# Date 2008-01-16 Time 00:27:21 PST -0800 (1200472041.63 s)
#phil __OFF__

Command line arguments: "../31.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9349
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 31

-------------------------------------------------------------------------------
  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: (68.4938, 46.2261, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8408 1.9509
Completeness in resolution range: 0.935482
Completeness with d_max=infinity: 0.932676

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8408
                             d_min =   1.9509

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: (68.4938, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8408 1.9509
Completeness in resolution range: 0.935482
Completeness with d_max=infinity: 0.932676

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8413 -  4.1748 [2201/2229]  1978   223  10.1%
  bin  2:  4.1748 -  3.3259 [2122/2138]  1909   213  10.0%
  bin  3:  3.3259 -  2.9091 [2089/2108]  1886   203   9.7%
  bin  4:  2.9091 -  2.6448 [2062/2092]  1848   214  10.4%
  bin  5:  2.6448 -  2.4561 [2041/2060]  1838   203   9.9%
  bin  6:  2.4561 -  2.3119 [2050/2075]  1846   204  10.0%
  bin  7:  2.3119 -  2.1965 [2022/2056]  1825   197   9.7%
  bin  8:  2.1965 -  2.1011 [2045/2076]  1838   207  10.1%
  bin  9:  2.1011 -  2.0205 [1978/2059]  1781   197  10.0%
  bin 10:  2.0205 -  1.9509 [ 979/2047]   881    98  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_31/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: 0.15 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:
        1.06 -     1.83: 12
        1.83 -     2.59: 103
        2.59 -     3.36: 4191
        3.36 -     4.13: 9557
        4.13 -     4.90: 14939
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.058 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.068 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.317 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.339 3.040 -x+1,y+1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.506 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28797 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_31/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_31/model_refine_001.geo

CPU time processing inputs: 11.28


============================ 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 = 68.49375 46.22605 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5137   r_free= 0.5092   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.306741                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8413 -  4.6565 0.99   1427  157 0.4246 0.4095      6.6398       6.626|
|  2:  4.6565 -  3.7151 0.99   1378  155 0.4399 0.4797      6.8283      6.9036|
|  3:  3.7151 -  3.2511 0.99   1346  149 0.4969 0.4454      6.7223      6.7137|
|  4:  3.2511 -  2.9564 0.99   1341  145 0.5168 0.5194      6.5632      6.5273|
|  5:  2.9564 -  2.7460 0.99   1329  152 0.5365 0.5379      6.3838      6.4536|
|  6:  2.7460 -  2.5850 0.99   1341  148 0.5535 0.5069      6.2978      6.2081|
|  7:  2.5850 -  2.4561 0.99   1297  150 0.5481 0.5351       6.255      6.1508|
|  8:  2.4561 -  2.3496 0.98   1323  146 0.5536 0.5710      6.1865      6.2221|
|  9:  2.3496 -  2.2595 0.98   1310  142 0.5455 0.5501      6.1328      6.2076|
| 10:  2.2595 -  2.1818 0.99   1323  142 0.5595 0.5561      6.1039      6.1089|
| 11:  2.1818 -  2.1138 0.99   1283  152 0.5496 0.5325      6.0227       6.042|
| 12:  2.1138 -  2.0535 0.97   1311  138 0.5421 0.5255      5.9709       5.989|
| 13:  2.0535 -  1.9996 0.88   1163  126 0.5501 0.5154       5.895      5.8382|
| 14:  1.9996 -  1.9509 0.36    458   57 0.5548 0.5989      5.9104      5.7653|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8413 -  4.6565  1427   157  0.65  38.92   0.78     0.70      90849.08|
|  2:  4.6565 -  3.7151  1378   155  0.62  41.77   0.86     0.70     139052.92|
|  3:  3.7151 -  3.2511  1346   149  0.48  53.42   0.82     0.61     149000.36|
|  4:  3.2511 -  2.9564  1341   145  0.35  63.14   0.76     0.45     135580.78|
|  5:  2.9564 -  2.7460  1329   152  0.24  71.89   0.72     0.31     105115.10|
|  6:  2.7460 -  2.5850  1341   148  0.18  76.38   0.69     0.22      90885.04|
|  7:  2.5850 -  2.4561  1297   150  0.15  78.96   0.72     0.18      79988.68|
|  8:  2.4561 -  2.3496  1323   146  0.15  78.67   0.71     0.19      72114.74|
|  9:  2.3496 -  2.2595  1310   142  0.16  77.94   0.72     0.20      66872.74|
| 10:  2.2595 -  2.1818  1323   142  0.19  75.62   0.73     0.24      56995.90|
| 11:  2.1818 -  2.1138  1283   152  0.18  76.70   0.73     0.25      56670.35|
| 12:  2.1138 -  2.0535  1311   138  0.19  75.74   0.75     0.26      49265.18|
| 13:  2.0535 -  1.9996  1163   126  0.20  75.00   0.72     0.28      43198.03|
| 14:  1.9996 -  1.9509   458    57  0.28  68.89   0.73     0.31      31362.49|
|alpha:            min =        0.18 max =            0.70 mean =         0.36|
|beta:             min =    31362.49 max =       149000.36 mean =     86741.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.29|
|phase err.(work): min =        0.00 max =           89.99 mean =        67.65|
|phase err.(test): min =        0.00 max =           89.97 mean =        68.01|
|-----------------------------------------------------------------------------|

