# Date 2008-01-16 Time 02:57:24 PST -0800 (1200481044.32 s)
#phil __OFF__

Command line arguments: "../1043.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15965
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1043

-------------------------------------------------------------------------------
  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: (71.3037, 47.1647, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 2.01232
Completeness in resolution range: 0.964975
Completeness with d_max=infinity: 0.96199

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2391
                             d_min =   2.0123

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: (71.3037, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 2.01232
Completeness in resolution range: 0.964975
Completeness with d_max=infinity: 0.96199

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2395 -  4.3059 [2132/2156]  1918   214  10.0%
  bin  2:  4.3059 -  3.4305 [2037/2057]  1835   202   9.9%
  bin  3:  3.4305 -  3.0006 [2031/2050]  1824   207  10.2%
  bin  4:  3.0006 -  2.7280 [1997/2027]  1800   197   9.9%
  bin  5:  2.7280 -  2.5334 [2005/2024]  1804   201  10.0%
  bin  6:  2.5334 -  2.3847 [1956/1981]  1761   195  10.0%
  bin  7:  2.3847 -  2.2656 [1979/2007]  1779   200  10.1%
  bin  8:  2.2656 -  2.1673 [1969/2005]  1774   195   9.9%
  bin  9:  2.1673 -  2.0841 [1937/1979]  1745   192   9.9%
  bin 10:  2.0841 -  2.0123 [1546/2014]  1390   156  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1043/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2160
        3.04 -     3.66: 4563
        3.66 -     4.28: 8838
        4.28 -     4.90: 12170
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.955 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.119 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.181 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.181 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27737 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_1043/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1043/model_refine_001.geo

CPU time processing inputs: 9.29


============================ 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 = 71.30375 47.16465 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4707   r_free= 0.4636   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.270912                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.8025 0.99   1387  153 0.3867 0.3533      6.5897      6.4758|
|  2:  4.8025 -  3.8319 0.99   1329  152 0.3805 0.4094      6.7579       6.863|
|  3:  3.8319 -  3.3534 0.99   1305  140 0.4272 0.4009      6.6607      6.6385|
|  4:  3.3534 -  3.0495 0.99   1293  149 0.4596 0.4056      6.5247      6.4093|
|  5:  3.0495 -  2.8324 0.99   1290  143 0.4927 0.4730      6.3655      6.3948|
|  6:  2.8324 -  2.6663 0.99   1300  137 0.4966 0.5666      6.2771      6.2042|
|  7:  2.6663 -  2.5334 0.99   1277  147 0.5181 0.5049      6.2337      6.2335|
|  8:  2.5334 -  2.4236 0.98   1271  141 0.5281 0.4520      6.1895      6.1179|
|  9:  2.4236 -  2.3306 0.98   1260  141 0.5004 0.6018      6.1075       6.185|
| 10:  2.3306 -  2.2505 1.00   1282  142 0.5225 0.4891      6.1211      6.0957|
| 11:  2.2505 -  2.1803 0.97   1251  138 0.5036 0.5180      6.0199      6.0812|
| 12:  2.1803 -  2.1182 0.98   1248  138 0.5198 0.4934      5.9873      5.9905|
| 13:  2.1182 -  2.0625 0.99   1289  139 0.5280 0.5059      5.8927      5.8301|
| 14:  2.0625 -  2.0123 0.67    848   99 0.5297 0.4947      5.8558      5.7619|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2395 -  4.8025  1387   153  0.73  31.83   0.79     0.75      62348.66|
|  2:  4.8025 -  3.8319  1329   152  0.74  32.11   0.88     0.78      92259.31|
|  3:  3.8319 -  3.3534  1305   140  0.65  39.95   0.82     0.73      98671.16|
|  4:  3.3534 -  3.0495  1293   149  0.56  47.39   0.80     0.63      89616.60|
|  5:  3.0495 -  2.8324  1290   143  0.46  54.93   0.74     0.53      75653.50|
|  6:  2.8324 -  2.6663  1300   137  0.42  58.34   0.72     0.47      69140.30|
|  7:  2.6663 -  2.5334  1277   147  0.38  61.36   0.71     0.43      64169.59|
|  8:  2.5334 -  2.4236  1271   141  0.37  62.10   0.72     0.43      58457.18|
|  9:  2.4236 -  2.3306  1260   141  0.37  62.22   0.72     0.42      54023.10|
| 10:  2.3306 -  2.2505  1282   142  0.37  62.12   0.73     0.43      47871.90|
| 11:  2.2505 -  2.1803  1251   138  0.37  62.06   0.74     0.44      44657.38|
| 12:  2.1803 -  2.1182  1248   138  0.39  61.00   0.74     0.46      40005.18|
| 13:  2.1182 -  2.0625  1289   139  0.36  62.82   0.70     0.44      35172.47|
| 14:  2.0625 -  2.0123   848    99  0.36  63.15   0.70     0.37      29261.45|
|alpha:            min =        0.37 max =            0.78 mean =         0.53|
|beta:             min =    29261.45 max =        98671.16 mean =     62554.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.92|
|phase err.(test): min =        0.00 max =           89.95 mean =        54.04|
|-----------------------------------------------------------------------------|

