# Date 2008-01-16 Time 01:21:07 PST -0800 (1200475267.98 s)
#phil __OFF__

Command line arguments: "../376.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4128
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 376

-------------------------------------------------------------------------------
  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: (69.5475, 45.9914, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


================================== 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: (69.5475, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.96157
Completeness in resolution range: 0.973415
Completeness with d_max=infinity: 0.970377

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8236
                             d_min =   1.9616

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: (69.5475, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.96157
Completeness in resolution range: 0.973415
Completeness with d_max=infinity: 0.970377

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8240 -  4.1971 [2109/2133]  1899   210  10.0%
  bin  2:  4.1971 -  3.3439 [2033/2053]  1828   205  10.1%
  bin  3:  3.3439 -  2.9249 [2005/2024]  1804   201  10.0%
  bin  4:  2.9249 -  2.6592 [1988/2018]  1793   195   9.8%
  bin  5:  2.6592 -  2.4695 [1977/1996]  1779   198  10.0%
  bin  6:  2.4695 -  2.3245 [1965/1990]  1762   203  10.3%
  bin  7:  2.3245 -  2.2085 [1947/1975]  1755   192   9.9%
  bin  8:  2.2085 -  2.1126 [1953/1989]  1759   194   9.9%
  bin  9:  2.1126 -  2.0315 [1930/1972]  1738   192   9.9%
  bin 10:  2.0315 -  1.9616 [1682/1974]  1513   169  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_376/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.52 -     2.19: 25
        2.19 -     2.87: 1255
        2.87 -     3.55: 4601
        3.55 -     4.22: 9410
        4.22 -     4.90: 13661
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.515 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.665 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.715 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  ... (remaining 28947 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_376/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_376/model_refine_001.geo

CPU time processing inputs: 9.27


============================ 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 = 69.5475 45.9914 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4966   r_free= 0.4929   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.294407                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.6811 0.99   1378  152 0.4191 0.4281      6.6194      6.6648|
|  2:  4.6811 -  3.7351 0.99   1315  147 0.4377 0.3927      6.8355      6.7869|
|  3:  3.7351 -  3.2687 0.99   1293  143 0.4637 0.4520      6.7194      6.7751|
|  4:  3.2687 -  2.9725 0.99   1281  146 0.4791 0.4426      6.5619      6.4914|
|  5:  2.9725 -  2.7609 0.99   1286  142 0.5230 0.5313      6.3933       6.397|
|  6:  2.7609 -  2.5991 0.99   1276  140 0.5292 0.5924      6.3081      6.2632|
|  7:  2.5991 -  2.4695 0.99   1274  139 0.5236 0.4527      6.2479      6.2269|
|  8:  2.4695 -  2.3625 0.98   1246  142 0.5492 0.5213       6.213      6.1688|
|  9:  2.3625 -  2.2718 0.98   1266  139 0.5257 0.5855      6.1267      6.1676|
| 10:  2.2718 -  2.1937 1.00   1254  144 0.5279 0.5415      6.1235      6.1572|
| 11:  2.1937 -  2.1253 0.97   1255  132 0.5328 0.5204      6.0555      6.0661|
| 12:  2.1253 -  2.0647 0.98   1240  142 0.5118 0.5480       5.992      6.0173|
| 13:  2.0647 -  2.0105 0.99   1271  140 0.5473 0.5349       5.907      5.8698|
| 14:  2.0105 -  1.9616 0.79    995  111 0.5486 0.4987      5.8504      5.7782|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8240 -  4.6811  1378   152  0.61  41.96   0.79     0.67      98454.24|
|  2:  4.6811 -  3.7351  1315   147  0.65  39.27   0.86     0.75     128790.70|
|  3:  3.7351 -  3.2687  1293   143  0.55  47.57   0.85     0.70     132365.60|
|  4:  3.2687 -  2.9725  1281   146  0.47  54.29   0.81     0.57     114472.94|
|  5:  2.9725 -  2.7609  1286   142  0.36  63.00   0.74     0.44      92082.40|
|  6:  2.7609 -  2.5991  1276   140  0.32  66.19   0.73     0.37      79676.74|
|  7:  2.5991 -  2.4695  1274   139  0.25  71.24   0.72     0.29      74164.55|
|  8:  2.4695 -  2.3625  1246   142  0.22  73.61   0.74     0.27      69422.03|
|  9:  2.3625 -  2.2718  1266   139  0.22  73.49   0.72     0.26      62927.31|
| 10:  2.2718 -  2.1937  1254   144  0.26  70.64   0.76     0.31      55031.25|
| 11:  2.1937 -  2.1253  1255   132  0.25  71.01   0.77     0.33      52027.44|
| 12:  2.1253 -  2.0647  1240   142  0.25  71.41   0.80     0.32      48061.61|
| 13:  2.0647 -  2.0105  1271   140  0.23  72.95   0.74     0.30      41562.56|
| 14:  2.0105 -  1.9616   995   111  0.26  70.59   0.72     0.29      31437.31|
|alpha:            min =        0.26 max =            0.75 mean =         0.42|
|beta:             min =    31437.31 max =       132365.60 mean =     78364.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.99 mean =        63.00|
|phase err.(test): min =        0.00 max =           89.94 mean =        63.15|
|-----------------------------------------------------------------------------|