============================== 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 = 27.277048             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.682   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.699025              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.734   (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 |  1.106 -  1.486:       10 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.486 -  1.865:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.865 -  2.244:      155 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.244 -  2.624:      623 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.624 -  3.003:     1445 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.003 -  3.383:     2588 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.383 -  3.762:     4017 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.762 -  4.141:     5187 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.141 -  4.521:     6781 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.521 -  4.900:     7988 |
|-----------------------------------------------------------------------------|
|-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 |       53.090 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.106 |       3.285 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    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 = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5189   r_free= 0.5106   ksol= 0.00   Bsol= 0.00   scale= 0.746    |
|                                                                             |
| 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:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.306887                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5055   r_free= 0.4977   ksol= 0.35   Bsol= 0.00   scale= 0.984    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.65,8.65,10.55,0.00,0.00,0.00); trace/3= 8.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.300523                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.726432             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.956   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.283901              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.106   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5055      final r-factor (work) = 0.4456          |
| start r-factor (free) = 0.4977      final r-factor (free) = 0.4681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 118.4036 = 20.73 * 0.50 * 6.3025 + 1.00 * 53.0896                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 64.9953 = 20.73 * 0.50 * 6.2562 + 1.00 * 0.1607                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4456      final r-factor (work) = 0.4058          |
| start r-factor (free) = 0.4681      final r-factor (free) = 0.4725          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.3030 = 2.28 * 1.00 * 6.2562 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.1947 = 2.28 * 1.00 * 6.2042 + 1.00 * 0.0249                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.71   17.16    None  None   None       |
|    all(noH): 2823   0      0.00    86.71   17.16    None  None   None       |
|    Sol.    : 438    0      0.00    86.71   24.89    None  None   None       |
|    Mac.    : 2385   0      0.00    69.45   15.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.671:  883   |   5:    43.353 -  52.024:   84        |
|      1:     8.671 -  17.341:  785   |   6:    52.024 -  60.695:   44        |
|      2:    17.341 -  26.012:  519   |   7:    60.695 -  69.365:   18        |
|      3:    26.012 -  34.683:  305   |   8:    69.365 -  78.036:    6        |
|      4:    34.683 -  43.353:  176   |   9:    78.036 -  86.707:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4058 r_free = 0.4725             target_work(ml) = 6.198         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4053 r_free = 0.4733             target_work(ml) = 6.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4053   r_free= 0.4733   ksol= 0.35   Bsol= 0.00   scale= 1.144    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.65,8.65,10.55,0.00,0.00,0.00); trace/3= 8.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.197487                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4022   r_free= 0.4727   ksol= 0.37   Bsol= 50.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.66,4.22,6.21,0.00,0.00,0.00); trace/3= 4.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.199427                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.685738             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.557  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.793570              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.771  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4022      final r-factor (work) = 0.3437          |
| start r-factor (free) = 0.4727      final r-factor (free) = 0.4174          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.3901 = 11.69 * 0.50 * 6.2006 + 1.00 * 0.1607                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.9905 = 11.69 * 0.50 * 6.1431 + 1.00 * 0.0974                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3437      final r-factor (work) = 0.3262          |
| start r-factor (free) = 0.4174      final r-factor (free) = 0.3955          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9001 = 0.79 * 1.00 * 6.1431 + 1.00 * 0.0251                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8544 = 0.79 * 1.00 * 6.0634 + 1.00 * 0.0427                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.05   16.12    None  None   None       |
|    all(noH): 2823   0      0.00    82.05   16.12    None  None   None       |
|    Sol.    : 438    0      0.00    82.05   29.40    None  None   None       |
|    Mac.    : 2385   0      0.00    65.10   13.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.206:  896   |   5:    41.027 -  49.233:   97        |
|      1:     8.206 -  16.411:  815   |   6:    49.233 -  57.438:   33        |
|      2:    16.411 -  24.616:  530   |   7:    57.438 -  65.644:   15        |
|      3:    24.616 -  32.822:  274   |   8:    65.644 -  73.849:    8        |
|      4:    32.822 -  41.027:  151   |   9:    73.849 -  82.054:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3262 r_free = 0.3955             target_work(ml) = 6.040         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3260 r_free = 0.3958             target_work(ml) = 6.040         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3260   r_free= 0.3958   ksol= 0.37   Bsol= 50.00   scale= 1.081   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.66,4.22,6.21,0.00,0.00,0.00); trace/3= 4.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.039889                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3246   r_free= 0.3940   ksol= 0.35   Bsol= 50.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,2.43,4.02,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.039327                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.103600              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.107  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.728945              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.177   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3246      final r-factor (work) = 0.2422          |
| start r-factor (free) = 0.3940      final r-factor (free) = 0.3051          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6913 = 9.10 * 0.50 * 6.0622 + 1.00 * 0.0974                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.1378 = 9.10 * 0.50 * 5.9396 + 1.00 * 0.1019                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2422      final r-factor (work) = 0.2099          |
| start r-factor (free) = 0.3051      final r-factor (free) = 0.2869          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2848 = 1.73 * 1.00 * 5.9396 + 1.00 * 0.0155                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9483 = 1.73 * 1.00 * 5.7435 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.74   16.88    None  None   None       |
|    all(noH): 2823   0      0.00    97.74   16.88    None  None   None       |
|    Sol.    : 438    0      0.00    97.74   41.90    None  None   None       |
|    Mac.    : 2385   0      0.00    84.31   12.29    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 -   9.774: 1291   |   5:    48.871 -  58.645:   94        |
|      1:     9.774 -  19.548:  759   |   6:    58.645 -  68.419:   65        |
|      2:    19.548 -  29.323:  284   |   7:    68.419 -  78.194:   30        |
|      3:    29.323 -  39.097:  167   |   8:    78.194 -  87.968:   12        |
|      4:    39.097 -  48.871:  118   |   9:    87.968 -  97.742:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2099 r_free = 0.2869             target_work(ml) = 5.708         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2096 r_free = 0.2868             target_work(ml) = 5.707         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2096   r_free= 0.2868   ksol= 0.35   Bsol= 50.00   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,2.43,4.02,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.707417                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2089   r_free= 0.2862   ksol= 0.33   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.17,1.07,2.68,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.704116                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.409098              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.807   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.199685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.407  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2089      final r-factor (work) = 0.1648          |
| start r-factor (free) = 0.2862      final r-factor (free) = 0.2287          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5215 = 6.41 * 0.50 * 5.7480 + 1.00 * 0.1017                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0991 = 6.41 * 0.50 * 5.6237 + 1.00 * 0.0778                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1648      final r-factor (work) = 0.1559          |