============================== 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 = 12.776424             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.681   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.127544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.279   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      673 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1473 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2568 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3825 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4985 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6463 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7571 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.598 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.634 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4761   r_free= 0.4650   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.273013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4624   r_free= 0.4500   ksol= 0.33   Bsol= 38.38   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.73,7.07,10.97,0.00,0.00,0.00); trace/3= 8.59                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.265075                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.533404             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.603   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.029725              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.281   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4624      final r-factor (work) = 0.3666          |
| start r-factor (free) = 0.4500      final r-factor (free) = 0.3954          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 90.7702 = 11.53 * 0.50 * 6.2726 + 1.00 * 54.5979                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.6450 = 11.53 * 0.50 * 6.1556 + 1.00 * 0.1472                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3666      final r-factor (work) = 0.3192          |
| start r-factor (free) = 0.3954      final r-factor (free) = 0.3664          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3531 = 1.03 * 1.00 * 6.1556 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2462 = 1.03 * 1.00 * 6.0506 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.64   12.16    None  None   None       |
|    all(noH): 2823   0      0.00    77.64   12.16    None  None   None       |
|    Sol.    : 438    0      0.00    77.64   28.02    None  None   None       |
|    Mac.    : 2385   0      0.00    69.47   9.24     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 -   7.764: 1328   |   5:    38.821 -  46.586:   70        |
|      1:     7.764 -  15.529:  725   |   6:    46.586 -  54.350:   37        |
|      2:    15.529 -  23.293:  342   |   7:    54.350 -  62.114:   19        |
|      3:    23.293 -  31.057:  188   |   8:    62.114 -  69.878:    9        |
|      4:    31.057 -  38.821:  103   |   9:    69.878 -  77.643:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3192 r_free = 0.3664             target_work(ml) = 6.021         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3186 r_free = 0.3671             target_work(ml) = 6.020         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3186   r_free= 0.3671   ksol= 0.33   Bsol= 38.38   scale= 1.071   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.73,7.07,10.97,0.00,0.00,0.00); trace/3= 8.59                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.019516                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3170   r_free= 0.3645   ksol= 0.31   Bsol= 52.58   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.73,4.48,7.67,0.00,0.00,0.00); trace/3= 5.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.021030                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.814001              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.869   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.484920              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.067  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3170      final r-factor (work) = 0.2325          |
| start r-factor (free) = 0.3645      final r-factor (free) = 0.2853          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6999 = 4.81 * 0.50 * 6.0460 + 1.00 * 0.1472                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2607 = 4.81 * 0.50 * 5.8935 + 1.00 * 0.0749                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2325      final r-factor (work) = 0.2117          |
| start r-factor (free) = 0.2853      final r-factor (free) = 0.2639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9342 = 0.48 * 1.00 * 5.8935 + 1.00 * 0.0763                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1216 = 0.48 * 1.00 * 5.7184 + 1.00 * 0.3486                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.49   12.12    None  None   None       |
|    all(noH): 2823   0      0.00    78.49   12.12    None  None   None       |
|    Sol.    : 438    0      0.00    78.49   32.54    None  None   None       |
|    Mac.    : 2385   0      0.00    69.67   8.37     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 -   7.849: 1498   |   5:    39.243 -  47.091:   81        |
|      1:     7.849 -  15.697:  654   |   6:    47.091 -  54.940:   51        |
|      2:    15.697 -  23.546:  228   |   7:    54.940 -  62.788:   23        |
|      3:    23.546 -  31.394:  132   |   8:    62.788 -  70.637:    6        |
|      4:    31.394 -  39.243:  148   |   9:    70.637 -  78.485:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2117 r_free = 0.2639             target_work(ml) = 5.688         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2115 r_free = 0.2640             target_work(ml) = 5.688         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2115   r_free= 0.2640   ksol= 0.31   Bsol= 52.58   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.73,4.48,7.67,0.00,0.00,0.00); trace/3= 5.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.688179                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2105   r_free= 0.2639   ksol= 0.34   Bsol= 70.80   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.22,5.20,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.689827                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.483214              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.143   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 10.529051             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.329   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2105      final r-factor (work) = 0.1510          |
| start r-factor (free) = 0.2639      final r-factor (free) = 0.1983          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7655 = 5.48 * 0.50 * 5.7230 + 1.00 * 0.0752                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3297 = 5.48 * 0.50 * 5.5596 + 1.00 * 0.0875                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1510      final r-factor (work) = 0.1354          |
| start r-factor (free) = 0.1983      final r-factor (free) = 0.1859          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 58.5582 = 10.53 * 1.00 * 5.5596 + 1.00 * 0.0208                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 56.2532 = 10.53 * 1.00 * 5.3409 + 1.00 * 0.0185                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.08   13.31    None  None   None       |
|    all(noH): 2823   0      0.00    96.08   13.31    None  None   None       |
|    Sol.    : 438    0      0.00    96.08   40.23    None  None   None       |
|    Mac.    : 2385   0      0.00    82.90   8.37     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 -   9.609: 1739   |   5:    48.043 -  57.651:   94        |
|      1:     9.609 -  19.217:  538   |   6:    57.651 -  67.260:   68        |
|      2:    19.217 -  28.826:  150   |   7:    67.260 -  76.868:   26        |
|      3:    28.826 -  38.434:  104   |   8:    76.868 -  86.476:   12        |
|      4:    38.434 -  48.043:   87   |   9:    86.476 -  96.085:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1354 r_free = 0.1859             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1353 r_free = 0.1859             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1353   r_free= 0.1859   ksol= 0.34   Bsol= 70.80   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.22,5.20,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.312424                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1355   r_free= 0.1859   ksol= 0.33   Bsol= 70.80   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.75,2.85,4.52,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.312601                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.560438              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.561  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.236149              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.413  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1355      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1859      final r-factor (free) = 0.1765          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9271 = 2.56 * 0.50 * 5.3425 + 1.00 * 0.0875                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8367 = 2.56 * 0.50 * 5.2844 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1255      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1765      final r-factor (free) = 0.1721          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2674 = 0.24 * 1.00 * 5.2844 + 1.00 * 0.0195                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3491 = 0.24 * 1.00 * 5.2550 + 1.00 * 0.1082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.65   13.20    None  None   None       |