============================== 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 = 21.102811             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.290   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.211630              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.118   (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 |  1.092 -  1.472:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.472 -  1.853:       17 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.853 -  2.234:      132 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.234 -  2.615:      620 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.615 -  2.996:     1444 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.996 -  3.377:     2602 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.377 -  3.757:     4023 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.757 -  4.138:     5272 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.138 -  4.519:     6783 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.519 -  4.900:     8132 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.724 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.092 |       2.434 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5014   r_free= 0.4932   ksol= 0.00   Bsol= 0.00   scale= 0.763    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.295376                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4877   r_free= 0.4807   ksol= 0.38   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.75,9.81,8.24,0.00,0.00,0.00); trace/3= 8.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.287773                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.005537             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.193   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.907487              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.069   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4877      final r-factor (work) = 0.4242          |
| start r-factor (free) = 0.4807      final r-factor (free) = 0.4451          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.0762 = 16.01 * 0.50 * 6.2919 + 1.00 * 52.7236                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.0328 = 16.01 * 0.50 * 6.2338 + 1.00 * 0.1452                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4242      final r-factor (work) = 0.3828          |
| start r-factor (free) = 0.4451      final r-factor (free) = 0.4341          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.9052 = 1.91 * 1.00 * 6.2338 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.7989 = 1.91 * 1.00 * 6.1734 + 1.00 * 0.0232                              |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.01   15.01    None  None   None       |
|    all(noH): 2823   0      0.00    93.01   15.01    None  None   None       |
|    Sol.    : 438    0      0.00    90.27   24.59    None  None   None       |
|    Mac.    : 2385   0      0.00    93.01   13.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.301: 1155   |   5:    46.504 -  55.804:   53        |
|      1:     9.301 -  18.602:  771   |   6:    55.804 -  65.105:   15        |
|      2:    18.602 -  27.902:  488   |   7:    65.105 -  74.406:    8        |
|      3:    27.902 -  37.203:  222   |   8:    74.406 -  83.707:    1        |
|      4:    37.203 -  46.504:  108   |   9:    83.707 -  93.007:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3828 r_free = 0.4341             target_work(ml) = 6.160         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3823 r_free = 0.4340             target_work(ml) = 6.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3823   r_free= 0.4340   ksol= 0.38   Bsol= 0.00   scale= 1.113    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.75,9.81,8.24,0.00,0.00,0.00); trace/3= 8.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.160014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3798   r_free= 0.4298   ksol= 0.37   Bsol= 34.14   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.59,5.79,5.19,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.159495                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.609717             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.984   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.698832              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.851  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3798      final r-factor (work) = 0.3077          |
| start r-factor (free) = 0.4298      final r-factor (free) = 0.3641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.8697 = 10.61 * 0.50 * 6.1688 + 1.00 * 0.1452                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.3345 = 10.61 * 0.50 * 6.0766 + 1.00 * 0.0990                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3077      final r-factor (work) = 0.2837          |
| start r-factor (free) = 0.3641      final r-factor (free) = 0.3461          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2777 = 0.70 * 1.00 * 6.0766 + 1.00 * 0.0312                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2186 = 0.70 * 1.00 * 5.9650 + 1.00 * 0.0500                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.93   14.33    None  None   None       |
|    all(noH): 2823   0      0.00    95.93   14.33    None  None   None       |
|    Sol.    : 438    0      0.00    88.48   29.60    None  None   None       |
|    Mac.    : 2385   0      0.00    95.93   11.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.593: 1267   |   5:    47.965 -  57.558:   36        |
|      1:     9.593 -  19.186:  816   |   6:    57.558 -  67.151:   10        |
|      2:    19.186 -  28.779:  388   |   7:    67.151 -  76.744:    5        |
|      3:    28.779 -  38.372:  203   |   8:    76.744 -  86.337:    2        |
|      4:    38.372 -  47.965:   93   |   9:    86.337 -  95.929:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2837 r_free = 0.3461             target_work(ml) = 5.942         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2834 r_free = 0.3460             target_work(ml) = 5.942         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2834   r_free= 0.3460   ksol= 0.37   Bsol= 34.14   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.59,5.79,5.19,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.942158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2819   r_free= 0.3446   ksol= 0.33   Bsol= 34.14   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,3.13,3.23,0.00,0.00,0.00); trace/3= 2.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.941937                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.135026              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.510  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.106639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.692   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2819      final r-factor (work) = 0.2246          |
| start r-factor (free) = 0.3446      final r-factor (free) = 0.2874          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4293 = 4.14 * 0.50 * 5.9641 + 1.00 * 0.0985                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1581 = 4.14 * 0.50 * 5.8473 + 1.00 * 0.0687                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2246      final r-factor (work) = 0.2035          |
| start r-factor (free) = 0.2874      final r-factor (free) = 0.2715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4987 = 1.11 * 1.00 * 5.8473 + 1.00 * 0.0278                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3279 = 1.11 * 1.00 * 5.7036 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.69  14.96    None  None   None       |
|    all(noH): 2823   0      0.00    111.69  14.96    None  None   None       |
|    Sol.    : 438    0      1.29    99.21   38.04    None  None   None       |
|    Mac.    : 2385   0      0.00    111.69  10.72    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 -  11.169: 1628   |   5:    55.847 -  67.017:   44        |
|      1:    11.169 -  22.339:  600   |   6:    67.017 -  78.186:   25        |
|      2:    22.339 -  33.508:  245   |   7:    78.186 -  89.355:    3        |
|      3:    33.508 -  44.678:  149   |   8:    89.355 - 100.525:    5        |
|      4:    44.678 -  55.847:  123   |   9:   100.525 - 111.694:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2035 r_free = 0.2715             target_work(ml) = 5.679         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2032 r_free = 0.2712             target_work(ml) = 5.678         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2032   r_free= 0.2712   ksol= 0.33   Bsol= 34.14   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,3.13,3.23,0.00,0.00,0.00); trace/3= 2.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.677694                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2032   r_free= 0.2706   ksol= 0.32   Bsol= 34.14   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,1.92,2.58,0.00,0.00,0.00); trace/3= 1.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.676734                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.175255              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.680  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.214332              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.946  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2032      final r-factor (work) = 0.1614          |
| start r-factor (free) = 0.2706      final r-factor (free) = 0.2195          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1251 = 3.18 * 0.50 * 5.7044 + 1.00 * 0.0687                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9230 = 3.18 * 0.50 * 5.5823 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1614      final r-factor (work) = 0.1521          |
| start r-factor (free) = 0.2195      final r-factor (free) = 0.2016          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2125 = 0.21 * 1.00 * 5.5823 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1758 = 0.21 * 1.00 * 5.4408 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.90  14.01    None  None   None       |
