0.4878      6.2602      6.2044|
|  8:  2.4585 -  2.3519 0.98   1274  148 0.5415 0.5044      6.1787      6.1643|
|  9:  2.3519 -  2.2617 0.98   1285  150 0.5343 0.5372      6.1443      6.1798|
| 10:  2.2617 -  2.1839 1.00   1304  150 0.5329 0.5398      6.0974      6.0984|
| 11:  2.1839 -  2.1158 0.98   1299  136 0.5268 0.5166      6.0499      6.0528|
| 12:  2.1158 -  2.0555 0.98   1263  142 0.5282 0.5924       5.958      6.0209|
| 13:  2.0555 -  2.0015 0.96   1257  134 0.5627 0.5200      5.8828      5.8126|
| 14:  2.0015 -  1.9527 0.44    579   66 0.5674 0.4728      5.8612      5.8176|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0399 -  4.6626  1413   159  0.57  45.41   0.77     0.64     113947.25|
|  2:  4.6626 -  3.7193  1354   150  0.62  42.00   0.84     0.72     145350.12|
|  3:  3.7193 -  3.2546  1325   142  0.51  51.22   0.82     0.66     146448.57|
|  4:  3.2546 -  2.9595  1334   156  0.41  59.29   0.78     0.52     127146.76|
|  5:  2.9595 -  2.7487  1319   147  0.30  67.56   0.73     0.38     100213.29|
|  6:  2.7487 -  2.5875  1316   144  0.28  68.87   0.71     0.34      85432.72|
|  7:  2.5875 -  2.4585  1308   135  0.28  69.38   0.74     0.33      72187.45|
|  8:  2.4585 -  2.3519  1274   148  0.29  68.52   0.71     0.35      65175.81|
|  9:  2.3519 -  2.2617  1285   150  0.28  68.73   0.73     0.33      58152.88|
| 10:  2.2617 -  2.1839  1304   150  0.27  69.87   0.74     0.34      54695.89|
| 11:  2.1839 -  2.1158  1299   136  0.23  72.84   0.78     0.29      53065.14|
| 12:  2.1158 -  2.0555  1263   142  0.21  74.74   0.76     0.27      49114.26|
| 13:  2.0555 -  2.0015  1257   134  0.20  75.38   0.72     0.27      41535.93|
| 14:  2.0015 -  1.9527   579    66  0.30  68.04   0.72     0.34      31380.61|
|alpha:            min =        0.27 max =            0.72 mean =         0.42|
|beta:             min =    31380.61 max =       146448.57 mean =     84567.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           89.99 mean =        64.00|
|phase err.(test): min =        0.00 max =           89.97 mean =        64.19|
|-----------------------------------------------------------------------------|

============================== 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 = 25.539675             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.340   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.262936              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.176   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      180 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      728 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1534 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2677 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3987 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5153 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6632 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7882 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.038 |
| 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 |       2.391 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.538)------------------------------------------|
|    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 = 11.538)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5102   r_free= 0.5045   ksol= 0.00   Bsol= 0.00   scale= 0.750    |
|                                                                             |
| 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: 6.306622                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4981   r_free= 0.4924   ksol= 0.40   Bsol= 20.00   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.54,8.86,7.16,0.00,0.00,0.00); trace/3= 7.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.301809                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.736066             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.356   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.039269              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.962   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4981      final r-factor (work) = 0.4418          |
| start r-factor (free) = 0.4924      final r-factor (free) = 0.4733          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 118.3724 = 20.74 * 0.50 * 6.3015 + 1.00 * 53.0383                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 65.0504 = 20.74 * 0.50 * 6.2594 + 1.00 * 0.1527                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4418      final r-factor (work) = 0.4085          |
| start r-factor (free) = 0.4733      final r-factor (free) = 0.4701          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7790 = 2.04 * 1.00 * 6.2594 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7049 = 2.04 * 1.00 * 6.2195 + 1.00 * 0.0218                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.538)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.24   15.72    None  None   None       |
|    all(noH): 2823   0      0.00    97.24   15.72    None  None   None       |
|    Sol.    : 438    0      0.00    97.24   21.97    None  None   None       |
|    Mac.    : 2385   0      0.00    87.06   14.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.724: 1062   |   5:    48.621 -  58.345:   47        |
|      1:     9.724 -  19.449:  893   |   6:    58.345 -  68.070:   11        |
|      2:    19.449 -  29.173:  502   |   7:    68.070 -  77.794:    5        |
|      3:    29.173 -  38.897:  201   |   8:    77.794 -  87.518:    4        |
|      4:    38.897 -  48.621:   97   |   9:    87.518 -  97.242:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4085 r_free = 0.4701             target_work(ml) = 6.215         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4086 r_free = 0.4702             target_work(ml) = 6.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4086   r_free= 0.4702   ksol= 0.40   Bsol= 20.00   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.54,8.86,7.16,0.00,0.00,0.00); trace/3= 7.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.214531                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4073   r_free= 0.4659   ksol= 0.38   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.46,4.96,4.21,0.00,0.00,0.00); trace/3= 4.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.214730                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.469954             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.217  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.919625              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.158  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4073      final r-factor (work) = 0.3614          |
| start r-factor (free) = 0.4659      final r-factor (free) = 0.4314          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.8005 = 11.47 * 0.50 * 6.2159 + 1.00 * 0.1527                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.4839 = 11.47 * 0.50 * 6.1719 + 1.00 * 0.0879                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3614      final r-factor (work) = 0.3499          |
| start r-factor (free) = 0.4314      final r-factor (free) = 0.4223          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6981 = 0.92 * 1.00 * 6.1719 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6495 = 0.92 * 1.00 * 6.1225 + 1.00 * 0.0191                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.538)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.24   15.56    None  None   None       |
|    all(noH): 2823   0      0.00    99.24   15.56    None  None   None       |
|    Sol.    : 438    0      0.00    99.24   23.93    None  None   None       |
|    Mac.    : 2385   0      0.00    91.02   14.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.924: 1087   |   5:    49.619 -  59.542:   30        |
|      1:     9.924 -  19.847:  921   |   6:    59.542 -  69.466:    7        |
|      2:    19.847 -  29.771:  503   |   7:    69.466 -  79.390:    2        |
|      3:    29.771 -  39.695:  186   |   8:    79.390 -  89.313:    3        |