| start r-factor (free) = 0.2287      final r-factor (free) = 0.2114          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1409 = 0.20 * 1.00 * 5.6237 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1086 = 0.20 * 1.00 * 5.4705 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.23   16.33    None  None   None       |
|    all(noH): 2823   0      0.00    96.23   16.33    None  None   None       |
|    Sol.    : 438    0      2.22    96.23   41.37    None  None   None       |
|    Mac.    : 2385   0      0.00    84.78   11.73    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 -   9.623: 1352   |   5:    48.115 -  57.738:   96        |
|      1:     9.623 -  19.246:  779   |   6:    57.738 -  67.361:   57        |
|      2:    19.246 -  28.869:  216   |   7:    67.361 -  76.984:   32        |
|      3:    28.869 -  38.492:  155   |   8:    76.984 -  86.607:   11        |
|      4:    38.492 -  48.115:  122   |   9:    86.607 -  96.230:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1559 r_free = 0.2114             target_work(ml) = 5.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1555 r_free = 0.2107             target_work(ml) = 5.422         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1555   r_free= 0.2107   ksol= 0.33   Bsol= 50.00   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.17,1.07,2.68,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.421901                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1552   r_free= 0.2104   ksol= 0.32   Bsol= 45.13   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,0.18,2.01,0.00,0.00,0.00); trace/3= 0.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.421392                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.805688              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.914  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.372351              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.256   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1552      final r-factor (work) = 0.1374          |
| start r-factor (free) = 0.2104      final r-factor (free) = 0.1917          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4866 = 3.81 * 0.50 * 5.4701 + 1.00 * 0.0778                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2995 = 3.81 * 0.50 * 5.3754 + 1.00 * 0.0710                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1374      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1917      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0145 = 0.37 * 1.00 * 5.3754 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1275 = 0.37 * 1.00 * 5.3039 + 1.00 * 0.1525                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.54   15.84    None  None   None       |
|    all(noH): 2823   0      0.00    95.54   15.84    None  None   None       |
|    Sol.    : 438    0      3.33    95.54   41.25    None  None   None       |
|    Mac.    : 2385   0      0.00    94.08   11.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.554: 1426   |   5:    47.772 -  57.326:   96        |
|      1:     9.554 -  19.109:  739   |   6:    57.326 -  66.881:   58        |
|      2:    19.109 -  28.663:  200   |   7:    66.881 -  76.435:   31        |
|      3:    28.663 -  38.218:  146   |   8:    76.435 -  85.989:    8        |
|      4:    38.218 -  47.772:  114   |   9:    85.989 -  95.544:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1303 r_free = 0.1830             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1299 r_free = 0.1827             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1299   r_free= 0.1827   ksol= 0.32   Bsol= 45.13   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,0.18,2.01,0.00,0.00,0.00); trace/3= 0.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280053                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8413 -  4.6565 0.99   1427  157 0.1026 0.1413      5.4368      5.6384|
|  2:  4.6565 -  3.7151 0.99   1378  155 0.0951 0.1305      5.5506      5.7725|
|  3:  3.7151 -  3.2511 0.99   1346  149 0.1271 0.1818      5.6402      5.9946|
|  4:  3.2511 -  2.9564 0.99   1341  145 0.1465 0.1998      5.5963      5.7749|
|  5:  2.9564 -  2.7460 0.99   1329  152 0.1562 0.1767      5.4915      5.6187|
|  6:  2.7460 -  2.5850 0.99   1341  148 0.1506 0.2445      5.3564      5.6664|
|  7:  2.5850 -  2.4561 0.99   1297  150 0.1490 0.1879      5.3083      5.4408|
|  8:  2.4561 -  2.3496 0.98   1323  146 0.1408 0.2019      5.2071      5.4546|
|  9:  2.3496 -  2.2595 0.98   1310  142 0.1388 0.2023      5.1552      5.4272|
| 10:  2.2595 -  2.1818 0.99   1323  142 0.1286 0.1781      5.0709      5.2451|
| 11:  2.1818 -  2.1138 0.99   1283  152 0.1326 0.2331      5.0458      5.4739|
| 12:  2.1138 -  2.0535 0.97   1311  138 0.1324 0.1777      5.0053       5.233|
| 13:  2.0535 -  1.9996 0.88   1163  126 0.1194 0.1896      4.8634       5.042|
| 14:  1.9996 -  1.9509 0.36    458   57 0.1105 0.1879      4.7487      5.0414|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8413 -  4.6565  1427   157  0.93  10.58   0.98     0.96       8897.07|
|  2:  4.6565 -  3.7151  1378   155  0.94   9.96   1.03     1.02      11823.76|
|  3:  3.7151 -  3.2511  1346   149  0.91  14.50   1.05     1.05      14631.70|
|  4:  3.2511 -  2.9564  1341   145  0.89  16.81   1.03     1.02      13901.99|
|  5:  2.9564 -  2.7460  1329   152  0.87  19.52   1.01     0.98      12118.31|
|  6:  2.7460 -  2.5850  1341   148  0.87  19.74   0.99     0.95       9330.14|
|  7:  2.5850 -  2.4561  1297   150  0.87  19.48   1.01     0.97       8474.63|
|  8:  2.4561 -  2.3496  1323   146  0.88  18.32   1.02     0.99       7083.21|
|  9:  2.3496 -  2.2595  1310   142  0.88  18.68   1.01     0.96       6319.78|
| 10:  2.2595 -  2.1818  1323   142  0.88  18.17   1.02     0.98       5603.70|
| 11:  2.1818 -  2.1138  1283   152  0.87  19.61   1.03     0.99       5825.14|
| 12:  2.1138 -  2.0535  1311   138  0.87  19.17   1.03     1.01       5249.37|
| 13:  2.0535 -  1.9996  1163   126  0.89  18.04   1.01     0.96       3987.75|
| 14:  1.9996 -  1.9509   458    57  0.92  14.58   1.01     0.97       2878.75|
|alpha:            min =        0.95 max =            1.05 mean =         0.99|
|beta:             min =     2878.75 max =        14631.70 mean =      8639.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.97|
|phase err.(test): min =        0.00 max =           89.83 mean =        16.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1303   r_free= 0.1833   ksol= 0.32   Bsol= 45.38   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-0.41,1.57,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280917                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1303   r_free= 0.1833   ksol= 0.32   Bsol= 45.38   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-0.41,1.57,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280917                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8413 -  4.6565 0.99   1427  157 0.1027 0.1420       5.439      5.6367|
|  2:  4.6565 -  3.7151 0.99   1378  155 0.0957 0.1336      5.5581        5.79|
|  3:  3.7151 -  3.2511 0.99   1346  149 0.1285 0.1833       5.648      5.9935|
|  4:  3.2511 -  2.9564 0.99   1341  145 0.1469 0.2016      5.5993       5.779|
|  5:  2.9564 -  2.7460 0.99   1329  152 0.1564 0.1771      5.4927      5.6207|
|  6:  2.7460 -  2.5850 0.99   1341  148 0.1507 0.2435      5.3554      5.6624|
|  7:  2.5850 -  2.4561 0.99   1297  150 0.1489 0.1875      5.3064      5.4391|
|  8:  2.4561 -  2.3496 0.98   1323  146 0.1404 0.2007      5.2043      5.4521|
|  9:  2.3496 -  2.2595 0.98   1310  142 0.1387 0.2021      5.1533       5.426|
| 10:  2.2595 -  2.1818 0.99   1323  142 0.1285 0.1781      5.0699      5.2453|
| 11:  2.1818 -  2.1138 0.99   1283  152 0.1326 0.2335      5.0454      5.4735|
| 12:  2.1138 -  2.0535 0.97   1311  138 0.1322 0.1771      5.0049      5.2331|
| 13:  2.0535 -  1.9996 0.88   1163  126 0.1194 0.1890      4.8622        5.04|
| 14:  1.9996 -  1.9509 0.36    458   57 0.1106 0.1883      4.7476      5.0437|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8413 -  4.6565  1427   157  0.93  10.62   0.97     0.95       9014.99|
|  2:  4.6565 -  3.7151  1378   155  0.94  10.12   1.03     1.01      12040.00|
|  3:  3.7151 -  3.2511  1346   149  0.91  14.67   1.05     1.04      14881.35|
|  4:  3.2511 -  2.9564  1341   145  0.89  16.94   1.02     1.01      14017.58|
|  5:  2.9564 -  2.7460  1329   152  0.87  19.55   1.01     0.97      12150.88|
|  6:  2.7460 -  2.5850  1341   148  0.87  19.70   0.98     0.94       9310.95|
|  7:  2.5850 -  2.4561  1297   150  0.87  19.42   1.00     0.96       8430.09|
|  8:  2.4561 -  2.3496  1323   146  0.88  18.25   1.01     0.97       7036.85|
|  9:  2.3496 -  2.2595  1310   142  0.88  18.62   1.00     0.95       6293.25|
| 10:  2.2595 -  2.1818  1323   142  0.88  18.16   1.01     0.96       5594.14|
| 11:  2.1818 -  2.1138  1283   152  0.87  19.60   1.01     0.98       5822.22|
| 12:  2.1138 -  2.0535  1311   138  0.87  19.17   1.01     1.00       5248.96|
| 13:  2.0535 -  1.9996  1163   126  0.89  18.02   0.99     0.95       3980.96|
| 14:  1.9996 -  1.9509   458    57  0.92  14.57   0.99     0.96       2872.87|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     2872.87 max =        14881.35 mean =      8684.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.67 mean =        16.99|
|phase err.(test): min =        0.00 max =           89.63 mean =        16.28|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.25    95.80   16.09    None  None   None       |
|    all(noH): 2823   0      0.25    95.80   16.09    None  None   None       |
|    Sol.    : 438    0      3.59    95.80   41.50    None  None   None       |
|    Mac.    : 2385   0      0.25    94.34   11.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.254 -   9.809: 1426   |   5:    48.026 -  57.581:   96        |
|      1:     9.809 -  19.363:  739   |   6:    57.581 -  67.135:   58        |
|      2:    19.363 -  28.917:  200   |   7:    67.135 -  76.689:   31        |
|      3:    28.917 -  38.472:  146   |   8:    76.689 -  86.244:    8        |
|      4:    38.472 -  48.026:  114   |   9:    86.244 -  95.798:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.116 - 4.177
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 314
   mapped sites are within: 0.715 - 4.177