|    all(noH): 2823   0      0.00    107.90  14.01    None  None   None       |
|    Sol.    : 438    0      3.39    94.72   37.36    None  None   None       |
|    Mac.    : 2385   0      0.00    107.90  9.72     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 -  10.790: 1765   |   5:    53.948 -  64.738:   45        |
|      1:    10.790 -  21.579:  537   |   6:    64.738 -  75.528:   21        |
|      2:    21.579 -  32.369:  175   |   7:    75.528 -  86.317:    3        |
|      3:    32.369 -  43.159:  138   |   8:    86.317 -  97.107:    4        |
|      4:    43.159 -  53.948:  134   |   9:    97.107 - 107.897:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1521 r_free = 0.2016             target_work(ml) = 5.397         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1518 r_free = 0.2011             target_work(ml) = 5.395         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1518   r_free= 0.2011   ksol= 0.32   Bsol= 34.14   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,1.92,2.58,0.00,0.00,0.00); trace/3= 1.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.395098                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1519   r_free= 0.2005   ksol= 0.32   Bsol= 34.14   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.03,1.09,2.17,0.00,0.00,0.00); trace/3= 1.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.393804                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.064027              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.281  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.142664              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.752  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1519      final r-factor (work) = 0.1280          |
| start r-factor (free) = 0.2005      final r-factor (free) = 0.1755          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3969 = 3.06 * 0.50 * 5.4415 + 1.00 * 0.0604                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2111 = 3.06 * 0.50 * 5.3177 + 1.00 * 0.0642                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1280      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1755      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0860 = 1.14 * 1.00 * 5.3177 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9840 = 1.14 * 1.00 * 5.2266 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.35  14.25    None  None   None       |
|    all(noH): 2823   0      0.00    109.35  14.25    None  None   None       |
|    Sol.    : 438    0      3.18    95.85   39.85    None  None   None       |
|    Mac.    : 2385   0      0.00    109.35  9.55     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 -  10.935: 1806   |   5:    54.677 -  65.612:   73        |
|      1:    10.935 -  21.871:  517   |   6:    65.612 -  76.547:   29        |
|      2:    21.871 -  32.806:  141   |   7:    76.547 -  87.483:    8        |
|      3:    32.806 -  43.741:  126   |   8:    87.483 -  98.418:    4        |
|      4:    43.741 -  54.677:  118   |   9:    98.418 - 109.353:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1220 r_free = 0.1719             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1717             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1717   ksol= 0.32   Bsol= 34.14   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.03,1.09,2.17,0.00,0.00,0.00); trace/3= 1.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.214253                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.6811 0.99   1378  152 0.1046 0.1360      5.4359      5.5777|
|  2:  4.6811 -  3.7351 0.99   1315  147 0.0917 0.1255      5.4984      5.7239|
|  3:  3.7351 -  3.2687 0.99   1293  143 0.1176 0.1507      5.5737      5.8601|
|  4:  3.2687 -  2.9725 0.99   1281  146 0.1349 0.1905      5.5472      5.7429|
|  5:  2.9725 -  2.7609 0.99   1286  142 0.1427 0.1949      5.4028      5.6215|
|  6:  2.7609 -  2.5991 0.99   1276  140 0.1312 0.1819      5.2851       5.471|
|  7:  2.5991 -  2.4695 0.99   1274  139 0.1390 0.1844      5.2461      5.4946|
|  8:  2.4695 -  2.3625 0.98   1246  142 0.1342 0.1866      5.1714      5.4495|
|  9:  2.3625 -  2.2718 0.98   1266  139 0.1273 0.1802      5.1025      5.3004|
| 10:  2.2718 -  2.1937 1.00   1254  144 0.1212 0.1913      5.0465      5.3164|
| 11:  2.1937 -  2.1253 0.97   1255  132 0.1248 0.1982      5.0276      5.3658|
| 12:  2.1253 -  2.0647 0.98   1240  142 0.1212 0.1825      4.9608      5.2677|
| 13:  2.0647 -  2.0105 0.99   1271  140 0.1182 0.1991      4.8447      5.1623|
| 14:  2.0105 -  1.9616 0.79    995  111 0.1067 0.1601      4.6912      4.9061|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8240 -  4.6811  1378   152  0.93  10.00   0.98     0.96       8220.52|
|  2:  4.6811 -  3.7351  1315   147  0.95   8.90   1.04     1.02      10248.83|
|  3:  3.7351 -  3.2687  1293   143  0.92  12.77   1.05     1.04      12320.68|
|  4:  3.2687 -  2.9725  1281   146  0.91  15.23   1.03     1.01      12337.00|
|  5:  2.9725 -  2.7609  1286   142  0.89  16.92   1.01     0.96       9445.24|
|  6:  2.7609 -  2.5991  1276   140  0.89  17.17   0.99     0.95       8134.07|
|  7:  2.5991 -  2.4695  1274   139  0.88  18.22   1.01     0.98       7519.82|
|  8:  2.4695 -  2.3625  1246   142  0.89  16.78   1.01     0.98       6261.15|
|  9:  2.3625 -  2.2718  1266   139  0.90  16.75   1.02     0.99       5805.00|
| 10:  2.2718 -  2.1937  1254   144  0.89  16.88   1.01     0.97       5243.33|
| 11:  2.1937 -  2.1253  1255   132  0.88  18.49   1.02     0.97       5357.34|
| 12:  2.1253 -  2.0647  1240   142  0.89  17.14   1.03     1.01       4748.27|
| 13:  2.0647 -  2.0105  1271   140  0.90  16.76   1.03     1.02       3743.91|
| 14:  2.0105 -  1.9616   995   111  0.91  14.94   1.01     0.98       2718.78|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2718.78 max =        12337.00 mean =      7399.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.45|
|phase err.(test): min =        0.00 max =           89.95 mean =        14.82|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1720   ksol= 0.31   Bsol= 38.16   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.39,-0.34,0.73,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.216126                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1720   ksol= 0.31   Bsol= 38.16   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.39,-0.34,0.73,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.216126                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.6811 0.99   1378  152 0.1053 0.1367      5.4414       5.587|
|  2:  4.6811 -  3.7351 0.99   1315  147 0.0934 0.1259      5.5144       5.735|
|  3:  3.7351 -  3.2687 0.99   1293  143 0.1186 0.1527      5.5818      5.8715|
|  4:  3.2687 -  2.9725 0.99   1281  146 0.1351 0.1911      5.5514      5.7446|
|  5:  2.9725 -  2.7609 0.99   1286  142 0.1427 0.1962      5.4053      5.6252|
|  6:  2.7609 -  2.5991 0.99   1276  140 0.1312 0.1824      5.2866      5.4731|
|  7:  2.5991 -  2.4695 0.99   1274  139 0.1386 0.1834      5.2448      5.4926|
|  8:  2.4695 -  2.3625 0.98   1246  142 0.1340 0.1851      5.1684      5.4435|
|  9:  2.3625 -  2.2718 0.98   1266  139 0.1267 0.1798      5.1007      5.3007|
| 10:  2.2718 -  2.1937 1.00   1254  144 0.1212 0.1919      5.0447       5.318|
| 11:  2.1937 -  2.1253 0.97   1255  132 0.1245 0.1982      5.0273      5.3656|
| 12:  2.1253 -  2.0647 0.98   1240  142 0.1208 0.1829      4.9598      5.2682|
| 13:  2.0647 -  2.0105 0.99   1271  140 0.1183 0.1987      4.8435      5.1609|
| 14:  2.0105 -  1.9616 0.79    995  111 0.1066 0.1592      4.6876      4.9012|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8240 -  4.6811  1378   152  0.93  10.12   0.98     0.96       8407.00|
|  2:  4.6811 -  3.7351  1315   147  0.94   9.05   1.04     1.02      10485.48|
|  3:  3.7351 -  3.2687  1293   143  0.92  12.93   1.05     1.04      12592.25|
|  4:  3.2687 -  2.9725  1281   146  0.91  15.35   1.02     1.01      12523.22|
|  5:  2.9725 -  2.7609  1286   142  0.89  17.00   1.00     0.96       9527.62|
|  6:  2.7609 -  2.5991  1276   140  0.89  17.19   0.99     0.95       8160.23|
|  7:  2.5991 -  2.4695  1274   139  0.88  18.18   1.00     0.97       7502.23|
|  8:  2.4695 -  2.3625  1246   142  0.90  16.70   1.00     0.98       6209.18|
|  9:  2.3625 -  2.2718  1266   139  0.90  16.70   1.02     0.99       5781.64|
| 10:  2.2718 -  2.1937  1254   144  0.89  16.85   1.01     0.97       5218.24|
| 11:  2.1937 -  2.1253  1255   132  0.88  18.51   1.01     0.97       5366.81|
| 12:  2.1253 -  2.0647  1240   142  0.89  17.14   1.02     1.00       4747.59|
| 13:  2.0647 -  2.0105  1271   140  0.90  16.73   1.02     1.01       3730.43|
| 14:  2.0105 -  1.9616   995   111  0.91  14.84   1.00     0.97       2690.56|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2690.56 max =        12592.25 mean =      7462.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.73 mean =        15.47|
|phase err.(test): min =        0.00 max =           89.46 mean =        14.88|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.374)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.33    110.68  15.57    None  None   None       |
|    all(noH): 2823   0      1.33    110.68  15.57    None  None   None       |
|    Sol.    : 438    0      4.51    97.18   41.18    None  None   None       |
|    Mac.    : 2385   0      1.33    110.68  10.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.325 -  12.260: 1806   |   5:    56.002 -  66.937:   73        |
|      1:    12.260 -  23.196:  517   |   6:    66.937 -  77.872:   29        |
|      2:    23.196 -  34.131:  141   |   7:    77.872 -  88.808:    8        |
|      3:    34.131 -  45.066:  126   |   8:    88.808 -  99.743:    4        |
|      4:    45.066 -  56.002:  118   |   9:    99.743 - 110.678:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.240 - 5.457
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 322
   mapped sites are within: 0.733 - 5.457