|      4:    39.695 -  49.619:   82   |   9:    89.313 -  99.237:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3499 r_free = 0.4223             target_work(ml) = 6.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3496 r_free = 0.4222             target_work(ml) = 6.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3496   r_free= 0.4222   ksol= 0.38   Bsol= 50.00   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.46,4.96,4.21,0.00,0.00,0.00); trace/3= 4.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.111432                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3499   r_free= 0.4218   ksol= 0.38   Bsol= 65.20   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.49,3.02,3.16,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.113431                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.523147             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.913  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.980861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.710   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3499      final r-factor (work) = 0.2818          |
| start r-factor (free) = 0.4218      final r-factor (free) = 0.3623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.6684 = 16.52 * 0.50 * 6.1224 + 1.00 * 0.0878                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.0352 = 16.52 * 0.50 * 6.0406 + 1.00 * 0.1305                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2818      final r-factor (work) = 0.2556          |
| start r-factor (free) = 0.3623      final r-factor (free) = 0.3393          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9391 = 0.98 * 1.00 * 6.0406 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8148 = 0.98 * 1.00 * 5.9130 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.538)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.77  15.58    None  None   None       |
|    all(noH): 2823   0      0.00    106.77  15.58    None  None   None       |
|    Sol.    : 438    0      0.00    106.77  32.82    None  None   None       |
|    Mac.    : 2385   0      0.00    95.32   12.42    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 -  10.677: 1324   |   5:    53.383 -  64.060:   38        |
|      1:    10.677 -  21.353:  820   |   6:    64.060 -  74.736:    9        |
|      2:    21.353 -  32.030:  350   |   7:    74.736 -  85.413:    5        |
|      3:    32.030 -  42.707:  176   |   8:    85.413 -  96.090:    3        |
|      4:    42.707 -  53.383:   96   |   9:    96.090 - 106.766:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2556 r_free = 0.3393             target_work(ml) = 5.879         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2550 r_free = 0.3391             target_work(ml) = 5.878         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2550   r_free= 0.3391   ksol= 0.38   Bsol= 65.20   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.49,3.02,3.16,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.878236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2542   r_free= 0.3364   ksol= 0.36   Bsol= 65.20   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.47,1.28,2.12,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.875271                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.146385              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.125  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.558657              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.201  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2542      final r-factor (work) = 0.2166          |
| start r-factor (free) = 0.3364      final r-factor (free) = 0.2850          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3881 = 4.15 * 0.50 * 5.9124 + 1.00 * 0.1305                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1185 = 4.15 * 0.50 * 5.8150 + 1.00 * 0.0629                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2166      final r-factor (work) = 0.2006          |
| start r-factor (free) = 0.2850      final r-factor (free) = 0.2637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2636 = 0.56 * 1.00 * 5.8150 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1926 = 0.56 * 1.00 * 5.6921 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.538)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.06  15.39    None  None   None       |
|    all(noH): 2823   0      0.00    109.06  15.39    None  None   None       |
|    Sol.    : 438    0      2.56    109.06  38.78    None  None   None       |
|    Mac.    : 2385   0      0.00    95.57   11.10    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 -  10.907: 1536   |   5:    54.533 -  65.439:   56        |
|      1:    10.907 -  21.813:  693   |   6:    65.439 -  76.346:   17        |
|      2:    21.813 -  32.720:  212   |   7:    76.346 -  87.252:    7        |
|      3:    32.720 -  43.626:  175   |   8:    87.252 -  98.158:    2        |
|      4:    43.626 -  54.533:  123   |   9:    98.158 - 109.065:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2006 r_free = 0.2637             target_work(ml) = 5.656         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2002 r_free = 0.2626             target_work(ml) = 5.654         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2002   r_free= 0.2626   ksol= 0.36   Bsol= 65.20   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.47,1.28,2.12,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.654176                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2000   r_free= 0.2617   ksol= 0.33   Bsol= 48.73   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,0.50,1.65,0.00,0.00,0.00); trace/3= 1.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.652732                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.978596              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.231  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.410685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.421  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2000      final r-factor (work) = 0.1567          |
| start r-factor (free) = 0.2617      final r-factor (free) = 0.2122          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2300 = 4.98 * 0.50 * 5.6913 + 1.00 * 0.0627                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8954 = 4.98 * 0.50 * 5.5522 + 1.00 * 0.0743                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1567      final r-factor (work) = 0.1450          |
| start r-factor (free) = 0.2122      final r-factor (free) = 0.1993          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2927 = 0.41 * 1.00 * 5.5522 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2336 = 0.41 * 1.00 * 5.4122 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.538)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.67  15.10    None  None   None       |
|    all(noH): 2823   0      0.00    109.67  15.10    None  None   None       |
|    Sol.    : 438    0      3.82    109.67  41.07    None  None   None       |
|    Mac.    : 2385   0      0.00    97.87   10.33    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 -  10.967: 1682   |   5:    54.836 -  65.803:   76        |
|      1:    10.967 -  21.935:  616   |   6:    65.803 -  76.771:   27        |
|      2:    21.935 -  32.902:  167   |   7:    76.771 -  87.738:    8        |
|      3:    32.902 -  43.869:  116   |   8:    87.738 -  98.705:    3        |
|      4:    43.869 -  54.836:  126   |   9:    98.705 - 109.672:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1450 r_free = 0.1993             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1448 r_free = 0.1985             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1448   r_free= 0.1985   ksol= 0.33   Bsol= 48.73   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,0.50,1.65,0.00,0.00,0.00); trace/3= 1.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.372243                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.6626 0.99   1413  159 0.1120 0.1539      5.5313      5.7312|
|  2:  4.6626 -  3.7193 0.99   1354  150 0.1030 0.1426       5.629      5.8901|
|  3:  3.7193 -  3.2546 0.99   1325  142 0.1404 0.1819      5.7071      5.9924|
|  4:  3.2546 -  2.9595 0.99   1334  156 0.1607 0.2152      5.6947      5.8658|
|  5:  2.9595 -  2.7487 0.99   1319  147 0.1720 0.2332      5.5648      5.8006|
|  6:  2.7487 -  2.5875 0.99   1316  144 0.1578 0.2269      5.4458      5.6162|
|  7:  2.5875 -  2.4585 0.99   1308  135 0.1657 0.2086      5.3963      5.5698|
|  8:  2.4585 -  2.3519 0.98   1274  148 0.1608 0.2436      5.3257      5.6377|
|  9:  2.3519 -  2.2617 0.98   1285  150 0.1538 0.2244      5.2625      5.4947|
| 10:  2.2617 -  2.1839 1.00   1304  150 0.1470 0.2135      5.1777      5.4328|