peak=   10.118 closest distance to " CB  VAL A 230 " =    1.508
peak=    9.814 closest distance to " O   HOH Z 203 " =    0.715
peak=    8.931 closest distance to " CB  VAL A 296 " =    1.575
peak=    7.648 closest distance to " O   HOH Z 103 " =    1.010
peak=    7.486 closest distance to " O   HOH Z 130 " =    2.039
peak=    7.027 closest distance to " O   HOH Z 255 " =    0.997
peak=    6.640 closest distance to " O   HOH Z 178 " =    1.086
peak=    6.090 closest distance to " O   HOH Z 375 " =    1.775
peak=    6.055 closest distance to " O  BHOH Z  74 " =    0.928
peak=    5.927 closest distance to " CD2 LEU A   5 " =    1.348
peak=    5.544 closest distance to " CG  PRO A  54 " =    1.367
peak=    5.515 closest distance to " O   HOH Z  65 " =    1.340
peak=    5.458 closest distance to " CB  ARG A 275 " =    1.093
peak=    5.457 closest distance to " O   HOH Z 182 " =    1.306
peak=    5.299 closest distance to " CD1AILE A 234 " =    0.966
peak=    5.268 closest distance to " O   HOH Z 236 " =    1.757
peak=    5.201 closest distance to " O   HOH Z 188 " =    1.650
peak=    5.186 closest distance to " O   HOH Z  49 " =    1.475
peak=    5.139 closest distance to " O   HOH Z 107 " =    0.941
peak=    5.007 closest distance to " O   HOH Z 258 " =    1.156
peak=    4.984 closest distance to " CB  VAL A 230 " =    1.255
peak=    4.954 closest distance to " O   HOH Z  11 " =    1.490
peak=    4.948 closest distance to " O   HOH Z 422 " =    0.948
peak=    4.916 closest distance to " O   HOH Z   9 " =    2.047
peak=    4.839 closest distance to " CB  GLN A 223 " =    1.512
peak=    4.814 closest distance to " CB  ASN A 142 " =    1.110
peak=    4.792 closest distance to " NE2 GLN A  11 " =    1.103
peak=    4.782 closest distance to " O   HOH Z 142 " =    1.752
peak=    4.711 closest distance to " O   HOH Z 403 " =    1.909
peak=    4.700 closest distance to " O   HOH Z 417 " =    1.889
peak=    4.675 closest distance to " O   HOH Z 193 " =    1.874
peak=    4.651 closest distance to " CG2 ILE A 234 " =    0.994
peak=    4.642 closest distance to " NH2 ARG A  56 " =    2.088
peak=    4.634 closest distance to " CB  PRO A  54 " =    1.027
peak=    4.587 closest distance to " O   HOH Z 147 " =    1.150
peak=    4.542 closest distance to " O   HOH Z  39 " =    1.392
peak=    4.535 closest distance to " O   HOH Z 369 " =    2.246
peak=    4.512 closest distance to " O   HOH Z  69 " =    1.257
peak=    4.492 closest distance to " O   HOH Z 249 " =    1.312
peak=    4.488 closest distance to " O   HOH Z 222 " =    1.358
peak=    4.461 closest distance to " O   HOH Z  43 " =    1.520
peak=    4.458 closest distance to " CG AARG A 275 " =    1.265
peak=    4.457 closest distance to " O   HOH Z 406 " =    1.600
peak=    4.438 closest distance to " O   HOH Z 248 " =    1.166
peak=    4.380 closest distance to " O   HOH Z 427 " =    2.841
peak=    4.376 closest distance to " O   HOH Z 116 " =    1.192
peak=    4.369 closest distance to " CG  LEU A   5 " =    1.201
peak=    4.353 closest distance to " O   HOH Z 123 " =    1.585
peak=    4.340 closest distance to " O   HOH Z 373 " =    2.187
peak=    4.316 closest distance to " O   HOH Z 126 " =    1.888
peak=    4.315 closest distance to " O   HOH Z 143 " =    1.824
peak=    4.279 closest distance to " CG2 ILE A 120 " =    0.867
peak=    4.269 closest distance to " CB  VAL A 265 " =    1.544
peak=    4.233 closest distance to " O   HOH Z 238 " =    1.466
peak=    4.229 closest distance to " O   HOH Z 124 " =    1.388
peak=    4.211 closest distance to " O   HOH Z 232 " =    2.220
peak=    4.207 closest distance to " O   HOH Z 425 " =    1.995
peak=    4.203 closest distance to " O   HOH Z  61 " =    1.813
peak=    4.193 closest distance to " NH2AARG A 145 " =    1.072
peak=    4.175 closest distance to " CG  LYS A  76 " =    1.540
peak=    4.175 closest distance to " O   HOH Z  83 " =    0.971
peak=    4.158 closest distance to " O   HOH Z 287 " =    1.705
peak=    4.147 closest distance to " O   HOH Z  24 " =    1.714
peak=    4.144 closest distance to " O   HOH Z 344 " =    1.361
peak=    4.138 closest distance to " O   HOH Z 368 " =    2.060
peak=    4.138 closest distance to " O   HOH Z 272 " =    1.721
peak=    4.136 closest distance to " NZ  LYS A 117 " =    2.751
peak=    4.129 closest distance to " CA  PHE A 283 " =    1.113
peak=    4.087 closest distance to " O   HOH Z 298 " =    1.660
peak=    4.085 closest distance to " O   HOH Z  40 " =    1.534
peak=    4.077 closest distance to " CB  ASN A 148 " =    1.284
peak=    4.072 closest distance to " O   HOH Z 385 " =    1.093
peak=    4.047 closest distance to " O   HOH Z  68 " =    2.066
peak=    4.027 closest distance to " O   HOH Z   7 " =    1.212
peak=    3.994 closest distance to " O   HOH Z  26 " =    1.644
peak=    3.992 closest distance to " O   HOH Z 380 " =    2.151
peak=    3.990 closest distance to " CB  LYS A 117 " =    1.041
peak=    3.981 closest distance to " O   HOH Z  69 " =    1.614
peak=    3.978 closest distance to " O   SER A  87 " =    2.506
peak=    3.973 closest distance to " CB  GLN A 183 " =    1.257
peak=    3.965 closest distance to " CB  GLN A 278 " =    0.847
peak=    3.963 closest distance to " O   HOH Z 132 " =    0.983
peak=    3.963 closest distance to " O   HOH Z 211 " =    1.301
peak=    3.960 closest distance to " O   HOH Z  44 " =    2.073
peak=    3.951 closest distance to " O   HOH Z 423 " =    1.486
peak=    3.946 closest distance to " O   HOH Z  85 " =    1.429
peak=    3.945 closest distance to " O   HOH Z 425 " =    1.441
peak=    3.943 closest distance to " O   HOH Z 389 " =    1.766
peak=    3.929 closest distance to " O   HOH Z 371 " =    1.949
peak=    3.923 closest distance to " CG  LEU A 228 " =    1.378
peak=    3.922 closest distance to " CB  GLU A 277 " =    3.483
peak=    3.919 closest distance to " CB  ALA A 114 " =    1.050
peak=    3.918 closest distance to " O   PRO A 198 " =    1.638
peak=    3.917 closest distance to " O   HOH Z 112 " =    1.150
peak=    3.909 closest distance to " O   HOH Z 346 " =    1.588
peak=    3.908 closest distance to " CB  SER A 276 " =    1.085
peak=    3.907 closest distance to " NE1 TRP A 274 " =    0.911
peak=    3.896 closest distance to " NZ  LYS A 117 " =    1.414
peak=    3.889 closest distance to " O   HOH Z 170 " =    2.150
peak=    3.883 closest distance to " CG2 VAL A 257 " =    0.933
peak=    3.863 closest distance to " O   HOH Z 246 " =    1.024
peak=    3.851 closest distance to " CG  GLN A  58 " =    1.199
peak=    3.846 closest distance to " O   HOH Z 331 " =    0.970
peak=    3.844 closest distance to " O   HOH Z  78 " =    1.684
peak=    3.832 closest distance to " O   HOH Z 350 " =    1.417
peak=    3.824 closest distance to " O   HOH Z 213 " =    1.840
peak=    3.822 closest distance to " O   HOH Z  33 " =    1.733
peak=    3.818 closest distance to " OG  SER A  62 " =    2.815
peak=    3.808 closest distance to " O   HOH Z 303 " =    2.137
peak=    3.808 closest distance to " CG  PRO A 243 " =    1.003
peak=    3.801 closest distance to " O   HOH Z 392 " =    0.888
peak=    3.799 closest distance to " CB  SER A  63 " =    1.246
peak=    3.777 closest distance to " CA  ALA A  51 " =    0.994
peak=    3.767 closest distance to " O   HOH Z  51 " =    1.499
peak=    3.765 closest distance to " CZ  PHE A  38 " =    1.118
peak=    3.758 closest distance to " O   HOH Z 414 " =    0.930
peak=    3.755 closest distance to " CB  ARG A 219 " =    1.011
peak=    3.726 closest distance to " O   HOH Z 402 " =    1.317
peak=    3.714 closest distance to " O   HOH Z 234 " =    3.484
peak=    3.714 closest distance to " O   ARG A 275 " =    1.546
peak=    3.709 closest distance to " CD1 ILE A 199 " =    1.465
peak=    3.699 closest distance to " O   HOH Z 218 " =    2.135
peak=    3.698 closest distance to " O   HOH Z  10 " =    1.748
peak=    3.698 closest distance to " CB  SER A  99 " =    0.772
peak=    3.697 closest distance to " O   HOH Z 152 " =    1.792
peak=    3.697 closest distance to " O   HOH Z 362 " =    2.203
peak=    3.693 closest distance to " NH2AARG A 190 " =    1.921
peak=    3.692 closest distance to " CB  VAL A 202 " =    1.566
peak=    3.671 closest distance to " CE AMET A  47 " =    1.278
peak=    3.670 closest distance to " O   HOH Z 361 " =    3.663
peak=    3.668 closest distance to " CA  ILE A 234 " =    1.110
peak=    3.668 closest distance to " O   HOH Z 423 " =    1.542
peak=    3.666 closest distance to " CB  GLU A 152 " =    1.430
peak=    3.661 closest distance to " O   HOH Z 128 " =    1.839
peak=    3.651 closest distance to " O   HOH Z 418 " =    1.172
peak=    3.649 closest distance to " NE AARG A 145 " =    0.825
peak=    3.645 closest distance to " CD2 TYR A 186 " =    1.065
peak=    3.645 closest distance to " O   HOH Z 223 " =    1.172
peak=    3.640 closest distance to " N   ASP A 162 " =    1.179
peak=    3.630 closest distance to " CA  GLN A  58 " =    0.732
peak=    3.629 closest distance to " CB  ARG A  79 " =    0.997
peak=    3.628 closest distance to " O   HOH Z   1 " =    1.705
peak=    3.623 closest distance to " O   HOH Z 422 " =    2.158
peak=    3.621 closest distance to " O   HOH Z   1 " =    1.722
peak=    3.617 closest distance to " CG1 ILE A 120 " =    1.405
peak=    3.615 closest distance to " O   HOH Z  76 " =    1.172
peak=    3.612 closest distance to " O   HOH Z 407 " =    1.411
peak=    3.602 closest distance to " O   HOH Z  59 " =    1.678
peak=    3.600 closest distance to " O   HOH Z 295 " =    1.222