peak=   10.569 closest distance to " CB  VAL A 296 " =    1.545
peak=    9.774 closest distance to " CB  VAL A 230 " =    1.408
peak=    7.733 closest distance to " O   HOH Z 390 " =    1.209
peak=    7.357 closest distance to " O   HOH Z 130 " =    1.557
peak=    7.165 closest distance to " O   HOH Z 385 " =    1.391
peak=    7.089 closest distance to " CG  ARG A 138 " =    1.153
peak=    6.437 closest distance to " O   HOH Z  65 " =    1.656
peak=    6.298 closest distance to " CD2 LEU A   5 " =    1.328
peak=    6.093 closest distance to " O   HOH Z 124 " =    1.715
peak=    5.620 closest distance to " O   HOH Z   7 " =    1.798
peak=    5.421 closest distance to " O   HOH Z 424 " =    1.406
peak=    5.406 closest distance to " O   HOH Z 193 " =    1.786
peak=    5.397 closest distance to " NE2 GLN A  11 " =    1.117
peak=    5.372 closest distance to " O   HOH Z 142 " =    1.969
peak=    5.278 closest distance to " O   HOH Z  28 " =    1.545
peak=    5.234 closest distance to " O   HOH Z   9 " =    1.562
peak=    5.208 closest distance to " CG  LEU A   5 " =    1.216
peak=    5.134 closest distance to " CB  VAL A 230 " =    1.182
peak=    5.098 closest distance to " O   HOH Z 403 " =    1.435
peak=    4.942 closest distance to " CB  PRO A  54 " =    1.074
peak=    4.922 closest distance to " CB  ARG A 275 " =    1.020
peak=    4.916 closest distance to " O   HOH Z 278 " =    1.233
peak=    4.877 closest distance to " NH2 ARG A  56 " =    1.943
peak=    4.862 closest distance to " O   PRO A 198 " =    1.263
peak=    4.852 closest distance to " O   HOH Z 126 " =    1.879
peak=    4.852 closest distance to " O   HOH Z 414 " =    1.339
peak=    4.783 closest distance to " O   HOH Z 123 " =    1.390
peak=    4.779 closest distance to " O   HOH Z  78 " =    1.696
peak=    4.746 closest distance to " O   HOH Z 112 " =    1.381
peak=    4.737 closest distance to " CG  PRO A  54 " =    1.255
peak=    4.730 closest distance to " CD2 LEU A 228 " =    1.184
peak=    4.703 closest distance to " CD1AILE A 234 " =    0.908
peak=    4.672 closest distance to " O   HOH Z  63 " =    1.601
peak=    4.592 closest distance to " O   HOH Z 429 " =    1.013
peak=    4.558 closest distance to " O   HOH Z 369 " =    2.264
peak=    4.558 closest distance to " O   HOH Z 214 " =    1.487
peak=    4.511 closest distance to " O   HOH Z 427 " =    1.173
peak=    4.480 closest distance to " O   HOH Z 427 " =    2.260
peak=    4.469 closest distance to " O   HOH Z   2 " =    2.055
peak=    4.465 closest distance to " O   HOH Z 423 " =    1.685
peak=    4.435 closest distance to " CA  PHE A 283 " =    1.286
peak=    4.432 closest distance to " CG  GLN A  11 " =    2.157
peak=    4.420 closest distance to " CG  PRO A 213 " =    1.215
peak=    4.413 closest distance to " O   HOH Z 347 " =    0.974
peak=    4.403 closest distance to " O   HOH Z 410 " =    1.415
peak=    4.398 closest distance to " O   HOH Z  51 " =    1.656
peak=    4.388 closest distance to " O   HOH Z 143 " =    1.302
peak=    4.363 closest distance to " O   HOH Z 316 " =    2.872
peak=    4.325 closest distance to " O   HOH Z 236 " =    1.486
peak=    4.304 closest distance to " CB  SER A   3 " =    1.218
peak=    4.304 closest distance to " O   HOH Z 130 " =    2.112
peak=    4.299 closest distance to " O   HOH Z 132 " =    1.206
peak=    4.295 closest distance to " CE AMET A  47 " =    1.258
peak=    4.287 closest distance to " O   HOH Z 380 " =    1.910
peak=    4.276 closest distance to " CG  PRO A 198 " =    1.280
peak=    4.255 closest distance to " O   HOH Z 232 " =    2.196
peak=    4.239 closest distance to " NH1 ARG A 138 " =    1.024
peak=    4.237 closest distance to " O   HOH Z   1 " =    1.628
peak=    4.233 closest distance to " O   HOH Z 227 " =    1.979
peak=    4.215 closest distance to " O   HOH Z 145 " =    1.787
peak=    4.214 closest distance to " O   HOH Z 426 " =    1.107
peak=    4.191 closest distance to " O   SER A  87 " =    2.435
peak=    4.180 closest distance to " O   HOH Z 298 " =    1.786
peak=    4.168 closest distance to " OG  SER A  62 " =    3.031
peak=    4.151 closest distance to " O   HOH Z 425 " =    1.468
peak=    4.148 closest distance to " O   HOH Z  39 " =    1.522
peak=    4.136 closest distance to " O   HOH Z 405 " =    1.610
peak=    4.112 closest distance to " O   HOH Z 272 " =    1.833
peak=    4.095 closest distance to " O   HOH Z 384 " =    1.623
peak=    4.087 closest distance to " CB  ASN A 148 " =    1.241
peak=    4.078 closest distance to " O   HOH Z 193 " =    1.762
peak=    4.062 closest distance to " O   HOH Z 222 " =    1.248
peak=    4.061 closest distance to " O   HOH Z  69 " =    1.174
peak=    4.027 closest distance to " O   HOH Z 291 " =    1.398
peak=    4.010 closest distance to " O   HOH Z 366 " =    2.631
peak=    4.003 closest distance to " CG  LEU A 228 " =    0.990
peak=    3.993 closest distance to " CB  GLN A 183 " =    1.141
peak=    3.984 closest distance to " NE1 TRP A 274 " =    1.017
peak=    3.979 closest distance to " CB  TRP A 179 " =    1.377
peak=    3.978 closest distance to " O   HOH Z 419 " =    2.054
peak=    3.970 closest distance to " O   HOH Z  59 " =    1.497
peak=    3.963 closest distance to " O   HOH Z 117 " =    1.878
peak=    3.959 closest distance to " O   HOH Z 108 " =    1.878
peak=    3.937 closest distance to " O   HOH Z 422 " =    2.258
peak=    3.936 closest distance to " CB  GLN A 223 " =    1.602
peak=    3.923 closest distance to " O   HOH Z 417 " =    1.261
peak=    3.910 closest distance to " O   HOH Z 344 " =    1.252
peak=    3.895 closest distance to " CG2 THR A 221 " =    1.262
peak=    3.895 closest distance to " OG BSER A 212 " =    2.778
peak=    3.890 closest distance to " CB  VAL A 265 " =    1.253
peak=    3.885 closest distance to " CG  TRP A 179 " =    2.295
peak=    3.885 closest distance to " O   HOH Z  30 " =    1.673
peak=    3.882 closest distance to " O   HOH Z 290 " =    1.010
peak=    3.880 closest distance to " O   HOH Z  71 " =    1.339
peak=    3.878 closest distance to " NH2BARG A 145 " =    1.448
peak=    3.866 closest distance to " O   HOH Z 406 " =    1.707
peak=    3.854 closest distance to " O   HOH Z 263 " =    1.546
peak=    3.852 closest distance to " O   HOH Z  50 " =    1.587
peak=    3.851 closest distance to " O   HOH Z 425 " =    2.011
peak=    3.848 closest distance to " OD2 ASP A 286 " =    2.454
peak=    3.837 closest distance to " O   HOH Z 415 " =    1.059
peak=    3.800 closest distance to " CG2 VAL A 257 " =    0.897
peak=    3.794 closest distance to " CB  ALA A   1 " =    0.958
peak=    3.787 closest distance to " O   HOH Z 383 " =    2.367
peak=    3.786 closest distance to " O   HOH Z 276 " =    1.418
peak=    3.783 closest distance to " O   HOH Z 287 " =    1.789
peak=    3.770 closest distance to " O   HOH Z 411 " =    3.620
peak=    3.764 closest distance to " O   HOH Z 381 " =    1.129
peak=    3.759 closest distance to " NE2 GLN A  73 " =    1.521
peak=    3.759 closest distance to " CB  VAL A 202 " =    1.751
peak=    3.755 closest distance to " O   HOH Z 389 " =    1.250
peak=    3.754 closest distance to " O   HOH Z 371 " =    3.033
peak=    3.751 closest distance to " CG  GLN A  88 " =    1.152
peak=    3.750 closest distance to " CA  ASN A 127 " =    1.110
peak=    3.740 closest distance to " CB  VAL A 121 " =    0.987
peak=    3.737 closest distance to " CB  SER A 276 " =    1.197
peak=    3.734 closest distance to " O   HOH Z  55 " =    2.019
peak=    3.733 closest distance to " O   HOH Z  64 " =    2.050
peak=    3.707 closest distance to " CB BVAL A  41 " =    1.092
peak=    3.702 closest distance to " O   HOH Z 345 " =    3.088
peak=    3.694 closest distance to " O   HOH Z 358 " =    1.286
peak=    3.687 closest distance to " O   HOH Z 130 " =    1.666
peak=    3.681 closest distance to " O   HOH Z 251 " =    1.713
peak=    3.678 closest distance to " CB  SER A  63 " =    1.258
peak=    3.670 closest distance to " O   HOH Z 119 " =    1.459
peak=    3.659 closest distance to " CG1 ILE A 120 " =    1.406
peak=    3.658 closest distance to " O   HOH Z 334 " =    1.593
peak=    3.647 closest distance to " O   HOH Z 258 " =    2.188
peak=    3.647 closest distance to " N   PHE A 130 " =    1.263
peak=    3.642 closest distance to " O   HOH Z 392 " =    1.363
peak=    3.641 closest distance to " CA  LEU A 282 " =    1.082
peak=    3.610 closest distance to " O   HOH Z 207 " =    2.164
peak=    3.609 closest distance to " O   HOH Z 423 " =    1.529
peak=    3.564 closest distance to " ND1 HIS A  81 " =    1.472
peak=    3.560 closest distance to " O   HOH Z 139 " =    1.131
peak=    3.555 closest distance to " O   HOH Z  47 " =    1.746
peak=    3.553 closest distance to " O   HOH Z 303 " =    1.717
peak=    3.547 closest distance to " O   HOH Z  59 " =    2.005
peak=    3.543 closest distance to " CB  GLU A 277 " =    3.454
peak=    3.542 closest distance to " O   HOH Z 259 " =    2.061
peak=    3.541 closest distance to " NZ  LYS A 117 " =    0.988
peak=    3.539 closest distance to " CG2 ILE A 234 " =    0.830
peak=    3.534 closest distance to " CD  GLN A 194 " =    1.369
peak=    3.518 closest distance to " N   ALA A   1 " =    1.142
peak=    3.516 closest distance to " O   HOH Z 326 " =    1.317
peak=    3.510 closest distance to " O   HOH Z  48 " =    1.531
peak=    3.509 closest distance to " O   HOH Z 189 " =    2.647
peak=    3.507 closest distance to " CB  ASN A 142 " =    1.057
peak=    3.502 closest distance to " O   HOH Z  22 " =    2.065
peak=    3.501 closest distance to " O   HOH Z 143 " =    2.269
peak=    3.500 closest distance to " NZ  LYS A 117 " =    3.295
peak=    3.498 closest distance to " O   HOH Z 222 " =    2.014
peak=    3.487 closest distance to " O   HOH Z 371 " =    1.790
peak=    3.481 closest distance to " OG ASER A 134 " =    1.430
peak=    3.474 closest distance to " O   HOH Z 334 " =    2.793
peak=    3.470 closest distance to " CB  SER A 216 " =    0.949
peak=    3.469 closest distance to " CA  ALA A 158 " =    1.159
peak=    3.468 closest distance to " CB  MET A  40 " =    0.952
peak=    3.468 closest distance to " O   HOH Z 250 " =    1.380
peak=    3.466 closest distance to " O   HOH Z 108 " =    1.301
