# Date 2008-01-16 Time 03:17:08 PST -0800 (1200482228.34 s)
#phil __OFF__

Command line arguments: "../1176.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15626
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1176

-------------------------------------------------------------------------------
  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: (71.655, 47.3993, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 2.02233
Completeness in resolution range: 0.965118
Completeness with d_max=infinity: 0.962132

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3141
                             d_min =   2.0223

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: (71.655, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 2.02233
Completeness in resolution range: 0.965118
Completeness with d_max=infinity: 0.962132

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3145 -  4.3273 [2132/2156]  1918   214  10.0%
  bin  2:  4.3273 -  3.4476 [2037/2057]  1835   202   9.9%
  bin  3:  3.4476 -  3.0156 [2030/2049]  1823   207  10.2%
  bin  4:  3.0156 -  2.7416 [1998/2028]  1801   197   9.9%
  bin  5:  2.7416 -  2.5460 [2005/2024]  1804   201  10.0%
  bin  6:  2.5460 -  2.3965 [1954/1979]  1760   194   9.9%
  bin  7:  2.3965 -  2.2769 [1980/2008]  1779   201  10.2%
  bin  8:  2.2769 -  2.1781 [1970/2006]  1775   195   9.9%
  bin  9:  2.1781 -  2.0944 [1934/1976]  1742   192   9.9%
  bin 10:  2.0944 -  2.0223 [1549/2014]  1393   156  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1176/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: 12
        2.42 -     3.04: 2144
        3.04 -     3.66: 4542
        3.66 -     4.28: 8792
        4.28 -     4.90: 12094
  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 "  1.810 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.211 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.211 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27579 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_1176/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1176/model_refine_001.geo

CPU time processing inputs: 9.30


============================ 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 = 71.655 47.3993 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5000   r_free= 0.4920   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.297875                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.8264 0.99   1387  153 0.4114 0.3881      6.6279      6.5502|
|  2:  4.8264 -  3.8509 0.99   1329  152 0.4339 0.4694      6.8459      6.9577|
|  3:  3.8509 -  3.3701 0.99   1305  140 0.4687 0.4266      6.7193      6.7065|
|  4:  3.3701 -  3.0646 0.99   1293  149 0.4976 0.4188      6.5666      6.4609|
|  5:  3.0646 -  2.8465 0.99   1290  143 0.5178 0.5055      6.3922      6.4293|
|  6:  2.8465 -  2.6796 0.99   1300  137 0.5297 0.5852      6.3032      6.2176|
|  7:  2.6796 -  2.5460 0.99   1277  147 0.5451 0.5096      6.2506      6.2368|
|  8:  2.5460 -  2.4357 0.98   1269  141 0.5414 0.4667      6.2052      6.1415|
|  9:  2.4357 -  2.3422 0.98   1261  141 0.5237 0.6313      6.1222      6.1962|
| 10:  2.3422 -  2.2617 1.00   1282  142 0.5474 0.5212      6.1312      6.1396|
| 11:  2.2617 -  2.1912 0.97   1251  138 0.5245 0.5501      6.0344      6.0883|
| 12:  2.1912 -  2.1287 0.98   1248  137 0.5361 0.5296      5.9927      6.0117|
| 13:  2.1287 -  2.0728 0.99   1290  140 0.5360 0.5285      5.8968       5.843|
| 14:  2.0728 -  2.0223 0.67    848   99 0.5532 0.5097      5.8606      5.7799|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.8264  1387   153  0.69  35.26   0.77     0.72      75146.72|
|  2:  4.8264 -  3.8509  1329   152  0.68  37.19   0.85     0.73     117087.88|
|  3:  3.8509 -  3.3701  1305   140  0.57  46.12   0.79     0.67     124820.25|
|  4:  3.3701 -  3.0646  1293   149  0.46  54.95   0.77     0.54     110972.71|
|  5:  3.0646 -  2.8465  1290   143  0.37  62.24   0.71     0.43      89002.98|
|  6:  2.8465 -  2.6796  1300   137  0.32  65.90   0.69     0.36      79310.13|
|  7:  2.6796 -  2.5460  1277   147  0.29  68.31   0.69     0.33      71850.94|
|  8:  2.5460 -  2.4357  1269   141  0.28  69.39   0.70     0.32      65984.23|
|  9:  2.4357 -  2.3422  1261   141  0.25  71.47   0.70     0.29      61920.67|
| 10:  2.3422 -  2.2617  1282   142  0.23  73.15   0.71     0.26      56424.61|
| 11:  2.2617 -  2.1912  1251   138  0.22  73.34   0.73     0.27      53397.51|
| 12:  2.1912 -  2.1287  1248   137  0.23  72.99   0.72     0.27      48161.07|
| 13:  2.1287 -  2.0728  1290   140  0.17  77.22   0.69     0.20      42226.34|
| 14:  2.0728 -  2.0223   848    99  0.04  87.18   0.68     0.04      35634.79|
|alpha:            min =        0.04 max =            0.73 mean =         0.40|
|beta:             min =    35634.79 max =       124820.25 mean =     74965.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.02|
|phase err.(test): min =        0.00 max =           89.99 mean =        62.97|
|-----------------------------------------------------------------------------|