peak=    3.593 closest distance to " CG  LYS A 119 " =    1.012
peak=    3.592 closest distance to " CB  THR A  31 " =    1.693
peak=    3.588 closest distance to " CA  ALA A 291 " =    0.822
peak=    3.587 closest distance to " CG  PRO A 213 " =    1.195
peak=    3.584 closest distance to " O   HOH Z 357 " =    1.890
peak=    3.584 closest distance to " O   HOH Z 132 " =    2.435
peak=    3.580 closest distance to " CB  SER A   3 " =    1.226
peak=    3.579 closest distance to " CB  ASN A 110 " =    1.143
peak=    3.568 closest distance to " O   HOH Z 117 " =    1.807
peak=    3.565 closest distance to " CB  SER A  26 " =    1.856
peak=    3.557 closest distance to " O   HOH Z 405 " =    1.665
peak=    3.553 closest distance to " O   HOH Z 177 " =    1.118
peak=    3.524 closest distance to " OG1 THR A 220 " =    1.981
peak=    3.519 closest distance to " CA  ARG A 195 " =    1.242
peak=    3.517 closest distance to " ND2BASN A 224 " =    0.830
peak=    3.516 closest distance to " CA  VAL A 125 " =    1.016
peak=    3.515 closest distance to " O   HOH Z 158 " =    1.009
peak=    3.510 closest distance to " CA  ASN A 127 " =    1.035
peak=    3.509 closest distance to " O   HOH Z 398 " =    1.352
peak=    3.507 closest distance to " CG  GLN A  89 " =    1.302
peak=    3.504 closest distance to " CH2 TRP A 266 " =    1.080
peak=    3.503 closest distance to " CB  PHE A 130 " =    0.901
peak=    3.503 closest distance to " O   HOH Z 130 " =    2.071
peak=    3.501 closest distance to " O   THR A 220 " =    1.279
peak=    3.499 closest distance to " O   HOH Z 365 " =    2.735
peak=    3.476 closest distance to " O   HOH Z 261 " =    2.019
peak=    3.466 closest distance to " CG  PRO A 198 " =    1.329
peak=    3.463 closest distance to " NH1BARG A 145 " =    1.859
peak=    3.453 closest distance to " CE  LYS A 119 " =    1.335
peak=    3.449 closest distance to " O   HOH Z 358 " =    1.226
peak=    3.441 closest distance to " CE3 TRP A 150 " =    1.182
peak=    3.435 closest distance to " CD2 LEU A 143 " =    1.236
peak=    3.431 closest distance to " O   HOH Z 323 " =    1.521
peak=    3.427 closest distance to " CG  LEU A 167 " =    1.256
peak=    3.418 closest distance to " O   HOH Z  70 " =    0.839
peak=    3.414 closest distance to " N   ARG A 156 " =    1.388
peak=    3.413 closest distance to " CB  ALA A 160 " =    1.396
peak=    3.410 closest distance to " O   HOH Z  80 " =    1.534
peak=    3.410 closest distance to " CB  ASP A 107 " =    1.223
peak=    3.406 closest distance to " CA  GLY A 241 " =    3.996
peak=    3.400 closest distance to " N   PHE A 130 " =    1.446
peak=    3.394 closest distance to " NH1BARG A 102 " =    0.928
peak=    3.391 closest distance to " CB  ALA A   1 " =    0.958
peak=    3.388 closest distance to " O   HOH Z 214 " =    2.724
peak=    3.386 closest distance to " O   THR A 182 " =    1.513
peak=    3.386 closest distance to " NH2AARG A 190 " =    1.857
peak=    3.383 closest distance to " CB  SER A  62 " =    0.745
peak=    3.380 closest distance to " CB  ALA A 248 " =    1.425
peak=    3.379 closest distance to " CA  TYR A  30 " =    0.968
peak=    3.373 closest distance to " OG ASER A 258 " =    3.032
peak=    3.368 closest distance to " O   HOH Z  97 " =    1.477
peak=    3.366 closest distance to " CA  ALA A 129 " =    1.510
peak=    3.366 closest distance to " O   HOH Z 427 " =    1.357
peak=    3.358 closest distance to " CB  ARG A 275 " =    0.749
peak=    3.358 closest distance to " CD  ARG A 269 " =    0.865
peak=    3.350 closest distance to " O   HOH Z 337 " =    1.762
peak=    3.348 closest distance to " CD2 TRP A 179 " =    1.343
peak=    3.348 closest distance to " O   HOH Z 153 " =    3.436
peak=    3.348 closest distance to " O   HOH Z 305 " =    3.361
peak=    3.346 closest distance to " O   HOH Z 141 " =    1.454
peak=    3.343 closest distance to " CB  PRO A  90 " =    1.136
peak=    3.335 closest distance to " O   HOH Z 158 " =    2.813
peak=    3.333 closest distance to " CE  LYS A  48 " =    1.237
peak=    3.330 closest distance to " O   HOH Z  55 " =    1.663
peak=    3.324 closest distance to " CB  ARG A 156 " =    1.291
peak=    3.323 closest distance to " O   HOH Z 409 " =    1.610
peak=    3.317 closest distance to " O   HOH Z  51 " =    1.714
peak=    3.308 closest distance to " O   HOH Z 148 " =    2.196
peak=    3.301 closest distance to " O   HOH Z 263 " =    1.497
peak=    3.300 closest distance to " O   HOH Z  50 " =    1.574
peak=    3.296 closest distance to " O   HOH Z 410 " =    1.218
peak=    3.294 closest distance to " CZ  PHE A 218 " =    1.120
peak=    3.294 closest distance to " CD1 LEU A  96 " =    0.731
peak=    3.291 closest distance to " O   HOH Z 188 " =    2.436
peak=    3.287 closest distance to " O   HOH Z 272 " =    2.208
peak=    3.285 closest distance to " O   HOH Z 104 " =    1.935
peak=    3.272 closest distance to " CE  MET A 185 " =    2.083
peak=    3.271 closest distance to " O   HOH Z 174 " =    2.181
peak=    3.269 closest distance to " CB  GLU A 175 " =    0.751
peak=    3.266 closest distance to " CB  GLN A  88 " =    1.365
peak=    3.265 closest distance to " CB  LEU A 300 " =    1.011
peak=    3.263 closest distance to " O   HOH Z 227 " =    1.967
peak=    3.261 closest distance to " CB  TYR A  30 " =    1.507
peak=    3.255 closest distance to " O   HOH Z  98 " =    1.740
peak=    3.246 closest distance to " O   HOH Z 162 " =    1.644
peak=    3.244 closest distance to " CB  GLN A  55 " =    0.944
peak=    3.234 closest distance to " O   HOH Z 244 " =    1.843
peak=    3.232 closest distance to " O   HOH Z  33 " =    1.836
peak=    3.230 closest distance to " O   HOH Z 156 " =    3.101
peak=    3.230 closest distance to " N   ASN A 148 " =    1.049
peak=    3.227 closest distance to " O   HOH Z 218 " =    2.401
peak=    3.225 closest distance to " O   HOH Z 287 " =    1.830
peak=    3.216 closest distance to " CB  ALA A  43 " =    1.057
peak=    3.214 closest distance to " O   HOH Z 252 " =    2.291
peak=    3.213 closest distance to " N   ALA A   1 " =    1.407
peak=    3.213 closest distance to " CD  LYS A 119 " =    2.072
peak=    3.210 closest distance to " CB  ASP A 191 " =    1.318
peak=    3.208 closest distance to " O   HOH Z 284 " =    2.858
peak=    3.207 closest distance to " NH1AARG A 145 " =    0.972
peak=    3.201 closest distance to " OG BSER A 258 " =    2.924
peak=    3.200 closest distance to " O   HOH Z 176 " =    1.539
peak=    3.199 closest distance to " CB  ASP A 124 " =    0.810
peak=    3.198 closest distance to " CG AARG A 102 " =    0.895
peak=    3.197 closest distance to " O   GLY A 147 " =    1.314
peak=    3.197 closest distance to " CG BARG A 102 " =    1.972
peak=    3.193 closest distance to " O   HOH Z 145 " =    1.844
peak=    3.193 closest distance to " O   HOH Z 251 " =    1.410
peak=    3.193 closest distance to " O   HOH Z 298 " =    4.177
peak=    3.192 closest distance to " O   HOH Z  61 " =    1.446
peak=    3.190 closest distance to " O   HOH Z  41 " =    2.443
peak=    3.189 closest distance to " O   HOH Z 389 " =    2.743
peak=    3.187 closest distance to " NH1 ARG A 138 " =    1.070
peak=    3.187 closest distance to " O   LYS A 119 " =    1.807
peak=    3.184 closest distance to " OG  SER A  22 " =    2.617
peak=    3.181 closest distance to " CB  HIS A 108 " =    0.862
peak=    3.179 closest distance to " CE  MET A  93 " =    1.390
peak=    3.177 closest distance to " O   HOH Z 216 " =    3.386
peak=    3.175 closest distance to " O   HOH Z 287 " =    1.246
peak=    3.171 closest distance to " ND1 HIS A  81 " =    1.405
peak=    3.170 closest distance to " CD2 LEU A 297 " =    1.177
peak=    3.170 closest distance to " O   HOH Z 325 " =    2.063
peak=    3.169 closest distance to " OD1 ASN A  60 " =    2.127
peak=    3.168 closest distance to " CA  LYS A 117 " =    1.132
peak=    3.166 closest distance to " CE AMET A  47 " =    1.423
peak=    3.166 closest distance to " O   HOH Z 146 " =    1.506
peak=    3.164 closest distance to " O   HOH Z 191 " =    3.084
peak=    3.164 closest distance to " NE2 HIS A  86 " =    1.860
peak=    3.163 closest distance to " CG2 ILE A 106 " =    0.900
peak=    3.156 closest distance to " NH2BARG A 190 " =    1.496
peak=    3.156 closest distance to " CA  ALA A 233 " =    0.977
peak=    3.153 closest distance to " O   HOH Z 260 " =    2.451
peak=    3.149 closest distance to " O   HOH Z 265 " =    1.566
peak=    3.144 closest distance to " O   HOH Z 193 " =    1.454
peak=    3.141 closest distance to " O   HOH Z 194 " =    2.144
peak=    3.123 closest distance to " O   HOH Z 303 " =    2.111
peak=    3.115 closest distance to " O   HOH Z 117 " =    1.382
peak=    3.110 closest distance to " CB  ALA A  10 " =    0.933
peak=    3.107 closest distance to " CD1 LEU A   5 " =    1.628
peak=    3.087 closest distance to " CG2 THR A 246 " =    1.196
peak=    3.079 closest distance to " CG2 VAL A 232 " =    1.034
peak=    3.074 closest distance to " O   HOH Z 328 " =    1.671
peak=    3.072 closest distance to " CZ3 TRP A 177 " =    1.139
peak=    3.068 closest distance to " N   ILE A 109 " =    1.126
peak=    3.064 closest distance to " O   HOH Z 215 " =    1.368
peak=    3.064 closest distance to " CB  PHE A  16 " =    1.007
peak=    3.059 closest distance to " O   HOH Z 189 " =    2.916
peak=    3.056 closest distance to " O   GLY A  75 " =    1.502
peak=    3.056 closest distance to " CG2 ILE A  20 " =    1.885