peak=    3.463 closest distance to " CB  LEU A 255 " =    0.850
peak=    3.463 closest distance to " O   HOH Z 147 " =    1.439
peak=    3.458 closest distance to " O   HOH Z 220 " =    1.253
peak=    3.456 closest distance to " O   HOH Z 394 " =    1.604
peak=    3.455 closest distance to " CD2 LEU A 297 " =    0.961
peak=    3.454 closest distance to " CG1 VAL A 153 " =    0.821
peak=    3.448 closest distance to " O   HOH Z 214 " =    1.930
peak=    3.444 closest distance to " O   HOH Z 176 " =    1.710
peak=    3.442 closest distance to " NE2 GLN A  58 " =    3.238
peak=    3.440 closest distance to " CB  TYR A 169 " =    0.936
peak=    3.439 closest distance to " O   HOH Z 263 " =    2.338
peak=    3.433 closest distance to " NE2 GLN A  58 " =    5.457
peak=    3.431 closest distance to " N   TYR A  15 " =    1.085
peak=    3.429 closest distance to " CG  LYS A 166 " =    1.294
peak=    3.427 closest distance to " O   HOH Z 368 " =    1.989
peak=    3.425 closest distance to " CB  GLU A 128 " =    1.054
peak=    3.424 closest distance to " O   HOH Z 234 " =    3.383
peak=    3.422 closest distance to " NH2BARG A 190 " =    1.480
peak=    3.422 closest distance to " CG  ARG A  66 " =    2.247
peak=    3.418 closest distance to " CE  MET A  93 " =    1.470
peak=    3.418 closest distance to " CD1 ILE A  33 " =    1.767
peak=    3.413 closest distance to " O   HOH Z  58 " =    1.731
peak=    3.412 closest distance to " CE3 TRP A 274 " =    2.291
peak=    3.412 closest distance to " O   HOH Z  89 " =    2.104
peak=    3.409 closest distance to " O   HOH Z 124 " =    2.242
peak=    3.409 closest distance to " O   HOH Z 281 " =    1.921
peak=    3.402 closest distance to " O   GLY A 302 " =    1.960
peak=    3.401 closest distance to " O   ALA A 165 " =    1.282
peak=    3.400 closest distance to " O   HOH Z 245 " =    1.329
peak=    3.397 closest distance to " O   HOH Z 192 " =    1.116
peak=    3.392 closest distance to " CD  ARG A 269 " =    0.983
peak=    3.392 closest distance to " O   HOH Z  61 " =    1.524
peak=    3.390 closest distance to " O   HOH Z 361 " =    1.544
peak=    3.386 closest distance to " NH1AARG A 145 " =    1.027
peak=    3.385 closest distance to " O   HOH Z 368 " =    3.593
peak=    3.384 closest distance to " O   HOH Z 327 " =    1.545
peak=    3.376 closest distance to " O   HOH Z  89 " =    1.735
peak=    3.373 closest distance to " O   HOH Z 362 " =    2.281
peak=    3.372 closest distance to " O   HOH Z 422 " =    0.919
peak=    3.371 closest distance to " O   HOH Z 305 " =    3.177
peak=    3.369 closest distance to " O   HOH Z 393 " =    1.361
peak=    3.366 closest distance to " NH1 ARG A  14 " =    1.078
peak=    3.365 closest distance to " CB  ASN A 148 " =    1.888
peak=    3.363 closest distance to " CG  MET A 185 " =    0.955
peak=    3.359 closest distance to " O   HOH Z 126 " =    1.482
peak=    3.359 closest distance to " CA  TYR A  30 " =    1.073
peak=    3.359 closest distance to " CB  ARG A  79 " =    1.382
peak=    3.358 closest distance to " O   HOH Z 134 " =    2.136
peak=    3.357 closest distance to " O   HOH Z 412 " =    1.902
peak=    3.357 closest distance to " O   HOH Z 193 " =    1.860
peak=    3.353 closest distance to " O   HOH Z 359 " =    1.131
peak=    3.352 closest distance to " CG1 VAL A 126 " =    1.289
peak=    3.344 closest distance to " OE1 GLN A  58 " =    3.803
peak=    3.338 closest distance to " CD  ARG A 138 " =    0.806
peak=    3.333 closest distance to " O   HOH Z  85 " =    1.046
peak=    3.330 closest distance to " O   HOH Z 302 " =    1.448
peak=    3.328 closest distance to " O   HOH Z 203 " =    1.624
peak=    3.327 closest distance to " O   HOH Z 326 " =    1.835
peak=    3.325 closest distance to " CB  SER A  62 " =    1.107
peak=    3.325 closest distance to " CG  LEU A 167 " =    1.150
peak=    3.325 closest distance to " O   HOH Z 390 " =    2.468
peak=    3.324 closest distance to " O   HOH Z 180 " =    2.159
peak=    3.320 closest distance to " CB  ILE A 234 " =    0.964
peak=    3.313 closest distance to " O   HOH Z 346 " =    1.631
peak=    3.312 closest distance to " CA  ILE A 234 " =    0.959
peak=    3.310 closest distance to " CB  GLU A 152 " =    1.241
peak=    3.310 closest distance to " CD1 LEU A   5 " =    1.760
peak=    3.305 closest distance to " NH2AARG A 190 " =    1.807
peak=    3.302 closest distance to " O   HOH Z  65 " =    1.520
peak=    3.291 closest distance to " CE  MET A  40 " =    0.966
peak=    3.291 closest distance to " O   HOH Z 260 " =    1.108
peak=    3.291 closest distance to " CZ AARG A 102 " =    1.827
peak=    3.286 closest distance to " O   HOH Z 344 " =    2.850
peak=    3.284 closest distance to " OG1 THR A 294 " =    2.357
peak=    3.282 closest distance to " CD1 LEU A 281 " =    1.011
peak=    3.279 closest distance to " CG  ARG A 159 " =    0.917
peak=    3.276 closest distance to " O   HOH Z 213 " =    1.745
peak=    3.271 closest distance to " O   HOH Z  64 " =    2.227
peak=    3.267 closest distance to " O   HOH Z 148 " =    1.585
peak=    3.264 closest distance to " O   HOH Z 279 " =    1.002
peak=    3.256 closest distance to " O   HOH Z 132 " =    1.555
peak=    3.251 closest distance to " O   HOH Z  88 " =    3.099
peak=    3.248 closest distance to " O   HOH Z 133 " =    1.370
peak=    3.246 closest distance to " OE2 GLU A  53 " =    2.026
peak=    3.242 closest distance to " NE2 GLN A 223 " =    1.635
peak=    3.242 closest distance to " O   HOH Z 222 " =    2.160
peak=    3.240 closest distance to " CB  TYR A 247 " =    0.835
peak=    3.235 closest distance to " O   HOH Z  93 " =    2.012
peak=    3.234 closest distance to " O   HOH Z 158 " =    1.295
peak=    3.230 closest distance to " O   HOH Z 212 " =    1.425
peak=    3.230 closest distance to " O   HOH Z 255 " =    1.776
peak=    3.230 closest distance to " O   GLY A 147 " =    1.445
peak=    3.228 closest distance to " CB  SER A 273 " =    0.783
peak=    3.224 closest distance to " O   HOH Z 247 " =    1.267
peak=    3.224 closest distance to " O   HOH Z  47 " =    1.801
peak=    3.218 closest distance to " O   HOH Z 233 " =    1.617
peak=    3.218 closest distance to " O   HOH Z 118 " =    1.903
peak=    3.217 closest distance to " OE2 GLU A   2 " =    1.967
peak=    3.217 closest distance to " NH2 ARG A 156 " =    1.043
peak=    3.213 closest distance to " O   HOH Z 428 " =    1.138
peak=    3.212 closest distance to " OE1 GLU A   2 " =    2.143
peak=    3.210 closest distance to " CB  LEU A 300 " =    0.891
peak=    3.210 closest distance to " O   HOH Z 410 " =    3.037
peak=    3.210 closest distance to " OG1 THR A 221 " =    1.308
peak=    3.205 closest distance to " N   GLU A   2 " =    1.267
peak=    3.203 closest distance to " O   HOH Z  94 " =    1.612
peak=    3.202 closest distance to " O   HOH Z 129 " =    0.799
peak=    3.201 closest distance to " CB  ARG A 138 " =    1.048
peak=    3.198 closest distance to " O   HOH Z 128 " =    2.202
peak=    3.194 closest distance to " O   HOH Z 153 " =    3.536
peak=    3.190 closest distance to " O   HOH Z 166 " =    1.286
peak=    3.187 closest distance to " O   HOH Z 128 " =    1.916
peak=    3.185 closest distance to " CA  ASN A 215 " =    0.964
peak=    3.182 closest distance to " CG  LYS A  76 " =    1.524
peak=    3.180 closest distance to " O   HOH Z 179 " =    0.782
peak=    3.179 closest distance to " CB  THR A  31 " =    1.577
peak=    3.178 closest distance to " O   HOH Z 158 " =    2.537
peak=    3.174 closest distance to " O   HOH Z 258 " =    1.236
peak=    3.171 closest distance to " CA  ALA A  21 " =    1.058
peak=    3.171 closest distance to " O   GLN A  58 " =    1.389
peak=    3.168 closest distance to " O   HOH Z 412 " =    2.200
peak=    3.167 closest distance to " C   ALA A 299 " =    0.985
peak=    3.167 closest distance to " O   HOH Z 217 " =    1.551
peak=    3.164 closest distance to " OG BSER A  99 " =    2.728
peak=    3.162 closest distance to " CD1 LEU A 228 " =    1.622
peak=    3.157 closest distance to " CA  ASN A  74 " =    1.214
peak=    3.157 closest distance to " O   HOH Z 412 " =    3.618
peak=    3.156 closest distance to " O   HOH Z 357 " =    1.865
peak=    3.154 closest distance to " O   HOH Z   1 " =    1.659
peak=    3.150 closest distance to " O   HOH Z 261 " =    1.972
peak=    3.141 closest distance to " O   HOH Z 356 " =    1.227
peak=    3.140 closest distance to " CB  ALA A 248 " =    0.996
peak=    3.135 closest distance to " CG1BVAL A  72 " =    0.821
peak=    3.131 closest distance to " O   HOH Z 281 " =    2.166
peak=    3.127 closest distance to " NE2 GLN A 278 " =    3.800
peak=    3.121 closest distance to " NZ  LYS A  76 " =    1.426
peak=    3.121 closest distance to " OG BSER A 164 " =    2.363
peak=    3.120 closest distance to " O   HOH Z 113 " =    1.647
peak=    3.117 closest distance to " CG1BVAL A 121 " =    1.005
peak=    3.114 closest distance to " O   HOH Z   9 " =    1.734
peak=    3.106 closest distance to " O   HOH Z 280 " =    2.647
peak=    3.102 closest distance to " OG1 THR A 220 " =    1.851
peak=    3.099 closest distance to " O   HOH Z 183 " =    1.642
peak=    3.090 closest distance to " O   HOH Z 158 " =    3.302
peak=    3.089 closest distance to " N   VAL A 257 " =    1.661
peak=    3.079 closest distance to " CD  LYS A 119 " =    1.717
peak=    3.079 closest distance to " O   HOH Z 410 " =    2.151
peak=    3.077 closest distance to " CB  ASN A 215 " =    1.019
peak=    3.075 closest distance to " CE  MET A  40 " =    1.069
peak=    3.075 closest distance to " CG2 ILE A  20 " =    1.095
peak=    3.071 closest distance to " O   HOH Z 213 " =    1.752
peak=    3.071 closest distance to " NZ BLYS A 290 " =    1.037
peak=    3.068 closest distance to " CB  LYS A 290 " =    1.507
peak=    3.060 closest distance to " O   HOH Z 352 " =    1.367
peak=    3.045 closest distance to " O   HOH Z  69 " =    2.073
peak=    3.044 closest distance to " O   HOH Z 426 " =    2.783
peak=    3.041 closest distance to " CD  ARG A 159 " =    0.733
peak=    3.038 closest distance to " O   HOH Z  80 " =    1.982
peak=    3.030 closest distance to " O   HOH Z 173 " =    2.139
peak=    3.007 closest distance to " O   HOH Z  44 " =    2.284