|    all(noH): 2823   0      0.00    95.65   13.20    None  None   None       |
|    Sol.    : 438    0      0.63    95.65   39.66    None  None   None       |
|    Mac.    : 2385   0      0.00    82.43   8.34     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 -   9.565: 1794   |   5:    47.827 -  57.392:   92        |
|      1:     9.565 -  19.131:  486   |   6:    57.392 -  66.958:   67        |
|      2:    19.131 -  28.696:  146   |   7:    66.958 -  76.523:   27        |
|      3:    28.696 -  38.262:  112   |   8:    76.523 -  86.088:   10        |
|      4:    38.262 -  47.827:   84   |   9:    86.088 -  95.654:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1252 r_free = 0.1721             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1250 r_free = 0.1720             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1720   ksol= 0.33   Bsol= 70.80   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.75,2.85,4.52,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.238631                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1721   ksol= 0.33   Bsol= 70.80   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.69,2.77,4.32,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.238609                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.018757              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.351  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.969142              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.316   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0019 = 3.02 * 0.50 * 5.2535 + 1.00 * 0.0723                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9587 = 3.02 * 0.50 * 5.2183 + 1.00 * 0.0823                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3039 = 1.97 * 1.00 * 5.2183 + 1.00 * 0.0283                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9761 = 1.97 * 1.00 * 5.1985 + 1.00 * 0.7395                              |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.33   13.11    None  None   None       |
|    all(noH): 2823   0      0.00    98.33   13.11    None  None   None       |
|    Sol.    : 438    0      0.77    98.33   39.02    None  None   None       |
|    Mac.    : 2385   0      0.00    91.85   8.36     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 -   9.833: 1807   |   5:    49.163 -  58.995:   90        |
|      1:     9.833 -  19.665:  484   |   6:    58.995 -  68.828:   48        |
|      2:    19.665 -  29.498:  153   |   7:    68.828 -  78.660:   21        |
|      3:    29.498 -  39.330:  119   |   8:    78.660 -  88.493:    9        |
|      4:    39.330 -  49.163:   87   |   9:    88.493 -  98.325:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1677             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1173 r_free = 0.1680             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1680   ksol= 0.33   Bsol= 70.80   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.69,2.77,4.32,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.199878                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.8025 0.99   1387  153 0.1003 0.1408      5.4167      5.5901|
|  2:  4.8025 -  3.8319 0.99   1329  152 0.0846 0.1145      5.4548      5.6602|
|  3:  3.8319 -  3.3534 0.99   1305  140 0.1083 0.1514         5.5       5.869|
|  4:  3.3534 -  3.0495 0.99   1293  149 0.1232 0.1750       5.478      5.6664|
|  5:  3.0495 -  2.8324 0.99   1290  143 0.1419 0.1724      5.3912      5.5693|
|  6:  2.8324 -  2.6663 0.99   1300  137 0.1292 0.2244      5.2801      5.5999|
|  7:  2.6663 -  2.5334 0.99   1277  147 0.1375 0.1700      5.2374      5.4134|
|  8:  2.5334 -  2.4236 0.98   1271  141 0.1272 0.1814      5.1569      5.4034|
|  9:  2.4236 -  2.3306 0.98   1260  141 0.1239 0.1859      5.1028      5.3503|
| 10:  2.3306 -  2.2505 1.00   1282  142 0.1210 0.1809      5.0354      5.2622|
| 11:  2.2505 -  2.1803 0.97   1251  138 0.1231 0.1897      5.0108      5.3026|
| 12:  2.1803 -  2.1182 0.98   1248  138 0.1192 0.1932      4.9396      5.3106|
| 13:  2.1182 -  2.0625 0.99   1289  139 0.1218 0.1866      4.8482      5.0933|
| 14:  2.0625 -  2.0123 0.67    848   99 0.1122 0.1739       4.743      4.9621|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2395 -  4.8025  1387   153  0.94   9.86   0.97     0.94       8263.43|
|  2:  4.8025 -  3.8319  1329   152  0.95   8.52   1.00     0.98       9866.68|
|  3:  3.8319 -  3.3534  1305   140  0.93  11.77   1.02     1.02      11043.84|
|  4:  3.3534 -  3.0495  1293   149  0.92  13.87   1.01     0.99      10860.03|
|  5:  3.0495 -  2.8324  1290   143  0.89  16.90   1.00     0.97       9387.25|
|  6:  2.8324 -  2.6663  1300   137  0.89  17.45   0.98     0.95       8347.76|
|  7:  2.6663 -  2.5334  1277   147  0.89  17.33   0.98     0.96       7268.67|
|  8:  2.5334 -  2.4236  1271   141  0.89  16.86   0.99     0.96       6384.15|
|  9:  2.4236 -  2.3306  1260   141  0.90  16.56   1.00     0.95       5817.63|
| 10:  2.3306 -  2.2505  1282   142  0.89  17.20   1.00     0.95       5144.12|
| 11:  2.2505 -  2.1803  1251   138  0.89  17.57   0.99     0.94       5006.97|
| 12:  2.1803 -  2.1182  1248   138  0.90  16.64   1.00     0.99       4527.82|
| 13:  2.1182 -  2.0625  1289   139  0.89  17.63   0.98     0.95       3791.30|
| 14:  2.0625 -  2.0123   848    99  0.91  15.17   0.97     0.93       2944.15|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2944.15 max =        11043.84 mean =      7181.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.71 mean =        15.18|
|phase err.(test): min =        0.00 max =           89.66 mean =        14.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1679   ksol= 0.32   Bsol= 68.39   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-0.49,1.06,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.199720                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1679   ksol= 0.32   Bsol= 68.39   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-0.49,1.06,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.199720                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.8025 0.99   1387  153 0.1001 0.1403      5.4123      5.5874|
|  2:  4.8025 -  3.8319 0.99   1329  152 0.0844 0.1142      5.4526       5.657|
|  3:  3.8319 -  3.3534 0.99   1305  140 0.1081 0.1514      5.4991      5.8691|
|  4:  3.3534 -  3.0495 0.99   1293  149 0.1234 0.1751       5.479      5.6667|
|  5:  3.0495 -  2.8324 0.99   1290  143 0.1420 0.1726      5.3925      5.5708|
|  6:  2.8324 -  2.6663 0.99   1300  137 0.1293 0.2247      5.2813       5.601|
|  7:  2.6663 -  2.5334 0.99   1277  147 0.1376 0.1701      5.2383      5.4144|
|  8:  2.5334 -  2.4236 0.98   1271  141 0.1273 0.1814      5.1574      5.4034|
|  9:  2.4236 -  2.3306 0.98   1260  141 0.1239 0.1858      5.1029      5.3502|
| 10:  2.3306 -  2.2505 1.00   1282  142 0.1210 0.1810      5.0356      5.2626|
| 11:  2.2505 -  2.1803 0.97   1251  138 0.1231 0.1897       5.011      5.3026|
| 12:  2.1803 -  2.1182 0.98   1248  138 0.1192 0.1932      4.9397      5.3108|
| 13:  2.1182 -  2.0625 0.99   1289  139 0.1218 0.1866      4.8484      5.0934|
| 14:  2.0625 -  2.0123 0.67    848   99 0.1122 0.1740      4.7431      4.9622|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2395 -  4.8025  1387   153  0.94   9.81   0.97     0.94       8200.01|
|  2:  4.8025 -  3.8319  1329   152  0.95   8.48   1.00     0.99       9818.16|
|  3:  3.8319 -  3.3534  1305   140  0.93  11.75   1.02     1.02      11012.96|
|  4:  3.3534 -  3.0495  1293   149  0.92  13.88   1.01     0.99      10872.19|
|  5:  3.0495 -  2.8324  1290   143  0.89  16.91   1.00     0.97       9410.03|
|  6:  2.8324 -  2.6663  1300   137  0.89  17.47   0.98     0.95       8370.44|
|  7:  2.6663 -  2.5334  1277   147  0.89  17.35   0.98     0.96       7283.24|
|  8:  2.5334 -  2.4236  1271   141  0.89  16.87   0.99     0.96       6390.15|
|  9:  2.4236 -  2.3306  1260   141  0.90  16.56   1.00     0.95       5820.26|
| 10:  2.3306 -  2.2505  1282   142  0.89  17.20   0.99     0.95       5145.85|
| 11:  2.2505 -  2.1803  1251   138  0.89  17.57   0.99     0.94       5009.13|
| 12:  2.1803 -  2.1182  1248   138  0.90  16.64   1.00     0.99       4529.49|
| 13:  2.1182 -  2.0625  1289   139  0.89  17.64   0.98     0.95       3792.79|
| 14:  2.0625 -  2.0123   848    99  0.91  15.17   0.97     0.93       2945.33|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2945.33 max =        11012.96 mean =      7177.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.80 mean =        15.18|
|phase err.(test): min =        0.00 max =           89.59 mean =        14.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.26    101.59  16.38    None  None   None       |
|    all(noH): 2823   0      3.26    101.59  16.38    None  None   None       |
|    Sol.    : 438    0      4.03    101.59  42.28    None  None   None       |
|    Mac.    : 2385   0      3.26    95.11   11.62    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:     3.261 -  13.093: 1807   |   5:    52.423 -  62.256:   90        |
|      1:    13.093 -  22.926:  484   |   6:    62.256 -  72.088:   48        |
|      2:    22.926 -  32.758:  153   |   7:    72.088 -  81.921:   21        |
|      3:    32.758 -  42.591:  119   |   8:    81.921 -  91.753:    9        |
|      4:    42.591 -  52.423:   87   |   9:    91.753 - 101.586:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.282 - 4.884
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 326
   mapped sites are within: 0.717 - 4.884