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.491 - 5.316
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 185 from: 192
   mapped sites are within: 0.728 - 5.316

peak=   -5.247 closest distance to " O   HOH Z 211 " =    0.867
peak=   -4.827 closest distance to " O   HOH Z 203 " =    1.431
peak=   -4.502 closest distance to " O   HOH Z  69 " =    1.585
peak=   -4.398 closest distance to " O   PRO A 198 " =    1.182
peak=   -4.338 closest distance to " CB  ALA A  43 " =    2.375
peak=   -4.224 closest distance to " O   HOH Z 147 " =    2.028
peak=   -4.224 closest distance to " CD1 LEU A 255 " =    2.943
peak=   -4.160 closest distance to " CG2 ILE A  20 " =    2.867
peak=   -4.120 closest distance to " C   HIS A 108 " =    1.159
peak=   -4.116 closest distance to " CB  GLN A  55 " =    1.478
peak=   -4.068 closest distance to " O   HOH Z 100 " =    0.823
peak=   -3.997 closest distance to " O   HOH Z 177 " =    1.282
peak=   -3.994 closest distance to " O   HOH Z 147 " =    1.068
peak=   -3.982 closest distance to " OG  SER A  97 " =    2.182
peak=   -3.972 closest distance to " O   HOH Z 134 " =    4.279
peak=   -3.961 closest distance to " SG  CYS A 254 " =    3.271
peak=   -3.915 closest distance to " CG  GLN A  58 " =    0.937
peak=   -3.902 closest distance to " O   SER A 135 " =    1.679
peak=   -3.859 closest distance to " OD2 ASP A  50 " =    1.562
peak=   -3.795 closest distance to " CD2 TYR A 293 " =    1.855
peak=   -3.793 closest distance to " O   HOH Z 394 " =    1.674
peak=   -3.782 closest distance to " OG  SER A  87 " =    1.476
peak=   -3.777 closest distance to " O   HOH Z 166 " =    2.184
peak=   -3.738 closest distance to " CE2 TYR A  30 " =    2.703
peak=   -3.726 closest distance to " O   ALA A 227 " =    1.418
peak=   -3.716 closest distance to " O   SER A 276 " =    1.528
peak=   -3.715 closest distance to " O   HOH Z 359 " =    3.369
peak=   -3.711 closest distance to " O   SER A  22 " =    2.434
peak=   -3.711 closest distance to " O   VAL A  67 " =    2.530
peak=   -3.707 closest distance to " CG2 THR A  18 " =    2.782
peak=   -3.699 closest distance to " O   HOH Z 286 " =    1.611
peak=   -3.693 closest distance to " O   HOH Z 183 " =    1.729
peak=   -3.688 closest distance to " N   ALA A 244 " =    1.180
peak=   -3.683 closest distance to " CB  ASN A  45 " =    1.961
peak=   -3.661 closest distance to " CD  PRO A 243 " =    1.868
peak=   -3.661 closest distance to " O   HOH Z 131 " =    4.237
peak=   -3.639 closest distance to " OG  SER A  63 " =    1.176
peak=   -3.623 closest distance to " CD2 LEU A 237 " =    2.484
peak=   -3.621 closest distance to " O   LEU A 297 " =    0.728
peak=   -3.618 closest distance to " O   GLN A  58 " =    1.366
peak=   -3.586 closest distance to " O   LYS A  76 " =    1.752
peak=   -3.585 closest distance to " CZ2 TRP A  92 " =    2.734
peak=   -3.580 closest distance to " CA  GLY A 203 " =    2.354
peak=   -3.569 closest distance to " O   HOH Z  64 " =    2.783
peak=   -3.568 closest distance to " CG2 VAL A 296 " =    2.193
peak=   -3.557 closest distance to " O   HOH Z 185 " =    1.766
peak=   -3.557 closest distance to " NZ  LYS A 119 " =    0.886
peak=   -3.552 closest distance to " NE2 GLN A 223 " =    1.726
peak=   -3.551 closest distance to " O   HOH Z 255 " =    1.850
peak=   -3.551 closest distance to " OE1 GLU A 277 " =    2.211
peak=   -3.549 closest distance to " O   SER A 273 " =    1.575
peak=   -3.534 closest distance to " O   HOH Z 174 " =    2.526
peak=   -3.525 closest distance to " O   VAL A 125 " =    2.353
peak=   -3.525 closest distance to " O   HOH Z 116 " =    1.685
peak=   -3.524 closest distance to " O   HOH Z  56 " =    2.290
peak=   -3.519 closest distance to " O   HOH Z 281 " =    2.854
peak=   -3.498 closest distance to " O   HOH Z 109 " =    0.843
peak=   -3.484 closest distance to " CD  GLN A 278 " =    1.796
peak=   -3.478 closest distance to " O   HOH Z  40 " =    1.273
peak=   -3.472 closest distance to " O   HOH Z 276 " =    1.418
peak=   -3.467 closest distance to " O   HOH Z 405 " =    1.690
peak=   -3.467 closest distance to " OE2 GLU A 152 " =    1.360
peak=   -3.461 closest distance to " O   HOH Z  64 " =    1.321
peak=   -3.457 closest distance to " O   HOH Z 179 " =    1.837
peak=   -3.456 closest distance to " O   HOH Z 266 " =    5.316
peak=   -3.447 closest distance to " O   VAL A 189 " =    2.468
peak=   -3.442 closest distance to " CG BARG A 275 " =    0.925
peak=   -3.436 closest distance to " CD1 ILE A 263 " =    2.574
peak=   -3.410 closest distance to " O   HOH Z 140 " =    0.822
peak=   -3.406 closest distance to " O   HOH Z 407 " =    2.028
peak=   -3.397 closest distance to " N   ALA A 248 " =    1.616
peak=   -3.390 closest distance to " NE1 TRP A  70 " =    1.621
peak=   -3.387 closest distance to " O   HOH Z 246 " =    1.291
peak=   -3.385 closest distance to " O   HOH Z 414 " =    2.382
peak=   -3.379 closest distance to " O   ALA A  51 " =    1.213
peak=   -3.379 closest distance to " O   GLY A 241 " =    2.315
peak=   -3.373 closest distance to " O   HOH Z  91 " =    1.747
peak=   -3.370 closest distance to " O   TRP A 179 " =    1.435
peak=   -3.369 closest distance to " O   HOH Z 387 " =    2.138
peak=   -3.368 closest distance to " CG  GLN A  55 " =    1.245
peak=   -3.367 closest distance to " O   HOH Z 428 " =    1.926
peak=   -3.365 closest distance to " CA  GLY A  57 " =    2.230
peak=   -3.364 closest distance to " O   GLN A 144 " =    1.791
peak=   -3.362 closest distance to " CA  GLY A  98 " =    1.875
peak=   -3.359 closest distance to " O   HOH Z 429 " =    1.523
peak=   -3.357 closest distance to " CE3 TRP A 274 " =    1.999
peak=   -3.357 closest distance to " O  BHOH Z  74 " =    0.818
peak=   -3.355 closest distance to " CG  ARG A 219 " =    2.383
peak=   -3.351 closest distance to " O   HOH Z 128 " =    2.707
peak=   -3.348 closest distance to " OE1 GLN A 183 " =    1.582
peak=   -3.348 closest distance to " N   GLN A  58 " =    1.293