| 11:  2.1839 -  2.1158 0.98   1299  136 0.1437 0.2187       5.153      5.4568|
| 12:  2.1158 -  2.0555 0.98   1263  142 0.1468 0.2072      5.0949      5.3415|
| 13:  2.0555 -  2.0015 0.96   1257  134 0.1569 0.2117      5.0025      5.2145|
| 14:  2.0015 -  1.9527 0.44    579   66 0.1476 0.1805      4.8977      5.0879|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0399 -  4.6626  1413   159  0.92  12.18   0.98     0.96      10813.36|
|  2:  4.6626 -  3.7193  1354   150  0.93  11.19   1.03     1.01      14014.12|
|  3:  3.7193 -  3.2546  1325   142  0.90  15.81   1.06     1.04      16826.31|
|  4:  3.2546 -  2.9595  1334   156  0.87  19.45   1.03     0.99      17337.98|
|  5:  2.9595 -  2.7487  1319   147  0.86  20.95   1.00     0.97      13720.61|
|  6:  2.7487 -  2.5875  1316   144  0.85  21.91   1.00     0.95      11911.70|
|  7:  2.5875 -  2.4585  1308   135  0.85  21.98   1.02     0.98      10753.34|
|  8:  2.4585 -  2.3519  1274   148  0.85  21.76   1.00     0.95       9202.29|
|  9:  2.3519 -  2.2617  1285   150  0.85  21.11   1.02     0.98       8323.91|
| 10:  2.2617 -  2.1839  1304   150  0.85  21.24   1.02     0.97       7207.95|
| 11:  2.1839 -  2.1158  1299   136  0.85  21.03   1.04     0.98       6929.85|
| 12:  2.1158 -  2.0555  1263   142  0.86  21.10   1.03     1.01       6414.08|
| 13:  2.0555 -  2.0015  1257   134  0.86  20.99   1.01     0.98       4947.36|
| 14:  2.0015 -  1.9527   579    66  0.88  18.55   1.01     0.98       3687.70|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3687.70 max =        17337.98 mean =     10481.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.94 mean =        19.18|
|phase err.(test): min =        0.00 max =           89.97 mean =        18.24|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1451   r_free= 0.1980   ksol= 0.32   Bsol= 43.54   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.00,-0.67,0.67,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.370428                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1451   r_free= 0.1980   ksol= 0.32   Bsol= 43.54   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.00,-0.67,0.67,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.370428                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.6626 0.99   1413  159 0.1125 0.1486      5.5102      5.6946|
|  2:  4.6626 -  3.7193 0.99   1354  150 0.1037 0.1414      5.6205      5.8778|
|  3:  3.7193 -  3.2546 0.99   1325  142 0.1407 0.1808      5.7065      5.9894|
|  4:  3.2546 -  2.9595 0.99   1334  156 0.1611 0.2164      5.6947      5.8712|
|  5:  2.9595 -  2.7487 0.99   1319  147 0.1719 0.2331      5.5654      5.8038|
|  6:  2.7487 -  2.5875 0.99   1316  144 0.1580 0.2271      5.4474      5.6176|
|  7:  2.5875 -  2.4585 0.99   1308  135 0.1658 0.2088      5.3982      5.5724|
|  8:  2.4585 -  2.3519 0.98   1274  148 0.1606 0.2450      5.3268      5.6434|
|  9:  2.3519 -  2.2617 0.98   1285  150 0.1535 0.2238      5.2635       5.493|
| 10:  2.2617 -  2.1839 1.00   1304  150 0.1469 0.2142      5.1786      5.4352|
| 11:  2.1839 -  2.1158 0.98   1299  136 0.1439 0.2195      5.1539      5.4589|
| 12:  2.1158 -  2.0555 0.98   1263  142 0.1466 0.2076      5.0953      5.3424|
| 13:  2.0555 -  2.0015 0.96   1257  134 0.1569 0.2113      5.0026      5.2135|
| 14:  2.0015 -  1.9527 0.44    579   66 0.1475 0.1805      4.8962      5.0867|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0399 -  4.6626  1413   159  0.92  11.39   0.97     0.96       9744.20|
|  2:  4.6626 -  3.7193  1354   150  0.93  10.83   1.03     1.01      13320.70|
|  3:  3.7193 -  3.2546  1325   142  0.90  15.73   1.05     1.04      16713.58|
|  4:  3.2546 -  2.9595  1334   156  0.87  19.43   1.02     0.98      17317.57|
|  5:  2.9595 -  2.7487  1319   147  0.85  20.99   0.99     0.96      13788.09|
|  6:  2.7487 -  2.5875  1316   144  0.85  21.93   0.99     0.94      11962.09|
|  7:  2.5875 -  2.4585  1308   135  0.84  22.05   1.00     0.96      10827.46|
|  8:  2.4585 -  2.3519  1274   148  0.85  21.86   0.99     0.94       9275.89|
|  9:  2.3519 -  2.2617  1285   150  0.85  21.17   1.01     0.96       8368.50|
| 10:  2.2617 -  2.1839  1304   150  0.85  21.29   1.00     0.96       7236.27|
| 11:  2.1839 -  2.1158  1299   136  0.85  21.07   1.02     0.97       6952.11|
| 12:  2.1158 -  2.0555  1263   142  0.86  21.12   1.01     0.99       6428.87|
| 13:  2.0555 -  2.0015  1257   134  0.86  20.98   0.99     0.97       4946.08|
| 14:  2.0015 -  1.9527   579    66  0.88  18.49   0.99     0.96       3667.70|
|alpha:            min =        0.94 max =            1.04 mean =         0.97|
|beta:             min =     3667.70 max =        17317.57 mean =     10359.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.96 mean =        19.11|
|phase err.(test): min =        0.00 max =           89.09 mean =        18.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.538)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.73    110.40  15.82    None  None   None       |
|    all(noH): 2823   0      0.73    110.40  15.82    None  None   None       |
|    Sol.    : 438    0      4.54    110.40  41.80    None  None   None       |
|    Mac.    : 2385   0      0.73    98.60   11.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.725 -  11.692: 1682   |   5:    55.561 -  66.529:   76        |
|      1:    11.692 -  22.660:  616   |   6:    66.529 -  77.496:   27        |
|      2:    22.660 -  33.627:  167   |   7:    77.496 -  88.463:    8        |
|      3:    33.627 -  44.594:  116   |   8:    88.463 -  99.430:    3        |
|      4:    44.594 -  55.561:  126   |   9:    99.430 - 110.397:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.500 - 5.958
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 341
   mapped sites are within: 0.735 - 5.958

peak=    8.991 closest distance to " CB  VAL A 296 " =    1.430
peak=    8.696 closest distance to " O   HOH Z 390 " =    1.745
peak=    7.004 closest distance to " O   HOH Z 130 " =    1.876
peak=    6.908 closest distance to " CG2 VAL A 230 " =    1.329
peak=    6.652 closest distance to " O   HOH Z 289 " =    1.770
peak=    6.591 closest distance to " O   HOH Z 415 " =    1.613
peak=    6.152 closest distance to " O   HOH Z 381 " =    1.173
peak=    6.052 closest distance to " O   HOH Z 120 " =    1.202
peak=    6.043 closest distance to " O   HOH Z 387 " =    1.647
peak=    5.983 closest distance to " O   HOH Z 350 " =    1.835
peak=    5.938 closest distance to " O   HOH Z  61 " =    1.433
peak=    5.824 closest distance to " CG  LEU A   5 " =    1.546
peak=    5.755 closest distance to " O   HOH Z  65 " =    1.744
peak=    5.743 closest distance to " O   HOH Z 375 " =    1.361
peak=    5.738 closest distance to " CG  ARG A 138 " =    1.310
peak=    5.619 closest distance to " O   PRO A 198 " =    1.460
peak=    5.570 closest distance to " O   HOH Z 424 " =    2.058
peak=    5.440 closest distance to " O   HOH Z   9 " =    1.608
peak=    5.439 closest distance to " O   HOH Z 410 " =    1.609
peak=    5.422 closest distance to " O   HOH Z 268 " =    1.148
peak=    5.258 closest distance to " O   HOH Z 291 " =    1.080
peak=    5.137 closest distance to " O   HOH Z 403 " =    1.731
peak=    5.092 closest distance to " O   HOH Z 111 " =    1.906
peak=    5.033 closest distance to " O   HOH Z 250 " =    2.126
peak=    5.022 closest distance to " O   HOH Z   7 " =    2.099
peak=    5.018 closest distance to " O   HOH Z 117 " =    1.201
peak=    4.997 closest distance to " O   HOH Z 124 " =    1.960
peak=    4.973 closest distance to " O   HOH Z  15 " =    1.059
peak=    4.949 closest distance to " O   HOH Z 255 " =    1.072
peak=    4.936 closest distance to " OE1 GLU A   2 " =    1.920
peak=    4.906 closest distance to " O   HOH Z  27 " =    1.118
peak=    4.895 closest distance to " NE2 GLN A  11 " =    1.324
peak=    4.890 closest distance to " CB  PRO A  54 " =    1.121
peak=    4.888 closest distance to " O   HOH Z  46 " =    1.260
peak=    4.862 closest distance to " O   HOH Z 214 " =    1.570
peak=    4.837 closest distance to " O   HOH Z  28 " =    2.025
peak=    4.820 closest distance to " O   HOH Z 144 " =    1.837
peak=    4.817 closest distance to " NZ BLYS A 290 " =    1.140
peak=    4.784 closest distance to " O   HOH Z  54 " =    1.440
peak=    4.763 closest distance to " O   HOH Z  57 " =    1.332
peak=    4.749 closest distance to " O   HOH Z  69 " =    1.453
peak=    4.683 closest distance to " O   HOH Z 222 " =    1.442
