# Date 2008-01-16 Time 02:10:10 PST -0800 (1200478210.41 s)
#phil __OFF__

Command line arguments: "../725.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13474
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 725

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 48.1033, 88.5498, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00079
Completeness in resolution range: 0.939701
Completeness with d_max=infinity: 0.936824

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   2.0008

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00079
Completeness in resolution range: 0.939701
Completeness with d_max=infinity: 0.936824

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2809 [2195/2223]  1972   223  10.2%
  bin  2:  4.2809 -  3.4107 [2081/2104]  1875   206   9.9%
  bin  3:  3.4107 -  2.9834 [2079/2101]  1873   206   9.9%
  bin  4:  2.9834 -  2.7123 [2067/2086]  1857   210  10.2%
  bin  5:  2.7123 -  2.5189 [2017/2046]  1814   203  10.1%
  bin  6:  2.5189 -  2.3710 [2037/2079]  1837   200   9.8%
  bin  7:  2.3710 -  2.2526 [2012/2048]  1812   200   9.9%
  bin  8:  2.2526 -  2.1549 [2021/2057]  1813   208  10.3%
  bin  9:  2.1549 -  2.0721 [2023/2055]  1830   193   9.5%
  bin 10:  2.0721 -  2.0008 [1057/2047]   947   110  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_725/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 10
        2.14 -     2.83: 937
        2.83 -     3.52: 4303
        3.52 -     4.21: 9079
        4.21 -     4.90: 13337
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.453 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.716 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.716 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.826 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 27661 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_725/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_725/model_refine_001.geo

CPU time processing inputs: 10.00


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 48.10325 88.54975 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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5221   r_free= 0.5150   ksol= 0.00   Bsol= 0.00   scale= 0.744    |
|                                                                             |
| 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:   0.98 A                  |
| x-ray target function (ml) for work reflections: 6.315304                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7745 0.99   1423  158 0.4369 0.4390      6.6757      6.6815|
|  2:  4.7745 -  3.8097 0.99   1375  153 0.4773 0.5211       6.896      6.9845|
|  3:  3.8097 -  3.3340 0.99   1331  150 0.4995 0.4757      6.7427      6.7042|
|  4:  3.3340 -  3.0319 0.99   1338  140 0.5269 0.4802      6.5725      6.5369|
|  5:  3.0319 -  2.8161 0.99   1311  148 0.5525 0.4966      6.3934      6.4238|
|  6:  2.8161 -  2.6510 0.98   1307  151 0.5493 0.5522         6.3      6.1963|
|  7:  2.6510 -  2.5189 0.99   1306  148 0.5364 0.4876      6.2536      6.1666|
|  8:  2.5189 -  2.4097 0.99   1322  140 0.5426 0.5164      6.1933       6.182|
|  9:  2.4097 -  2.3173 0.98   1308  145 0.5495 0.6419       6.126      6.1988|
| 10:  2.3173 -  2.2376 0.98   1291  142 0.5799 0.5466      6.1039      6.1386|
| 11:  2.2376 -  2.1678 0.98   1307  149 0.5483 0.5690      6.0379      6.0409|
| 12:  2.1678 -  2.1060 0.99   1294  145 0.5463 0.5394      5.9642      5.9957|
| 13:  2.1060 -  2.0507 0.97   1271  130 0.5522 0.5123      5.8899      5.8405|
| 14:  2.0507 -  2.0008 0.34    446   60 0.5611 0.5278      5.8964      5.7388|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.7745  1423   158  0.62  41.27   0.77     0.63      95663.72|
|  2:  4.7745 -  3.8097  1375   153  0.59  44.18   0.82     0.64     147327.61|
|  3:  3.8097 -  3.3340  1331   150  0.48  53.59   0.76     0.59     153261.45|
|  4:  3.3340 -  3.0319  1338   140  0.36  62.73   0.75     0.44     130458.64|
|  5:  3.0319 -  2.8161  1311   148  0.30  67.48   0.69     0.36      97934.00|
|  6:  2.8161 -  2.6510  1307   151  0.28  69.08   0.68     0.33      83197.23|
|  7:  2.6510 -  2.5189  1306   148  0.30  67.43   0.71     0.34      72049.96|
|  8:  2.5189 -  2.4097  1322   140  0.27  69.97   0.70     0.32      66012.40|
|  9:  2.4097 -  2.3173  1308   145  0.21  74.66   0.67     0.25      64202.68|
| 10:  2.3173 -  2.2376  1291   142  0.16  78.49   0.69     0.19      59101.51|
| 11:  2.2376 -  2.1678  1307   149  0.13  79.98   0.71     0.17      57054.01|
| 12:  2.1678 -  2.1060  1294   145  0.15  78.62   0.72     0.20      50697.57|
| 13:  2.1060 -  2.0507  1271   130  0.17  77.45   0.69     0.22      43590.19|
| 14:  2.0507 -  2.0008   446    60  0.22  73.53   0.71     0.23      31919.80|
|alpha:            min =        0.17 max =            0.64 mean =         0.36|
|beta:             min =    31919.80 max =       153261.45 mean =     85413.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           89.99 mean =        66.39|
|phase err.(test): min =        0.00 max =           89.92 mean =        66.79|
|-----------------------------------------------------------------------------|