============================== 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 = 20.281014             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.320   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.177793              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 85.274   (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:      667 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1476 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2553 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3809 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4936 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6423 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7532 |
|-----------------------------------------------------------------------------|
|-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 |       54.851 |
| 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 |       1.637 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.524)------------------------------------------|
|    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 = 12.524)------------------------------------------|
|    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: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5039   r_free= 0.4944   ksol= 0.00   Bsol= 0.00   scale= 0.734    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.298114                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4932   r_free= 0.4827   ksol= 0.30   Bsol= 50.00   scale= 0.940   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,6.90,10.47,0.00,0.00,0.00); trace/3= 8.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.293552                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.645772             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.872   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.798955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.493   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4932      final r-factor (work) = 0.4210          |
| start r-factor (free) = 0.4827      final r-factor (free) = 0.4477          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 110.4002 = 17.65 * 0.50 * 6.2960 + 1.00 * 54.8510                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.1133 = 17.65 * 0.50 * 6.2282 + 1.00 * 0.1626                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4210      final r-factor (work) = 0.3802          |
| start r-factor (free) = 0.4477      final r-factor (free) = 0.4348          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2187 = 1.80 * 1.00 * 6.2282 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1183 = 1.80 * 1.00 * 6.1668 + 1.00 * 0.0245                              |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.524)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.64   15.71    None  None   None       |
|    all(noH): 2823   0      0.00    96.64   15.71    None  None   None       |
|    Sol.    : 438    0      0.00    96.64   28.19    None  None   None       |
|    Mac.    : 2385   0      0.00    80.96   13.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.664: 1190   |   5:    48.318 -  57.981:   65        |
|      1:     9.664 -  19.327:  745   |   6:    57.981 -  67.645:   25        |
|      2:    19.327 -  28.991:  459   |   7:    67.645 -  77.308:   14        |
|      3:    28.991 -  38.654:  223   |   8:    77.308 -  86.972:    5        |
|      4:    38.654 -  48.318:   95   |   9:    86.972 -  96.635:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3802 r_free = 0.4348             target_work(ml) = 6.151         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3798 r_free = 0.4359             target_work(ml) = 6.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3798   r_free= 0.4359   ksol= 0.30   Bsol= 50.00   scale= 1.068   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,6.90,10.47,0.00,0.00,0.00); trace/3= 8.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.150628                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3792   r_free= 0.4344   ksol= 0.31   Bsol= 50.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.92,4.75,7.65,0.00,0.00,0.00); trace/3= 5.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.152208                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.122753             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.219  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.721120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.339  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3792      final r-factor (work) = 0.3010          |
| start r-factor (free) = 0.4344      final r-factor (free) = 0.3626          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.5085 = 12.12 * 0.50 * 6.1613 + 1.00 * 0.1626                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.8600 = 12.12 * 0.50 * 6.0635 + 1.00 * 0.1066                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3010      final r-factor (work) = 0.2751          |