peak=    4.653 closest distance to " CD1AILE A 234 " =    1.053
peak=    4.601 closest distance to " O   HOH Z 400 " =    0.895
peak=    4.577 closest distance to " O   HOH Z 105 " =    1.235
peak=    4.545 closest distance to " O   HOH Z 316 " =    3.135
peak=    4.541 closest distance to " CG1AVAL A 121 " =    0.954
peak=    4.537 closest distance to " NH1 ARG A 138 " =    1.004
peak=    4.533 closest distance to " O   HOH Z 427 " =    2.337
peak=    4.520 closest distance to " O   HOH Z 416 " =    1.544
peak=    4.520 closest distance to " O   HOH Z 361 " =    1.660
peak=    4.506 closest distance to " OG  SER A 276 " =    0.955
peak=    4.497 closest distance to " O   HOH Z 215 " =    1.485
peak=    4.487 closest distance to " CD2 TRP A 179 " =    2.106
peak=    4.486 closest distance to " O   HOH Z 116 " =    1.378
peak=    4.470 closest distance to " O   HOH Z  45 " =    1.060
peak=    4.465 closest distance to " NE1 TRP A 266 " =    1.932
peak=    4.463 closest distance to " O   HOH Z 132 " =    1.601
peak=    4.441 closest distance to " O   HOH Z 293 " =    1.414
peak=    4.418 closest distance to " O   HOH Z 139 " =    1.659
peak=    4.414 closest distance to " CB  SER A 216 " =    1.120
peak=    4.392 closest distance to " O   HOH Z 427 " =    1.405
peak=    4.351 closest distance to " CE  MET A  93 " =    1.483
peak=    4.314 closest distance to " CB  VAL A 230 " =    1.204
peak=    4.314 closest distance to " O   HOH Z 358 " =    1.502
peak=    4.297 closest distance to " O   HOH Z 238 " =    1.150
peak=    4.285 closest distance to " CB  SER A   3 " =    1.349
peak=    4.263 closest distance to " O   HOH Z 278 " =    1.290
peak=    4.256 closest distance to " CA  ASN A 127 " =    1.132
peak=    4.240 closest distance to " O   HOH Z 119 " =    1.434
peak=    4.225 closest distance to " O   HOH Z  63 " =    1.818
peak=    4.223 closest distance to " O   HOH Z 263 " =    1.429
peak=    4.218 closest distance to " CD2 LEU A 228 " =    1.224
peak=    4.215 closest distance to " O   HOH Z 357 " =    1.950
peak=    4.203 closest distance to " O   HOH Z 133 " =    2.029
peak=    4.202 closest distance to " CG2 THR A 279 " =    1.089
peak=    4.190 closest distance to " O   HOH Z 112 " =    1.211
peak=    4.179 closest distance to " O   HOH Z 353 " =    2.208
peak=    4.161 closest distance to " CB  ASP A 124 " =    0.959
peak=    4.073 closest distance to " CG  GLN A  88 " =    1.017
peak=    4.073 closest distance to " O   HOH Z 123 " =    1.128
peak=    4.060 closest distance to " O   HOH Z 259 " =    2.173
peak=    4.055 closest distance to " O   HOH Z 414 " =    1.957
peak=    4.036 closest distance to " O   HOH Z 431 " =    1.001
peak=    4.023 closest distance to " O   HOH Z 108 " =    1.731
peak=    4.023 closest distance to " O   ASN A 285 " =    0.912
peak=    4.020 closest distance to " O   HOH Z  48 " =    1.682
peak=    4.016 closest distance to " O   HOH Z 389 " =    1.669
peak=    4.006 closest distance to " O   HOH Z  30 " =    1.485
peak=    4.002 closest distance to " CZ  PHE A  16 " =    0.941
peak=    4.000 closest distance to " O   HOH Z 147 " =    1.610
peak=    3.996 closest distance to " O   HOH Z 418 " =    1.357
peak=    3.955 closest distance to " O   HOH Z 258 " =    2.249
peak=    3.955 closest distance to " CB  LEU A 300 " =    0.911
peak=    3.952 closest distance to " OG BSER A 258 " =    1.153
peak=    3.950 closest distance to " O   HOH Z  24 " =    2.003
peak=    3.947 closest distance to " CB  ARG A 275 " =    1.206
peak=    3.941 closest distance to " NE2 GLN A  58 " =    5.370
peak=    3.941 closest distance to " O   HOH Z 363 " =    2.783
peak=    3.927 closest distance to " OD1 ASP A 286 " =    1.052
peak=    3.916 closest distance to " O   HOH Z 193 " =    1.869
peak=    3.909 closest distance to " CD  ARG A  66 " =    2.494
peak=    3.896 closest distance to " O   HOH Z 126 " =    1.761
peak=    3.894 closest distance to " O   HOH Z 287 " =    1.981
peak=    3.889 closest distance to " O   HOH Z 226 " =    1.176
peak=    3.889 closest distance to " CD  ARG A 138 " =    0.886
peak=    3.883 closest distance to " O   HOH Z 344 " =    1.117
peak=    3.857 closest distance to " O   HOH Z 363 " =    1.236
peak=    3.855 closest distance to " O   HOH Z 374 " =    1.174
peak=    3.853 closest distance to " CG  PRO A 213 " =    1.225
peak=    3.849 closest distance to " CA  ILE A 234 " =    1.139
peak=    3.848 closest distance to " O   HOH Z 182 " =    1.181
peak=    3.840 closest distance to " O   HOH Z   6 " =    1.989
peak=    3.834 closest distance to " O   HOH Z  37 " =    1.370
peak=    3.814 closest distance to " O   HOH Z 419 " =    2.118
peak=    3.809 closest distance to " O   HOH Z 272 " =    1.855
peak=    3.801 closest distance to " O   HOH Z 417 " =    1.446
peak=    3.796 closest distance to " CA  ALA A  21 " =    1.161
peak=    3.780 closest distance to " CB  ALA A   1 " =    1.071
peak=    3.776 closest distance to " O   HOH Z 359 " =    1.498
peak=    3.771 closest distance to " O   HOH Z 127 " =    1.097
peak=    3.770 closest distance to " CB  ASN A 148 " =    1.431
peak=    3.768 closest distance to " O   HOH Z 423 " =    1.499
peak=    3.764 closest distance to " N   GLN A  73 " =    1.268
peak=    3.761 closest distance to " O   HOH Z 402 " =    1.434
peak=    3.758 closest distance to " CB  ASP A 200 " =    0.951
peak=    3.742 closest distance to " O   HOH Z 233 " =    1.405
peak=    3.740 closest distance to " O   HOH Z 247 " =    1.485
peak=    3.726 closest distance to " O   HOH Z 426 " =    1.095
peak=    3.724 closest distance to " N   GLY A 136 " =    1.095
peak=    3.717 closest distance to " O   HOH Z 178 " =    1.193
peak=    3.717 closest distance to " O   ASP A 132 " =    3.772
peak=    3.714 closest distance to " NZ  LYS A 117 " =    1.331
peak=    3.710 closest distance to " O   HOH Z  53 " =    2.099
peak=    3.691 closest distance to " NE BARG A 275 " =    1.056
peak=    3.680 closest distance to " O   HOH Z 422 " =    1.305
peak=    3.676 closest distance to " O   HOH Z 227 " =    1.901
peak=    3.671 closest distance to " CE AMET A  47 " =    1.508
peak=    3.665 closest distance to " O   HOH Z  59 " =    1.377
peak=    3.663 closest distance to " N   TYR A  15 " =    1.103
peak=    3.659 closest distance to " O   HOH Z 384 " =    2.019
peak=    3.658 closest distance to " O   HOH Z 411 " =    3.192
peak=    3.655 closest distance to " O   HOH Z 167 " =    1.604
peak=    3.651 closest distance to " CB  MET A  40 " =    0.788
peak=    3.647 closest distance to " CA  ALA A 295 " =    0.943
peak=    3.643 closest distance to " O   HOH Z 240 " =    1.926
peak=    3.641 closest distance to " CA  ARG A  36 " =    1.347
peak=    3.634 closest distance to " CA  SER A  87 " =    0.928
peak=    3.630 closest distance to " N   CYS A 260 " =    1.206
peak=    3.630 closest distance to " O   HOH Z 378 " =    1.206
peak=    3.625 closest distance to " CB  TRP A 266 " =    0.905
peak=    3.624 closest distance to " NE1 TRP A 274 " =    1.086
peak=    3.623 closest distance to " O   HOH Z 326 " =    1.355
peak=    3.618 closest distance to " O   HOH Z 356 " =    1.652
peak=    3.611 closest distance to " O   HOH Z 248 " =    2.283
peak=    3.608 closest distance to " CB  ALA A 104 " =    0.954
peak=    3.607 closest distance to " CG  ASN A  60 " =    1.501
peak=    3.604 closest distance to " O   HOH Z 232 " =    1.734
peak=    3.603 closest distance to " O   HOH Z 133 " =    2.132
peak=    3.602 closest distance to " CB  SER A 276 " =    1.421
peak=    3.598 closest distance to " O   HOH Z 213 " =    1.729
peak=    3.596 closest distance to " NH1 ARG A  56 " =    1.171
peak=    3.595 closest distance to " O   HOH Z 369 " =    2.190
peak=    3.592 closest distance to " O   HOH Z 110 " =    1.485
peak=    3.590 closest distance to " O   HOH Z   1 " =    1.782
peak=    3.587 closest distance to " O   HOH Z  15 " =    2.112
peak=    3.584 closest distance to " O   GLY A 302 " =    2.425
peak=    3.584 closest distance to " OG ASER A 134 " =    1.255
peak=    3.577 closest distance to " N   SER A  12 " =    1.518
peak=    3.576 closest distance to " O   HOH Z 225 " =    1.434
peak=    3.574 closest distance to " O   HOH Z 143 " =    1.377
peak=    3.573 closest distance to " O   HOH Z 360 " =    1.175
peak=    3.569 closest distance to " CB  GLN A 223 " =    1.413
peak=    3.569 closest distance to " OD2 ASP A 286 " =    2.500
peak=    3.568 closest distance to " O   HOH Z 191 " =    4.458