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.584 - 5.376
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 199
   mapped sites are within: 0.706 - 5.376

peak=   -4.604 closest distance to " O   HOH Z 385 " =    0.886
peak=   -4.410 closest distance to " O   HOH Z  43 " =    1.981
peak=   -4.398 closest distance to " OG BSER A 134 " =    1.273
peak=   -4.349 closest distance to " CD  ARG A 138 " =    1.306
peak=   -4.287 closest distance to " NH2 ARG A  79 " =    1.965
peak=   -4.285 closest distance to " C   HIS A 108 " =    1.112
peak=   -4.229 closest distance to " CG  ARG A 138 " =    0.891
peak=   -4.221 closest distance to " CG2 VAL A 230 " =    0.836
peak=   -4.167 closest distance to " OG ASER A 134 " =    1.126
peak=   -4.164 closest distance to " O   HOH Z 298 " =    1.062
peak=   -4.133 closest distance to " O   VAL A  67 " =    2.731
peak=   -4.088 closest distance to " OD1 ASN A  39 " =    2.063
peak=   -4.064 closest distance to " CD  ARG A 156 " =    1.894
peak=   -4.015 closest distance to " CA  GLY A  98 " =    1.809
peak=   -4.007 closest distance to " CB  PRO A 243 " =    2.545
peak=   -3.997 closest distance to " O   HOH Z 103 " =    1.471
peak=   -3.974 closest distance to " NH1 ARG A  56 " =    2.422
peak=   -3.921 closest distance to " O   HOH Z 412 " =    5.134
peak=   -3.892 closest distance to " O   VAL A  67 " =    2.852
peak=   -3.890 closest distance to " CD1 LEU A 101 " =    2.297
peak=   -3.880 closest distance to " CA  GLY A 133 " =    1.917
peak=   -3.878 closest distance to " CD1 ILE A 239 " =    2.492
peak=   -3.859 closest distance to " O   HOH Z  56 " =    2.014
peak=   -3.855 closest distance to " CD  ARG A  14 " =    2.871
peak=   -3.845 closest distance to " O   HOH Z 131 " =    3.954
peak=   -3.836 closest distance to " O   HOH Z 427 " =    1.769
peak=   -3.824 closest distance to " O   HOH Z  60 " =    1.788
peak=   -3.818 closest distance to " O   PRO A 198 " =    1.125
peak=   -3.795 closest distance to " N   ALA A   1 " =    1.183
peak=   -3.786 closest distance to " CD  LYS A 289 " =    2.488
peak=   -3.763 closest distance to " O   HOH Z 211 " =    1.346
peak=   -3.761 closest distance to " O   HOH Z 388 " =    1.901
peak=   -3.748 closest distance to " O   HOH Z 407 " =    2.994
peak=   -3.745 closest distance to " N   GLN A  58 " =    1.803
peak=   -3.743 closest distance to " O   GLY A  57 " =    1.316
peak=   -3.736 closest distance to " O   SER A 135 " =    1.518
peak=   -3.728 closest distance to " CD2 LEU A   5 " =    1.023
peak=   -3.723 closest distance to " CB  ALA A 248 " =    2.092
peak=   -3.723 closest distance to " O   GLY A  80 " =    2.420
peak=   -3.718 closest distance to " CE2 PHE A 218 " =    2.568
peak=   -3.712 closest distance to " O   HOH Z 231 " =    1.732
peak=   -3.660 closest distance to " O   HOH Z 359 " =    1.688
peak=   -3.660 closest distance to " OE1 GLU A 277 " =    2.142
peak=   -3.656 closest distance to " CD  GLU A 152 " =    2.315
peak=   -3.653 closest distance to " O   HOH Z  69 " =    1.925
peak=   -3.647 closest distance to " O   HOH Z 347 " =    0.894
peak=   -3.633 closest distance to " OG  SER A   3 " =    1.356
peak=   -3.626 closest distance to " O   HOH Z 140 " =    1.199
peak=   -3.617 closest distance to " O   HOH Z 290 " =    1.137
peak=   -3.611 closest distance to " O   ALA A  51 " =    1.262
peak=   -3.609 closest distance to " O   HOH Z  11 " =    1.855
peak=   -3.606 closest distance to " O   HOH Z 350 " =    1.809
peak=   -3.604 closest distance to " C   ALA A 158 " =    1.389
peak=   -3.602 closest distance to " O   ILE A  49 " =    1.749
peak=   -3.598 closest distance to " O   HOH Z 125 " =    3.242
peak=   -3.581 closest distance to " O   PRO A 163 " =    1.985
peak=   -3.570 closest distance to " CG2AVAL A  41 " =    2.946
peak=   -3.568 closest distance to " CA  ASP A  27 " =    2.338
peak=   -3.566 closest distance to " OD2 ASP A  27 " =    1.452
peak=   -3.560 closest distance to " N   MET A 188 " =    1.864
peak=   -3.555 closest distance to " O   HOH Z 111 " =    4.301
peak=   -3.553 closest distance to " CG  PHE A 283 " =    2.473
peak=   -3.553 closest distance to " O   HOH Z 351 " =    1.415
peak=   -3.545 closest distance to " O   HOH Z  88 " =    2.010
peak=   -3.542 closest distance to " CG  ARG A 219 " =    2.490
peak=   -3.539 closest distance to " C   ASN A 285 " =    2.062
peak=   -3.525 closest distance to " CD  GLN A  58 " =    1.075
peak=   -3.519 closest distance to " CZ  PHE A  59 " =    1.456
peak=   -3.516 closest distance to " N   HIS A 115 " =    2.011
peak=   -3.513 closest distance to " O   HOH Z  51 " =    1.000
peak=   -3.498 closest distance to " O   HOH Z 415 " =    1.136
peak=   -3.496 closest distance to " CE2 TYR A  30 " =    2.824
peak=   -3.492 closest distance to " O   HOH Z 414 " =    2.086
peak=   -3.488 closest distance to " CD2 LEU A 282 " =    2.319
peak=   -3.488 closest distance to " OD2 ASP A  50 " =    1.602
peak=   -3.487 closest distance to " O   HOH Z 102 " =    1.458
peak=   -3.478 closest distance to " O   HOH Z  54 " =    0.941
peak=   -3.477 closest distance to " CG1 VAL A 268 " =    2.857
peak=   -3.474 closest distance to " O   SER A  22 " =    2.451
peak=   -3.473 closest distance to " O   HOH Z  76 " =    1.268
peak=   -3.467 closest distance to " O   HOH Z  47 " =    1.549
peak=   -3.463 closest distance to " N   GLN A  88 " =    1.719
peak=   -3.463 closest distance to " CG  GLN A  88 " =    0.904
peak=   -3.461 closest distance to " O   HOH Z 191 " =    5.376
peak=   -3.458 closest distance to " O   HOH Z 308 " =    1.631
peak=   -3.452 closest distance to " N   ALA A 248 " =    1.628
peak=   -3.450 closest distance to " CD2 TRP A 150 " =    1.016
peak=   -3.444 closest distance to " CG  MET A 105 " =    0.880
peak=   -3.438 closest distance to " O   HOH Z 313 " =    1.579
peak=   -3.437 closest distance to " CE2 TYR A 116 " =    2.949
peak=   -3.437 closest distance to " CB  ALA A   7 " =    2.017
peak=   -3.437 closest distance to " O   ALA A 161 " =    1.870
peak=   -3.437 closest distance to " CG  PRO A 163 " =    2.595
peak=   -3.436 closest distance to " O   HOH Z 385 " =    2.055
peak=   -3.430 closest distance to " OG  SER A 245 " =    1.312
peak=   -3.421 closest distance to " O   HOH Z  65 " =    0.706
peak=   -3.417 closest distance to " O   GLY A  98 " =    2.115
peak=   -3.414 closest distance to " O   HOH Z  52 " =    1.433