| start r-factor (free) = 0.3626      final r-factor (free) = 0.3384          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4159 = 0.72 * 1.00 * 6.0635 + 1.00 * 0.0433                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4095 = 0.72 * 1.00 * 5.9287 + 1.00 * 0.1342                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.524)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.80   15.06    None  None   None       |
|    all(noH): 2823   0      0.00    98.80   15.06    None  None   None       |
|    Sol.    : 438    0      0.00    98.80   33.31    None  None   None       |
|    Mac.    : 2385   0      0.00    79.14   11.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.880: 1313   |   5:    49.400 -  59.280:   47        |
|      1:     9.880 -  19.760:  752   |   6:    59.280 -  69.160:   30        |
|      2:    19.760 -  29.640:  370   |   7:    69.160 -  79.040:   10        |
|      3:    29.640 -  39.520:  192   |   8:    79.040 -  88.920:    2        |
|      4:    39.520 -  49.400:  105   |   9:    88.920 -  98.800:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2751 r_free = 0.3384             target_work(ml) = 5.900         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2749 r_free = 0.3381             target_work(ml) = 5.899         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2749   r_free= 0.3381   ksol= 0.31   Bsol= 50.00   scale= 1.063   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.92,4.75,7.65,0.00,0.00,0.00); trace/3= 5.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.899472                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2730   r_free= 0.3361   ksol= 0.31   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.53,2.72,4.67,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.901020                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.894726              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.751  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.197720              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.748   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2730      final r-factor (work) = 0.2020          |
| start r-factor (free) = 0.3361      final r-factor (free) = 0.2627          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.5471 = 6.89 * 0.50 * 5.9293 + 1.00 * 0.1066                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0622 = 6.89 * 0.50 * 5.7902 + 1.00 * 0.1012                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2020      final r-factor (work) = 0.1749          |
| start r-factor (free) = 0.2627      final r-factor (free) = 0.2354          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.3279 = 4.20 * 1.00 * 5.7902 + 1.00 * 0.0223                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 23.4655 = 4.20 * 1.00 * 5.5853 + 1.00 * 0.0201                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.524)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.75   15.68    None  None   None       |
|    all(noH): 2823   0      0.00    97.75   15.68    None  None   None       |
|    Sol.    : 438    0      0.00    97.75   42.66    None  None   None       |
|    Mac.    : 2385   0      0.00    93.74   10.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.775: 1466   |   5:    48.873 -  58.647:  106        |
|      1:     9.775 -  19.549:  687   |   6:    58.647 -  68.422:   61        |
|      2:    19.549 -  29.324:  216   |   7:    68.422 -  78.196:   34        |
|      3:    29.324 -  39.098:  121   |   8:    78.196 -  87.971:    6        |
|      4:    39.098 -  48.873:  119   |   9:    87.971 -  97.745:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1749 r_free = 0.2354             target_work(ml) = 5.534         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1747 r_free = 0.2356             target_work(ml) = 5.534         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1747   r_free= 0.2356   ksol= 0.31   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.53,2.72,4.67,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.533537                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1745   r_free= 0.2351   ksol= 0.33   Bsol= 83.41   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,1.65,3.29,0.00,0.00,0.00); trace/3= 2.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.531464                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.374127              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.311   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.443364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.269  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1745      final r-factor (work) = 0.1503          |
| start r-factor (free) = 0.2351      final r-factor (free) = 0.2066          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5341 = 3.37 * 0.50 * 5.5913 + 1.00 * 0.1012                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3138 = 3.37 * 0.50 * 5.4748 + 1.00 * 0.0775                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1503      final r-factor (work) = 0.1423          |