peak=    3.565 closest distance to " CB  GLN A 183 " =    1.131
peak=    3.564 closest distance to " O   HOH Z 334 " =    2.513
peak=    3.562 closest distance to " CB  ALA A  10 " =    1.098
peak=    3.561 closest distance to " CG  LEU A 228 " =    0.999
peak=    3.560 closest distance to " CD1 LEU A   5 " =    1.205
peak=    3.558 closest distance to " O   HOH Z 193 " =    1.586
peak=    3.551 closest distance to " O   HOH Z 368 " =    1.743
peak=    3.550 closest distance to " CB  ASN A  39 " =    0.755
peak=    3.546 closest distance to " O   HOH Z 116 " =    2.465
peak=    3.540 closest distance to " O   HOH Z 239 " =    1.594
peak=    3.537 closest distance to " CG1BVAL A 121 " =    2.109
peak=    3.530 closest distance to " CB  ILE A 234 " =    0.899
peak=    3.527 closest distance to " O   HOH Z  22 " =    2.105
peak=    3.525 closest distance to " O   HOH Z 128 " =    2.136
peak=    3.524 closest distance to " O   HOH Z 161 " =    0.962
peak=    3.516 closest distance to " CG2 THR A 235 " =    0.874
peak=    3.515 closest distance to " CB  ASN A  60 " =    0.877
peak=    3.513 closest distance to " O   HOH Z 244 " =    1.545
peak=    3.511 closest distance to " O   HOH Z 158 " =    1.416
peak=    3.506 closest distance to " O   HOH Z 334 " =    1.569
peak=    3.503 closest distance to " CG2 THR A 294 " =    1.195
peak=    3.493 closest distance to " O   HOH Z 135 " =    1.684
peak=    3.493 closest distance to " O   HOH Z 128 " =    2.100
peak=    3.488 closest distance to " CA  GLU A 152 " =    1.092
peak=    3.481 closest distance to " SD  MET A  93 " =    1.091
peak=    3.478 closest distance to " CA  GLY A 267 " =    1.308
peak=    3.476 closest distance to " CG2 ILE A 151 " =    0.870
peak=    3.475 closest distance to " OG BSER A  99 " =    2.091
peak=    3.472 closest distance to " CB  ALA A 137 " =    1.012
peak=    3.468 closest distance to " OE1 GLN A 240 " =    1.639
peak=    3.467 closest distance to " CA  LEU A 282 " =    0.921
peak=    3.463 closest distance to " CB  SER A 210 " =    1.089
peak=    3.461 closest distance to " O   HOH Z  32 " =    1.401
peak=    3.460 closest distance to " NH1 ARG A  14 " =    0.975
peak=    3.456 closest distance to " O   HOH Z 207 " =    2.671
peak=    3.455 closest distance to " NE AARG A 275 " =    1.530
peak=    3.449 closest distance to " O   HOH Z  32 " =    1.761
peak=    3.449 closest distance to " CA  ASN A 284 " =    0.995
peak=    3.448 closest distance to " CB  MET A 105 " =    1.278
peak=    3.447 closest distance to " CB  PHE A  16 " =    1.048
peak=    3.447 closest distance to " O   HOH Z 380 " =    1.973
peak=    3.446 closest distance to " O   HOH Z 261 " =    1.892
peak=    3.431 closest distance to " CB  PHE A 225 " =    1.490
peak=    3.429 closest distance to " CB  VAL A 202 " =    1.703
peak=    3.425 closest distance to " N   GLN A 278 " =    1.002
peak=    3.417 closest distance to " CG  ASN A 301 " =    1.149
peak=    3.416 closest distance to " CA  GLU A  46 " =    1.061
peak=    3.414 closest distance to " O   HOH Z 217 " =    2.011
peak=    3.411 closest distance to " O   HOH Z 108 " =    1.945
peak=    3.406 closest distance to " CB  GLN A 278 " =    0.823
peak=    3.402 closest distance to " O   HOH Z 282 " =    1.574
peak=    3.397 closest distance to " NH2BARG A 145 " =    1.722
peak=    3.397 closest distance to " O   HOH Z 373 " =    2.066
peak=    3.394 closest distance to " C   ASP A  50 " =    1.239
peak=    3.390 closest distance to " CG  PRO A 243 " =    1.065
peak=    3.389 closest distance to " O   HOH Z  48 " =    1.624
peak=    3.386 closest distance to " CE  LYS A  48 " =    0.970
peak=    3.382 closest distance to " CB  ASP A 140 " =    0.831
peak=    3.380 closest distance to " CB  GLU A 152 " =    1.178
peak=    3.379 closest distance to " CB  ALA A 233 " =    1.218
peak=    3.374 closest distance to " CB  GLU A   2 " =    0.998
peak=    3.372 closest distance to " O   ALA A 165 " =    1.150
peak=    3.371 closest distance to " OG  SER A  26 " =    1.370
peak=    3.370 closest distance to " O   HOH Z 371 " =    2.922
peak=    3.368 closest distance to " O   HOH Z 303 " =    1.744
peak=    3.364 closest distance to " CZ3 TRP A 274 " =    1.477
peak=    3.363 closest distance to " OE1 GLN A 278 " =    1.361
peak=    3.363 closest distance to " O   HOH Z  95 " =    1.543
peak=    3.361 closest distance to " NH2 ARG A 219 " =    1.832
peak=    3.360 closest distance to " CB  SER A 273 " =    0.910
peak=    3.359 closest distance to " O   HOH Z  89 " =    2.116
peak=    3.356 closest distance to " NE2 GLN A  55 " =    1.262
peak=    3.354 closest distance to " O   HOH Z 124 " =    1.877
peak=    3.350 closest distance to " O   HOH Z 158 " =    2.253
peak=    3.347 closest distance to " O   HOH Z 302 " =    1.620
peak=    3.345 closest distance to " O   HOH Z 371 " =    1.738
peak=    3.344 closest distance to " O   THR A 251 " =    1.087
peak=    3.334 closest distance to " N   GLU A   2 " =    1.566
peak=    3.331 closest distance to " O   HOH Z 406 " =    1.902
peak=    3.329 closest distance to " CB  ASP A 298 " =    1.190
peak=    3.327 closest distance to " O   HOH Z  88 " =    2.805
peak=    3.322 closest distance to " CG2 THR A 246 " =    1.708
peak=    3.318 closest distance to " CG1 ILE A 120 " =    1.564
peak=    3.316 closest distance to " CB  ASN A 187 " =    1.028
peak=    3.313 closest distance to " O   HOH Z  69 " =    1.803
peak=    3.309 closest distance to " CG2 THR A 251 " =    1.784
peak=    3.308 closest distance to " O   HOH Z 361 " =    2.565
peak=    3.308 closest distance to " NH1BARG A 190 " =    1.600
peak=    3.303 closest distance to " CA  TRP A  92 " =    1.275
peak=    3.302 closest distance to " CA  TYR A  30 " =    1.140
peak=    3.298 closest distance to " O   GLY A 229 " =    1.049
peak=    3.296 closest distance to " OE1 GLN A  77 " =    0.960
peak=    3.293 closest distance to " CB  SER A  63 " =    1.353
peak=    3.293 closest distance to " CA  ASP A 124 " =    0.735
peak=    3.290 closest distance to " O   HOH Z  88 " =    3.283
peak=    3.290 closest distance to " N   TRP A 177 " =    1.747
peak=    3.284 closest distance to " OD1 ASP A 238 " =    0.950
peak=    3.277 closest distance to " CB  TRP A 179 " =    1.385
peak=    3.271 closest distance to " O   HOH Z 185 " =    1.362
peak=    3.268 closest distance to " O   HOH Z  97 " =    1.229
peak=    3.265 closest distance to " CE2 PHE A  16 " =    0.892
peak=    3.264 closest distance to " O   HOH Z 368 " =    1.080
peak=    3.261 closest distance to " O   HOH Z 434 " =    5.682
peak=    3.258 closest distance to " CG  ARG A 159 " =    0.840
peak=    3.257 closest distance to " CB  ASN A 142 " =    1.070
peak=    3.257 closest distance to " CG  PRO A  54 " =    1.295
peak=    3.252 closest distance to " O   HOH Z 287 " =    1.683
peak=    3.247 closest distance to " O   HOH Z 180 " =    2.219
peak=    3.246 closest distance to " O   HOH Z 129 " =    1.267
peak=    3.244 closest distance to " O   HOH Z 183 " =    1.246
peak=    3.242 closest distance to " O   HOH Z 106 " =    2.507
peak=    3.242 closest distance to " N   PHE A 130 " =    1.267
peak=    3.241 closest distance to " CG  LEU A 167 " =    1.372
peak=    3.241 closest distance to " O   HOH Z 130 " =    1.653
peak=    3.239 closest distance to " CG  LYS A 119 " =    1.030
peak=    3.236 closest distance to " O   HOH Z  49 " =    1.259
peak=    3.233 closest distance to " CG  LYS A 166 " =    1.376
peak=    3.232 closest distance to " O   HOH Z 413 " =    1.785
peak=    3.225 closest distance to " O   HOH Z 172 " =    5.958
peak=    3.223 closest distance to " O   HOH Z 184 " =    1.880
peak=    3.216 closest distance to " O   HOH Z 434 " =    1.524
peak=    3.216 closest distance to " O   HOH Z 392 " =    1.689
peak=    3.214 closest distance to " O   MET A  40 " =    1.627
peak=    3.213 closest distance to " CG2 THR A 221 " =    1.291
peak=    3.208 closest distance to " O   HOH Z  28 " =    2.087
peak=    3.205 closest distance to " OE2 GLU A  53 " =    2.095
peak=    3.199 closest distance to " O   HOH Z 334 " =    1.835
peak=    3.199 closest distance to " CB  PRO A 198 " =    1.295
peak=    3.196 closest distance to " O   HOH Z  49 " =    2.700
peak=    3.193 closest distance to " OG  SER A  22 " =    2.759
peak=    3.188 closest distance to " CB  PRO A 163 " =    3.872
peak=    3.185 closest distance to " O   HOH Z  59 " =    1.773
peak=    3.184 closest distance to " O   HOH Z 179 " =    1.077
peak=    3.182 closest distance to " CB  MET A  47 " =    1.562