============================== 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 = 26.461960             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.614   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.018738              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.681   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        8 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      673 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1471 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2572 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3817 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4946 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6428 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7577 |
|-----------------------------------------------------------------------------|
|-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 |       54.720 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.896 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.395)------------------------------------------|
|    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 = 12.395)------------------------------------------|
|    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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5268   r_free= 0.5176   ksol= 0.00   Bsol= 0.00   scale= 0.718    |
|                                                                             |
| 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:   0.97 A                  |
| x-ray target function (ml) for work reflections: 6.316044                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5164   r_free= 0.5096   ksol= 0.29   Bsol= 20.00   scale= 0.926   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.96,10.46,10.17,0.00,0.00,0.00); trace/3= 8.53                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.311257                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 22.774239             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.427   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.388562              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.277   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5164      final r-factor (work) = 0.4663          |
| start r-factor (free) = 0.5096      final r-factor (free) = 0.4809          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 126.6123 = 22.77 * 0.50 * 6.3134 + 1.00 * 54.7204                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.6109 = 22.77 * 0.50 * 6.2755 + 1.00 * 0.1516                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4663      final r-factor (work) = 0.4253          |
| start r-factor (free) = 0.4809      final r-factor (free) = 0.4816          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.0041 = 2.39 * 1.00 * 6.2755 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.9145 = 2.39 * 1.00 * 6.2312 + 1.00 * 0.0310                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    131.23  20.30    None  None   None       |
|    all(noH): 2823   0      0.00    131.23  20.30    None  None   None       |
|    Sol.    : 438    0      0.00    131.23  30.37    None  None   None       |
|    Mac.    : 2385   0      0.00    101.96  18.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  13.123: 1198   |   5:    65.617 -  78.740:   43        |
|      1:    13.123 -  26.247:  839   |   6:    78.740 -  91.863:   17        |
|      2:    26.247 -  39.370:  413   |   7:    91.863 - 104.987:    9        |
|      3:    39.370 -  52.493:  213   |   8:   104.987 - 118.110:    1        |
|      4:    52.493 -  65.617:   88   |   9:   118.110 - 131.233:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4253 r_free = 0.4816             target_work(ml) = 6.228         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4246 r_free = 0.4819             target_work(ml) = 6.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4246   r_free= 0.4819   ksol= 0.29   Bsol= 20.00   scale= 1.109   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.96,10.46,10.17,0.00,0.00,0.00); trace/3= 8.53                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.227391                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4220   r_free= 0.4767   ksol= 0.31   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.63,5.55,5.61,0.00,0.00,0.00); trace/3= 4.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.229164                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.751111             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.938  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.663409              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.617  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4220      final r-factor (work) = 0.3670          |
| start r-factor (free) = 0.4767      final r-factor (free) = 0.4461          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 64.7534 = 20.75 * 0.50 * 6.2264 + 1.00 * 0.1512                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 64.2033 = 20.75 * 0.50 * 6.1753 + 1.00 * 0.1308                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3670      final r-factor (work) = 0.3598          |
| start r-factor (free) = 0.4461      final r-factor (free) = 0.4302          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1277 = 0.66 * 1.00 * 6.1753 + 1.00 * 0.0310                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0810 = 0.66 * 1.00 * 6.1360 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.46  16.67    None  None   None       |
|    all(noH): 2823   0      0.00    119.46  16.67    None  None   None       |
|    Sol.    : 438    0      0.00    119.46  27.70    None  None   None       |
|    Mac.    : 2385   0      0.00    76.14   14.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.946: 1249   |   5:    59.732 -  71.678:   17        |
|      1:    11.946 -  23.893:  951   |   6:    71.678 -  83.625:    9        |
|      2:    23.893 -  35.839:  423   |   7:    83.625 -  95.571:    1        |
|      3:    35.839 -  47.786:  129   |   8:    95.571 - 107.518:    1        |
|      4:    47.786 -  59.732:   42   |   9:   107.518 - 119.464:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3598 r_free = 0.4302             target_work(ml) = 6.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3596 r_free = 0.4299             target_work(ml) = 6.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3596   r_free= 0.4299   ksol= 0.31   Bsol= 50.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.63,5.55,5.61,0.00,0.00,0.00); trace/3= 4.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.122169                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3592   r_free= 0.4293   ksol= 0.30   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.91,3.61,3.47,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.124203                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.295395             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.112  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.499237              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.904  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3592      final r-factor (work) = 0.2888          |
| start r-factor (free) = 0.4293      final r-factor (free) = 0.3457          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.9920 = 14.30 * 0.50 * 6.1364 + 1.00 * 0.1308                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.3675 = 14.30 * 0.50 * 6.0497 + 1.00 * 0.1261                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2888      final r-factor (work) = 0.2624          |
| start r-factor (free) = 0.3457      final r-factor (free) = 0.3233          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0299 = 0.50 * 1.00 * 6.0497 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9555 = 0.50 * 1.00 * 5.8984 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.17  16.21    None  None   None       |
|    all(noH): 2823   0      0.00    105.17  16.21    None  None   None       |
|    Sol.    : 438    0      0.00    105.17  35.27    None  None   None       |
|    Mac.    : 2385   0      0.00    68.26   12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.517: 1244   |   5:    52.583 -  63.100:   47        |
|      1:    10.517 -  21.033:  871   |   6:    63.100 -  73.617:   22        |
|      2:    21.033 -  31.550:  349   |   7:    73.617 -  84.134:    5        |
|      3:    31.550 -  42.067:  175   |   8:    84.134 -  94.650:    0        |
|      4:    42.067 -  52.583:  109   |   9:    94.650 - 105.167:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2624 r_free = 0.3233             target_work(ml) = 5.871         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2619 r_free = 0.3243             target_work(ml) = 5.871         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2619   r_free= 0.3243   ksol= 0.30   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.91,3.61,3.47,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.871063                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2603   r_free= 0.3227   ksol= 0.33   Bsol= 71.41   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,1.63,1.81,0.00,0.00,0.00); trace/3= 0.99                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.868270                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.820905              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.596  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.675019              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.616  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2603      final r-factor (work) = 0.2064          |
| start r-factor (free) = 0.3227      final r-factor (free) = 0.2560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2981 = 5.82 * 0.50 * 5.9001 + 1.00 * 0.1261                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9058 = 5.82 * 0.50 * 5.7797 + 1.00 * 0.0843                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2064      final r-factor (work) = 0.1907          |
| start r-factor (free) = 0.2560      final r-factor (free) = 0.2451          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9122 = 0.68 * 1.00 * 5.7797 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8077 = 0.68 * 1.00 * 5.6201 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.40  16.54    None  None   None       |