peak=   10.095 closest distance to " CB  VAL A 230 " =    1.477
peak=    6.092 closest distance to " CG  LEU A   5 " =    1.129
peak=    5.757 closest distance to " CB  GLN A 223 " =    1.471
peak=    5.668 closest distance to " CG  LEU A 228 " =    1.152
peak=    5.522 closest distance to " O   HOH Z 111 " =    2.180
peak=    5.169 closest distance to " CB  VAL A 296 " =    1.085
peak=    5.130 closest distance to " NE2 GLN A  11 " =    1.088
peak=    4.846 closest distance to " O   HOH Z 232 " =    2.254
peak=    4.834 closest distance to " CG2 VAL A 296 " =    0.984
peak=    4.812 closest distance to " O   HOH Z 369 " =    2.164
peak=    4.799 closest distance to " CZ  PHE A 218 " =    1.118
peak=    4.717 closest distance to " CB  GLN A 183 " =    1.269
peak=    4.642 closest distance to " O   HOH Z 427 " =    3.140
peak=    4.627 closest distance to " CB  SER A  63 " =    1.264
peak=    4.535 closest distance to " O   HOH Z 142 " =    1.768
peak=    4.514 closest distance to " O   HOH Z 303 " =    2.082
peak=    4.369 closest distance to " CD2 LEU A   5 " =    1.055
peak=    4.357 closest distance to " CB  ASP A 124 " =    0.819
peak=    4.324 closest distance to " CB  VAL A 230 " =    1.208
peak=    4.315 closest distance to " O   HOH Z 265 " =    2.185
peak=    4.300 closest distance to " O   HOH Z 425 " =    1.517
peak=    4.299 closest distance to " CA  TYR A  30 " =    1.051
peak=    4.286 closest distance to " O   HOH Z 298 " =    2.000
peak=    4.272 closest distance to " O   HOH Z 411 " =    3.782
peak=    4.204 closest distance to " CB  TYR A 169 " =    0.723
peak=    4.198 closest distance to " CG  PRO A 198 " =    1.217
peak=    4.181 closest distance to " CG  MET A 185 " =    1.350
peak=    4.169 closest distance to " CG  PRO A 213 " =    1.178
peak=    4.158 closest distance to " CA  ALA A  51 " =    0.988
peak=    4.139 closest distance to " CB  ARG A 190 " =    1.502
peak=    4.131 closest distance to " CB  GLU A 277 " =    3.788
peak=    4.127 closest distance to " O   HOH Z 368 " =    2.376
peak=    4.117 closest distance to " O   HOH Z 359 " =    1.618
peak=    4.116 closest distance to " O   HOH Z 287 " =    2.058
peak=    4.099 closest distance to " CD  ARG A 159 " =    0.765
peak=    4.091 closest distance to " CB  VAL A 202 " =    1.641
peak=    4.083 closest distance to " O   HOH Z 126 " =    1.601
peak=    4.076 closest distance to " CB  GLU A 128 " =    1.060
peak=    4.076 closest distance to " CB  ASN A 148 " =    1.328
peak=    4.066 closest distance to " CG1 VAL A 296 " =    1.265
peak=    4.064 closest distance to " CZ3 TRP A 266 " =    1.157
peak=    4.058 closest distance to " O   HOH Z  78 " =    1.683
peak=    4.058 closest distance to " O   SER A  87 " =    2.362
peak=    4.032 closest distance to " O   HOH Z 184 " =    1.508
peak=    4.029 closest distance to " CB  ASN A 142 " =    1.177
peak=    4.028 closest distance to " CB  ARG A  79 " =    1.509
peak=    4.014 closest distance to " O   HOH Z   9 " =    1.351
peak=    4.014 closest distance to " O   HOH Z 261 " =    1.894
peak=    4.009 closest distance to " O   HOH Z 158 " =    3.094
peak=    3.999 closest distance to " CG  PRO A 243 " =    1.118
peak=    3.999 closest distance to " O   PRO A 198 " =    1.571
peak=    3.992 closest distance to " NH1AARG A 145 " =    1.292
peak=    3.976 closest distance to " CA  ARG A 195 " =    1.224
peak=    3.961 closest distance to " CB  TRP A 266 " =    1.060
peak=    3.955 closest distance to " O   HOH Z 188 " =    3.044
peak=    3.950 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.937 closest distance to " O   HOH Z 290 " =    1.173
peak=    3.921 closest distance to " O   HOH Z  19 " =    2.362
peak=    3.910 closest distance to " CD2 LEU A 228 " =    1.176
peak=    3.907 closest distance to " CG  ARG A 138 " =    1.234
peak=    3.903 closest distance to " CG1 ILE A  49 " =    1.568
peak=    3.894 closest distance to " CA  ALA A 295 " =    1.149
peak=    3.891 closest distance to " CB  ASP A 140 " =    1.040
peak=    3.879 closest distance to " CB  ARG A 275 " =    0.999
peak=    3.872 closest distance to " O   HOH Z  43 " =    2.019
peak=    3.871 closest distance to " O   HOH Z 171 " =    3.947
peak=    3.861 closest distance to " ND2 ASN A 187 " =    1.513
peak=    3.860 closest distance to " CG2 ILE A 234 " =    0.922
peak=    3.858 closest distance to " O   HOH Z 316 " =    3.131
peak=    3.854 closest distance to " O   HOH Z 193 " =    2.147
peak=    3.796 closest distance to " O   HOH Z 346 " =    1.586
peak=    3.790 closest distance to " CD  LYS A 166 " =    1.339
peak=    3.786 closest distance to " OE1 GLN A  55 " =    1.235
peak=    3.779 closest distance to " O   HOH Z 422 " =    2.614
peak=    3.778 closest distance to " CG2 THR A 221 " =    1.171
peak=    3.776 closest distance to " CG  GLU A  37 " =    0.931
peak=    3.764 closest distance to " CZ  PHE A  38 " =    1.187
peak=    3.756 closest distance to " O   HOH Z  76 " =    1.116
peak=    3.755 closest distance to " O   HOH Z 214 " =    2.597
peak=    3.748 closest distance to " CA  VAL A 125 " =    1.260
peak=    3.747 closest distance to " O   HOH Z 406 " =    1.510
peak=    3.747 closest distance to " O   HOH Z 227 " =    1.752
peak=    3.745 closest distance to " O   HOH Z 313 " =    1.798
peak=    3.744 closest distance to " CA  ALA A 291 " =    0.911
peak=    3.743 closest distance to " CA  ARG A  36 " =    1.156
peak=    3.740 closest distance to " CB  VAL A 265 " =    1.253
peak=    3.738 closest distance to " O   HOH Z 272 " =    1.884
peak=    3.734 closest distance to " CD  ARG A  66 " =    2.349
peak=    3.732 closest distance to " CG  LEU A 167 " =    1.210
peak=    3.731 closest distance to " O   MET A 105 " =    1.888
peak=    3.717 closest distance to " CD  ARG A 269 " =    0.946
peak=    3.708 closest distance to " O   HOH Z 280 " =    2.925
peak=    3.706 closest distance to " CD ALYS A 290 " =    1.033
peak=    3.700 closest distance to " CD1 LEU A 300 " =    1.138
peak=    3.697 closest distance to " OG BSER A 164 " =    2.222
peak=    3.693 closest distance to " CB  GLU A  46 " =    0.968
peak=    3.690 closest distance to " CD2 TRP A 179 " =    1.325
peak=    3.686 closest distance to " CB  THR A  82 " =    1.337
peak=    3.686 closest distance to " CA  GLY A 267 " =    0.717
peak=    3.686 closest distance to " O   HOH Z  49 " =    0.958
peak=    3.677 closest distance to " O   HOH Z 234 " =    3.623
peak=    3.676 closest distance to " O   HOH Z 180 " =    2.115
peak=    3.675 closest distance to " CG1 VAL A 153 " =    0.966
peak=    3.657 closest distance to " CB  ARG A 138 " =    0.964
peak=    3.649 closest distance to " CA  MET A 105 " =    1.022
peak=    3.646 closest distance to " N   PHE A 130 " =    1.274
peak=    3.642 closest distance to " CB  ALA A   9 " =    1.657
peak=    3.636 closest distance to " O   HOH Z 126 " =    2.077
peak=    3.633 closest distance to " O   HOH Z 248 " =    1.591
peak=    3.622 closest distance to " CB AVAL A  41 " =    1.339
peak=    3.622 closest distance to " O   HOH Z 423 " =    1.740
peak=    3.620 closest distance to " O   HOH Z 247 " =    1.302
peak=    3.620 closest distance to " CB  GLU A 152 " =    1.214
peak=    3.620 closest distance to " CB  GLN A  89 " =    1.257
peak=    3.617 closest distance to " O   HOH Z 213 " =    1.908
peak=    3.608 closest distance to " O   HOH Z 353 " =    2.618
peak=    3.606 closest distance to " CD1 LEU A  96 " =    0.736
peak=    3.605 closest distance to " O  BHOH Z 338 " =    2.320
peak=    3.604 closest distance to " OD1 ASN A  69 " =    2.659
peak=    3.582 closest distance to " O   HOH Z  78 " =    2.282
peak=    3.572 closest distance to " O   HOH Z 214 " =    1.124
peak=    3.545 closest distance to " O   HOH Z  21 " =    1.733
peak=    3.542 closest distance to " CB  PRO A  54 " =    0.772
peak=    3.539 closest distance to " CA  LEU A 282 " =    1.073
peak=    3.539 closest distance to " ND2 ASN A 249 " =    1.898
peak=    3.534 closest distance to " CB  LEU A  83 " =    0.751
peak=    3.533 closest distance to " CB  LYS A 117 " =    1.168
peak=    3.526 closest distance to " CD1 LEU A   5 " =    1.323
peak=    3.523 closest distance to " CG2 VAL A 257 " =    0.860
peak=    3.522 closest distance to " O   ASP A 124 " =    1.172
peak=    3.521 closest distance to " CA  ALA A 160 " =    0.982
peak=    3.516 closest distance to " CB  SER A 212 " =    1.209
peak=    3.513 closest distance to " O   HOH Z  80 " =    1.821
peak=    3.506 closest distance to " O   HOH Z  30 " =    1.253
peak=    3.505 closest distance to " CB  THR A  52 " =    0.787
peak=    3.495 closest distance to " CB  ALA A 104 " =    0.830
peak=    3.491 closest distance to " O   ASP A 200 " =    1.734
peak=    3.487 closest distance to " CB  ASN A  39 " =    0.916
peak=    3.483 closest distance to " CA  ALA A 158 " =    1.252
peak=    3.469 closest distance to " O   HOH Z 258 " =    1.966
peak=    3.468 closest distance to " CB  TRP A 150 " =    1.281
peak=    3.465 closest distance to " O   HOH Z 155 " =    3.454
peak=    3.464 closest distance to " O   ALA A 158 " =    1.408
peak=    3.458 closest distance to " O   HOH Z 368 " =    3.610
peak=    3.451 closest distance to " CA  TYR A  30 " =    1.062
peak=    3.446 closest distance to " O   HOH Z 131 " =    2.411
peak=    3.445 closest distance to " O   HOH Z 134 " =    2.794
peak=    3.443 closest distance to " CB  THR A  31 " =    1.552
peak=    3.442 closest distance to " O   HOH Z 285 " =    2.264
peak=    3.437 closest distance to " CD1 ILE A 199 " =    0.998
peak=    3.435 closest distance to " CB  VAL A 268 " =    0.871
peak=    3.431 closest distance to " N   ASN A  39 " =    1.262
peak=    3.430 closest distance to " O   HOH Z 371 " =    3.076
peak=    3.430 closest distance to " O   HOH Z  61 " =    1.730
peak=    3.428 closest distance to " CG  MET A 185 " =    1.074
peak=    3.419 closest distance to " O   HOH Z  88 " =    3.399
peak=    3.418 closest distance to " CE1 TYR A 186 " =    1.241
peak=    3.415 closest distance to " O   HOH Z 102 " =    1.313
peak=    3.415 closest distance to " CB  TRP A 179 " =    1.468
peak=    3.413 closest distance to " O   HOH Z  88 " =    3.258
peak=    3.413 closest distance to " O   HOH Z 313 " =    1.548