| start r-factor (free) = 0.2066      final r-factor (free) = 0.1985          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3978 = 2.44 * 1.00 * 5.4748 + 1.00 * 0.0209                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3093 = 2.44 * 1.00 * 5.3860 + 1.00 * 0.1492                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.524)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.00  15.59    None  None   None       |
|    all(noH): 2823   0      0.00    109.00  15.59    None  None   None       |
|    Sol.    : 438    0      0.00    109.00  45.37    None  None   None       |
|    Mac.    : 2385   0      0.00    102.65  10.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.901: 1684   |   5:    54.502 -  65.403:   86        |
|      1:    10.901 -  21.801:  594   |   6:    65.403 -  76.303:   54        |
|      2:    21.801 -  32.701:  147   |   7:    76.303 -  87.203:   27        |
|      3:    32.701 -  43.602:  114   |   8:    87.203 -  98.104:   16        |
|      4:    43.602 -  54.502:   96   |   9:    98.104 - 109.004:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1423 r_free = 0.1985             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1421 r_free = 0.1986             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1421   r_free= 0.1986   ksol= 0.33   Bsol= 83.41   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,1.65,3.29,0.00,0.00,0.00); trace/3= 2.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.366232                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1423   r_free= 0.1988   ksol= 0.34   Bsol= 86.47   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,1.68,3.27,0.00,0.00,0.00); trace/3= 2.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.366728                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.113672              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.191  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.497294              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.593   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1423      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1988      final r-factor (free) = 0.1856          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1554 = 4.11 * 0.50 * 5.3859 + 1.00 * 0.0775                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0514 = 4.11 * 0.50 * 5.3268 + 1.00 * 0.0951                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1856      final r-factor (free) = 0.1818          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3381 = 2.50 * 1.00 * 5.3268 + 1.00 * 0.0355                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.2049 = 2.50 * 1.00 * 5.2770 + 1.00 * 0.0267                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.524)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.38  15.10    None  None   None       |
|    all(noH): 2823   0      0.00    116.38  15.10    None  None   None       |
|    Sol.    : 438    0      0.00    116.38  44.43    None  None   None       |
|    Mac.    : 2385   0      0.00    99.31   9.72     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.638: 1824   |   5:    58.192 -  69.830:   70        |
|      1:    11.638 -  23.277:  500   |   6:    69.830 -  81.469:   39        |
|      2:    23.277 -  34.915:  144   |   7:    81.469 -  93.107:   21        |
|      3:    34.915 -  46.553:  118   |   8:    93.107 - 104.745:   15        |
|      4:    46.553 -  58.192:   90   |   9:   104.745 - 116.384:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1252 r_free = 0.1818             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1251 r_free = 0.1817             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1817   ksol= 0.34   Bsol= 86.47   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,1.68,3.27,0.00,0.00,0.00); trace/3= 2.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.264926                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.8264 0.99   1387  153 0.0994 0.1416      5.4134      5.5897|
|  2:  4.8264 -  3.8509 0.99   1329  152 0.0839 0.1160      5.4569      5.6942|
|  3:  3.8509 -  3.3701 0.99   1305  140 0.1119 0.1587      5.5449      5.8986|
|  4:  3.3701 -  3.0646 0.99   1293  149 0.1307 0.1948      5.5392      5.7639|
|  5:  3.0646 -  2.8465 0.99   1290  143 0.1572 0.1931      5.4859      5.6469|
|  6:  2.8465 -  2.6796 0.99   1300  137 0.1410 0.2482      5.3628      5.6862|
|  7:  2.6796 -  2.5460 0.99   1277  147 0.1469 0.1829      5.3109      5.4828|
|  8:  2.5460 -  2.4357 0.98   1269  141 0.1389 0.1943      5.2347      5.4789|
|  9:  2.4357 -  2.3422 0.98   1261  141 0.1359 0.2019      5.1742      5.4019|
| 10:  2.3422 -  2.2617 1.00   1282  142 0.1305 0.1992      5.1067       5.349|
| 11:  2.2617 -  2.1912 0.97   1251  138 0.1340 0.2082      5.0838      5.3668|
| 12:  2.1912 -  2.1287 0.98   1248  137 0.1293 0.2120      5.0163      5.3955|
| 13:  2.1287 -  2.0728 0.99   1290  140 0.1338 0.2017      4.9442      5.1722|
| 14:  2.0728 -  2.0223 0.67    848   99 0.1267 0.1987      4.8569      5.0947|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.8264  1387   153  0.93  10.04   0.96     0.94       8392.29|
|  2:  4.8264 -  3.8509  1329   152  0.95   8.74   1.00     0.98      10173.38|