peak=   -3.412 closest distance to " OG  SER A 206 " =    1.654
peak=   -3.409 closest distance to " CB  ASN A  39 " =    2.242
peak=   -3.407 closest distance to " O   GLN A  73 " =    1.436
peak=   -3.405 closest distance to " C   GLU A  44 " =    1.853
peak=   -3.404 closest distance to " OE2 GLU A 152 " =    0.944
peak=   -3.395 closest distance to " O   HOH Z  60 " =    2.515
peak=   -3.384 closest distance to " O   HOH Z 416 " =    0.971
peak=   -3.381 closest distance to " O   HOH Z 189 " =    2.490
peak=   -3.379 closest distance to " C   ILE A 239 " =    2.132
peak=   -3.374 closest distance to " O   HOH Z 222 " =    2.563
peak=   -3.372 closest distance to " O   SER A 146 " =    1.154
peak=   -3.371 closest distance to " CD1 LEU A 255 " =    2.751
peak=   -3.369 closest distance to " O   HOH Z 406 " =    0.960
peak=   -3.369 closest distance to " O   HOH Z 429 " =    1.047
peak=   -3.364 closest distance to " CG2 THR A  31 " =    2.328
peak=   -3.362 closest distance to " C   TYR A  30 " =    1.006
peak=   -3.361 closest distance to " CG1BVAL A  72 " =    2.058
peak=   -3.356 closest distance to " CD1 TRP A 179 " =    1.070
peak=   -3.355 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.355 closest distance to " O   HOH Z 266 " =    4.546
peak=   -3.351 closest distance to " O   PRO A 198 " =    1.332
peak=   -3.347 closest distance to " O   HOH Z 166 " =    1.853
peak=   -3.344 closest distance to " N   PRO A 163 " =    1.505
peak=   -3.342 closest distance to " O   HOH Z 397 " =    1.348
peak=   -3.339 closest distance to " O   HOH Z  40 " =    4.230
peak=   -3.336 closest distance to " O   HOH Z 234 " =    3.874
peak=   -3.334 closest distance to " CD2 LEU A 237 " =    2.628
peak=   -3.332 closest distance to " CB  GLN A  55 " =    1.192
peak=   -3.325 closest distance to " CG1 ILE A 263 " =    2.021
peak=   -3.323 closest distance to " N   VAL A  72 " =    1.713
peak=   -3.318 closest distance to " O   HOH Z 185 " =    1.820
peak=   -3.317 closest distance to " OD2 ASP A 191 " =    1.501
peak=   -3.315 closest distance to " O   HOH Z 339 " =    1.774
peak=   -3.311 closest distance to " O   SER A 216 " =    1.676
peak=   -3.307 closest distance to " O   HOH Z  13 " =    1.655
peak=   -3.304 closest distance to " O   ASN A  39 " =    1.223
peak=   -3.303 closest distance to " O   HOH Z 134 " =    2.555
peak=   -3.302 closest distance to " O   HOH Z  90 " =    2.426
peak=   -3.297 closest distance to " CG  ARG A  66 " =    2.190
peak=   -3.296 closest distance to " O   THR A 235 " =    1.481
peak=   -3.295 closest distance to " O   ASN A 187 " =    1.358
peak=   -3.292 closest distance to " O   HOH Z 368 " =    2.576
peak=   -3.288 closest distance to " OG  SER A  87 " =    1.278
peak=   -3.286 closest distance to " CG2 THR A 178 " =    2.026
peak=   -3.284 closest distance to " CD1 ILE A 151 " =    2.373
peak=   -3.281 closest distance to " C   LEU A 143 " =    1.027
peak=   -3.275 closest distance to " CD2 LEU A 237 " =    2.419
peak=   -3.275 closest distance to " C   ARG A 269 " =    1.304
peak=   -3.273 closest distance to " OD1 ASP A 200 " =    1.337
peak=   -3.271 closest distance to " O   HOH Z   9 " =    1.557
peak=   -3.270 closest distance to " O   HOH Z 352 " =    1.811
peak=   -3.267 closest distance to " CB  SER A 134 " =    1.869
peak=   -3.252 closest distance to " O   HOH Z 137 " =    1.561
peak=   -3.250 closest distance to " ND2 ASN A  45 " =    1.137
peak=   -3.246 closest distance to " CG  ARG A 219 " =    2.256
peak=   -3.238 closest distance to " O   HOH Z 165 " =    2.181
peak=   -3.236 closest distance to " ND2 ASN A  60 " =    1.249
peak=   -3.227 closest distance to " O   HOH Z 210 " =    1.914
peak=   -3.217 closest distance to " N   SER A 276 " =    1.074
peak=   -3.217 closest distance to " CZ2 TRP A 179 " =    2.396
peak=   -3.216 closest distance to " N   LYS A 166 " =    1.892
peak=   -3.203 closest distance to " O   HOH Z 431 " =    1.302
peak=   -3.202 closest distance to " O   PRO A 198 " =    1.077
peak=   -3.201 closest distance to " ND2 ASN A 209 " =    1.689
peak=   -3.197 closest distance to " CG  GLN A  11 " =    2.033
peak=   -3.190 closest distance to " O   HOH Z 143 " =    0.750
peak=   -3.185 closest distance to " O   HOH Z 364 " =    1.977
peak=   -3.176 closest distance to " CG  LEU A 228 " =    1.099
peak=   -3.175 closest distance to " O   TRP A  92 " =    1.680
peak=   -3.174 closest distance to " O   HOH Z 193 " =    2.534
peak=   -3.171 closest distance to " CD1 TRP A 274 " =    1.382
peak=   -3.166 closest distance to " O   ASN A 301 " =    1.453
peak=   -3.162 closest distance to " O   HOH Z 431 " =    3.683
peak=   -3.162 closest distance to " CG1 VAL A 197 " =    1.768
peak=   -3.159 closest distance to " CZ  PHE A  16 " =    1.608
peak=   -3.154 closest distance to " CG  GLN A 223 " =    1.996
peak=   -3.153 closest distance to " C   LEU A 222 " =    0.776
peak=   -3.151 closest distance to " CE BMET A  47 " =    1.374
peak=   -3.146 closest distance to " CE3 TRP A 274 " =    2.476
peak=   -3.145 closest distance to " O   HOH Z 424 " =    1.468
peak=   -3.141 closest distance to " O   HOH Z 377 " =    1.179
peak=   -3.134 closest distance to " O   HOH Z 359 " =    3.479
peak=   -3.134 closest distance to " CB  ALA A  43 " =    2.131
peak=   -3.132 closest distance to " O   GLN A 183 " =    1.203
peak=   -3.130 closest distance to " NE2 GLN A  55 " =    0.897
peak=   -3.128 closest distance to " O   HOH Z 235 " =    1.061
peak=   -3.117 closest distance to " O   HOH Z  52 " =    1.121
peak=   -3.113 closest distance to " O   HOH Z 183 " =    1.670
peak=   -3.111 closest distance to " NH2 ARG A 159 " =    2.358
peak=   -3.106 closest distance to " CG  TRP A 266 " =    1.707
peak=   -3.105 closest distance to " CD2 TYR A 293 " =    1.904
peak=   -3.101 closest distance to " O   HOH Z 414 " =    2.211
peak=   -3.087 closest distance to " O   ALA A   1 " =    1.331
peak=   -3.083 closest distance to " O   MET A  40 " =    2.683
peak=   -3.082 closest distance to " O   HOH Z 314 " =    1.141
peak=   -3.077 closest distance to " O   HOH Z 426 " =    1.705
peak=   -3.051 closest distance to " CB  GLN A  11 " =    1.960
peak=   -3.045 closest distance to " O   GLN A 240 " =    1.574
peak=   -3.044 closest distance to " O   HOH Z 111 " =    1.246
peak=   -3.041 closest distance to " CA  THR A 235 " =    1.597