peak=    3.181 closest distance to " CG2 ILE A 234 " =    0.820
peak=    3.178 closest distance to " CA  ASN A  74 " =    1.282
peak=    3.172 closest distance to " O   HOH Z 176 " =    1.688
peak=    3.172 closest distance to " CB  LEU A   5 " =    1.192
peak=    3.171 closest distance to " O   ALA A 291 " =    1.583
peak=    3.164 closest distance to " O   HOH Z 299 " =    2.959
peak=    3.163 closest distance to " CZ3 TRP A 123 " =    1.396
peak=    3.158 closest distance to " OG BSER A  12 " =    0.850
peak=    3.157 closest distance to " O   HOH Z 367 " =    2.724
peak=    3.156 closest distance to " O   HOH Z 375 " =    2.054
peak=    3.154 closest distance to " O   HOH Z 362 " =    2.047
peak=    3.149 closest distance to " NH1AARG A 275 " =    1.170
peak=    3.145 closest distance to " NH2 ARG A  24 " =    0.806
peak=    3.132 closest distance to " CB  GLU A 277 " =    1.175
peak=    3.131 closest distance to " O   HOH Z 112 " =    2.600
peak=    3.114 closest distance to " O   HOH Z  94 " =    1.978
peak=    3.114 closest distance to " NE2 GLN A  89 " =    1.210
peak=    3.113 closest distance to " CD  PRO A 243 " =    1.492
peak=    3.108 closest distance to " CG2AVAL A  72 " =    2.878
peak=    3.103 closest distance to " O   HOH Z 217 " =    2.260
peak=    3.094 closest distance to " O   HOH Z 340 " =    1.882
peak=    3.094 closest distance to " O   HOH Z 143 " =    2.190
peak=    3.062 closest distance to " O   HOH Z 172 " =    1.365
peak=    3.061 closest distance to " CG  MET A 188 " =    1.375
peak=    3.038 closest distance to " O   HOH Z 172 " =    1.841
peak=    3.036 closest distance to " CD2 LEU A  25 " =    1.231
peak=    3.036 closest distance to " CB  ALA A  34 " =    1.151

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.555 - 5.456
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 206
   mapped sites are within: 0.748 - 5.456

peak=   -4.822 closest distance to " O   HOH Z 381 " =    0.852
peak=   -4.577 closest distance to " OG ASER A 134 " =    0.999
peak=   -4.436 closest distance to " CG2 VAL A 230 " =    0.981
peak=   -4.394 closest distance to " CG1 VAL A 296 " =    0.759
peak=   -4.391 closest distance to " CD  GLU A 277 " =    2.580
peak=   -4.381 closest distance to " CD  ARG A 138 " =    1.131
peak=   -4.331 closest distance to " OG  SER A  97 " =    2.337
peak=   -4.258 closest distance to " O   HOH Z 313 " =    1.266
peak=   -4.159 closest distance to " O   HOH Z 163 " =    1.515
peak=   -4.154 closest distance to " O   HOH Z 431 " =    1.028
peak=   -4.145 closest distance to " CD2 LEU A   5 " =    0.818
peak=   -4.139 closest distance to " O   PRO A 198 " =    1.259
peak=   -4.077 closest distance to " O   HOH Z 231 " =    0.844
peak=   -4.063 closest distance to " CG  PRO A 163 " =    2.463
peak=   -4.014 closest distance to " CD  ARG A  14 " =    2.970
peak=   -4.011 closest distance to " O   GLY A  80 " =    2.533
peak=   -4.002 closest distance to " CB  ASP A  27 " =    2.486
peak=   -3.926 closest distance to " O   ASN A 301 " =    1.786
peak=   -3.925 closest distance to " O   HOH Z 385 " =    0.959
peak=   -3.902 closest distance to " O   HOH Z 290 " =    1.132
peak=   -3.864 closest distance to " O   HOH Z 235 " =    0.974
peak=   -3.847 closest distance to " OE1 GLN A  88 " =    0.917
peak=   -3.825 closest distance to " OE1 GLN A 223 " =    2.435
peak=   -3.817 closest distance to " O   HOH Z 300 " =    0.882
peak=   -3.811 closest distance to " CA  GLY A  98 " =    1.953
peak=   -3.808 closest distance to " OG  SER A  87 " =    1.593
peak=   -3.800 closest distance to " O   HOH Z  56 " =    0.767
peak=   -3.793 closest distance to " O   HOH Z 255 " =    0.842
peak=   -3.791 closest distance to " CA  GLY A  35 " =    1.895
peak=   -3.790 closest distance to " O   HOH Z  24 " =    1.149
peak=   -3.790 closest distance to " CA  GLY A 133 " =    2.056
peak=   -3.786 closest distance to " O   HOH Z 268 " =    1.012
peak=   -3.774 closest distance to " NH2 ARG A  79 " =    2.065
peak=   -3.754 closest distance to " O   GLY A  98 " =    2.140
peak=   -3.731 closest distance to " CD1 LEU A  96 " =    2.412
peak=   -3.727 closest distance to " O   HOH Z 354 " =    2.595
peak=   -3.727 closest distance to " N   VAL A 125 " =    0.959
peak=   -3.713 closest distance to " CG BLYS A 290 " =    0.889
peak=   -3.707 closest distance to " CD2 LEU A 143 " =    2.485
peak=   -3.673 closest distance to " CB  ALA A 100 " =    2.127
peak=   -3.652 closest distance to " CD1 TRP A 179 " =    1.038
peak=   -3.644 closest distance to " O   GLN A  11 " =    1.704
peak=   -3.642 closest distance to " O   HOH Z  51 " =    0.748
peak=   -3.640 closest distance to " CD2 TRP A 150 " =    1.427
peak=   -3.637 closest distance to " O   HOH Z 117 " =    1.152
peak=   -3.624 closest distance to " O   HOH Z 286 " =    1.385
peak=   -3.608 closest distance to " CD  ARG A 139 " =    1.496
peak=   -3.604 closest distance to " O   THR A 220 " =    1.580
peak=   -3.595 closest distance to " O   HOH Z  71 " =    1.027
peak=   -3.588 closest distance to " C   PHE A 155 " =    0.888
peak=   -3.586 closest distance to " CG  MET A 105 " =    0.864
peak=   -3.582 closest distance to " CG  GLN A  88 " =    0.831
peak=   -3.569 closest distance to " N   SER A  12 " =    1.249
peak=   -3.568 closest distance to " O   HOH Z 426 " =    2.165
peak=   -3.549 closest distance to " O   HOH Z 407 " =    3.068
peak=   -3.548 closest distance to " C   ARG A  79 " =    2.528
peak=   -3.547 closest distance to " O   HOH Z  60 " =    1.840
peak=   -3.547 closest distance to " O   HOH Z  93 " =    2.111
peak=   -3.546 closest distance to " O   HOH Z 166 " =    1.977
peak=   -3.538 closest distance to " CG  PHE A  59 " =    1.796
peak=   -3.537 closest distance to " CB  ALA A 248 " =    2.009
peak=   -3.529 closest distance to " O   HOH Z  54 " =    0.751
peak=   -3.529 closest distance to " O   HOH Z 131 " =    3.907
peak=   -3.528 closest distance to " O   ILE A  49 " =    1.578
peak=   -3.527 closest distance to " O   HOH Z 359 " =    2.552
peak=   -3.526 closest distance to " OG  SER A 206 " =    1.867
peak=   -3.523 closest distance to " CG  TRP A 266 " =    1.592
peak=   -3.513 closest distance to " O   HOH Z 314 " =    1.004
peak=   -3.512 closest distance to " CG  ARG A 138 " =    1.079
peak=   -3.508 closest distance to " CD2 LEU A 237 " =    2.457
peak=   -3.508 closest distance to " O   ALA A  51 " =    1.465
peak=   -3.496 closest distance to " CD1 ILE A 239 " =    2.441
peak=   -3.494 closest distance to " O   SER A 135 " =    1.677
peak=   -3.491 closest distance to " ND2 ASN A 285 " =    2.109
peak=   -3.488 closest distance to " CD2 LEU A 228 " =    1.001
peak=   -3.481 closest distance to " O   HOH Z  76 " =    1.024
peak=   -3.481 closest distance to " CD  GLN A  77 " =    1.184
peak=   -3.478 closest distance to " C   ILE A 239 " =    1.966
peak=   -3.472 closest distance to " O   THR A  42 " =    2.566
peak=   -3.464 closest distance to " O   HOH Z 435 " =    2.243
peak=   -3.462 closest distance to " O   HOH Z 401 " =    0.902
peak=   -3.449 closest distance to " O   GLN A  73 " =    1.095
peak=   -3.446 closest distance to " CG2 ILE A 239 " =    2.185
peak=   -3.444 closest distance to " OG1 THR A 157 " =    1.747
peak=   -3.442 closest distance to " O   ILE A 106 " =    2.237
peak=   -3.433 closest distance to " O   TRP A 179 " =    1.803
peak=   -3.428 closest distance to " O   GLY A  57 " =    1.376
peak=   -3.426 closest distance to " C   ASP A 231 " =    1.932
peak=   -3.425 closest distance to " O   HOH Z 376 " =    2.355
peak=   -3.420 closest distance to " N   GLN A  58 " =    1.214
peak=   -3.409 closest distance to " O   HOH Z 359 " =    1.637
peak=   -3.398 closest distance to " CD  LYS A 289 " =    2.397
peak=   -3.397 closest distance to " O   HOH Z 413 " =    4.568
peak=   -3.395 closest distance to " OG BSER A 134 " =    1.563
peak=   -3.393 closest distance to " O   THR A 178 " =    0.942
peak=   -3.391 closest distance to " O   HOH Z 298 " =    0.761
peak=   -3.389 closest distance to " O   HOH Z 404 " =    1.133
peak=   -3.386 closest distance to " O   LYS A 119 " =    0.850
peak=   -3.384 closest distance to " O   HOH Z  52 " =    1.027
peak=   -3.378 closest distance to " O   HOH Z 291 " =    0.866
peak=   -3.378 closest distance to " O   HOH Z 383 " =    2.347
peak=   -3.367 closest distance to " O   HOH Z 264 " =    1.219
peak=   -3.365 closest distance to " CB  ALA A   9 " =    2.501