peak=    3.413 closest distance to " CG  ARG A 269 " =    1.866
peak=    3.413 closest distance to " CA  GLY A 211 " =    1.389
peak=    3.410 closest distance to " OE2 GLU A  53 " =    2.004
peak=    3.407 closest distance to " CA  SER A  87 " =    0.970
peak=    3.407 closest distance to " CB  PRO A 243 " =    1.354
peak=    3.403 closest distance to " CA  ARG A 139 " =    1.186
peak=    3.403 closest distance to " O   HOH Z  63 " =    1.740
peak=    3.403 closest distance to " CA  TYR A 116 " =    1.420
peak=    3.402 closest distance to " CB  SER A   3 " =    1.526
peak=    3.401 closest distance to " CG1 ILE A  33 " =    1.225
peak=    3.395 closest distance to " CB  ALA A 227 " =    1.130
peak=    3.391 closest distance to " CZ  PHE A 192 " =    0.955
peak=    3.390 closest distance to " OG1 THR A 279 " =    1.495
peak=    3.388 closest distance to " O   GLN A  88 " =    1.627
peak=    3.387 closest distance to " CG  PHE A 204 " =    0.909
peak=    3.384 closest distance to " CB  GLN A  88 " =    1.229
peak=    3.383 closest distance to " O   ALA A 165 " =    1.512
peak=    3.379 closest distance to " N   SER A 135 " =    1.472
peak=    3.379 closest distance to " ND1 HIS A  81 " =    1.780
peak=    3.378 closest distance to " CG BARG A 102 " =    1.875
peak=    3.376 closest distance to " CA  GLU A 152 " =    0.921
peak=    3.372 closest distance to " CD  GLU A 152 " =    0.812
peak=    3.372 closest distance to " NZ  LYS A 117 " =    3.140
peak=    3.370 closest distance to " O   HOH Z 251 " =    1.470
peak=    3.366 closest distance to " O   HOH Z 273 " =    2.913
peak=    3.364 closest distance to " CA  ALA A  21 " =    1.203
peak=    3.361 closest distance to " CB  LEU A 228 " =    1.242
peak=    3.361 closest distance to " O   HOH Z 325 " =    2.305
peak=    3.357 closest distance to " CB  LEU A 143 " =    1.301
peak=    3.356 closest distance to " CA  ASN A  74 " =    1.286
peak=    3.356 closest distance to " NE2 HIS A 207 " =    1.235
peak=    3.353 closest distance to " CA  ASN A 127 " =    1.067
peak=    3.351 closest distance to " CG BARG A 275 " =    1.471
peak=    3.350 closest distance to " O   HOH Z 193 " =    1.968
peak=    3.348 closest distance to " CB  TYR A 116 " =    0.873
peak=    3.346 closest distance to " O   HOH Z 183 " =    1.116
peak=    3.345 closest distance to " O   HOH Z 291 " =    1.503
peak=    3.339 closest distance to " O   HOH Z 133 " =    2.773
peak=    3.338 closest distance to " O   HOH Z  10 " =    1.802
peak=    3.336 closest distance to " O   HOH Z  97 " =    2.098
peak=    3.335 closest distance to " OD1 ASN A 217 " =    1.560
peak=    3.334 closest distance to " O   HOH Z 299 " =    4.306
peak=    3.334 closest distance to " ND2 ASN A 249 " =    0.836
peak=    3.333 closest distance to " O   HOH Z 437 " =    1.357
peak=    3.333 closest distance to " O   HOH Z 130 " =    1.059
peak=    3.329 closest distance to " O   HOH Z   4 " =    1.709
peak=    3.325 closest distance to " O   HOH Z 238 " =    2.280
peak=    3.325 closest distance to " O   ASN A  74 " =    1.419
peak=    3.322 closest distance to " OG  SER A 245 " =    1.715
peak=    3.321 closest distance to " CG1 ILE A 151 " =    1.185
peak=    3.320 closest distance to " CB  ALA A  43 " =    0.864
peak=    3.317 closest distance to " O   HOH Z 403 " =    1.579
peak=    3.317 closest distance to " CA  ALA A 100 " =    1.007
peak=    3.316 closest distance to " CG AARG A 275 " =    1.233
peak=    3.316 closest distance to " NZ  LYS A  48 " =    1.361
peak=    3.315 closest distance to " O   GLU A   2 " =    1.725
peak=    3.314 closest distance to " O   HOH Z 201 " =    2.804
peak=    3.313 closest distance to " O   HOH Z 298 " =    2.481
peak=    3.312 closest distance to " CA  VAL A 112 " =    1.141
peak=    3.310 closest distance to " O   HOH Z  20 " =    1.638
peak=    3.309 closest distance to " CB  PRO A  90 " =    1.231
peak=    3.308 closest distance to " CB  ALA A 248 " =    1.112
peak=    3.306 closest distance to " CA  ALA A 129 " =    1.439
peak=    3.305 closest distance to " N   SER A 271 " =    0.957
peak=    3.304 closest distance to " O   HOH Z 365 " =    2.953
peak=    3.303 closest distance to " CA  MET A  40 " =    1.275
peak=    3.303 closest distance to " O   HOH Z 357 " =    2.754
peak=    3.298 closest distance to " CG1BVAL A  72 " =    1.765
peak=    3.297 closest distance to " CA  ASP A 191 " =    1.154
peak=    3.297 closest distance to " CB  SER A 273 " =    0.878
peak=    3.294 closest distance to " OG  SER A  62 " =    3.041
peak=    3.282 closest distance to " O   HOH Z 250 " =    1.363
peak=    3.277 closest distance to " O   HOH Z 147 " =    1.726
peak=    3.277 closest distance to " NE  ARG A  79 " =    1.155
peak=    3.276 closest distance to " O   HOH Z 172 " =    3.849
peak=    3.275 closest distance to " CD  ARG A  66 " =    2.285
peak=    3.274 closest distance to " O   HOH Z 166 " =    3.694
peak=    3.273 closest distance to " CA  ASN A 215 " =    1.166
peak=    3.271 closest distance to " CB  ALA A 242 " =    0.872
peak=    3.268 closest distance to " OG  SER A  22 " =    2.902
peak=    3.267 closest distance to " O   PHE A  61 " =    1.381
peak=    3.266 closest distance to " O   HOH Z  44 " =    2.136
peak=    3.265 closest distance to " O   PRO A 213 " =    1.570
peak=    3.260 closest distance to " O   HOH Z 109 " =    2.787
peak=    3.258 closest distance to " CA  ARG A 102 " =    1.165
peak=    3.257 closest distance to " O   THR A 182 " =    1.425
peak=    3.256 closest distance to " O   HOH Z 130 " =    2.211
peak=    3.256 closest distance to " CB  ILE A 120 " =    1.330
peak=    3.256 closest distance to " O   HOH Z 391 " =    3.016
peak=    3.254 closest distance to " CB  TYR A  30 " =    1.161
peak=    3.254 closest distance to " O   HOH Z 124 " =    2.011
peak=    3.253 closest distance to " CA  ALA A 154 " =    1.071
peak=    3.252 closest distance to " N   ALA A 256 " =    1.118
peak=    3.250 closest distance to " CB  MET A  47 " =    1.008
peak=    3.249 closest distance to " CB  GLN A 205 " =    1.008
peak=    3.244 closest distance to " CD2 LEU A 255 " =    1.626
peak=    3.242 closest distance to " O   GLN A 278 " =    1.349
peak=    3.239 closest distance to " CA  THR A 221 " =    0.925
peak=    3.237 closest distance to " CB  ALA A 291 " =    1.303
peak=    3.237 closest distance to " O   HOH Z 197 " =    2.874
peak=    3.233 closest distance to " CB  ASN A 187 " =    1.113
peak=    3.233 closest distance to " O   HOH Z 329 " =    4.222
peak=    3.230 closest distance to " CB  SER A 288 " =    1.351
peak=    3.228 closest distance to " CA  ASN A 217 " =    1.290
peak=    3.224 closest distance to " CB  ALA A 248 " =    1.515
peak=    3.224 closest distance to " CE3 TRP A 150 " =    1.053
peak=    3.216 closest distance to " CB  ASP A 298 " =    1.185
peak=    3.215 closest distance to " O   HOH Z  48 " =    1.635
peak=    3.214 closest distance to " NH2 ARG A 156 " =    1.102
peak=    3.214 closest distance to " CA  ASP A 140 " =    1.342
peak=    3.212 closest distance to " CB  ASN A 285 " =    0.970
peak=    3.209 closest distance to " CB  VAL A 257 " =    0.786
peak=    3.207 closest distance to " O   HOH Z 211 " =    1.106
peak=    3.207 closest distance to " O   HOH Z 409 " =    3.180
peak=    3.201 closest distance to " O   HOH Z 193 " =    1.740
peak=    3.199 closest distance to " CB  ASN A 110 " =    1.206
peak=    3.194 closest distance to " CB  SER A  62 " =    0.913
peak=    3.194 closest distance to " O   HOH Z 145 " =    1.861
peak=    3.192 closest distance to " N   VAL A 126 " =    1.407
peak=    3.191 closest distance to " CE  LYS A  48 " =    1.151
peak=    3.190 closest distance to " CZ3 TRP A  85 " =    1.107
peak=    3.190 closest distance to " OG  SER A 135 " =    1.262
peak=    3.185 closest distance to " O   HOH Z 368 " =    4.041
peak=    3.185 closest distance to " CZ3 TRP A  92 " =    1.332
peak=    3.184 closest distance to " CA  VAL A  41 " =    0.812
peak=    3.182 closest distance to " N   ASP A 162 " =    1.197
peak=    3.179 closest distance to " O   HOH Z 203 " =    1.771
peak=    3.177 closest distance to " CZ3 TRP A 274 " =    4.691
peak=    3.175 closest distance to " CB  SER A 216 " =    0.940
peak=    3.174 closest distance to " O   THR A 220 " =    1.222
peak=    3.174 closest distance to " O   HOH Z 329 " =    3.018
peak=    3.164 closest distance to " CB  ALA A   1 " =    4.884
peak=    3.163 closest distance to " O   HOH Z 332 " =    1.597
peak=    3.162 closest distance to " O   TYR A 116 " =    1.290
peak=    3.160 closest distance to " O   HOH Z   9 " =    1.787
peak=    3.158 closest distance to " CG  GLN A  88 " =    1.129
peak=    3.149 closest distance to " CA  ALA A 184 " =    1.098
peak=    3.141 closest distance to " CD  LYS A 193 " =    1.987
peak=    3.137 closest distance to " C   ALA A 299 " =    0.965
peak=    3.136 closest distance to " CB  MET A 113 " =    1.874
peak=    3.136 closest distance to " O   HOH Z 162 " =    4.097
peak=    3.131 closest distance to " OG BSER A 210 " =    1.353
peak=    3.121 closest distance to " O   HOH Z 294 " =    1.548
peak=    3.116 closest distance to " O   HOH Z 371 " =    3.548
peak=    3.114 closest distance to " O   HOH Z 148 " =    3.345
peak=    3.112 closest distance to " CG2 VAL A 197 " =    1.046
peak=    3.106 closest distance to " O   THR A 251 " =    1.253
peak=    3.105 closest distance to " NH1BARG A 145 " =    1.038
peak=    3.105 closest distance to " O   HOH Z 171 " =    4.347
peak=    3.100 closest distance to " O   PHE A 192 " =    1.480
peak=    3.090 closest distance to " O   HOH Z 116 " =    1.850
peak=    3.088 closest distance to " NE2 HIS A 115 " =    1.000
peak=    3.086 closest distance to " CB  GLU A  37 " =    0.857
peak=    3.081 closest distance to " N   ASN A 127 " =    1.303
peak=    3.077 closest distance to " CD  ARG A 195 " =    0.943
peak=    3.065 closest distance to " O   HOH Z 148 " =    2.103
peak=    3.059 closest distance to " CB  ALA A 100 " =    1.281
peak=    3.056 closest distance to " CG  ARG A 159 " =    0.979
peak=    3.050 closest distance to " CB  ARG A 145 " =    0.779
peak=    3.035 closest distance to " O   LYS A 290 " =    2.421