|    all(noH): 2823   0      0.00    100.40  16.54    None  None   None       |
|    Sol.    : 438    0      1.30    100.40  40.81    None  None   None       |
|    Mac.    : 2385   0      0.00    77.94   12.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.040: 1304   |   5:    50.201 -  60.241:   79        |
|      1:    10.040 -  20.080:  812   |   6:    60.241 -  70.281:   57        |
|      2:    20.080 -  30.120:  249   |   7:    70.281 -  80.321:   19        |
|      3:    30.120 -  40.161:  162   |   8:    80.321 -  90.361:    3        |
|      4:    40.161 -  50.201:  137   |   9:    90.361 - 100.401:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1907 r_free = 0.2451             target_work(ml) = 5.604         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1905 r_free = 0.2453             target_work(ml) = 5.603         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1905   r_free= 0.2453   ksol= 0.33   Bsol= 71.41   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,1.63,1.81,0.00,0.00,0.00); trace/3= 0.99                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.603033                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1905   r_free= 0.2456   ksol= 0.33   Bsol= 76.54   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,0.83,1.46,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.603990                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.720898              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.162  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.866502              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.405  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1905      final r-factor (work) = 0.1648          |
| start r-factor (free) = 0.2456      final r-factor (free) = 0.2170          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7320 = 2.72 * 0.50 * 5.6211 + 1.00 * 0.0849                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6105 = 2.72 * 0.50 * 5.5436 + 1.00 * 0.0688                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1648      final r-factor (work) = 0.1562          |
| start r-factor (free) = 0.2170      final r-factor (free) = 0.2143          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 38.0787 = 6.87 * 1.00 * 5.5436 + 1.00 * 0.0138                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 37.4700 = 6.87 * 1.00 * 5.4540 + 1.00 * 0.0198                              |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.63  17.80    None  None   None       |
|    all(noH): 2823   0      0.00    104.63  17.80    None  None   None       |
|    Sol.    : 438    0      1.20    104.63  49.60    None  None   None       |
|    Mac.    : 2385   0      0.00    101.25  11.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.463: 1403   |   5:    52.314 -  62.777:   86        |
|      1:    10.463 -  20.926:  782   |   6:    62.777 -  73.240:   73        |
|      2:    20.926 -  31.389:  191   |   7:    73.240 -  83.703:   47        |
|      3:    31.389 -  41.851:  119   |   8:    83.703 -  94.165:   40        |
|      4:    41.851 -  52.314:   75   |   9:    94.165 - 104.628:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1562 r_free = 0.2143             target_work(ml) = 5.448         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1561 r_free = 0.2144             target_work(ml) = 5.447         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1561   r_free= 0.2144   ksol= 0.33   Bsol= 76.54   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,0.83,1.46,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.447397                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7745 0.99   1423  158 0.1082 0.1530      5.5007      5.7135|
|  2:  4.7745 -  3.8097 0.99   1375  153 0.1049 0.1323      5.6325      5.8355|
|  3:  3.8097 -  3.3340 0.99   1331  150 0.1449 0.2025      5.7681      6.1077|
|  4:  3.3340 -  3.0319 0.99   1338  140 0.1751 0.2205      5.7526      5.9146|
|  5:  3.0319 -  2.8161 0.99   1311  148 0.1936 0.2066      5.6542      5.7635|
|  6:  2.8161 -  2.6510 0.98   1307  151 0.1760 0.2882      5.5174      5.7614|
|  7:  2.6510 -  2.5189 0.99   1306  148 0.1778 0.2354      5.4892      5.6741|
|  8:  2.5189 -  2.4097 0.99   1322  140 0.1800 0.2344      5.4372      5.6296|
|  9:  2.4097 -  2.3173 0.98   1308  145 0.1776 0.2734      5.3571      5.6666|
| 10:  2.3173 -  2.2376 0.98   1291  142 0.1644 0.2259      5.2941      5.4519|
| 11:  2.2376 -  2.1678 0.98   1307  149 0.1641 0.2518      5.2361      5.5628|
| 12:  2.1678 -  2.1060 0.99   1294  145 0.1606 0.2263      5.1675      5.3945|
| 13:  2.1060 -  2.0507 0.97   1271  130 0.1686 0.2343      5.1053      5.2963|
| 14:  2.0507 -  2.0008 0.34    446   60 0.1478 0.2548      5.0432      5.3074|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.7745  1423   158  0.92  11.42   0.95     0.91       9817.79|
|  2:  4.7745 -  3.8097  1375   153  0.93  11.24   1.01     0.98      13779.57|
|  3:  3.8097 -  3.3340  1331   150  0.90  16.18   1.03     1.02      18660.69|
|  4:  3.3340 -  3.0319  1338   140  0.87  19.64   1.01     0.99      18612.10|
|  5:  3.0319 -  2.8161  1311   148  0.83  23.14   1.01     0.99      16290.40|
|  6:  2.8161 -  2.6510  1307   151  0.83  23.53   0.97     0.92      13467.76|
|  7:  2.6510 -  2.5189  1306   148  0.85  22.27   0.99     0.94      12132.15|
|  8:  2.5189 -  2.4097  1322   140  0.82  24.28   0.98     0.91      11488.16|
|  9:  2.4097 -  2.3173  1308   145  0.83  23.52   0.99     0.93       9754.04|
| 10:  2.3173 -  2.2376  1291   142  0.83  23.54   0.98     0.93       9116.03|
| 11:  2.2376 -  2.1678  1307   149  0.84  23.16   0.98     0.90       7950.71|
| 12:  2.1678 -  2.1060  1294   145  0.84  22.56   0.97     0.96       7337.96|
| 13:  2.1060 -  2.0507  1271   130  0.83  23.72   0.96     0.91       6496.24|
| 14:  2.0507 -  2.0008   446    60  0.83  23.66   0.92     0.84       5856.44|
|alpha:            min =        0.84 max =            1.02 mean =         0.94|
|beta:             min =     5856.44 max =        18660.69 mean =     11794.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.98 mean =        20.60|
|phase err.(test): min =        0.00 max =           89.41 mean =        19.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1565   r_free= 0.2149   ksol= 0.34   Bsol= 90.49   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,0.18,1.04,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.450971                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1565   r_free= 0.2149   ksol= 0.34   Bsol= 90.49   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,0.18,1.04,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.450971                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7745 0.99   1423  158 0.1110 0.1574      5.5307      5.7399|
|  2:  4.7745 -  3.8097 0.99   1375  153 0.1064 0.1331      5.6481      5.8482|
|  3:  3.8097 -  3.3340 0.99   1331  150 0.1451 0.2027       5.772      6.1066|
|  4:  3.3340 -  3.0319 0.99   1338  140 0.1747 0.2211       5.752      5.9159|
|  5:  3.0319 -  2.8161 0.99   1311  148 0.1935 0.2061      5.6537      5.7628|
|  6:  2.8161 -  2.6510 0.98   1307  151 0.1756 0.2879      5.5161      5.7596|
|  7:  2.6510 -  2.5189 0.99   1306  148 0.1776 0.2351      5.4881      5.6732|
|  8:  2.5189 -  2.4097 0.99   1322  140 0.1798 0.2342      5.4365      5.6292|
|  9:  2.4097 -  2.3173 0.98   1308  145 0.1775 0.2738      5.3571       5.667|
| 10:  2.3173 -  2.2376 0.98   1291  142 0.1643 0.2258      5.2941      5.4521|
| 11:  2.2376 -  2.1678 0.98   1307  149 0.1640 0.2517       5.236      5.5624|
| 12:  2.1678 -  2.1060 0.99   1294  145 0.1605 0.2268      5.1673      5.3955|
| 13:  2.1060 -  2.0507 0.97   1271  130 0.1686 0.2339       5.105      5.2953|
| 14:  2.0507 -  2.0008 0.34    446   60 0.1478 0.2545      5.0434      5.3067|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.7745  1423   158  0.92  11.95   0.95     0.91      10417.17|
|  2:  4.7745 -  3.8097  1375   153  0.93  11.55   1.01     0.98      14306.01|
|  3:  3.8097 -  3.3340  1331   150  0.90  16.33   1.03     1.02      18950.56|
|  4:  3.3340 -  3.0319  1338   140  0.87  19.67   1.01     0.99      18650.34|
|  5:  3.0319 -  2.8161  1311   148  0.83  23.12   1.01     0.99      16278.31|
|  6:  2.8161 -  2.6510  1307   151  0.83  23.49   0.98     0.93      13421.80|
|  7:  2.6510 -  2.5189  1306   148  0.85  22.25   1.00     0.95      12109.60|
|  8:  2.5189 -  2.4097  1322   140  0.82  24.26   0.99     0.91      11465.19|
|  9:  2.4097 -  2.3173  1308   145  0.83  23.52   1.00     0.94       9753.71|
| 10:  2.3173 -  2.2376  1291   142  0.83  23.55   0.99     0.93       9117.74|
| 11:  2.2376 -  2.1678  1307   149  0.84  23.17   0.99     0.91       7950.88|
| 12:  2.1678 -  2.1060  1294   145  0.84  22.56   0.98     0.96       7337.82|
| 13:  2.1060 -  2.0507  1271   130  0.83  23.71   0.97     0.92       6490.76|
| 14:  2.0507 -  2.0008   446    60  0.83  23.64   0.93     0.85       5841.40|
|alpha:            min =        0.85 max =            1.02 mean =         0.95|
|beta:             min =     5841.40 max =        18950.56 mean =     11900.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.98 mean =        20.67|
|phase err.(test): min =        0.00 max =           89.72 mean =        19.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    105.31  18.48    None  None   None       |
|    all(noH): 2823   0      0.68    105.31  18.48    None  None   None       |
|    Sol.    : 438    0      1.88    105.31  50.28    None  None   None       |
|    Mac.    : 2385   0      0.68    101.93  12.64    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:     0.683 -  11.146: 1403   |   5:    52.997 -  63.460:   86        |
|      1:    11.146 -  21.608:  782   |   6:    63.460 -  73.922:   73        |
|      2:    21.608 -  32.071:  191   |   7:    73.922 -  84.385:   47        |
|      3:    32.071 -  42.534:  119   |   8:    84.385 -  94.848:   40        |
|      4:    42.534 -  52.997:   75   |   9:    94.848 - 105.311:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.687 - 4.967
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 344 from: 346
   mapped sites are within: 0.702 - 4.967