peak=   -3.363 closest distance to " CG  ASP A 200 " =    0.873
peak=   -3.360 closest distance to " O   HOH Z 377 " =    1.102
peak=   -3.360 closest distance to " O   GLY A 118 " =    1.517
peak=   -3.355 closest distance to " O   HOH Z 120 " =    1.209
peak=   -3.346 closest distance to " O   HOH Z  68 " =    1.212
peak=   -3.346 closest distance to " NH2AARG A 275 " =    5.456
peak=   -3.346 closest distance to " CD  LYS A 166 " =    2.628
peak=   -3.342 closest distance to " C   GLU A  44 " =    1.861
peak=   -3.340 closest distance to " CA  ASN A 217 " =    1.841
peak=   -3.334 closest distance to " CB  TYR A  15 " =    2.032
peak=   -3.324 closest distance to " CA  GLY A 133 " =    2.177
peak=   -3.318 closest distance to " OG1 THR A 178 " =    0.999
peak=   -3.316 closest distance to " CG1AVAL A  72 " =    2.018
peak=   -3.314 closest distance to " O   HOH Z 124 " =    3.881
peak=   -3.314 closest distance to " O   HOH Z 177 " =    2.628
peak=   -3.308 closest distance to " OG  SER A  63 " =    1.395
peak=   -3.306 closest distance to " OG  SER A  26 " =    0.948
peak=   -3.302 closest distance to " O   HOH Z 126 " =    1.794
peak=   -3.302 closest distance to " O   HOH Z 409 " =    1.800
peak=   -3.301 closest distance to " CD1 LEU A 222 " =    2.511
peak=   -3.288 closest distance to " CG  ASP A 200 " =    1.067
peak=   -3.288 closest distance to " O   ARG A  56 " =    2.022
peak=   -3.284 closest distance to " CA  ASN A 110 " =    0.936
peak=   -3.284 closest distance to " O   HOH Z 373 " =    0.794
peak=   -3.284 closest distance to " O   HOH Z 174 " =    2.831
peak=   -3.279 closest distance to " CB  LEU A 261 " =    2.238
peak=   -3.279 closest distance to " O   THR A 279 " =    0.811
peak=   -3.277 closest distance to " OD2 ASP A 171 " =    1.894
peak=   -3.268 closest distance to " O   HOH Z 111 " =    1.262
peak=   -3.266 closest distance to " O   VAL A  72 " =    0.823
peak=   -3.266 closest distance to " NH1 ARG A  56 " =    2.463
peak=   -3.265 closest distance to " O   HOH Z 221 " =    0.958
peak=   -3.257 closest distance to " O   HOH Z 388 " =    1.794
peak=   -3.254 closest distance to " CG2 THR A  31 " =    2.073
peak=   -3.253 closest distance to " OD2 ASP A 286 " =    1.207
peak=   -3.251 closest distance to " CG2 ILE A  20 " =    2.766
peak=   -3.247 closest distance to " C   GLN A  94 " =    1.491
peak=   -3.233 closest distance to " OE1 GLN A  77 " =    1.689
peak=   -3.225 closest distance to " O   HOH Z  69 " =    1.958
peak=   -3.219 closest distance to " O   HOH Z  52 " =    1.585
peak=   -3.216 closest distance to " O   HOH Z  97 " =    1.030
peak=   -3.216 closest distance to " SG BCYS A 201 " =    1.984
peak=   -3.213 closest distance to " CG  MET A  93 " =    2.039
peak=   -3.211 closest distance to " CA  GLY A  23 " =    2.733
peak=   -3.206 closest distance to " O   LEU A 297 " =    0.942
peak=   -3.198 closest distance to " CD2 TYR A  30 " =    2.552
peak=   -3.195 closest distance to " O   HOH Z  40 " =    4.157
peak=   -3.194 closest distance to " CA  GLN A  55 " =    1.284
peak=   -3.192 closest distance to " O   HOH Z 113 " =    2.185
peak=   -3.190 closest distance to " O   HOH Z 402 " =    1.430
peak=   -3.189 closest distance to " N   PRO A 163 " =    1.504
peak=   -3.187 closest distance to " CE1 PHE A  59 " =    1.371
peak=   -3.185 closest distance to " CB  TRP A  85 " =    2.548
peak=   -3.183 closest distance to " OD1 ASN A  60 " =    1.495
peak=   -3.177 closest distance to " O   HOH Z  77 " =    1.355
peak=   -3.175 closest distance to " CB  ASN A 285 " =    2.205
peak=   -3.175 closest distance to " O   HOH Z  61 " =    0.913
peak=   -3.173 closest distance to " O   HOH Z 139 " =    2.424
peak=   -3.166 closest distance to " O   HOH Z 177 " =    1.355
peak=   -3.164 closest distance to " OG  SER A   3 " =    1.014
peak=   -3.162 closest distance to " O   SER A  22 " =    1.264
peak=   -3.159 closest distance to " O   ALA A 226 " =    1.280
peak=   -3.156 closest distance to " O   HOH Z 438 " =    1.023
peak=   -3.154 closest distance to " O   HOH Z 275 " =    1.783
peak=   -3.150 closest distance to " O   ALA A   1 " =    1.214
peak=   -3.147 closest distance to " NH1BARG A 145 " =    5.018
peak=   -3.143 closest distance to " O   TYR A  30 " =    1.716
peak=   -3.141 closest distance to " O   HOH Z 140 " =    1.477
peak=   -3.141 closest distance to " SD  MET A 105 " =    2.482
peak=   -3.140 closest distance to " CG1BVAL A  72 " =    4.559
peak=   -3.140 closest distance to " CD  ARG A 219 " =    2.549
peak=   -3.136 closest distance to " O   HOH Z  43 " =    1.766
peak=   -3.133 closest distance to " O   HOH Z 292 " =    1.537
peak=   -3.127 closest distance to " CA  VAL A 296 " =    1.220
peak=   -3.126 closest distance to " CD1 LEU A   5 " =    2.537
peak=   -3.124 closest distance to " CD1 TRP A 274 " =    1.070
peak=   -3.122 closest distance to " CZ  ARG A  66 " =    0.819
peak=   -3.121 closest distance to " O   HOH Z 137 " =    1.326
peak=   -3.119 closest distance to " O  BHOH Z  74 " =    2.242
peak=   -3.118 closest distance to " CB  PHE A 130 " =    1.178
peak=   -3.118 closest distance to " O   HOH Z 209 " =    2.417
peak=   -3.118 closest distance to " O   HOH Z  47 " =    1.487
peak=   -3.117 closest distance to " OD2 ASP A 298 " =    1.224
peak=   -3.114 closest distance to " CZ  PHE A 130 " =    0.988
peak=   -3.110 closest distance to " O   MET A  47 " =    2.678
peak=   -3.105 closest distance to " OD2 ASP A  50 " =    1.379
peak=   -3.092 closest distance to " OD2 ASP A  27 " =    1.616
peak=   -3.091 closest distance to " CB  ALA A 291 " =    1.830
peak=   -3.085 closest distance to " O   SER A 216 " =    2.339
peak=   -3.084 closest distance to " C   ASN A 148 " =    1.990
peak=   -3.082 closest distance to " O   HOH Z 393 " =    3.296
peak=   -3.079 closest distance to " O   HOH Z  92 " =    2.071
peak=   -3.078 closest distance to " O   SER A  97 " =    1.428
peak=   -3.072 closest distance to " O   HOH Z  57 " =    0.987
peak=   -3.072 closest distance to " CG2 ILE A 120 " =    1.742
peak=   -3.059 closest distance to " CB  VAL A  72 " =    0.797
peak=   -3.044 closest distance to " CG1 VAL A 232 " =    2.032
peak=   -3.041 closest distance to " N   ASN A 127 " =    1.374
peak=   -3.023 closest distance to " O   HOH Z 156 " =    1.669

================= 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    :  0.5070 0.5031   6.306069e+00   6.298787e+00
   1_bss:  0.4981 0.4924   6.301809e+00   6.292220e+00
   1_xyz:  0.4418 0.4733   6.247991e+00   6.271751e+00
   1_adp:  0.4085 0.4701   6.214996e+00   6.270953e+00
   1_occ:  0.4086 0.4702   6.214531e+00   6.270866e+00
   2_bss:  0.4073 0.4659   6.214730e+00   6.269331e+00
   2_xyz:  0.3614 0.4314   6.127869e+00   6.227977e+00
   2_adp:  0.3499 0.4223   6.111931e+00   6.216472e+00
   2_occ:  0.3496 0.4222   6.111432e+00   6.216018e+00
   3_bss:  0.3499 0.4218   6.113431e+00   6.216422e+00
   3_xyz:  0.2818 0.3623   5.952201e+00   6.105475e+00
   3_adp:  0.2556 0.3393   5.879091e+00   6.056663e+00
   3_occ:  0.2550 0.3391   5.878236e+00   6.056103e+00
   4_bss:  0.2542 0.3364   5.875271e+00   6.052132e+00
   4_xyz:  0.2166 0.2850   5.724633e+00   5.915903e+00
   4_adp:  0.2006 0.2637   5.656049e+00   5.854734e+00
   4_occ:  0.2002 0.2626   5.654176e+00   5.852773e+00
   5_bss:  0.2000 0.2617   5.652732e+00   5.851001e+00
   5_xyz:  0.1567 0.2122   5.442879e+00   5.675680e+00
   5_adp:  0.1450 0.1993   5.374591e+00   5.609895e+00
   5_occ:  0.1448 0.1985   5.372243e+00   5.606317e+00
   5_bss:  0.1451 0.1980   5.370428e+00   5.603727e+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:  0.405  20.000   6.542   8.859   7.163   0.000   0.000   0.000
   1_xyz:  0.405  20.000   6.542   8.859   7.163   0.000   0.000   0.000
   1_adp:  0.405  20.000   6.542   8.859   7.163   0.000   0.000   0.000
   1_occ:  0.405  20.000   6.542   8.859   7.163   0.000   0.000   0.000
   2_bss:  0.381  50.000   3.456   4.959   4.210   0.000   0.000   0.000
   2_xyz:  0.381  50.000   3.456   4.959   4.210   0.000   0.000   0.000
   2_adp:  0.381  50.000   3.456   4.959   4.210   0.000   0.000   0.000
   2_occ:  0.381  50.000   3.456   4.959   4.210   0.000   0.000   0.000
   3_bss:  0.375  65.200   2.488   3.016   3.158   0.000   0.000   0.000
   3_xyz:  0.375  65.200   2.488   3.016   3.158   0.000   0.000   0.000
   3_adp:  0.375  65.200   2.488   3.016   3.158   0.000   0.000   0.000
   3_occ:  0.375  65.200   2.488   3.016   3.158   0.000   0.000   0.000