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.686 - 5.535
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 220
   mapped sites are within: 0.730 - 5.535

peak=   -4.991 closest distance to " CG2 VAL A 230 " =    0.837
peak=   -4.659 closest distance to " CG1 VAL A 112 " =    2.679
peak=   -4.502 closest distance to " CB  PRO A 243 " =    2.707
peak=   -4.470 closest distance to " CD  ARG A  14 " =    3.354
peak=   -4.436 closest distance to " CD  ARG A 156 " =    2.079
peak=   -4.360 closest distance to " CD  GLN A  58 " =    0.950
peak=   -4.358 closest distance to " O   HOH Z 211 " =    0.730
peak=   -4.280 closest distance to " CG1 VAL A 296 " =    1.196
peak=   -4.216 closest distance to " OE1 GLN A 223 " =    2.276
peak=   -4.199 closest distance to " CG1 VAL A 250 " =    2.744
peak=   -4.124 closest distance to " O   ILE A 109 " =    2.663
peak=   -4.096 closest distance to " O   VAL A  67 " =    2.761
peak=   -4.090 closest distance to " O   HOH Z  73 " =    2.347
peak=   -4.077 closest distance to " CA  ASP A 298 " =    1.075
peak=   -4.064 closest distance to " CZ2 TRP A  92 " =    2.868
peak=   -4.040 closest distance to " O   HOH Z 231 " =    2.133
peak=   -4.014 closest distance to " O   SER A 271 " =    2.070
peak=   -4.013 closest distance to " O   HOH Z 196 " =    2.360
peak=   -4.004 closest distance to " CG1 VAL A 112 " =    2.848
peak=   -3.988 closest distance to " O   HOH Z 216 " =    1.040
peak=   -3.980 closest distance to " CG  ARG A 269 " =    2.337
peak=   -3.963 closest distance to " O   HOH Z 166 " =    1.771
peak=   -3.943 closest distance to " OE1 GLN A  88 " =    1.027
peak=   -3.908 closest distance to " O   HOH Z 411 " =    5.535
peak=   -3.904 closest distance to " O   HOH Z 394 " =    1.562
peak=   -3.862 closest distance to " CE2 TYR A  30 " =    2.713
peak=   -3.846 closest distance to " O   HOH Z  52 " =    1.553
peak=   -3.810 closest distance to " O   HOH Z  37 " =    1.982
peak=   -3.795 closest distance to " CA  GLY A 241 " =    2.362
peak=   -3.762 closest distance to " CE3 TRP A  70 " =    1.783
peak=   -3.758 closest distance to " O   HOH Z  44 " =    2.387
peak=   -3.709 closest distance to " O   VAL A 189 " =    2.664
peak=   -3.706 closest distance to " CG  HIS A  86 " =    1.130
peak=   -3.693 closest distance to " CA  GLY A 241 " =    3.175
peak=   -3.684 closest distance to " OG BSER A 134 " =    1.436
peak=   -3.673 closest distance to " CE3 TRP A 150 " =    2.121
peak=   -3.666 closest distance to " O   HOH Z 133 " =    1.185
peak=   -3.646 closest distance to " OD1 ASN A 148 " =    1.401
peak=   -3.630 closest distance to " O   HOH Z 251 " =    5.010
peak=   -3.625 closest distance to " O   HOH Z  38 " =    1.726
peak=   -3.623 closest distance to " O   PRO A 198 " =    1.265
peak=   -3.617 closest distance to " O   PRO A 163 " =    2.248
peak=   -3.611 closest distance to " OG  SER A  97 " =    2.323
peak=   -3.602 closest distance to " C   GLY A  17 " =    1.227
peak=   -3.597 closest distance to " O   HOH Z 198 " =    2.448
peak=   -3.593 closest distance to " CD2 PHE A  61 " =    2.002
peak=   -3.588 closest distance to " CB  VAL A 230 " =    1.097
peak=   -3.586 closest distance to " O   HOH Z 407 " =    3.203
peak=   -3.581 closest distance to " OG  SER A  62 " =    4.525
peak=   -3.577 closest distance to " O   HOH Z 128 " =    2.653
peak=   -3.568 closest distance to " CA  GLY A 203 " =    2.527
peak=   -3.564 closest distance to " N   ALA A  43 " =    2.682
peak=   -3.562 closest distance to " O   ASP A  27 " =    1.994
peak=   -3.556 closest distance to " CD2 LEU A 167 " =    1.830
peak=   -3.546 closest distance to " O   HOH Z 426 " =    1.614
peak=   -3.545 closest distance to " O   HOH Z 359 " =    2.957
peak=   -3.537 closest distance to " O   HOH Z  10 " =    1.532
peak=   -3.524 closest distance to " C   ALA A 158 " =    1.259
peak=   -3.523 closest distance to " ND2 ASN A 249 " =    2.499
peak=   -3.520 closest distance to " CG1 VAL A 125 " =    1.979
peak=   -3.519 closest distance to " O   GLY A  80 " =    2.586
peak=   -3.519 closest distance to " CD2 TYR A 293 " =    2.034
peak=   -3.519 closest distance to " CA  VAL A  67 " =    2.718
peak=   -3.514 closest distance to " O   HOH Z 351 " =    1.609
peak=   -3.509 closest distance to " CB  ALA A  43 " =    2.634
peak=   -3.508 closest distance to " O   HOH Z 106 " =    1.940
peak=   -3.505 closest distance to " CB  PHE A 192 " =    1.970
peak=   -3.505 closest distance to " N   ALA A 226 " =    2.131
peak=   -3.503 closest distance to " CD1 ILE A  33 " =    2.562
peak=   -3.494 closest distance to " CG  MET A 105 " =    1.010
peak=   -3.489 closest distance to " CG  PRO A 163 " =    2.315
peak=   -3.484 closest distance to " O   HOH Z 177 " =    1.777
peak=   -3.484 closest distance to " O   HOH Z 377 " =    1.888
peak=   -3.481 closest distance to " ND2 ASN A  45 " =    2.280
peak=   -3.480 closest distance to " OG  SER A  87 " =    1.575
peak=   -3.474 closest distance to " CD1 LEU A   5 " =    2.542
peak=   -3.473 closest distance to " NE2 GLN A 194 " =    1.895
peak=   -3.471 closest distance to " CD  LYS A 289 " =    2.397
peak=   -3.466 closest distance to " CG  GLU A 277 " =    1.298
peak=   -3.466 closest distance to " CB  ARG A  79 " =    2.608
peak=   -3.464 closest distance to " O   HOH Z   9 " =    1.594
peak=   -3.461 closest distance to " CG  GLN A 103 " =    2.519
peak=   -3.460 closest distance to " N   ASP A 171 " =    2.403
peak=   -3.453 closest distance to " O   HOH Z  93 " =    2.254
peak=   -3.443 closest distance to " CD  GLN A 223 " =    1.358
peak=   -3.439 closest distance to " CH2 TRP A 179 " =    1.200
peak=   -3.435 closest distance to " O   HOH Z 252 " =    3.759
peak=   -3.434 closest distance to " NH2AARG A 275 " =    5.393
peak=   -3.422 closest distance to " O   HOH Z 350 " =    1.880
peak=   -3.418 closest distance to " CG2BVAL A  41 " =    1.828
peak=   -3.416 closest distance to " O   HOH Z 185 " =    2.355
peak=   -3.412 closest distance to " CZ2 TRP A 274 " =    0.966
peak=   -3.410 closest distance to " C   LEU A 143 " =    1.142
peak=   -3.406 closest distance to " CA  GLY A 133 " =    2.322
peak=   -3.398 closest distance to " CG2 VAL A 189 " =    2.099
peak=   -3.396 closest distance to " CD  GLN A  88 " =    0.817
peak=   -3.388 closest distance to " CD1 PHE A  59 " =    2.048
peak=   -3.381 closest distance to " CE BMET A  47 " =    1.639
peak=   -3.380 closest distance to " O   HOH Z  68 " =    1.639
peak=   -3.380 closest distance to " O   HOH Z  43 " =    1.735
peak=   -3.375 closest distance to " CB  ALA A 248 " =    2.136
peak=   -3.374 closest distance to " CD1 ILE A 151 " =    2.466
peak=   -3.373 closest distance to " CD1 LEU A 101 " =    2.418
peak=   -3.369 closest distance to " N   SER A 276 " =    1.442
peak=   -3.364 closest distance to " CD  PRO A 213 " =    2.175
peak=   -3.362 closest distance to " O   TYR A 186 " =    1.852
peak=   -3.361 closest distance to " O   HOH Z  94 " =    2.158
peak=   -3.354 closest distance to " CB  ALA A  10 " =    2.257