peak=    7.402 closest distance to " O   GLN A  11 " =    1.154
peak=    6.308 closest distance to " CB  VAL A 230 " =    1.284
peak=    6.098 closest distance to " OD1 ASN A 301 " =    1.171
peak=    6.025 closest distance to " O   HOH Z 426 " =    1.270
peak=    5.855 closest distance to " CG1 ILE A 234 " =    1.503
peak=    5.760 closest distance to " O   HOH Z  57 " =    1.114
peak=    5.588 closest distance to " O   HOH Z 117 " =    1.752
peak=    5.567 closest distance to " CG1 VAL A 296 " =    1.363
peak=    5.473 closest distance to " O   HOH Z 120 " =    1.680
peak=    5.455 closest distance to " CG  GLN A  77 " =    1.011
peak=    5.388 closest distance to " O   HOH Z  82 " =    1.133
peak=    5.278 closest distance to " O   HOH Z 248 " =    1.524
peak=    5.197 closest distance to " O   HOH Z 223 " =    1.371
peak=    5.162 closest distance to " O   HOH Z  54 " =    1.712
peak=    5.161 closest distance to " N   SER A 164 " =    0.997
peak=    5.063 closest distance to " O   HOH Z 425 " =    1.909
peak=    5.046 closest distance to " CD  ARG A  36 " =    1.083
peak=    5.016 closest distance to " O   HOH Z 203 " =    0.860
peak=    5.005 closest distance to " O   HOH Z 342 " =    0.958
peak=    4.761 closest distance to " O   HOH Z 272 " =    1.642
peak=    4.749 closest distance to " O   HOH Z 431 " =    2.003
peak=    4.733 closest distance to " O   HOH Z 159 " =    1.300
peak=    4.718 closest distance to " CB  VAL A 230 " =    1.402
peak=    4.707 closest distance to " OH  TYR A  68 " =    1.065
peak=    4.681 closest distance to " O   HOH Z 422 " =    1.045
peak=    4.651 closest distance to " O   HOH Z 139 " =    1.539
peak=    4.632 closest distance to " CG1 ILE A 120 " =    1.118
peak=    4.624 closest distance to " CD  ARG A  36 " =    1.099
peak=    4.599 closest distance to " OD1 ASN A  69 " =    1.034
peak=    4.581 closest distance to " CB  SER A  63 " =    1.278
peak=    4.576 closest distance to " O   HOH Z 210 " =    1.709
peak=    4.576 closest distance to " CG AARG A 275 " =    1.360
peak=    4.532 closest distance to " CE1 HIS A 115 " =    1.173
peak=    4.506 closest distance to " CA  ARG A 195 " =    1.196
peak=    4.464 closest distance to " O   HOH Z 277 " =    1.318
peak=    4.444 closest distance to " CZ3 TRP A 266 " =    1.111
peak=    4.417 closest distance to " CD2 TRP A 179 " =    1.207
peak=    4.402 closest distance to " CZ  PHE A 218 " =    1.191
peak=    4.392 closest distance to " CD2 LEU A 228 " =    1.232
peak=    4.383 closest distance to " O   HOH Z 158 " =    1.696
peak=    4.375 closest distance to " O   VAL A  72 " =    1.082
peak=    4.365 closest distance to " CB  SER A 288 " =    1.499
peak=    4.364 closest distance to " O   HOH Z 128 " =    2.074
peak=    4.346 closest distance to " NH2 ARG A 156 " =    1.150
peak=    4.340 closest distance to " O   HOH Z  52 " =    1.190
peak=    4.302 closest distance to " CG  ARG A  36 " =    1.290
peak=    4.272 closest distance to " N   TYR A 247 " =    1.282
peak=    4.267 closest distance to " O   HOH Z  69 " =    1.350
peak=    4.265 closest distance to " O   HOH Z 279 " =    1.009
peak=    4.246 closest distance to " CG  LEU A   5 " =    1.236
peak=    4.246 closest distance to " O   HOH Z 207 " =    1.457
peak=    4.201 closest distance to " O   HOH Z  67 " =    1.275
peak=    4.194 closest distance to " OE1 GLN A  88 " =    0.919
peak=    4.176 closest distance to " CB  THR A  52 " =    0.923
peak=    4.161 closest distance to " O   ASP A 298 " =    0.956
peak=    4.145 closest distance to " O   HOH Z 124 " =    1.548
peak=    4.141 closest distance to " O   HOH Z  38 " =    1.684
peak=    4.114 closest distance to " CA  TYR A  30 " =    0.960
peak=    4.104 closest distance to " O  BHOH Z  74 " =    1.104
peak=    4.094 closest distance to " O   HOH Z 107 " =    1.359
peak=    4.093 closest distance to " O   HOH Z 247 " =    1.488
peak=    4.088 closest distance to " NH1 ARG A 269 " =    0.994
peak=    4.085 closest distance to " O   HOH Z 412 " =    3.360
peak=    4.061 closest distance to " CB  GLN A 183 " =    1.179
peak=    4.052 closest distance to " CD2 TYR A  68 " =    1.031
peak=    4.050 closest distance to " O   HOH Z 102 " =    1.492
peak=    4.047 closest distance to " CA  GLN A  11 " =    0.966
peak=    4.026 closest distance to " CG  PRO A  54 " =    1.290
peak=    4.015 closest distance to " O  BHOH Z 338 " =    1.132
peak=    4.004 closest distance to " CA  ALA A 291 " =    0.877
peak=    3.991 closest distance to " O   HOH Z 147 " =    1.449
peak=    3.968 closest distance to " NH2AARG A 145 " =    1.252
peak=    3.956 closest distance to " CB  GLN A  73 " =    1.056
peak=    3.951 closest distance to " O   HOH Z  18 " =    2.242
peak=    3.948 closest distance to " O   HOH Z 126 " =    1.764
peak=    3.913 closest distance to " O   SER A   3 " =    1.078
peak=    3.898 closest distance to " CB  TRP A 179 " =    1.473
peak=    3.893 closest distance to " O   HOH Z  92 " =    1.348
peak=    3.892 closest distance to " NH2 ARG A  56 " =    1.330
peak=    3.889 closest distance to " CB  ASN A 285 " =    1.029
peak=    3.887 closest distance to " O   HOH Z 146 " =    1.708
peak=    3.886 closest distance to " CD  ARG A 269 " =    0.825
peak=    3.880 closest distance to " CB  ASN A 148 " =    1.578
peak=    3.877 closest distance to " O   HOH Z 261 " =    2.466
peak=    3.871 closest distance to " O   HOH Z 174 " =    1.587
peak=    3.861 closest distance to " O   HOH Z 222 " =    1.089
peak=    3.836 closest distance to " O   HOH Z  40 " =    2.095
peak=    3.826 closest distance to " O   HOH Z  53 " =    1.146
peak=    3.822 closest distance to " CB  MET A  40 " =    0.981
peak=    3.819 closest distance to " NH1AARG A 145 " =    1.334
peak=    3.811 closest distance to " CA  ALA A 100 " =    1.227
peak=    3.807 closest distance to " N   LYS A 119 " =    1.035
peak=    3.804 closest distance to " CB  ARG A 275 " =    0.833
peak=    3.797 closest distance to " CG  LYS A  76 " =    1.088
peak=    3.788 closest distance to " O   HOH Z 104 " =    2.605
peak=    3.788 closest distance to " CB  ALA A 114 " =    0.826
peak=    3.785 closest distance to " O   HOH Z 388 " =    1.513
peak=    3.779 closest distance to " CG1 ILE A  20 " =    1.268
peak=    3.779 closest distance to " OE1 GLU A   2 " =    1.336
peak=    3.778 closest distance to " O   HOH Z 199 " =    1.632
peak=    3.777 closest distance to " O   HOH Z 193 " =    2.288
peak=    3.767 closest distance to " O   HOH Z 343 " =    2.720
peak=    3.765 closest distance to " NE2 GLN A  11 " =    0.953
peak=    3.759 closest distance to " O   ASP A 200 " =    1.395
peak=    3.758 closest distance to " NH2 ARG A  56 " =    2.146
peak=    3.754 closest distance to " O   HOH Z 146 " =    1.833
peak=    3.751 closest distance to " NE2 GLN A  77 " =    3.115
peak=    3.747 closest distance to " ND2 ASN A 110 " =    0.958
peak=    3.743 closest distance to " CG2 VAL A 296 " =    1.006
peak=    3.742 closest distance to " O   HOH Z 377 " =    1.533
peak=    3.737 closest distance to " OG  SER A  62 " =    2.845
peak=    3.737 closest distance to " O   GLU A   2 " =    1.710
peak=    3.736 closest distance to " CB  ASN A  45 " =    1.050
peak=    3.732 closest distance to " ND2 ASN A 301 " =    1.052
peak=    3.732 closest distance to " O   HOH Z 402 " =    1.627
peak=    3.719 closest distance to " O   HOH Z  47 " =    1.401
peak=    3.717 closest distance to " N   TYR A  15 " =    1.053
peak=    3.714 closest distance to " CG2BVAL A 121 " =    1.167
peak=    3.704 closest distance to " O   HOH Z 401 " =    1.258
peak=    3.702 closest distance to " C   ALA A 299 " =    0.837
peak=    3.694 closest distance to " O   HOH Z 130 " =    2.574
peak=    3.691 closest distance to " O   HOH Z 111 " =    1.766
peak=    3.684 closest distance to " CB  ALA A 299 " =    1.155
peak=    3.684 closest distance to " CG  ARG A 138 " =    1.574
peak=    3.673 closest distance to " CB  ASN A  39 " =    0.759
peak=    3.670 closest distance to " O   PRO A 198 " =    1.679
peak=    3.669 closest distance to " CA  CYS A 260 " =    1.236
peak=    3.662 closest distance to " CG2 VAL A 197 " =    1.236
peak=    3.661 closest distance to " CA  LEU A   5 " =    0.946
peak=    3.647 closest distance to " O   HOH Z  70 " =    1.005
peak=    3.640 closest distance to " CD  ARG A 195 " =    1.496
peak=    3.639 closest distance to " O   HOH Z  49 " =    1.727
peak=    3.633 closest distance to " CB  ALA A  10 " =    1.288
peak=    3.632 closest distance to " CE  LYS A 119 " =    1.363
peak=    3.631 closest distance to " O   HOH Z  27 " =    1.140
peak=    3.623 closest distance to " O   HOH Z 221 " =    1.199
peak=    3.617 closest distance to " CA  PRO A 198 " =    1.100
peak=    3.611 closest distance to " CE1 HIS A 108 " =    1.075
peak=    3.597 closest distance to " CA  GLN A  11 " =    1.359
peak=    3.589 closest distance to " CA  VAL A 112 " =    1.135
peak=    3.589 closest distance to " O   HOH Z   9 " =    1.360
peak=    3.586 closest distance to " O   HOH Z 368 " =    4.231
peak=    3.585 closest distance to " O   HOH Z 134 " =    2.103
peak=    3.585 closest distance to " NH1 ARG A  36 " =    1.479
peak=    3.579 closest distance to " CB  GLN A  88 " =    1.368
peak=    3.578 closest distance to " O   HOH Z 174 " =    1.552
peak=    3.577 closest distance to " N   ALA A 292 " =    1.115
peak=    3.576 closest distance to " O   HOH Z 163 " =    2.261
peak=    3.572 closest distance to " O   HOH Z 359 " =    2.023
peak=    3.569 closest distance to " O   HOH Z 149 " =    2.110
peak=    3.565 closest distance to " O   HOH Z 427 " =    3.109
peak=    3.562 closest distance to " CG2 THR A  42 " =    0.900
peak=    3.548 closest distance to " CD2 LEU A   5 " =    1.415
peak=    3.545 closest distance to " O   VAL A  72 " =    1.045
peak=    3.543 closest distance to " OH  TYR A  15 " =    0.802
peak=    3.541 closest distance to " CG2 THR A  31 " =    1.103
peak=    3.541 closest distance to " CB  PRO A  54 " =    0.989
peak=    3.539 closest distance to " CG  GLN A 278 " =    1.118
peak=    3.538 closest distance to " O   GLN A 103 " =    1.171
peak=    3.534 closest distance to " CA  ARG A 156 " =    1.067
peak=    3.534 closest distance to " OH  TYR A 293 " =    1.085
peak=    3.529 closest distance to " N   THR A 221 " =    0.937
peak=    3.527 closest distance to " OD2 ASP A 298 " =    0.847
peak=    3.526 closest distance to " CG  MET A 185 " =    1.223
peak=    3.525 closest distance to " CB  ASP A 191 " =    1.328
peak=    3.524 closest distance to " O   HOH Z 296 " =    1.668
peak=    3.523 closest distance to " O   HOH Z 421 " =    1.687
peak=    3.519 closest distance to " CE1 TYR A 186 " =    1.103
peak=    3.513 closest distance to " CA  THR A 246 " =    1.056
peak=    3.512 closest distance to " N   GLY A  75 " =    0.891
peak=    3.510 closest distance to " CA  ALA A 295 " =    1.076
peak=    3.510 closest distance to " O   HOH Z 132 " =    3.371