   4_bss:  0.363  65.200   1.467   1.279   2.119   0.000   0.000   0.000
   4_xyz:  0.363  65.200   1.467   1.279   2.119   0.000   0.000   0.000
   4_adp:  0.363  65.200   1.467   1.279   2.119   0.000   0.000   0.000
   4_occ:  0.363  65.200   1.467   1.279   2.119   0.000   0.000   0.000
   5_bss:  0.332  48.727   0.930   0.503   1.647   0.000   0.000   0.000
   5_xyz:  0.332  48.727   0.930   0.503   1.647   0.000   0.000   0.000
   5_adp:  0.332  48.727   0.930   0.503   1.647   0.000   0.000   0.000
   5_occ:  0.332  48.727   0.930   0.503   1.647   0.000   0.000   0.000
   5_bss:  0.318  43.543  -0.002  -0.666   0.668  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.022 0.3424  0.4191    84570.908
   1_bss:  63.761 0.3449  0.5227    82627.513
   1_xyz:  59.038 0.4052  0.6022    72720.248
   1_adp:  58.731 0.4088  0.6630    72487.439
   1_occ:  58.709 0.4093  0.6634    72697.494
   2_bss:  58.369 0.4134  0.6009    71848.730
   2_xyz:  51.254 0.5032  0.7270    57507.458
   2_adp:  48.979 0.5326  0.7865    54805.322
   2_occ:  48.941 0.5330  0.7868    54709.729
   3_bss:  48.882 0.5337  0.7522    54683.627
   3_xyz:  39.205 0.6516  0.9017    37423.971
   3_adp:  35.578 0.6947  0.9356    32211.165
   3_occ:  35.557 0.6949  0.9354    32119.783
   4_bss:  35.357 0.6970  0.8964    31686.959
   4_xyz:  28.948 0.7688  0.9550    21420.126
   4_adp:  26.109 0.8001  0.9679    18220.236
   4_occ:  26.031 0.8008  0.9680    18070.019
   5_bss:  25.992 0.8011  0.9467    17950.299
   5_xyz:  20.956 0.8520  0.9809    11965.229
   5_adp:  19.172 0.8698  0.9814    10578.003
   5_occ:  19.083 0.8706  0.9816    10482.591
   5_bss:  19.012 0.8710  0.9709    10360.476
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3038e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3038e+01
   1_xyz:   1.744  0.014  0.108 18.470  0.007  4.105   1.5271e-01
   1_adp:   1.744  0.014  0.108 18.470  0.007  4.105   1.5271e-01
   1_occ:   1.744  0.014  0.108 18.470  0.007  4.105   1.5271e-01
   2_bss:   1.744  0.014  0.108 18.470  0.007  4.105   1.5271e-01
   2_xyz:   1.128  0.008  0.077 16.228  0.005  4.119   8.7909e-02
   2_adp:   1.128  0.008  0.077 16.228  0.005  4.119   8.7909e-02
   2_occ:   1.128  0.008  0.077 16.228  0.005  4.119   8.7909e-02
   3_bss:   1.128  0.008  0.077 16.228  0.005  4.119   8.7909e-02
   3_xyz:   1.482  0.013  0.104 17.127  0.006  4.100   1.3053e-01
   3_adp:   1.482  0.013  0.104 17.127  0.006  4.100   1.3053e-01
   3_occ:   1.482  0.013  0.104 17.127  0.006  4.100   1.3053e-01
   4_bss:   1.482  0.013  0.104 17.127  0.006  4.100   1.3053e-01
   4_xyz:   0.953  0.007  0.066 15.719  0.004  4.113   6.2885e-02
   4_adp:   0.953  0.007  0.066 15.719  0.004  4.113   6.2885e-02
   4_occ:   0.953  0.007  0.066 15.719  0.004  4.113   6.2885e-02
   5_bss:   0.953  0.007  0.066 15.719  0.004  4.113   6.2885e-02
   5_xyz:   1.106  0.008  0.076 16.015  0.004  4.113   7.4349e-02
   5_adp:   1.106  0.008  0.076 16.015  0.004  4.113   7.4349e-02
   5_occ:   1.106  0.008  0.076 16.015  0.004  4.113   7.4349e-02
   5_bss:   1.106  0.008  0.076 16.015  0.004  4.113   7.4349e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8716e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8716e+00
   1_xyz:  13.507  0.194  0.445 85.908  0.050  2.144   1.0216e-01
   1_adp:  13.507  0.194  0.445 85.908  0.050  2.144   1.0216e-01
   1_occ:  13.507  0.194  0.445 85.908  0.050  2.144   1.0216e-01
   2_bss:  13.507  0.194  0.445 85.908  0.050  2.144   1.0216e-01
   2_xyz:   7.426  0.066  0.250 75.445  0.055  2.049   8.1761e-02
   2_adp:   7.426  0.066  0.250 75.445  0.055  2.049   8.1761e-02
   2_occ:   7.426  0.066  0.250 75.445  0.055  2.049   8.1761e-02
   3_bss:   7.426  0.066  0.250 75.445  0.055  2.049   8.1761e-02
   3_xyz:  11.308  0.106  0.352 73.945  0.047  2.092   1.0449e-01
   3_adp:  11.308  0.106  0.352 73.945  0.047  2.092   1.0449e-01
   3_occ:  11.308  0.106  0.352 73.945  0.047  2.092   1.0449e-01
   4_bss:  11.308  0.106  0.352 73.945  0.047  2.092   1.0449e-01
   4_xyz:   7.159  0.050  0.229 79.426  0.036  2.307   6.6567e-02
   4_adp:   7.159  0.050  0.229 79.426  0.036  2.307   6.6567e-02
   4_occ:   7.159  0.050  0.229 79.426  0.036  2.307   6.6567e-02
   5_bss:   7.159  0.050  0.229 79.426  0.036  2.307   6.6567e-02
   5_xyz:   7.723  0.059  0.240 82.474  0.039  2.238   7.8304e-02
   5_adp:   7.723  0.059  0.240 82.474  0.039  2.238   7.8304e-02
   5_occ:   7.723  0.059  0.240 82.474  0.039  2.238   7.8304e-02
   5_bss:   7.723  0.059  0.240 82.474  0.039  2.238   7.8304e-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:  97.24   0.00  15.72  87.06   0.00  14.57  97.24   0.00  21.97
   1_occ:  97.24   0.00  15.72  87.06   0.00  14.57  97.24   0.00  21.97
   2_bss:  97.24   0.00  15.72  87.06   0.00  14.57  97.24   0.00  21.97
   2_xyz:  97.24   0.00  15.72  87.06   0.00  14.57  97.24   0.00  21.97
   2_adp:  99.24   0.00  15.56  91.02   0.00  14.02  99.24   0.00  23.93
   2_occ:  99.24   0.00  15.56  91.02   0.00  14.02  99.24   0.00  23.93
   3_bss:  99.24   0.00  15.56  91.02   0.00  14.02  99.24   0.00  23.93
   3_xyz:  99.24   0.00  15.56  91.02   0.00  14.02  99.24   0.00  23.93
   3_adp: 106.77   0.00  15.58  95.32   0.00  12.42 106.77   0.00  32.82
   3_occ: 106.77   0.00  15.58  95.32   0.00  12.42 106.77   0.00  32.82
   4_bss: 106.77   0.00  15.58  95.32   0.00  12.42 106.77   0.00  32.82
   4_xyz: 106.77   0.00  15.58  95.32   0.00  12.42 106.77   0.00  32.82
   4_adp: 109.06   0.00  15.39  95.57   0.00  11.10 109.06   2.56  38.78
   4_occ: 109.06   0.00  15.39  95.57   0.00  11.10 109.06   2.56  38.78
   5_bss: 109.06   0.00  15.39  95.57   0.00  11.10 109.06   2.56  38.78
   5_xyz: 109.06   0.00  15.39  95.57   0.00  11.10 109.06   2.56  38.78
   5_adp: 109.67   0.00  15.10  97.87   0.00  10.33 109.67   3.82  41.07
   5_occ: 109.67   0.00  15.10  97.87   0.00  10.33 109.67   3.82  41.07
   5_bss: 110.40   0.73  15.82  98.60   0.73  11.05 110.40   4.54  41.80
------------------------------------------------------------------------
 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:    1.276    0.032    0.413
   1_adp:    1.276    0.032    0.413
   1_occ:    1.276    0.032    0.413
   2_bss:    1.276    0.032    0.413
   2_xyz:    1.622    0.017    0.554
   2_adp:    1.622    0.017    0.554
   2_occ:    1.622    0.017    0.554
   3_bss:    1.622    0.017    0.554
   3_xyz:    1.746    0.042    0.758
   3_adp:    1.746    0.042    0.758
   3_occ:    1.746    0.042    0.758
   4_bss:    1.746    0.042    0.758
   4_xyz:    2.167    0.031    0.826
   4_adp:    2.167    0.031    0.826
   4_occ:    2.167    0.031    0.826
   5_bss:    2.167    0.031    0.826
   5_xyz:    2.256    0.047    0.919
   5_adp:    2.256    0.047    0.919
   5_occ:    2.256    0.047    0.919
   5_bss:    2.256    0.047    0.919
------------------------------------------------------------------------

CPU time actual refinement: 347.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_849/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_849/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_849/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_849/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_849/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.44 
  Macro-tasks:
    bulk solvent and scale       = 41.31  
    individual site refinement   = 148.05 
    weights calculation          = 33.76  
    collect and process          = 6.25   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 229.50 
  Micro-tasks:
    mask                            = 3.19   
    f_calc                          = 110.33 
    alpha_beta                      = 8.01   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 119.28 
    fmodel                         = 6.96   
    r_factors                      = 0.29   
    phase_errors                   = 9.53   
    foms                           = 0.29   
    TOTAL for micro-tasks          = 259.00 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.950 micro seconds
Total CPU time: 6.03 minutes
from_scatterers_fft:    606 calls, 110.01 s
gradients_fft:          550 calls, 106.52 s

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

# Date 2008-01-16 Time 02:34:10 PST -0800 (1200479650.71 s)
Start R-work = 0.5070, R-free = 0.5031 (no bulk solvent and anisotropic scale)
Final R-work = 0.1598, R-free = 0.2113 (no bulk solvent and anisotropic scale)

Start R-work = 0.4981, R-free = 0.4924
Final R-work = 0.1451, R-free = 0.1980