peak=   -3.346 closest distance to " O   HOH Z 107 " =    1.310
peak=   -3.345 closest distance to " CB  TRP A 266 " =    1.858
peak=   -3.343 closest distance to " OXT GLY A 302 " =    4.124
peak=   -3.341 closest distance to " CD2 HIS A 207 " =    1.806
peak=   -3.338 closest distance to " CB  ASN A  39 " =    2.224
peak=   -3.336 closest distance to " O   HOH Z  97 " =    1.051
peak=   -3.333 closest distance to " CG2 VAL A 202 " =    2.788
peak=   -3.328 closest distance to " ND2 ASN A  69 " =    1.654
peak=   -3.319 closest distance to " O   HOH Z 244 " =    1.300
peak=   -3.313 closest distance to " CB  ASP A 132 " =    2.376
peak=   -3.310 closest distance to " CG2 THR A 221 " =    2.095
peak=   -3.292 closest distance to " NE2 GLN A  55 " =    1.392
peak=   -3.283 closest distance to " CB  PRO A 213 " =    2.299
peak=   -3.283 closest distance to " CE  MET A 105 " =    2.381
peak=   -3.281 closest distance to " N   LYS A 290 " =    1.300
peak=   -3.281 closest distance to " O   HOH Z  65 " =    1.466
peak=   -3.281 closest distance to " O   PRO A 163 " =    1.986
peak=   -3.281 closest distance to " NH2 ARG A  79 " =    2.035
peak=   -3.278 closest distance to " O   HOH Z  24 " =    1.299
peak=   -3.277 closest distance to " O   HOH Z 165 " =    2.232
peak=   -3.267 closest distance to " OG BSER A 134 " =    1.568
peak=   -3.265 closest distance to " O   HOH Z 385 " =    1.626
peak=   -3.264 closest distance to " ND2 ASN A 249 " =    2.136
peak=   -3.263 closest distance to " NE2 GLN A  88 " =    1.285
peak=   -3.257 closest distance to " O   HOH Z 312 " =    1.441
peak=   -3.255 closest distance to " O   HOH Z 421 " =    2.766
peak=   -3.254 closest distance to " OG  SER A  62 " =    4.237
peak=   -3.252 closest distance to " CG1 ILE A 263 " =    2.199
peak=   -3.252 closest distance to " CD  PRO A 213 " =    2.154
peak=   -3.248 closest distance to " CG1 VAL A 112 " =    2.942
peak=   -3.247 closest distance to " O   HOH Z 259 " =    0.803
peak=   -3.247 closest distance to " OE1 GLN A  88 " =    1.479
peak=   -3.241 closest distance to " O   ASP A 270 " =    1.232
peak=   -3.241 closest distance to " CG  TRP A 274 " =    1.532
peak=   -3.240 closest distance to " O   ALA A 161 " =    1.786
peak=   -3.235 closest distance to " O   SER A  95 " =    1.347
peak=   -3.234 closest distance to " O   HOH Z 142 " =    0.805
peak=   -3.234 closest distance to " CZ2 TRP A 274 " =    1.224
peak=   -3.233 closest distance to " O   ILE A 234 " =    1.370
peak=   -3.228 closest distance to " CD2 TYR A 247 " =    2.497
peak=   -3.221 closest distance to " OE2 GLU A   2 " =    0.776
peak=   -3.220 closest distance to " CG1BVAL A  72 " =    2.450
peak=   -3.215 closest distance to " O   HOH Z 275 " =    1.817
peak=   -3.215 closest distance to " O   HOH Z 123 " =    0.792
peak=   -3.214 closest distance to " O   HOH Z  11 " =    1.812
peak=   -3.208 closest distance to " O   HOH Z 423 " =    2.612
peak=   -3.206 closest distance to " C   ALA A 158 " =    1.229
peak=   -3.202 closest distance to " CD1 TRP A  85 " =    0.933
peak=   -3.199 closest distance to " OG  SER A   3 " =    1.048
peak=   -3.189 closest distance to " CD  ARG A 156 " =    1.955
peak=   -3.181 closest distance to " O   HOH Z  39 " =    1.455
peak=   -3.180 closest distance to " CA  TYR A  68 " =    1.111
peak=   -3.178 closest distance to " O   HOH Z 171 " =    0.966
peak=   -3.173 closest distance to " O   ALA A  10 " =    1.691
peak=   -3.170 closest distance to " OE1 GLN A 223 " =    2.040
peak=   -3.170 closest distance to " CB  SER A 210 " =    1.017
peak=   -3.169 closest distance to " OG  SER A 245 " =    1.507
peak=   -3.168 closest distance to " O   HOH Z 244 " =    1.537
peak=   -3.163 closest distance to " O   HOH Z 133 " =    1.502
peak=   -3.163 closest distance to " CD2 LEU A   5 " =    1.067
peak=   -3.162 closest distance to " SG BCYS A 201 " =    2.284
peak=   -3.162 closest distance to " CZ  PHE A  38 " =    2.396
peak=   -3.152 closest distance to " O   HOH Z 426 " =    1.748
peak=   -3.152 closest distance to " CB  ALA A 114 " =    2.450
peak=   -3.148 closest distance to " O   HOH Z 434 " =    4.557
peak=   -3.148 closest distance to " CA  GLY A  23 " =    1.765
peak=   -3.148 closest distance to " O   HOH Z 201 " =    1.954
peak=   -3.147 closest distance to " CD  LYS A 289 " =    2.298
peak=   -3.146 closest distance to " O   HOH Z 149 " =    1.793
peak=   -3.146 closest distance to " CB  ALA A 131 " =    1.828
peak=   -3.141 closest distance to " C   ASN A 285 " =    1.967
peak=   -3.136 closest distance to " C   ALA A 233 " =    1.304
peak=   -3.134 closest distance to " CE1 TYR A 247 " =    2.482
peak=   -3.130 closest distance to " O   HOH Z 298 " =    3.813
peak=   -3.125 closest distance to " C   HIS A 207 " =    1.144
peak=   -3.121 closest distance to " N   GLN A  58 " =    2.022
peak=   -3.117 closest distance to " O   HOH Z  89 " =    2.671
peak=   -3.117 closest distance to " O   HOH Z 428 " =    2.850
peak=   -3.112 closest distance to " O   HOH Z 430 " =    1.896
peak=   -3.107 closest distance to " ND2 ASN A 285 " =    1.947
peak=   -3.101 closest distance to " O   HOH Z 231 " =    2.076
peak=   -3.101 closest distance to " O   HOH Z  37 " =    1.482
peak=   -3.099 closest distance to " C   LYS A  76 " =    1.686
peak=   -3.097 closest distance to " NE  ARG A 259 " =    0.922
peak=   -3.085 closest distance to " O   HOH Z 339 " =    1.290
peak=   -3.083 closest distance to " O   HOH Z 198 " =    1.064
peak=   -3.083 closest distance to " CD1 LEU A 101 " =    2.217
peak=   -3.074 closest distance to " N   GLY A  91 " =    1.479
peak=   -3.070 closest distance to " ND2 ASN A 173 " =    1.373
peak=   -3.070 closest distance to " O   HOH Z 293 " =    1.605
peak=   -3.053 closest distance to " O   HOH Z 174 " =    4.612
peak=   -3.046 closest distance to " O   HOH Z 231 " =    1.206
peak=   -3.022 closest distance to " O  BHOH Z  74 " =    0.974
peak=   -3.010 closest distance to " OG  SER A  28 " =    2.008