peak=    3.506 closest distance to " O   THR A 251 " =    1.129
peak=    3.503 closest distance to " OE2 GLU A   2 " =    2.089
peak=    3.501 closest distance to " CB  LEU A  83 " =    0.702
peak=    3.500 closest distance to " CB  TYR A  30 " =    1.010
peak=    3.493 closest distance to " O   HOH Z 142 " =    2.024
peak=    3.489 closest distance to " O   HOH Z 394 " =    1.760
peak=    3.486 closest distance to " OD2 ASP A 171 " =    1.182
peak=    3.478 closest distance to " O   HOH Z  85 " =    2.012
peak=    3.472 closest distance to " CA  SER A  62 " =    0.940
peak=    3.466 closest distance to " CA  LYS A 117 " =    1.558
peak=    3.465 closest distance to " CG  LEU A 228 " =    1.329
peak=    3.462 closest distance to " O   HOH Z  91 " =    2.487
peak=    3.454 closest distance to " CD2 TRP A 179 " =    2.400
peak=    3.454 closest distance to " O   HOH Z  76 " =    1.274
peak=    3.445 closest distance to " O   HOH Z 251 " =    1.806
peak=    3.438 closest distance to " O   HOH Z  26 " =    1.618
peak=    3.436 closest distance to " CA  LEU A  83 " =    1.237
peak=    3.434 closest distance to " O   HOH Z 234 " =    3.271
peak=    3.428 closest distance to " O   HOH Z  44 " =    2.049
peak=    3.425 closest distance to " O   ASP A 124 " =    1.416
peak=    3.420 closest distance to " CB  SER A 210 " =    1.118
peak=    3.418 closest distance to " CB  SER A  62 " =    1.187
peak=    3.417 closest distance to " CA  TYR A 116 " =    1.334
peak=    3.412 closest distance to " CD  LYS A 166 " =    1.940
peak=    3.411 closest distance to " NH1BARG A 102 " =    1.064
peak=    3.404 closest distance to " CB  VAL A 202 " =    1.416
peak=    3.402 closest distance to " O   HOH Z 417 " =    1.375
peak=    3.399 closest distance to " O   HOH Z 289 " =    1.555
peak=    3.395 closest distance to " CE  LYS A  76 " =    0.889
peak=    3.395 closest distance to " O   HOH Z 196 " =    1.312
peak=    3.393 closest distance to " CD1 ILE A  33 " =    1.764
peak=    3.393 closest distance to " O   HOH Z 250 " =    1.311
peak=    3.392 closest distance to " O   THR A 182 " =    1.551
peak=    3.389 closest distance to " CB  VAL A 265 " =    1.287
peak=    3.387 closest distance to " CB  GLN A 223 " =    1.590
peak=    3.386 closest distance to " CE3 TRP A  85 " =    1.175
peak=    3.383 closest distance to " C   ALA A 295 " =    1.764
peak=    3.382 closest distance to " CB  SER A 146 " =    1.038
peak=    3.377 closest distance to " CB  ALA A 248 " =    1.510
peak=    3.376 closest distance to " CD ALYS A 290 " =    1.077
peak=    3.376 closest distance to " O   HOH Z 191 " =    3.306
peak=    3.373 closest distance to " CD  ARG A 159 " =    0.801
peak=    3.372 closest distance to " CB  ARG A 219 " =    1.614
peak=    3.371 closest distance to " CG  PRO A 198 " =    1.393
peak=    3.371 closest distance to " O   HOH Z 435 " =    1.947
peak=    3.366 closest distance to " CB  VAL A 126 " =    0.860
peak=    3.363 closest distance to " OG1 THR A  82 " =    0.988
peak=    3.360 closest distance to " CB ASER A 164 " =    1.342
peak=    3.356 closest distance to " O   ASN A 301 " =    1.450
peak=    3.355 closest distance to " O   HOH Z  63 " =    2.211
peak=    3.352 closest distance to " OE1 GLN A  55 " =    1.411
peak=    3.351 closest distance to " O   VAL A 112 " =    1.548
peak=    3.349 closest distance to " CA  VAL A  41 " =    0.915
peak=    3.349 closest distance to " O   HOH Z 418 " =    3.281
peak=    3.348 closest distance to " CB  GLU A 175 " =    1.329
peak=    3.343 closest distance to " O   HOH Z 368 " =    2.442
peak=    3.343 closest distance to " CB  MET A 105 " =    1.168
peak=    3.332 closest distance to " O   HOH Z 116 " =    1.244
peak=    3.330 closest distance to " ND2 ASN A  69 " =    1.437
peak=    3.329 closest distance to " O   HOH Z 130 " =    1.107
peak=    3.329 closest distance to " CG2AVAL A 121 " =    1.833
peak=    3.326 closest distance to " CG  GLN A  11 " =    0.965
peak=    3.317 closest distance to " O   HOH Z 361 " =    3.262
peak=    3.316 closest distance to " CB  PHE A  16 " =    1.079
peak=    3.315 closest distance to " CG  MET A 188 " =    0.728
peak=    3.313 closest distance to " CB  VAL A 296 " =    1.202
peak=    3.312 closest distance to " O   HOH Z 404 " =    1.475
peak=    3.310 closest distance to " CA  ALA A 158 " =    2.008
peak=    3.309 closest distance to " CG  GLU A  37 " =    0.917
peak=    3.308 closest distance to " OG1 THR A 221 " =    1.158
peak=    3.308 closest distance to " CD1 ILE A 263 " =    1.034
peak=    3.307 closest distance to " CE3 TRP A 150 " =    1.092
peak=    3.306 closest distance to " N   ASP A 298 " =    0.978
peak=    3.305 closest distance to " N   ASN A 187 " =    0.815
peak=    3.303 closest distance to " O   HOH Z 369 " =    1.452
peak=    3.303 closest distance to " CB  LEU A 281 " =    0.793
peak=    3.300 closest distance to " CA  ALA A  21 " =    1.590
peak=    3.297 closest distance to " O   HOH Z 133 " =    1.718
peak=    3.294 closest distance to " CB  ALA A  71 " =    1.066
peak=    3.293 closest distance to " CB  THR A 235 " =    1.569
peak=    3.289 closest distance to " CG2 THR A 220 " =    0.822
peak=    3.287 closest distance to " N   SER A 271 " =    1.082
peak=    3.284 closest distance to " CA  VAL A 125 " =    1.101
peak=    3.284 closest distance to " CZ3 TRP A  85 " =    1.183
peak=    3.284 closest distance to " CA  GLY A 133 " =    3.715
peak=    3.279 closest distance to " O   HOH Z 272 " =    1.848
peak=    3.279 closest distance to " O   HOH Z  47 " =    2.986
peak=    3.279 closest distance to " N   ILE A  33 " =    0.917
peak=    3.273 closest distance to " O   ALA A  84 " =    1.521
peak=    3.273 closest distance to " CZ  PHE A  38 " =    1.000
peak=    3.270 closest distance to " OG  SER A  62 " =    2.710
peak=    3.269 closest distance to " O   HOH Z 134 " =    1.918
peak=    3.268 closest distance to " NH1 ARG A 138 " =    1.103
peak=    3.264 closest distance to " CG1 VAL A 153 " =    1.190
peak=    3.257 closest distance to " CB  ALA A 137 " =    0.983
peak=    3.253 closest distance to " NE2 GLN A  58 " =    3.588
peak=    3.253 closest distance to " O   HOH Z  88 " =    2.885
peak=    3.252 closest distance to " O   HOH Z 112 " =    1.216
peak=    3.252 closest distance to " CB  ASN A 187 " =    1.186
peak=    3.251 closest distance to " O   HOH Z 327 " =    2.917
peak=    3.251 closest distance to " O   HOH Z 232 " =    2.353
peak=    3.246 closest distance to " O   HOH Z 214 " =    1.705
peak=    3.245 closest distance to " CA  ASP A 162 " =    1.254
peak=    3.245 closest distance to " O   ALA A 292 " =    1.657
peak=    3.245 closest distance to " OE1 GLN A  73 " =    1.316
peak=    3.244 closest distance to " N   PHE A  59 " =    1.149
peak=    3.244 closest distance to " CD  LYS A 289 " =    1.132
peak=    3.243 closest distance to " O   HOH Z 154 " =    1.442
peak=    3.239 closest distance to " O   HOH Z 141 " =    1.601
peak=    3.238 closest distance to " CD  ARG A 139 " =    1.157
peak=    3.237 closest distance to " O   HOH Z 371 " =    1.771
peak=    3.236 closest distance to " O   HOH Z 166 " =    1.925
peak=    3.216 closest distance to " O   HOH Z  80 " =    2.448
peak=    3.208 closest distance to " CB  SER A  26 " =    0.863
peak=    3.206 closest distance to " O   HOH Z 379 " =    3.433
peak=    3.203 closest distance to " CA  GLY A  23 " =    0.972
peak=    3.202 closest distance to " O   PHE A 192 " =    1.351
peak=    3.201 closest distance to " O   HOH Z 255 " =    0.930
peak=    3.198 closest distance to " O   HOH Z 358 " =    1.657
peak=    3.197 closest distance to " OD1 ASP A 191 " =    1.696
peak=    3.194 closest distance to " O   LYS A 289 " =    1.045
peak=    3.193 closest distance to " O   HOH Z 110 " =    1.843
peak=    3.193 closest distance to " O   HOH Z 151 " =    1.748
peak=    3.187 closest distance to " CB  SER A  62 " =    3.970
peak=    3.187 closest distance to " CD  GLN A  73 " =    1.156
peak=    3.185 closest distance to " NE2 GLN A 278 " =    2.527
peak=    3.183 closest distance to " O   HOH Z 371 " =    2.521
peak=    3.180 closest distance to " CD  GLU A 152 " =    0.749
peak=    3.177 closest distance to " O   GLN A  77 " =    0.893
peak=    3.177 closest distance to " N   LYS A 166 " =    0.983
peak=    3.177 closest distance to " CD  LYS A  76 " =    1.833
peak=    3.174 closest distance to " O   HOH Z 158 " =    2.964
peak=    3.174 closest distance to " O   HOH Z  65 " =    1.146
peak=    3.170 closest distance to " ND2 ASN A 249 " =    2.129
peak=    3.169 closest distance to " CD  LYS A 119 " =    1.895
peak=    3.169 closest distance to " CG AARG A 102 " =    1.337
peak=    3.168 closest distance to " O   HOH Z 379 " =    2.859
peak=    3.168 closest distance to " CA  ARG A  66 " =    0.877
peak=    3.166 closest distance to " OE1 GLU A  37 " =    1.105
peak=    3.163 closest distance to " O   GLY A  91 " =    1.210
peak=    3.161 closest distance to " O   HOH Z 406 " =    1.860
peak=    3.159 closest distance to " CA  ALA A  51 " =    1.026
peak=    3.159 closest distance to " O   HOH Z 185 " =    1.639
peak=    3.150 closest distance to " ND2 ASN A  60 " =    4.967
peak=    3.149 closest distance to " CG1BVAL A 121 " =    1.046
peak=    3.147 closest distance to " CD1 LEU A 167 " =    1.088
peak=    3.144 closest distance to " OG ASER A  12 " =    1.133
peak=    3.139 closest distance to " O   HOH Z 250 " =    1.446
peak=    3.136 closest distance to " O   HOH Z 213 " =    1.736
peak=    3.136 closest distance to " CB  GLU A 128 " =    1.058
peak=    3.134 closest distance to " O   HOH Z 171 " =    3.647
peak=    3.127 closest distance to " O   HOH Z 284 " =    2.837
peak=    3.127 closest distance to " CB  TYR A 169 " =    0.847
peak=    3.121 closest distance to " O   HOH Z 191 " =    2.315
peak=    3.117 closest distance to " CB  GLU A  46 " =    1.165
peak=    3.113 closest distance to " O   THR A 220 " =    1.145
peak=    3.111 closest distance to " O   HOH Z 297 " =    4.365
peak=    3.109 closest distance to " CA  ALA A 248 " =    1.351
peak=    3.096 closest distance to " OG  SER A 135 " =    1.494
peak=    3.090 closest distance to " CB  PRO A 243 " =    1.142
peak=    3.089 closest distance to " CG  LYS A 119 " =    0.995
peak=    3.088 closest distance to " CA  ASP A 124 " =    0.918
peak=    3.087 closest distance to " O   HOH Z  84 " =    1.302
peak=    3.084 closest distance to " CB  GLN A  89 " =    1.188
peak=    3.083 closest distance to " CD1 ILE A 199 " =    1.091
peak=    3.082 closest distance to " CB  ASN A 176 " =    0.903
peak=    3.082 closest distance to " CE1 TYR A  30 " =    0.963
peak=    3.062 closest distance to " O   HOH Z 238 " =    1.670
peak=    3.060 closest distance to " CD  GLN A  73 " =    1.240
peak=    3.033 closest distance to " CB  PHE A  16 " =    1.293
peak=    3.032 closest distance to " O   HOH Z 369 " =    2.042
peak=    3.012 closest distance to " CB  LYS A 119 " =    1.390