peak=   -3.350 closest distance to " CA  ASN A 127 " =    1.098
peak=   -3.348 closest distance to " OXT GLY A 302 " =    3.132
peak=   -3.348 closest distance to " O   HOH Z 145 " =    1.044
peak=   -3.341 closest distance to " CE2 TRP A  70 " =    2.237
peak=   -3.340 closest distance to " O   HOH Z 193 " =    1.558
peak=   -3.338 closest distance to " O   HOH Z 232 " =    1.836
peak=   -3.331 closest distance to " CG2 VAL A 296 " =    1.303
peak=   -3.330 closest distance to " O   HOH Z 290 " =    1.422
peak=   -3.329 closest distance to " CG1 VAL A  67 " =    2.861
peak=   -3.324 closest distance to " O   HOH Z 166 " =    1.801
peak=   -3.314 closest distance to " CG  PRO A 163 " =    2.349
peak=   -3.313 closest distance to " O   HOH Z 353 " =    2.099
peak=   -3.313 closest distance to " C   HIS A 108 " =    1.207
peak=   -3.312 closest distance to " O   HOH Z 102 " =    1.579
peak=   -3.312 closest distance to " O   HOH Z 174 " =    2.446
peak=   -3.310 closest distance to " N   THR A  52 " =    1.680
peak=   -3.307 closest distance to " O   HOH Z  60 " =    2.224
peak=   -3.307 closest distance to " CG  ASP A 231 " =    0.861
peak=   -3.304 closest distance to " O   HOH Z 140 " =    1.924
peak=   -3.302 closest distance to " O   HOH Z 275 " =    1.588
peak=   -3.302 closest distance to " O   HOH Z 243 " =    1.768
peak=   -3.301 closest distance to " O   HOH Z 389 " =    2.092
peak=   -3.289 closest distance to " O   HOH Z 357 " =    2.131
peak=   -3.285 closest distance to " ND2 ASN A  69 " =    1.881
peak=   -3.278 closest distance to " CG2 ILE A 263 " =    2.464
peak=   -3.276 closest distance to " CD1 ILE A 239 " =    2.148
peak=   -3.272 closest distance to " CB  PRO A 163 " =    2.450
peak=   -3.268 closest distance to " CA  GLY A  98 " =    2.128
peak=   -3.268 closest distance to " O   HOH Z 285 " =    1.958
peak=   -3.263 closest distance to " CG  TRP A 266 " =    1.756
peak=   -3.262 closest distance to " CD2 PHE A 225 " =    1.123
peak=   -3.260 closest distance to " CD2 LEU A 237 " =    2.772
peak=   -3.259 closest distance to " O   HOH Z 189 " =    2.336
peak=   -3.258 closest distance to " C   MET A 188 " =    1.421
peak=   -3.257 closest distance to " OD1 ASN A 173 " =    1.256
peak=   -3.255 closest distance to " O   HOH Z  19 " =    2.270
peak=   -3.253 closest distance to " OE1 GLN A 223 " =    2.313
peak=   -3.252 closest distance to " CB  ALA A 248 " =    2.312
peak=   -3.248 closest distance to " O   PHE A 218 " =    1.641
peak=   -3.241 closest distance to " O   HOH Z  78 " =    1.932
peak=   -3.240 closest distance to " CE2 PHE A  61 " =    2.625
peak=   -3.234 closest distance to " O   HOH Z 191 " =    3.368
peak=   -3.232 closest distance to " O   HOH Z 431 " =    1.929
peak=   -3.231 closest distance to " CB  PRO A 163 " =    2.474
peak=   -3.230 closest distance to " O   HOH Z 411 " =    1.127
peak=   -3.230 closest distance to " CG  ARG A 259 " =    2.452
peak=   -3.229 closest distance to " OG  SER A 141 " =    1.685
peak=   -3.225 closest distance to " O   HOH Z 259 " =    4.145
peak=   -3.220 closest distance to " NH2 ARG A  79 " =    1.524
peak=   -3.220 closest distance to " CZ  PHE A  38 " =    2.503
peak=   -3.218 closest distance to " O   HOH Z  17 " =    1.450
peak=   -3.217 closest distance to " O   HOH Z 368 " =    1.827
peak=   -3.216 closest distance to " O   HOH Z  11 " =    1.866
peak=   -3.209 closest distance to " C   LYS A  76 " =    1.524
peak=   -3.206 closest distance to " OH  TYR A 214 " =    1.196
peak=   -3.203 closest distance to " O   HOH Z 364 " =    2.992
peak=   -3.196 closest distance to " O   HOH Z  60 " =    1.864
peak=   -3.195 closest distance to " CD2 TYR A 247 " =    2.327
peak=   -3.191 closest distance to " O   HOH Z 134 " =    2.989
peak=   -3.188 closest distance to " O   GLY A 211 " =    1.378
peak=   -3.187 closest distance to " C   ASN A 285 " =    2.487
peak=   -3.186 closest distance to " CE  LYS A  76 " =    2.571
peak=   -3.184 closest distance to " CB  HIS A  81 " =    1.021
peak=   -3.173 closest distance to " O   HOH Z 393 " =    1.311
peak=   -3.173 closest distance to " O   HOH Z 411 " =    1.736
peak=   -3.172 closest distance to " O   VAL A 125 " =    2.367
peak=   -3.171 closest distance to " CA  SER A  62 " =    2.516
peak=   -3.171 closest distance to " O   HOH Z 110 " =    1.393
peak=   -3.163 closest distance to " O   GLY A 196 " =    1.246
peak=   -3.163 closest distance to " O   HOH Z  89 " =    3.052
peak=   -3.162 closest distance to " CD1 TYR A 247 " =    2.310
peak=   -3.161 closest distance to " O   MET A  40 " =    2.770
peak=   -3.160 closest distance to " O   HOH Z  44 " =    1.001
peak=   -3.159 closest distance to " O   HOH Z 234 " =    4.364
peak=   -3.155 closest distance to " OH  TYR A 247 " =    1.823
peak=   -3.154 closest distance to " O   SER A 210 " =    1.925
peak=   -3.153 closest distance to " O   HOH Z  13 " =    1.719
peak=   -3.152 closest distance to " O   GLY A  80 " =    2.336
peak=   -3.149 closest distance to " O   HOH Z 298 " =    2.834
peak=   -3.147 closest distance to " O   HOH Z 111 " =    1.941
peak=   -3.144 closest distance to " CD1 LEU A 228 " =    2.383
peak=   -3.137 closest distance to " NE2 GLN A 103 " =    1.820
peak=   -3.136 closest distance to " O   HOH Z 262 " =    2.854
peak=   -3.133 closest distance to " CB  ALA A 291 " =    2.289
peak=   -3.133 closest distance to " N   LYS A 166 " =    1.931
peak=   -3.131 closest distance to " CE  MET A 105 " =    2.364
peak=   -3.130 closest distance to " CD1 ILE A 199 " =    2.554
peak=   -3.123 closest distance to " N   ALA A 248 " =    2.555
peak=   -3.119 closest distance to " NE1 TRP A  70 " =    1.152
peak=   -3.118 closest distance to " C   ASN A 187 " =    1.807
peak=   -3.116 closest distance to " O   HOH Z 109 " =    1.686
peak=   -3.113 closest distance to " O   HOH Z   6 " =    1.624
peak=   -3.112 closest distance to " C   ASP A 270 " =    1.223
peak=   -3.109 closest distance to " O   HOH Z 357 " =    2.147
peak=   -3.106 closest distance to " O   HOH Z 109 " =    1.319
peak=   -3.102 closest distance to " OD2 ASP A 171 " =    1.814
peak=   -3.101 closest distance to " OD1 ASP A 171 " =    1.612
peak=   -3.094 closest distance to " CG2 VAL A 112 " =    2.543
peak=   -3.092 closest distance to " O   HOH Z 136 " =    0.937
peak=   -3.090 closest distance to " CZ  TYR A 169 " =    1.836
peak=   -3.087 closest distance to " CB  TYR A  15 " =    2.220
peak=   -3.084 closest distance to " NE2 GLN A 240 " =    1.677
peak=   -3.084 closest distance to " NH2 ARG A  66 " =    2.251
peak=   -3.074 closest distance to " CB  GLN A  11 " =    1.690
peak=   -3.056 closest distance to " O   HOH Z 177 " =    1.400
peak=   -3.054 closest distance to " N   ALA A 248 " =    1.850
peak=   -3.053 closest distance to " CG2 VAL A 230 " =    2.734
peak=   -3.052 closest distance to " O   HOH Z 198 " =    1.494
peak=   -3.052 closest distance to " CA  GLY A 241 " =    2.878
peak=   -3.049 closest distance to " CA  SER A 135 " =    1.274
peak=   -3.006 closest distance to " O   HOH Z 100 " =    1.348