================= 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    :  0.5137 0.5092   6.306741e+00   6.302187e+00
   1_bss:  0.5055 0.4977   6.300523e+00   6.294645e+00
   1_xyz:  0.4456 0.4681   6.238907e+00   6.266516e+00
   1_adp:  0.4058 0.4725   6.198358e+00   6.265818e+00
   1_occ:  0.4053 0.4733   6.197487e+00   6.266143e+00
   2_bss:  0.4022 0.4727   6.199427e+00   6.267763e+00
   2_xyz:  0.3437 0.4174   6.078678e+00   6.199647e+00
   2_adp:  0.3262 0.3955   6.039818e+00   6.162088e+00
   2_occ:  0.3260 0.3958   6.039889e+00   6.162186e+00
   3_bss:  0.3246 0.3940   6.039327e+00   6.161962e+00
   3_xyz:  0.2422 0.3051   5.805688e+00   5.977416e+00
   3_adp:  0.2099 0.2869   5.708323e+00   5.915287e+00
   3_occ:  0.2096 0.2868   5.707417e+00   5.914619e+00
   4_bss:  0.2089 0.2862   5.704116e+00   5.911743e+00
   4_xyz:  0.1648 0.2287   5.491722e+00   5.722655e+00
   4_adp:  0.1559 0.2114   5.424150e+00   5.643921e+00
   4_occ:  0.1555 0.2107   5.421901e+00   5.641331e+00
   5_bss:  0.1552 0.2104   5.421392e+00   5.640563e+00
   5_xyz:  0.1374 0.1917   5.326205e+00   5.559191e+00
   5_adp:  0.1303 0.1830   5.281731e+00   5.518791e+00
   5_occ:  0.1299 0.1827   5.280053e+00   5.517101e+00
   5_bss:  0.1303 0.1833   5.280917e+00   5.517934e+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:  0.352   0.000   7.653   8.654  10.552   0.000   0.000   0.000
   1_xyz:  0.352   0.000   7.653   8.654  10.552   0.000   0.000   0.000
   1_adp:  0.352   0.000   7.653   8.654  10.552   0.000   0.000   0.000
   1_occ:  0.352   0.000   7.653   8.654  10.552   0.000   0.000   0.000
   2_bss:  0.366  50.000   3.656   4.218   6.213   0.000   0.000   0.000
   2_xyz:  0.366  50.000   3.656   4.218   6.213   0.000   0.000   0.000
   2_adp:  0.366  50.000   3.656   4.218   6.213   0.000   0.000   0.000
   2_occ:  0.366  50.000   3.656   4.218   6.213   0.000   0.000   0.000
   3_bss:  0.353  50.000   1.523   2.430   4.023   0.000   0.000   0.000
   3_xyz:  0.353  50.000   1.523   2.430   4.023   0.000   0.000   0.000
   3_adp:  0.353  50.000   1.523   2.430   4.023   0.000   0.000   0.000
   3_occ:  0.353  50.000   1.523   2.430   4.023   0.000   0.000   0.000
   4_bss:  0.327  50.000   0.169   1.067   2.684   0.000   0.000   0.000
   4_xyz:  0.327  50.000   0.169   1.067   2.684   0.000   0.000   0.000
   4_adp:  0.327  50.000   0.169   1.067   2.684   0.000   0.000   0.000
   4_occ:  0.327  50.000   0.169   1.067   2.684   0.000   0.000   0.000
   5_bss:  0.317  45.129  -0.631   0.179   2.013   0.000   0.000   0.000
   5_xyz:  0.317  45.129  -0.631   0.179   2.013   0.000   0.000   0.000
   5_adp:  0.317  45.129  -0.631   0.179   2.013   0.000   0.000   0.000
   5_occ:  0.317  45.129  -0.631   0.179   2.013   0.000   0.000   0.000
   5_bss:  0.317  45.383  -1.154  -0.411   1.565  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.690 0.2931  0.3569    86738.704
   1_bss:  66.774 0.3041  0.4741    84112.116
   1_xyz:  57.948 0.4184  0.6452    69865.350
   1_adp:  56.808 0.4332  0.7450    69846.235
   1_occ:  56.864 0.4324  0.7418    69881.992
   2_bss:  56.755 0.4337  0.6496    69629.885
   2_xyz:  47.220 0.5535  0.8222    50742.220
   2_adp:  43.500 0.5998  0.8926    44608.310
   2_occ:  43.530 0.5994  0.8916    44635.984
   3_bss:  43.362 0.6013  0.8309    44321.053
   3_xyz:  31.892 0.7361  0.9804    25322.184
   3_adp:  29.094 0.7677  0.9904    21888.911
   3_occ:  29.094 0.7676  0.9898    21835.245
   4_bss:  28.935 0.7691  0.9435    21582.778
   4_xyz:  22.546 0.8358  0.9909    13520.199
   4_adp:  20.151 0.8603  1.0074    11599.734
   4_occ:  20.085 0.8609  1.0076    11510.615
   5_bss:  20.041 0.8613  0.9795    11478.333
   5_xyz:  17.844 0.8822  0.9883     9490.353
   5_adp:  16.947 0.8902  0.9859     8678.989
   5_occ:  16.903 0.8906  0.9860     8639.199
   5_bss:  16.924 0.8904  0.9765     8684.190
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.3090e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.3090e+01
   1_xyz:   1.815  0.014  0.109 18.439  0.006  4.103   1.6066e-01
   1_adp:   1.815  0.014  0.109 18.439  0.006  4.103   1.6066e-01
   1_occ:   1.815  0.014  0.109 18.439  0.006  4.103   1.6066e-01
   2_bss:   1.815  0.014  0.109 18.439  0.006  4.103   1.6066e-01
   2_xyz:   1.230  0.009  0.081 16.366  0.005  4.119   9.7383e-02
   2_adp:   1.230  0.009  0.081 16.366  0.005  4.119   9.7383e-02
   2_occ:   1.230  0.009  0.081 16.366  0.005  4.119   9.7383e-02
   3_bss:   1.230  0.009  0.081 16.366  0.005  4.119   9.7383e-02
   3_xyz:   1.236  0.010  0.083 16.108  0.005  4.113   1.0185e-01
   3_adp:   1.236  0.010  0.083 16.108  0.005  4.113   1.0185e-01
   3_occ:   1.236  0.010  0.083 16.108  0.005  4.113   1.0185e-01
   4_bss:   1.236  0.010  0.083 16.108  0.005  4.113   1.0185e-01
   4_xyz:   1.149  0.008  0.079 15.788  0.005  4.119   7.7758e-02
   4_adp:   1.149  0.008  0.079 15.788  0.005  4.119   7.7758e-02
   4_occ:   1.149  0.008  0.079 15.788  0.005  4.119   7.7758e-02
   5_bss:   1.149  0.008  0.079 15.788  0.005  4.119   7.7758e-02
   5_xyz:   1.095  0.008  0.078 15.590  0.004  4.108   7.1024e-02
   5_adp:   1.095  0.008  0.078 15.590  0.004  4.108   7.1024e-02
   5_occ:   1.095  0.008  0.078 15.590  0.004  4.108   7.1024e-02
   5_bss:   1.095  0.008  0.078 15.590  0.004  4.108   7.1024e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.106   6.8711e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.106   6.8711e+00
   1_xyz:  14.493  0.177  0.445 85.187  0.035  2.106   1.0552e-01
   1_adp:  14.493  0.177  0.445 85.187  0.035  2.106   1.0552e-01
   1_occ:  14.493  0.177  0.445 85.187  0.035  2.106   1.0552e-01
   2_bss:  14.493  0.177  0.445 85.187  0.035  2.106   1.0552e-01
   2_xyz:   7.194  0.088  0.330 82.088  0.041  1.987   9.1769e-02
   2_adp:   7.194  0.088  0.330 82.088  0.041  1.987   9.1769e-02
   2_occ:   7.194  0.088  0.330 82.088  0.041  1.987   9.1769e-02
   3_bss:   7.194  0.088  0.330 82.088  0.041  1.987   9.1769e-02
   3_xyz:   7.499  0.076  0.277 80.152  0.033  2.043   2.1142e-01
   3_adp:   7.499  0.076  0.277 80.152  0.033  2.043   2.1142e-01
   3_occ:   7.499  0.076  0.277 80.152  0.033  2.043   2.1142e-01
   4_bss:   7.499  0.076  0.277 80.152  0.033  2.043   2.1142e-01
   4_xyz:   8.985  0.052  0.275 86.781  0.043  2.149   5.1885e-02
   4_adp:   8.985  0.052  0.275 86.781  0.043  2.149   5.1885e-02
   4_occ:   8.985  0.052  0.275 86.781  0.043  2.149   5.1885e-02
   5_bss:   8.985  0.052  0.275 86.781  0.043  2.149   5.1885e-02
   5_xyz:   7.439  0.055  0.244 84.238  0.041  2.252   5.1401e-02
   5_adp:   7.439  0.055  0.244 84.238  0.041  2.252   5.1401e-02
   5_occ:   7.439  0.055  0.244 84.238  0.041  2.252   5.1401e-02
   5_bss:   7.439  0.055  0.244 84.238  0.041  2.252   5.1401e-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:  86.71   0.00  17.16  69.45   0.00  15.74  86.71   0.00  24.89
   1_occ:  86.71   0.00  17.16  69.45   0.00  15.74  86.71   0.00  24.89
   2_bss:  86.71   0.00  17.16  69.45   0.00  15.74  86.71   0.00  24.89
   2_xyz:  86.71   0.00  17.16  69.45   0.00  15.74  86.71   0.00  24.89
   2_adp:  82.05   0.00  16.12  65.10   0.00  13.68  82.05   0.00  29.40
   2_occ:  82.05   0.00  16.12  65.10   0.00  13.68  82.05   0.00  29.40
   3_bss:  82.05   0.00  16.12  65.10   0.00  13.68  82.05   0.00  29.40
   3_xyz:  82.05   0.00  16.12  65.10   0.00  13.68  82.05   0.00  29.40
   3_adp:  97.74   0.00  16.88  84.31   0.00  12.29  97.74   0.00  41.90
   3_occ:  97.74   0.00  16.88  84.31   0.00  12.29  97.74   0.00  41.90
   4_bss:  97.74   0.00  16.88  84.31   0.00  12.29  97.74   0.00  41.90
   4_xyz:  97.74   0.00  16.88  84.31   0.00  12.29  97.74   0.00  41.90
   4_adp:  96.23   0.00  16.33  84.78   0.00  11.73  96.23   2.22  41.37
   4_occ:  96.23   0.00  16.33  84.78   0.00  11.73  96.23   2.22  41.37
   5_bss:  96.23   0.00  16.33  84.78   0.00  11.73  96.23   2.22  41.37
   5_xyz:  96.23   0.00  16.33  84.78   0.00  11.73  96.23   2.22  41.37
   5_adp:  95.54   0.00  15.84  94.08   0.00  11.17  95.54   3.33  41.25
   5_occ:  95.54   0.00  15.84  94.08   0.00  11.17  95.54   3.33  41.25
   5_bss:  95.80   0.25  16.09  94.34   0.25  11.43  95.80   3.59  41.50
------------------------------------------------------------------------
 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:    1.303    0.028    0.418
   1_adp:    1.303    0.028    0.418
   1_occ:    1.303    0.028    0.418
   2_bss:    1.303    0.028    0.418
   2_xyz:    1.830    0.037    0.570
   2_adp:    1.830    0.037    0.570
   2_occ:    1.830    0.037    0.570
   3_bss:    1.830    0.037    0.570
   3_xyz:    1.672    0.043    0.739
   3_adp:    1.672    0.043    0.739
   3_occ:    1.672    0.043    0.739
   4_bss:    1.672    0.043    0.739
   4_xyz:    1.727    0.027    0.828
   4_adp:    1.727    0.027    0.828
   4_occ:    1.727    0.027    0.828
   5_bss:    1.727    0.027    0.828
   5_xyz:    1.937    0.029    0.858
   5_adp:    1.937    0.029    0.858
   5_occ:    1.937    0.029    0.858
   5_bss:    1.937    0.029    0.858
------------------------------------------------------------------------

CPU time actual refinement: 344.13


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_31/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_31/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_31/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_31/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_31/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.98 
  Macro-tasks:
    bulk solvent and scale       = 40.06  
    individual site refinement   = 143.29 
    weights calculation          = 32.21  
    collect and process          = 6.33   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 222.00 
  Micro-tasks:
    mask                            = 3.01   
    f_calc                          = 108.13 
    alpha_beta                      = 8.30   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 118.25 
    fmodel                         = 7.01   
    r_factors                      = 0.28   
    phase_errors                   = 9.94   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 256.35 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.868 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    652 calls, 107.74 s
gradients_fft:          598 calls, 104.95 s

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

# Date 2008-01-16 Time 00:33:24 PST -0800 (1200472404.39 s)
Start R-work = 0.5137, R-free = 0.5092 (no bulk solvent and anisotropic scale)
Final R-work = 0.1479, R-free = 0.1982 (no bulk solvent and anisotropic scale)

Start R-work = 0.5055, R-free = 0.4977
Final R-work = 0.1303, R-free = 0.1833