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.738 - 5.632
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 209
   mapped sites are within: 0.738 - 5.632

peak=   -4.498 closest distance to " CG1 VAL A 112 " =    2.698
peak=   -4.420 closest distance to " O   HOH Z 203 " =    1.027
peak=   -4.365 closest distance to " O   HOH Z 400 " =    0.859
peak=   -4.345 closest distance to " CG2BVAL A  41 " =    2.012
peak=   -4.216 closest distance to " CG  PRO A 243 " =    1.764
peak=   -4.174 closest distance to " O   HOH Z  44 " =    1.877
peak=   -4.164 closest distance to " O   HOH Z 411 " =    5.256
peak=   -4.127 closest distance to " CD  ARG A 269 " =    2.658
peak=   -4.116 closest distance to " O   PRO A 198 " =    1.250
peak=   -4.110 closest distance to " O   HOH Z 196 " =    1.367
peak=   -4.051 closest distance to " CD  ARG A  14 " =    3.179
peak=   -4.039 closest distance to " CG2 VAL A 189 " =    2.285
peak=   -4.024 closest distance to " CG2 VAL A 230 " =    1.056
peak=   -3.996 closest distance to " CG1 VAL A 296 " =    1.002
peak=   -3.996 closest distance to " CA  GLU A 277 " =    0.993
peak=   -3.987 closest distance to " O   HOH Z  52 " =    1.976
peak=   -3.983 closest distance to " N   SER A 134 " =    1.123
peak=   -3.929 closest distance to " O   SER A   3 " =    0.889
peak=   -3.921 closest distance to " O   LYS A  76 " =    1.400
peak=   -3.920 closest distance to " CD  LYS A 289 " =    2.290
peak=   -3.903 closest distance to " CD  GLN A  58 " =    0.879
peak=   -3.888 closest distance to " CG2 THR A 279 " =    1.730
peak=   -3.882 closest distance to " O   HOH Z  52 " =    0.879
peak=   -3.870 closest distance to " CE3 TRP A 150 " =    2.192
peak=   -3.869 closest distance to " CD  GLN A 223 " =    1.267
peak=   -3.865 closest distance to " NH2 ARG A  36 " =    1.152
peak=   -3.840 closest distance to " O   HOH Z 250 " =    1.639
peak=   -3.790 closest distance to " OD2 ASP A 171 " =    1.932
peak=   -3.767 closest distance to " NH1 ARG A 195 " =    0.958
peak=   -3.736 closest distance to " N   VAL A  72 " =    1.001
peak=   -3.735 closest distance to " O   HOH Z 265 " =    1.495
peak=   -3.734 closest distance to " CG  GLN A  58 " =    1.196
peak=   -3.706 closest distance to " C   LEU A 101 " =    1.066
peak=   -3.700 closest distance to " O   HOH Z 192 " =    1.945
peak=   -3.697 closest distance to " O   HOH Z 136 " =    1.629
peak=   -3.695 closest distance to " CA  GLY A 241 " =    2.325
peak=   -3.691 closest distance to " O   HOH Z  64 " =    2.675
peak=   -3.679 closest distance to " O   HOH Z 156 " =    3.042
peak=   -3.678 closest distance to " CG2 ILE A  49 " =    2.911
peak=   -3.677 closest distance to " O   VAL A 174 " =    2.129
peak=   -3.662 closest distance to " CG  GLN A  77 " =    1.019
peak=   -3.658 closest distance to " CB  ALA A 291 " =    2.380
peak=   -3.654 closest distance to " O   HOH Z  40 " =    2.818
peak=   -3.647 closest distance to " CA  ASP A 298 " =    1.166
peak=   -3.641 closest distance to " CD2 PHE A  61 " =    2.147
peak=   -3.640 closest distance to " C   ASN A 285 " =    2.176
peak=   -3.638 closest distance to " O   HOH Z 155 " =    1.651
peak=   -3.632 closest distance to " O   HOH Z 122 " =    1.369
peak=   -3.628 closest distance to " O   HOH Z  65 " =    1.549
peak=   -3.619 closest distance to " OD1 ASN A 301 " =    0.775
peak=   -3.608 closest distance to " O   HOH Z 361 " =    4.055
peak=   -3.599 closest distance to " O   HOH Z 174 " =    1.677
peak=   -3.584 closest distance to " CE2 PHE A 283 " =    2.593
peak=   -3.582 closest distance to " ND2 ASN A  60 " =    1.539
peak=   -3.574 closest distance to " O   HOH Z 352 " =    1.841
peak=   -3.573 closest distance to " CA  SER A 276 " =    1.352
peak=   -3.568 closest distance to " CE  LYS A  76 " =    0.966
peak=   -3.567 closest distance to " CB  ILE A 120 " =    1.122
peak=   -3.567 closest distance to " O   HOH Z 213 " =    1.512
peak=   -3.549 closest distance to " OD1 ASP A 272 " =    1.561
peak=   -3.538 closest distance to " CD  GLU A 236 " =    1.178
peak=   -3.534 closest distance to " CG  ASN A 110 " =    1.038
peak=   -3.528 closest distance to " CD1 ILE A 263 " =    2.571
peak=   -3.512 closest distance to " O   HOH Z 231 " =    1.742
peak=   -3.511 closest distance to " CE2 PHE A  61 " =    2.631
peak=   -3.509 closest distance to " O   ASN A 187 " =    1.692
peak=   -3.490 closest distance to " O   HOH Z 222 " =    1.260
peak=   -3.486 closest distance to " O   HOH Z 418 " =    1.397
peak=   -3.482 closest distance to " O   HOH Z 340 " =    1.464
peak=   -3.472 closest distance to " CA  TRP A 274 " =    0.971
peak=   -3.460 closest distance to " O   HOH Z  10 " =    1.474
peak=   -3.455 closest distance to " OD1 ASP A 107 " =    1.113
peak=   -3.453 closest distance to " SG  CYS A 254 " =    2.914
peak=   -3.451 closest distance to " O   HOH Z  30 " =    0.784
peak=   -3.449 closest distance to " N   ALA A 295 " =    0.922
peak=   -3.444 closest distance to " CE3 TRP A 274 " =    2.533
peak=   -3.439 closest distance to " CG1 VAL A 153 " =    2.286
peak=   -3.438 closest distance to " CA  SER A 164 " =    2.062
peak=   -3.437 closest distance to " O   VAL A  72 " =    0.986
peak=   -3.432 closest distance to " NH2 ARG A  66 " =    1.703
peak=   -3.432 closest distance to " CD  ARG A  36 " =    0.948
peak=   -3.426 closest distance to " O   HOH Z 109 " =    3.927
peak=   -3.415 closest distance to " O   HOH Z  71 " =    1.349
peak=   -3.413 closest distance to " CE1 PHE A 218 " =    1.457
peak=   -3.412 closest distance to " O   HOH Z 423 " =    3.076
peak=   -3.412 closest distance to " CG1AVAL A 121 " =    1.236
peak=   -3.412 closest distance to " O   HOH Z 223 " =    2.341
peak=   -3.411 closest distance to " O   HOH Z 259 " =    1.544
peak=   -3.410 closest distance to " CZ  TYR A 169 " =    1.526
peak=   -3.408 closest distance to " O   HOH Z  19 " =    2.212
peak=   -3.405 closest distance to " O   HOH Z  81 " =    1.514
peak=   -3.405 closest distance to " O   HOH Z  53 " =    1.131
peak=   -3.404 closest distance to " NE2 GLN A 194 " =    2.216
peak=   -3.396 closest distance to " O   HOH Z 166 " =    1.402
peak=   -3.396 closest distance to " O   HOH Z  54 " =    1.624
peak=   -3.395 closest distance to " O   ASP A 298 " =    1.870
peak=   -3.394 closest distance to " O   HOH Z 384 " =    1.734
peak=   -3.391 closest distance to " CD2 HIS A 115 " =    0.990
peak=   -3.388 closest distance to " CZ2 TRP A 179 " =    2.138
peak=   -3.387 closest distance to " CG  PRO A 163 " =    1.953
peak=   -3.385 closest distance to " O   HOH Z  38 " =    3.339
peak=   -3.380 closest distance to " O   HOH Z  67 " =    1.755
peak=   -3.379 closest distance to " O   HOH Z 342 " =    0.903