================= 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    :  0.4707 0.4636   6.270912e+00   6.251215e+00
   1_bss:  0.4624 0.4500   6.265075e+00   6.241975e+00
   1_xyz:  0.3666 0.3954   6.122626e+00   6.160038e+00
   1_adp:  0.3192 0.3664   6.020514e+00   6.110420e+00
   1_occ:  0.3186 0.3671   6.019516e+00   6.111529e+00
   2_bss:  0.3170 0.3645   6.021030e+00   6.110316e+00
   2_xyz:  0.2325 0.2853   5.761743e+00   5.912608e+00
   2_adp:  0.2117 0.2639   5.688316e+00   5.854829e+00
   2_occ:  0.2115 0.2640   5.688179e+00   5.855173e+00
   3_bss:  0.2105 0.2639   5.689827e+00   5.855920e+00
   3_xyz:  0.1510 0.1983   5.390213e+00   5.599862e+00
   3_adp:  0.1354 0.1859   5.312396e+00   5.546206e+00
   3_occ:  0.1353 0.1859   5.312424e+00   5.546570e+00
   4_bss:  0.1355 0.1859   5.312601e+00   5.545707e+00
   4_xyz:  0.1255 0.1765   5.254699e+00   5.493150e+00
   4_adp:  0.1252 0.1721   5.239325e+00   5.467943e+00
   4_occ:  0.1250 0.1720   5.238631e+00   5.467671e+00
   5_bss:  0.1250 0.1721   5.238609e+00   5.467721e+00
   5_xyz:  0.1193 0.1676   5.204837e+00   5.444247e+00
   5_adp:  0.1175 0.1677   5.199817e+00   5.444963e+00
   5_occ:  0.1173 0.1680   5.199878e+00   5.445788e+00
   5_bss:  0.1173 0.1679   5.199720e+00   5.445689e+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:  0.325  38.376   7.735   7.066  10.974   0.000   0.000   0.000
   1_xyz:  0.325  38.376   7.735   7.066  10.974   0.000   0.000   0.000
   1_adp:  0.325  38.376   7.735   7.066  10.974   0.000   0.000   0.000
   1_occ:  0.325  38.376   7.735   7.066  10.974   0.000   0.000   0.000
   2_bss:  0.315  52.577   4.731   4.482   7.666   0.000   0.000   0.000
   2_xyz:  0.315  52.577   4.731   4.482   7.666   0.000   0.000   0.000
   2_adp:  0.315  52.577   4.731   4.482   7.666   0.000   0.000   0.000
   2_occ:  0.315  52.577   4.731   4.482   7.666   0.000   0.000   0.000
   3_bss:  0.336  70.800   3.168   3.217   5.204   0.000   0.000   0.000
   3_xyz:  0.336  70.800   3.168   3.217   5.204   0.000   0.000   0.000
   3_adp:  0.336  70.800   3.168   3.217   5.204   0.000   0.000   0.000
   3_occ:  0.336  70.800   3.168   3.217   5.204   0.000   0.000   0.000
   4_bss:  0.330  70.800   2.751   2.849   4.518   0.000   0.000   0.000
   4_xyz:  0.330  70.800   2.751   2.849   4.518   0.000   0.000   0.000
   4_adp:  0.330  70.800   2.751   2.849   4.518   0.000   0.000   0.000
   4_occ:  0.330  70.800   2.751   2.849   4.518   0.000   0.000   0.000
   5_bss:  0.330  70.800   2.688   2.773   4.321   0.000   0.000   0.000
   5_xyz:  0.330  70.800   2.688   2.773   4.321   0.000   0.000   0.000
   5_adp:  0.330  70.800   2.688   2.773   4.321   0.000   0.000   0.000
   5_occ:  0.330  70.800   2.688   2.773   4.321   0.000   0.000   0.000
   5_bss:  0.320  68.391  -0.573  -0.488   1.061   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.929 0.4715  0.5283    62556.239
   1_bss:  52.778 0.4856  0.7051    60606.380
   1_xyz:  44.778 0.5838  0.8199    44045.627
   1_adp:  40.049 0.6419  0.9117    37444.033
   1_occ:  40.063 0.6416  0.9109    37496.177
   2_bss:  39.924 0.6432  0.8236    37289.401
   2_xyz:  29.112 0.7671  0.9586    21298.493
   2_adp:  26.415 0.7970  0.9822    18303.467
   2_occ:  26.456 0.7965  0.9810    18309.847
   3_bss:  26.452 0.7968  0.9218    18386.709
   3_xyz:  18.832 0.8725  0.9763     9986.709
   3_adp:  17.499 0.8849  0.9761     8880.699
   3_occ:  17.507 0.8848  0.9760     8883.145
   4_bss:  17.496 0.8850  0.9588     8874.052
   4_xyz:  16.195 0.8969  0.9631     7878.870
   4_adp:  15.552 0.9026  0.9668     7509.431
   4_occ:  15.561 0.9025  0.9665     7505.772
   5_bss:  15.561 0.9025  0.9627     7506.990
   5_xyz:  15.081 0.9066  0.9663     7161.601
   5_adp:  15.086 0.9066  0.9650     7177.537
   5_occ:  15.115 0.9064  0.9646     7181.453
   5_bss:  15.114 0.9064  0.9645     7176.988
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4598e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4598e+01
   1_xyz:   1.729  0.014  0.111 18.233  0.007  4.112   1.4722e-01
   1_adp:   1.729  0.014  0.111 18.233  0.007  4.112   1.4722e-01
   1_occ:   1.729  0.014  0.111 18.233  0.007  4.112   1.4722e-01
   2_bss:   1.729  0.014  0.111 18.233  0.007  4.112   1.4722e-01
   2_xyz:   1.106  0.008  0.075 16.611  0.005  4.132   7.4948e-02
   2_adp:   1.106  0.008  0.075 16.611  0.005  4.132   7.4948e-02
   2_occ:   1.106  0.008  0.075 16.611  0.005  4.132   7.4948e-02
   3_bss:   1.106  0.008  0.075 16.611  0.005  4.132   7.4948e-02
   3_xyz:   1.199  0.011  0.091 16.493  0.004  4.141   8.7464e-02
   3_adp:   1.199  0.011  0.091 16.493  0.004  4.141   8.7464e-02
   3_occ:   1.199  0.011  0.091 16.493  0.004  4.141   8.7464e-02
   4_bss:   1.199  0.011  0.091 16.493  0.004  4.141   8.7464e-02
   4_xyz:   1.085  0.009  0.084 15.847  0.004  4.148   7.1564e-02
   4_adp:   1.085  0.009  0.084 15.847  0.004  4.148   7.1564e-02
   4_occ:   1.085  0.009  0.084 15.847  0.004  4.148   7.1564e-02
   5_bss:   1.085  0.009  0.084 15.847  0.004  4.148   7.1564e-02
   5_xyz:   1.160  0.011  0.091 15.782  0.004  4.131   8.2306e-02
   5_adp:   1.160  0.011  0.091 15.782  0.004  4.131   8.2306e-02
   5_occ:   1.160  0.011  0.091 15.782  0.004  4.131   8.2306e-02
   5_bss:   1.160  0.011  0.091 15.782  0.004  4.131   8.2306e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0794e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0794e+00
   1_xyz:  14.708  0.166  0.458 85.715  0.037  2.284   1.1044e-01
   1_adp:  14.708  0.166  0.458 85.715  0.037  2.284   1.1044e-01
   1_occ:  14.708  0.166  0.458 85.715  0.037  2.284   1.1044e-01
   2_bss:  14.708  0.166  0.458 85.715  0.037  2.284   1.1044e-01
   2_xyz:   7.153  0.061  0.249 83.738  0.041  2.172   7.9429e-02
   2_adp:   7.153  0.061  0.249 83.738  0.041  2.172   7.9429e-02
   2_occ:   7.153  0.061  0.249 83.738  0.041  2.172   7.9429e-02
   3_bss:   7.153  0.061  0.249 83.738  0.041  2.172   7.9429e-02
   3_xyz:  10.045  0.064  0.385 86.195  0.041  2.295   9.4805e-02
   3_adp:  10.045  0.064  0.385 86.195  0.041  2.295   9.4805e-02
   3_occ:  10.045  0.064  0.385 86.195  0.041  2.295   9.4805e-02
   4_bss:  10.045  0.064  0.385 86.195  0.041  2.295   9.4805e-02
   4_xyz:   7.822  0.045  0.389 82.709  0.040  2.374   4.3861e-02
   4_adp:   7.822  0.045  0.389 82.709  0.040  2.374   4.3861e-02
   4_occ:   7.822  0.045  0.389 82.709  0.040  2.374   4.3861e-02
   5_bss:   7.822  0.045  0.389 82.709  0.040  2.374   4.3861e-02
   5_xyz:   7.862  0.054  0.521 83.345  0.039  2.326   5.3817e-02
   5_adp:   7.862  0.054  0.521 83.345  0.039  2.326   5.3817e-02
   5_occ:   7.862  0.054  0.521 83.345  0.039  2.326   5.3817e-02
   5_bss:   7.862  0.054  0.521 83.345  0.039  2.326   5.3817e-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:  77.64   0.00  12.16  69.47   0.00   9.24  77.64   0.00  28.02
   1_occ:  77.64   0.00  12.16  69.47   0.00   9.24  77.64   0.00  28.02
   2_bss:  77.64   0.00  12.16  69.47   0.00   9.24  77.64   0.00  28.02
   2_xyz:  77.64   0.00  12.16  69.47   0.00   9.24  77.64   0.00  28.02
   2_adp:  78.49   0.00  12.12  69.67   0.00   8.37  78.49   0.00  32.54
   2_occ:  78.49   0.00  12.12  69.67   0.00   8.37  78.49   0.00  32.54
   3_bss:  78.49   0.00  12.12  69.67   0.00   8.37  78.49   0.00  32.54
   3_xyz:  78.49   0.00  12.12  69.67   0.00   8.37  78.49   0.00  32.54
   3_adp:  96.08   0.00  13.31  82.90   0.00   8.37  96.08   0.00  40.23
   3_occ:  96.08   0.00  13.31  82.90   0.00   8.37  96.08   0.00  40.23
   4_bss:  96.08   0.00  13.31  82.90   0.00   8.37  96.08   0.00  40.23
   4_xyz:  96.08   0.00  13.31  82.90   0.00   8.37  96.08   0.00  40.23
   4_adp:  95.65   0.00  13.20  82.43   0.00   8.34  95.65   0.63  39.66
   4_occ:  95.65   0.00  13.20  82.43   0.00   8.34  95.65   0.63  39.66
   5_bss:  95.65   0.00  13.20  82.43   0.00   8.34  95.65   0.63  39.66
   5_xyz:  95.65   0.00  13.20  82.43   0.00   8.34  95.65   0.63  39.66
   5_adp:  98.33   0.00  13.11  91.85   0.00   8.36  98.33   0.77  39.02
   5_occ:  98.33   0.00  13.11  91.85   0.00   8.36  98.33   0.77  39.02
   5_bss: 101.59   3.26  16.38  95.11   3.26  11.62 101.59   4.03  42.28
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.279    0.025    0.417
   1_adp:    1.279    0.025    0.417
   1_occ:    1.279    0.025    0.417
   2_bss:    1.279    0.025    0.417
   2_xyz:    1.730    0.037    0.554
   2_adp:    1.730    0.037    0.554
   2_occ:    1.730    0.037    0.554
   3_bss:    1.730    0.037    0.554
   3_xyz:    1.666    0.049    0.644
   3_adp:    1.666    0.049    0.644
   3_occ:    1.666    0.049    0.644
   4_bss:    1.666    0.049    0.644
   4_xyz:    1.817    0.052    0.665
   4_adp:    1.817    0.052    0.665
   4_occ:    1.817    0.052    0.665
   5_bss:    1.817    0.052    0.665
   5_xyz:    1.776    0.044    0.678
   5_adp:    1.776    0.044    0.678
   5_occ:    1.776    0.044    0.678
   5_bss:    1.776    0.044    0.678
------------------------------------------------------------------------

CPU time actual refinement: 352.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1043/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_1043/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1043/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1043/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1043/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.93 
  Macro-tasks:
    bulk solvent and scale       = 36.17  
    individual site refinement   = 154.59 
    weights calculation          = 33.27  
    collect and process          = 6.70   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 230.88 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 111.85 
    alpha_beta                      = 8.41   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 124.71 
    fmodel                         = 6.78   
    r_factors                      = 0.16   
    phase_errors                   = 10.81  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 265.99 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.876 micro seconds
Total CPU time: 6.09 minutes
from_scatterers_fft:    678 calls, 111.46 s
gradients_fft:          623 calls, 110.47 s

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

# Date 2008-01-16 Time 03:03:29 PST -0800 (1200481409.86 s)
Start R-work = 0.4707, R-free = 0.4636 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1825 (no bulk solvent and anisotropic scale)

Start R-work = 0.4624, R-free = 0.4500
Final R-work = 0.1173, R-free = 0.1679