================= 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    :  0.4966 0.4929   6.294407e+00   6.287034e+00
   1_bss:  0.4877 0.4807   6.287773e+00   6.276972e+00
   1_xyz:  0.4242 0.4451   6.214689e+00   6.238584e+00
   1_adp:  0.3828 0.4341   6.160478e+00   6.231980e+00
   1_occ:  0.3823 0.4340   6.160014e+00   6.232577e+00
   2_bss:  0.3798 0.4298   6.159495e+00   6.229058e+00
   2_xyz:  0.3077 0.3641   5.997188e+00   6.121626e+00
   2_adp:  0.2837 0.3461   5.942372e+00   6.079510e+00
   2_occ:  0.2834 0.3460   5.942158e+00   6.079902e+00
   3_bss:  0.2819 0.3446   5.941937e+00   6.078887e+00
   3_xyz:  0.2246 0.2874   5.748590e+00   5.925930e+00
   3_adp:  0.2035 0.2715   5.678760e+00   5.880500e+00
   3_occ:  0.2032 0.2712   5.677694e+00   5.879826e+00
   4_bss:  0.2032 0.2706   5.676734e+00   5.876794e+00
   4_xyz:  0.1614 0.2195   5.465986e+00   5.687838e+00
   4_adp:  0.1521 0.2016   5.397110e+00   5.610524e+00
   4_occ:  0.1518 0.2011   5.395098e+00   5.607658e+00
   5_bss:  0.1519 0.2005   5.393804e+00   5.605192e+00
   5_xyz:  0.1280 0.1755   5.247965e+00   5.479991e+00
   5_adp:  0.1220 0.1719   5.214845e+00   5.459647e+00
   5_occ:  0.1219 0.1717   5.214253e+00   5.458575e+00
   5_bss:  0.1223 0.1720   5.216126e+00   5.460719e+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:  0.375   0.000   6.745   9.812   8.237   0.000   0.000   0.000
   1_xyz:  0.375   0.000   6.745   9.812   8.237   0.000   0.000   0.000
   1_adp:  0.375   0.000   6.745   9.812   8.237   0.000   0.000   0.000
   1_occ:  0.375   0.000   6.745   9.812   8.237   0.000   0.000   0.000
   2_bss:  0.368  34.138   3.594   5.795   5.189   0.000   0.000   0.000
   2_xyz:  0.368  34.138   3.594   5.795   5.189   0.000   0.000   0.000
   2_adp:  0.368  34.138   3.594   5.795   5.189   0.000   0.000   0.000
   2_occ:  0.368  34.138   3.594   5.795   5.189   0.000   0.000   0.000
   3_bss:  0.334  34.138   2.038   3.129   3.230   0.000   0.000   0.000
   3_xyz:  0.334  34.138   2.038   3.129   3.230   0.000   0.000   0.000
   3_adp:  0.334  34.138   2.038   3.129   3.230   0.000   0.000   0.000
   3_occ:  0.334  34.138   2.038   3.129   3.230   0.000   0.000   0.000
   4_bss:  0.319  34.138   1.417   1.924   2.584   0.000   0.000   0.000
   4_xyz:  0.319  34.138   1.417   1.924   2.584   0.000   0.000   0.000
   4_adp:  0.319  34.138   1.417   1.924   2.584   0.000   0.000   0.000
   4_occ:  0.319  34.138   1.417   1.924   2.584   0.000   0.000   0.000
   5_bss:  0.316  34.138   1.026   1.095   2.171   0.000   0.000   0.000
   5_xyz:  0.316  34.138   1.026   1.095   2.171   0.000   0.000   0.000
   5_adp:  0.316  34.138   1.026   1.095   2.171   0.000   0.000   0.000
   5_occ:  0.316  34.138   1.026   1.095   2.171   0.000   0.000   0.000
   5_bss:  0.313  38.163  -0.394  -0.337   0.730   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.016 0.3549  0.4243    78368.947
   1_bss:  62.686 0.3576  0.5343    75197.790
   1_xyz:  53.950 0.4694  0.6954    60840.255
   1_adp:  51.046 0.5069  0.8086    57992.069
   1_occ:  51.131 0.5058  0.8059    58159.776
   2_bss:  50.464 0.5140  0.7330    57082.400
   2_xyz:  39.908 0.6431  0.9059    38182.811
   2_adp:  36.586 0.6831  0.9618    33619.797
   2_occ:  36.615 0.6828  0.9611    33649.077
   3_bss:  36.516 0.6837  0.8920    33468.103
   3_xyz:  28.866 0.7699  0.9716    21400.541
   3_adp:  26.811 0.7926  0.9783    19055.732
   3_occ:  26.774 0.7930  0.9783    19008.859
   4_bss:  26.703 0.7937  0.9498    18870.192
   4_xyz:  21.074 0.8509  0.9932    12088.087
   4_adp:  18.779 0.8737  1.0024    10284.887
   4_occ:  18.712 0.8743  1.0024    10197.703
   5_bss:  18.641 0.8748  0.9825    10102.137
   5_xyz:  15.921 0.8989  0.9944     7712.160
   5_adp:  15.399 0.9037  0.9899     7420.532
   5_occ:  15.383 0.9038  0.9899     7399.498
   5_bss:  15.413 0.9036  0.9859     7462.736
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.2724e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.2724e+01
   1_xyz:   1.713  0.013  0.106 18.288  0.007  4.105   1.4525e-01
   1_adp:   1.713  0.013  0.106 18.288  0.007  4.105   1.4525e-01
   1_occ:   1.713  0.013  0.106 18.288  0.007  4.105   1.4525e-01
   2_bss:   1.713  0.013  0.106 18.288  0.007  4.105   1.4525e-01
   2_xyz:   1.289  0.009  0.086 16.454  0.006  4.116   9.8953e-02
   2_adp:   1.289  0.009  0.086 16.454  0.006  4.116   9.8953e-02
   2_occ:   1.289  0.009  0.086 16.454  0.006  4.116   9.8953e-02
   3_bss:   1.289  0.009  0.086 16.454  0.006  4.116   9.8953e-02
   3_xyz:   1.049  0.007  0.076 15.867  0.004  4.112   6.8653e-02
   3_adp:   1.049  0.007  0.076 15.867  0.004  4.112   6.8653e-02
   3_occ:   1.049  0.007  0.076 15.867  0.004  4.112   6.8653e-02
   4_bss:   1.049  0.007  0.076 15.867  0.004  4.112   6.8653e-02
   4_xyz:   0.950  0.006  0.069 15.693  0.003  4.114   6.0406e-02
   4_adp:   0.950  0.006  0.069 15.693  0.003  4.114   6.0406e-02
   4_occ:   0.950  0.006  0.069 15.693  0.003  4.114   6.0406e-02
   5_bss:   0.950  0.006  0.069 15.693  0.003  4.114   6.0406e-02
   5_xyz:   1.032  0.006  0.073 15.910  0.004  4.107   6.4220e-02
   5_adp:   1.032  0.006  0.073 15.910  0.004  4.107   6.4220e-02
   5_occ:   1.032  0.006  0.073 15.910  0.004  4.107   6.4220e-02
   5_bss:   1.032  0.006  0.073 15.910  0.004  4.107   6.4220e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.092   6.8305e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.092   6.8305e+00
   1_xyz:  14.478  0.171  0.457 87.968  0.047  2.204   9.8246e-02
   1_adp:  14.478  0.171  0.457 87.968  0.047  2.204   9.8246e-02
   1_occ:  14.478  0.171  0.457 87.968  0.047  2.204   9.8246e-02
   2_bss:  14.478  0.171  0.457 87.968  0.047  2.204   9.8246e-02
   2_xyz:   8.090  0.101  0.405 85.247  0.051  2.198   6.7762e-02
   2_adp:   8.090  0.101  0.405 85.247  0.051  2.198   6.7762e-02
   2_occ:   8.090  0.101  0.405 85.247  0.051  2.198   6.7762e-02
   3_bss:   8.090  0.101  0.405 85.247  0.051  2.198   6.7762e-02
   3_xyz:   7.719  0.045  0.229 85.468  0.021  2.321   6.0632e-02
   3_adp:   7.719  0.045  0.229 85.468  0.021  2.321   6.0632e-02
   3_occ:   7.719  0.045  0.229 85.468  0.021  2.321   6.0632e-02
   4_bss:   7.719  0.045  0.229 85.468  0.021  2.321   6.0632e-02
   4_xyz:   7.206  0.044  0.222 82.012  0.025  2.331   5.9968e-02
   4_adp:   7.206  0.044  0.222 82.012  0.025  2.331   5.9968e-02
   4_occ:   7.206  0.044  0.222 82.012  0.025  2.331   5.9968e-02
   5_bss:   7.206  0.044  0.222 82.012  0.025  2.331   5.9968e-02
   5_xyz:   7.713  0.047  0.256 83.202  0.034  2.248   5.0365e-02
   5_adp:   7.713  0.047  0.256 83.202  0.034  2.248   5.0365e-02
   5_occ:   7.713  0.047  0.256 83.202  0.034  2.248   5.0365e-02
   5_bss:   7.713  0.047  0.256 83.202  0.034  2.248   5.0365e-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:  93.01   0.00  15.01  93.01   0.00  13.25  90.27   0.00  24.59
   1_occ:  93.01   0.00  15.01  93.01   0.00  13.25  90.27   0.00  24.59
   2_bss:  93.01   0.00  15.01  93.01   0.00  13.25  90.27   0.00  24.59
   2_xyz:  93.01   0.00  15.01  93.01   0.00  13.25  90.27   0.00  24.59
   2_adp:  95.93   0.00  14.33  95.93   0.00  11.52  88.48   0.00  29.60
   2_occ:  95.93   0.00  14.33  95.93   0.00  11.52  88.48   0.00  29.60
   3_bss:  95.93   0.00  14.33  95.93   0.00  11.52  88.48   0.00  29.60
   3_xyz:  95.93   0.00  14.33  95.93   0.00  11.52  88.48   0.00  29.60
   3_adp: 111.69   0.00  14.96 111.69   0.00  10.72  99.21   1.29  38.04
   3_occ: 111.69   0.00  14.96 111.69   0.00  10.72  99.21   1.29  38.04
   4_bss: 111.69   0.00  14.96 111.69   0.00  10.72  99.21   1.29  38.04
   4_xyz: 111.69   0.00  14.96 111.69   0.00  10.72  99.21   1.29  38.04
   4_adp: 107.90   0.00  14.01 107.90   0.00   9.72  94.72   3.39  37.36
   4_occ: 107.90   0.00  14.01 107.90   0.00   9.72  94.72   3.39  37.36
   5_bss: 107.90   0.00  14.01 107.90   0.00   9.72  94.72   3.39  37.36
   5_xyz: 107.90   0.00  14.01 107.90   0.00   9.72  94.72   3.39  37.36
   5_adp: 109.35   0.00  14.25 109.35   0.00   9.55  95.85   3.18  39.85
   5_occ: 109.35   0.00  14.25 109.35   0.00   9.55  95.85   3.18  39.85
   5_bss: 110.68   1.33  15.57 110.68   1.33  10.87  97.18   4.51  41.18
------------------------------------------------------------------------
 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:    1.258    0.016    0.412
   1_adp:    1.258    0.016    0.412
   1_occ:    1.258    0.016    0.412
   2_bss:    1.258    0.016    0.412
   2_xyz:    1.667    0.028    0.590
   2_adp:    1.667    0.028    0.590
   2_occ:    1.667    0.028    0.590
   3_bss:    1.667    0.028    0.590
   3_xyz:    1.579    0.025    0.685
   3_adp:    1.579    0.025    0.685
   3_occ:    1.579    0.025    0.685
   4_bss:    1.579    0.025    0.685
   4_xyz:    1.742    0.040    0.777
   4_adp:    1.742    0.040    0.777
   4_occ:    1.742    0.040    0.777
   5_bss:    1.742    0.040    0.777
   5_xyz:    1.879    0.024    0.821
   5_adp:    1.879    0.024    0.821
   5_occ:    1.879    0.024    0.821
   5_bss:    1.879    0.024    0.821
------------------------------------------------------------------------

CPU time actual refinement: 352.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_376/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_376/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_376/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_376/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_376/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 352.75 
  Macro-tasks:
    bulk solvent and scale       = 43.72  
    individual site refinement   = 148.99 
    weights calculation          = 33.08  
    collect and process          = 6.47   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 232.39 
  Micro-tasks:
    mask                            = 2.90   
    f_calc                          = 109.74 
    alpha_beta                      = 8.37   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 120.91 
    fmodel                         = 7.34   
    r_factors                      = 0.19   
    phase_errors                   = 10.29  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 261.08 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.916 micro seconds
Total CPU time: 6.11 minutes
from_scatterers_fft:    656 calls, 109.34 s
gradients_fft:          601 calls, 107.32 s

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

# Date 2008-01-16 Time 01:27:13 PST -0800 (1200475633.25 s)
Start R-work = 0.4966, R-free = 0.4929 (no bulk solvent and anisotropic scale)
Final R-work = 0.1380, R-free = 0.1857 (no bulk solvent and anisotropic scale)

Start R-work = 0.4877, R-free = 0.4807
Final R-work = 0.1223, R-free = 0.1720