peak=   -3.377 closest distance to " O   SER A   3 " =    1.068
peak=   -3.376 closest distance to " CD1 PHE A  59 " =    1.662
peak=   -3.373 closest distance to " O   HOH Z 260 " =    2.046
peak=   -3.373 closest distance to " O   SER A 271 " =    2.186
peak=   -3.373 closest distance to " CA  GLY A 241 " =    3.382
peak=   -3.363 closest distance to " CA  VAL A 197 " =    1.045
peak=   -3.360 closest distance to " CG  GLN A  11 " =    1.202
peak=   -3.359 closest distance to " O   HOH Z  30 " =    1.573
peak=   -3.358 closest distance to " N   ALA A  43 " =    2.646
peak=   -3.358 closest distance to " O   HOH Z 114 " =    1.646
peak=   -3.357 closest distance to " O   HOH Z  43 " =    1.470
peak=   -3.353 closest distance to " N   ILE A 120 " =    1.179
peak=   -3.353 closest distance to " CG  PRO A 198 " =    1.585
peak=   -3.344 closest distance to " O   HOH Z 137 " =    1.445
peak=   -3.342 closest distance to " CB  ALA A 161 " =    2.594
peak=   -3.339 closest distance to " O   HOH Z 216 " =    0.936
peak=   -3.331 closest distance to " O   HOH Z 405 " =    1.792
peak=   -3.329 closest distance to " CB  ALA A   9 " =    2.381
peak=   -3.328 closest distance to " O   HOH Z 124 " =    1.617
peak=   -3.325 closest distance to " O   HOH Z 197 " =    1.777
peak=   -3.325 closest distance to " OG1 THR A  82 " =    1.815
peak=   -3.316 closest distance to " O   HOH Z  17 " =    1.270
peak=   -3.314 closest distance to " OG  SER A  28 " =    2.029
peak=   -3.306 closest distance to " CB  PHE A 155 " =    2.451
peak=   -3.304 closest distance to " O   HOH Z 426 " =    0.879
peak=   -3.304 closest distance to " OE1 GLU A  44 " =    0.929
peak=   -3.302 closest distance to " ND2 ASN A 110 " =    1.067
peak=   -3.295 closest distance to " O   HOH Z  55 " =    1.588
peak=   -3.290 closest distance to " CB  ASP A 162 " =    2.735
peak=   -3.288 closest distance to " NH1 ARG A 219 " =    2.049
peak=   -3.285 closest distance to " O   HOH Z 203 " =    0.825
peak=   -3.283 closest distance to " O   HOH Z  16 " =    1.532
peak=   -3.278 closest distance to " OG BSER A 134 " =    1.397
peak=   -3.273 closest distance to " CD2 TYR A 293 " =    1.809
peak=   -3.271 closest distance to " O   HOH Z 118 " =    4.890
peak=   -3.265 closest distance to " CD2 LEU A 228 " =    2.602
peak=   -3.263 closest distance to " O   HOH Z  78 " =    2.054
peak=   -3.255 closest distance to " CG  GLN A 103 " =    2.159
peak=   -3.254 closest distance to " CA  THR A 264 " =    1.495
peak=   -3.248 closest distance to " OG  SER A  87 " =    1.825
peak=   -3.242 closest distance to " O   HOH Z   2 " =    2.436
peak=   -3.241 closest distance to " CA  ASN A 127 " =    1.058
peak=   -3.240 closest distance to " O   HOH Z 388 " =    1.896
peak=   -3.221 closest distance to " CG  ASP A 286 " =    1.432
peak=   -3.219 closest distance to " O   HOH Z 135 " =    1.218
peak=   -3.217 closest distance to " CA  ASP A  65 " =    1.092
peak=   -3.212 closest distance to " O   HOH Z 269 " =    1.336
peak=   -3.208 closest distance to " O   THR A  82 " =    1.429
peak=   -3.207 closest distance to " OD1 ASP A 231 " =    0.849
peak=   -3.201 closest distance to " CB  ALA A 248 " =    2.266
peak=   -3.194 closest distance to " CA  ALA A 114 " =    1.095
peak=   -3.192 closest distance to " OG1 THR A  82 " =    1.352
peak=   -3.189 closest distance to " CA  GLY A 229 " =    2.506
peak=   -3.188 closest distance to " O   HOH Z 289 " =    1.884
peak=   -3.187 closest distance to " OE1 GLN A  88 " =    1.282
peak=   -3.179 closest distance to " CB  ARG A 159 " =    2.070
peak=   -3.174 closest distance to " O   HOH Z 198 " =    2.026
peak=   -3.174 closest distance to " O   ALA A  43 " =    1.880
peak=   -3.172 closest distance to " CZ  TYR A  68 " =    1.227
peak=   -3.171 closest distance to " O  BHOH Z  74 " =    1.323
peak=   -3.170 closest distance to " CG2 VAL A 202 " =    2.717
peak=   -3.165 closest distance to " O   THR A 251 " =    1.643
peak=   -3.164 closest distance to " CG  GLU A  53 " =    1.483
peak=   -3.163 closest distance to " NE2 GLN A 278 " =    2.045
peak=   -3.162 closest distance to " CE2 PHE A 218 " =    2.339
peak=   -3.162 closest distance to " O   HOH Z 147 " =    2.163
peak=   -3.149 closest distance to " OXT GLY A 302 " =    2.962
peak=   -3.143 closest distance to " O   HOH Z  70 " =    2.046
peak=   -3.143 closest distance to " O   HOH Z 310 " =    3.709
peak=   -3.142 closest distance to " O   HOH Z 345 " =    2.627
peak=   -3.134 closest distance to " CA  GLY A  98 " =    2.250
peak=   -3.133 closest distance to " CG1BVAL A  72 " =    1.735
peak=   -3.124 closest distance to " CG  ARG A 259 " =    2.459
peak=   -3.124 closest distance to " N   ALA A 184 " =    0.950
peak=   -3.118 closest distance to " CG1BVAL A  72 " =    5.632
peak=   -3.111 closest distance to " OG  SER A 273 " =    2.301
peak=   -3.110 closest distance to " OD1 ASN A  39 " =    0.949
peak=   -3.109 closest distance to " CD2 LEU A 237 " =    2.486
peak=   -3.109 closest distance to " CZ  PHE A 225 " =    1.075
peak=   -3.109 closest distance to " O   HOH Z 132 " =    4.569
peak=   -3.105 closest distance to " O   HOH Z 244 " =    1.164
peak=   -3.104 closest distance to " CA  TYR A  68 " =    2.713
peak=   -3.103 closest distance to " CA  PRO A 243 " =    1.506
peak=   -3.098 closest distance to " O   HOH Z 128 " =    3.262
peak=   -3.097 closest distance to " CA  LEU A 143 " =    1.001
peak=   -3.097 closest distance to " OD1 ASN A 148 " =    1.249
peak=   -3.095 closest distance to " CB  VAL A 230 " =    0.981
peak=   -3.090 closest distance to " O   MET A 113 " =    1.286
peak=   -3.089 closest distance to " O   HOH Z 407 " =    3.052
peak=   -3.088 closest distance to " O   HOH Z  91 " =    2.309
peak=   -3.087 closest distance to " CZ  ARG A 259 " =    0.986
peak=   -3.084 closest distance to " O   HOH Z 278 " =    1.131
peak=   -3.082 closest distance to " O   GLN A  11 " =    0.990
peak=   -3.076 closest distance to " O   HOH Z  60 " =    1.805
peak=   -3.076 closest distance to " C   HIS A 108 " =    1.337
peak=   -3.073 closest distance to " O   PHE A 218 " =    1.258
peak=   -3.072 closest distance to " C   ILE A 120 " =    1.216
peak=   -3.067 closest distance to " N   VAL A 230 " =    0.920
peak=   -3.060 closest distance to " SD  MET A 188 " =    1.626
peak=   -3.057 closest distance to " O   HOH Z 215 " =    1.074
peak=   -3.050 closest distance to " N   VAL A  72 " =    0.738
peak=   -3.050 closest distance to " ND2BASN A 224 " =    2.187
peak=   -3.045 closest distance to " O   ILE A 120 " =    1.466
peak=   -3.037 closest distance to " O   HOH Z  32 " =    2.131
peak=   -3.026 closest distance to " O   TYR A  15 " =    1.875
peak=   -3.020 closest distance to " O   HOH Z 195 " =    1.807

================= 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    :  0.5221 0.5150   6.315304e+00   6.305861e+00
   1_bss:  0.5164 0.5096   6.311257e+00   6.303497e+00
   1_xyz:  0.4663 0.4809   6.268717e+00   6.278632e+00
   1_adp:  0.4253 0.4816   6.227539e+00   6.278682e+00
   1_occ:  0.4246 0.4819   6.227391e+00   6.279283e+00
   2_bss:  0.4220 0.4767   6.229164e+00   6.279676e+00
   2_xyz:  0.3670 0.4461   6.137101e+00   6.238769e+00
   2_adp:  0.3598 0.4302   6.122800e+00   6.219202e+00
   2_occ:  0.3596 0.4299   6.122169e+00   6.218545e+00
   3_bss:  0.3592 0.4293   6.124203e+00   6.218979e+00
   3_xyz:  0.2888 0.3457   5.942435e+00   6.076514e+00
   3_adp:  0.2624 0.3233   5.871064e+00   6.025203e+00
   3_occ:  0.2619 0.3243   5.871063e+00   6.026249e+00
   4_bss:  0.2603 0.3227   5.868270e+00   6.025326e+00
   4_xyz:  0.2064 0.2560   5.658564e+00   5.836351e+00
   4_adp:  0.1907 0.2451   5.603505e+00   5.798957e+00
   4_occ:  0.1905 0.2453   5.603033e+00   5.798994e+00
   5_bss:  0.1905 0.2456   5.603990e+00   5.799825e+00
   5_xyz:  0.1648 0.2170   5.481088e+00   5.688377e+00
   5_adp:  0.1562 0.2143   5.447560e+00   5.668586e+00
   5_occ:  0.1561 0.2144   5.447397e+00   5.668454e+00
   5_bss:  0.1565 0.2149   5.450971e+00   5.671292e+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:  0.294  20.001   4.960  10.459  10.175   0.000   0.000   0.000
   1_xyz:  0.294  20.001   4.960  10.459  10.175   0.000   0.000   0.000
   1_adp:  0.294  20.001   4.960  10.459  10.175   0.000   0.000   0.000
   1_occ:  0.294  20.001   4.960  10.459  10.175   0.000   0.000   0.000
   2_bss:  0.313  50.001   1.626   5.548   5.609   0.000   0.000   0.000
   2_xyz:  0.313  50.001   1.626   5.548   5.609   0.000   0.000   0.000
   2_adp:  0.313  50.001   1.626   5.548   5.609   0.000   0.000   0.000
   2_occ:  0.313  50.001   1.626   5.548   5.609   0.000   0.000   0.000
   3_bss:  0.304  50.001   0.911   3.613   3.470   0.000   0.000   0.000
   3_xyz:  0.304  50.001   0.911   3.613   3.470   0.000   0.000   0.000
   3_adp:  0.304  50.001   0.911   3.613   3.470   0.000   0.000   0.000
   3_occ:  0.304  50.001   0.911   3.613   3.470   0.000   0.000   0.000
   4_bss:  0.325  71.410  -0.462   1.633   1.814   0.000   0.000   0.000
   4_xyz:  0.325  71.410  -0.462   1.633   1.814   0.000   0.000   0.000
   4_adp:  0.325  71.410  -0.462   1.633   1.814   0.000   0.000   0.000
   4_occ:  0.325  71.410  -0.462   1.633   1.814   0.000   0.000   0.000
   5_bss:  0.332  76.542  -0.784   0.829   1.456   0.000   0.000   0.000
   5_xyz:  0.332  76.542  -0.784   0.829   1.456   0.000   0.000   0.000
   5_adp:  0.332  76.542  -0.784   0.829   1.456   0.000   0.000   0.000
   5_occ:  0.332  76.542  -0.784   0.829   1.456   0.000   0.000   0.000
   5_bss:  0.339  90.488  -1.213   0.176   1.037   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.434 0.3102  0.3609    85396.995
   1_bss:  66.233 0.3122  0.4607    85316.538
   1_xyz:  58.495 0.4121  0.6022    71265.901
   1_adp:  59.360 0.4005  0.6717    72424.974
   1_occ:  59.480 0.3989  0.6676    72733.386
   2_bss:  59.338 0.4007  0.5882    72593.605
   2_xyz:  52.620 0.4862  0.7198    60195.421
   2_adp:  49.778 0.5225  0.7606    55440.476
   2_occ:  49.710 0.5233  0.7614    55259.834
   3_bss:  49.676 0.5238  0.7238    55281.501
   3_xyz:  37.479 0.6722  0.9022    34208.177
   3_adp:  34.155 0.7113  0.9259    29164.495
   3_occ:  34.242 0.7103  0.9242    29254.178
   4_bss:  34.062 0.7122  0.8742    28947.302
   4_xyz:  25.824 0.8026  0.9468    17452.817
   4_adp:  24.455 0.8171  0.9448    15986.256
   4_occ:  24.440 0.8172  0.9447    15970.599
   5_bss:  24.433 0.8173  0.9287    15983.922
   5_xyz:  21.043 0.8518  0.9505    12312.774
   5_adp:  20.502 0.8572  0.9418    11792.764
   5_occ:  20.496 0.8572  0.9418    11792.222
   5_bss:  20.565 0.8567  0.9473    11898.073
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4720e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4720e+01
   1_xyz:   1.747  0.013  0.108 18.499  0.007  4.123   1.5156e-01
   1_adp:   1.747  0.013  0.108 18.499  0.007  4.123   1.5156e-01
   1_occ:   1.747  0.013  0.108 18.499  0.007  4.123   1.5156e-01
   2_bss:   1.747  0.013  0.108 18.499  0.007  4.123   1.5156e-01
   2_xyz:   1.499  0.011  0.098 17.702  0.006  4.105   1.3078e-01
   2_adp:   1.499  0.011  0.098 17.702  0.006  4.105   1.3078e-01
   2_occ:   1.499  0.011  0.098 17.702  0.006  4.105   1.3078e-01
   3_bss:   1.499  0.011  0.098 17.702  0.006  4.105   1.3078e-01
   3_xyz:   1.463  0.012  0.099 16.964  0.005  4.113   1.2605e-01
   3_adp:   1.463  0.012  0.099 16.964  0.005  4.113   1.2605e-01
   3_occ:   1.463  0.012  0.099 16.964  0.005  4.113   1.2605e-01
   4_bss:   1.463  0.012  0.099 16.964  0.005  4.113   1.2605e-01
   4_xyz:   1.163  0.009  0.083 16.016  0.004  4.136   8.4334e-02
   4_adp:   1.163  0.009  0.083 16.016  0.004  4.136   8.4334e-02
   4_occ:   1.163  0.009  0.083 16.016  0.004  4.136   8.4334e-02
   5_bss:   1.163  0.009  0.083 16.016  0.004  4.136   8.4334e-02
   5_xyz:   1.058  0.008  0.079 15.382  0.003  4.131   6.8805e-02
   5_adp:   1.058  0.008  0.079 15.382  0.003  4.131   6.8805e-02
   5_occ:   1.058  0.008  0.079 15.382  0.003  4.131   6.8805e-02
   5_bss:   1.058  0.008  0.079 15.382  0.003  4.131   6.8805e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0931e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0931e+00
   1_xyz:  14.332  0.122  0.452 88.300  0.058  2.208   1.0380e-01
   1_adp:  14.332  0.122  0.452 88.300  0.058  2.208   1.0380e-01
   1_occ:  14.332  0.122  0.452 88.300  0.058  2.208   1.0380e-01
   2_bss:  14.332  0.122  0.452 88.300  0.058  2.208   1.0380e-01
   2_xyz:   9.060  0.084  0.357 83.340  0.029  2.036   8.3898e-02
   2_adp:   9.060  0.084  0.357 83.340  0.029  2.036   8.3898e-02
   2_occ:   9.060  0.084  0.357 83.340  0.029  2.036   8.3898e-02
   3_bss:   9.060  0.084  0.357 83.340  0.029  2.036   8.3898e-02
   3_xyz:  10.447  0.078  0.347 89.017  0.034  2.071   8.1941e-02
   3_adp:  10.447  0.078  0.347 89.017  0.034  2.071   8.1941e-02
   3_occ:  10.447  0.078  0.347 89.017  0.034  2.071   8.1941e-02
   4_bss:  10.447  0.078  0.347 89.017  0.034  2.071   8.1941e-02
   4_xyz:   7.696  0.065  0.262 86.114  0.042  2.181   7.0157e-02
   4_adp:   7.696  0.065  0.262 86.114  0.042  2.181   7.0157e-02
   4_occ:   7.696  0.065  0.262 86.114  0.042  2.181   7.0157e-02
   5_bss:   7.696  0.065  0.262 86.114  0.042  2.181   7.0157e-02
   5_xyz:   7.211  0.054  0.272 84.223  0.036  2.278   5.3111e-02
   5_adp:   7.211  0.054  0.272 84.223  0.036  2.278   5.3111e-02
   5_occ:   7.211  0.054  0.272 84.223  0.036  2.278   5.3111e-02
   5_bss:   7.211  0.054  0.272 84.223  0.036  2.278   5.3111e-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: 131.23   0.00  20.30 101.96   0.00  18.45 131.23   0.00  30.37
   1_occ: 131.23   0.00  20.30 101.96   0.00  18.45 131.23   0.00  30.37
   2_bss: 131.23   0.00  20.30 101.96   0.00  18.45 131.23   0.00  30.37
   2_xyz: 131.23   0.00  20.30 101.96   0.00  18.45 131.23   0.00  30.37
   2_adp: 119.46   0.00  16.67  76.14   0.00  14.64 119.46   0.00  27.70
   2_occ: 119.46   0.00  16.67  76.14   0.00  14.64 119.46   0.00  27.70
   3_bss: 119.46   0.00  16.67  76.14   0.00  14.64 119.46   0.00  27.70
   3_xyz: 119.46   0.00  16.67  76.14   0.00  14.64 119.46   0.00  27.70
   3_adp: 105.17   0.00  16.21  68.26   0.00  12.71 105.17   0.00  35.27
   3_occ: 105.17   0.00  16.21  68.26   0.00  12.71 105.17   0.00  35.27
   4_bss: 105.17   0.00  16.21  68.26   0.00  12.71 105.17   0.00  35.27
   4_xyz: 105.17   0.00  16.21  68.26   0.00  12.71 105.17   0.00  35.27
   4_adp: 100.40   0.00  16.54  77.94   0.00  12.08 100.40   1.30  40.81
   4_occ: 100.40   0.00  16.54  77.94   0.00  12.08 100.40   1.30  40.81
   5_bss: 100.40   0.00  16.54  77.94   0.00  12.08 100.40   1.30  40.81
   5_xyz: 100.40   0.00  16.54  77.94   0.00  12.08 100.40   1.30  40.81
   5_adp: 104.63   0.00  17.80 101.25   0.00  11.96 104.63   1.20  49.60
   5_occ: 104.63   0.00  17.80 101.25   0.00  11.96 104.63   1.20  49.60
   5_bss: 105.31   0.68  18.48 101.93   0.68  12.64 105.31   1.88  50.28
------------------------------------------------------------------------
 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:    1.219    0.006    0.407
   1_adp:    1.219    0.006    0.407
   1_occ:    1.219    0.006    0.407
   2_bss:    1.219    0.006    0.407
   2_xyz:    1.604    0.031    0.604
   2_adp:    1.604    0.031    0.604
   2_occ:    1.604    0.031    0.604
   3_bss:    1.604    0.031    0.604
   3_xyz:    1.886    0.061    0.825
   3_adp:    1.886    0.061    0.825
   3_occ:    1.886    0.061    0.825
   4_bss:    1.886    0.061    0.825
   4_xyz:    1.945    0.080    0.904
   4_adp:    1.945    0.080    0.904
   4_occ:    1.945    0.080    0.904
   5_bss:    1.945    0.080    0.904
   5_xyz:    2.100    0.035    0.966
   5_adp:    2.100    0.035    0.966
   5_occ:    2.100    0.035    0.966
   5_bss:    2.100    0.035    0.966
------------------------------------------------------------------------

CPU time actual refinement: 354.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_725/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_725/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_725/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_725/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_725/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.35 
  Macro-tasks:
    bulk solvent and scale       = 48.13  
    individual site refinement   = 153.79 
    weights calculation          = 32.76  
    collect and process          = 6.19   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 240.99 
  Micro-tasks:
    mask                            = 3.11   
    f_calc                          = 110.20 
    alpha_beta                      = 8.35   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 120.33 
    fmodel                         = 7.83   
    r_factors                      = 0.29   
    phase_errors                   = 9.47   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 260.97 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.975 micro seconds
Total CPU time: 6.14 minutes
from_scatterers_fft:    617 calls, 109.82 s
gradients_fft:          561 calls, 107.01 s

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

# Date 2008-01-16 Time 02:16:17 PST -0800 (1200478577.00 s)
Start R-work = 0.5221, R-free = 0.5150 (no bulk solvent and anisotropic scale)
Final R-work = 0.1714, R-free = 0.2292 (no bulk solvent and anisotropic scale)

Start R-work = 0.5164, R-free = 0.5096
Final R-work = 0.1565, R-free = 0.2149