|  3:  3.8509 -  3.3701  1305   140  0.92  12.54   1.02     1.02      12368.22|
|  4:  3.3701 -  3.0646  1293   149  0.91  15.45   1.01     0.99      12703.73|
|  5:  3.0646 -  2.8465  1290   143  0.87  19.33   1.00     0.97      11678.37|
|  6:  2.8465 -  2.6796  1300   137  0.87  19.43   0.98     0.94      10045.81|
|  7:  2.6796 -  2.5460  1277   147  0.87  19.43   0.99     0.95       8801.61|
|  8:  2.5460 -  2.4357  1269   141  0.88  18.54   0.98     0.95       7488.89|
|  9:  2.4357 -  2.3422  1261   141  0.89  18.18   0.99     0.93       6674.21|
| 10:  2.3422 -  2.2617  1282   142  0.88  18.60   0.99     0.93       5932.58|
| 11:  2.2617 -  2.1912  1251   138  0.87  19.45   0.98     0.92       5872.11|
| 12:  2.1912 -  2.1287  1248   137  0.88  18.64   0.99     0.97       5452.04|
| 13:  2.1287 -  2.0728  1290   140  0.87  20.10   0.96     0.92       4748.22|
| 14:  2.0728 -  2.0223   848    99  0.89  17.83   0.94     0.90       3785.94|
|alpha:            min =        0.90 max =            1.02 mean =         0.95|
|beta:             min =     3785.94 max =        12703.73 mean =      8287.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.88 mean =        16.78|
|phase err.(test): min =        0.00 max =           88.25 mean =        16.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1816   ksol= 0.33   Bsol= 81.95   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.53,1.06,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.264705                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1816   ksol= 0.33   Bsol= 81.95   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.53,1.06,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.264705                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.8264 0.99   1387  153 0.0991 0.1414      5.4095      5.5887|
|  2:  4.8264 -  3.8509 0.99   1329  152 0.0837 0.1157      5.4555      5.6915|
|  3:  3.8509 -  3.3701 0.99   1305  140 0.1118 0.1587      5.5443      5.8984|
|  4:  3.3701 -  3.0646 0.99   1293  149 0.1310 0.1949      5.5402      5.7643|
|  5:  3.0646 -  2.8465 0.99   1290  143 0.1573 0.1931      5.4868      5.6475|
|  6:  2.8465 -  2.6796 0.99   1300  137 0.1410 0.2484      5.3634       5.687|
|  7:  2.6796 -  2.5460 0.99   1277  147 0.1470 0.1830      5.3115      5.4838|
|  8:  2.5460 -  2.4357 0.98   1269  141 0.1389 0.1944      5.2351      5.4784|
|  9:  2.4357 -  2.3422 0.98   1261  141 0.1359 0.2019      5.1743      5.4021|
| 10:  2.3422 -  2.2617 1.00   1282  142 0.1306 0.1992      5.1068      5.3493|
| 11:  2.2617 -  2.1912 0.97   1251  138 0.1340 0.2081      5.0838      5.3664|
| 12:  2.1912 -  2.1287 0.98   1248  137 0.1292 0.2119       5.016      5.3949|
| 13:  2.1287 -  2.0728 0.99   1290  140 0.1338 0.2017      4.9441      5.1719|
| 14:  2.0728 -  2.0223 0.67    848   99 0.1267 0.1986      4.8568      5.0945|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3145 -  4.8264  1387   153  0.93  10.03   0.96     0.94       8360.76|
|  2:  4.8264 -  3.8509  1329   152  0.95   8.71   1.00     0.98      10141.12|
|  3:  3.8509 -  3.3701  1305   140  0.93  12.53   1.03     1.02      12337.81|
|  4:  3.3701 -  3.0646  1293   149  0.91  15.46   1.02     0.99      12710.06|
|  5:  3.0646 -  2.8465  1290   143  0.87  19.34   1.01     0.98      11697.82|
|  6:  2.8465 -  2.6796  1300   137  0.87  19.44   0.98     0.95      10058.76|
|  7:  2.6796 -  2.5460  1277   147  0.87  19.45   0.99     0.96       8811.37|
|  8:  2.5460 -  2.4357  1269   141  0.88  18.55   0.99     0.96       7491.80|
|  9:  2.4357 -  2.3422  1261   141  0.89  18.18   1.00     0.94       6679.15|
| 10:  2.3422 -  2.2617  1282   142  0.88  18.59   1.00     0.94       5929.23|
| 11:  2.2617 -  2.1912  1251   138  0.87  19.44   0.99     0.93       5868.97|
| 12:  2.1912 -  2.1287  1248   137  0.88  18.63   1.00     0.98       5446.98|
| 13:  2.1287 -  2.0728  1290   140  0.87  20.09   0.97     0.93       4745.39|
| 14:  2.0728 -  2.0223   848    99  0.89  17.83   0.96     0.91       3783.56|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3783.56 max =        12710.06 mean =      8282.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.80 mean =        16.78|
|phase err.(test): min =        0.00 max =           88.46 mean =        16.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.524)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.40    118.78  17.50    None  None   None       |
|    all(noH): 2823   0      2.40    118.78  17.50    None  None   None       |
|    Sol.    : 438    0      2.40    118.78  46.83    None  None   None       |
|    Mac.    : 2385   0      2.40    101.71  12.11    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:     2.398 -  14.037: 1824   |   5:    60.590 -  72.229:   70        |
|      1:    14.037 -  25.675:  500   |   6:    72.229 -  83.867:   39        |
|      2:    25.675 -  37.314:  144   |   7:    83.867 -  95.505:   21        |
|      3:    37.314 -  48.952:  118   |   8:    95.505 - 107.144:   15        |
|      4:    48.952 -  60.590:   90   |   9:   107.144 - 118.782:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.413 - 5.983
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 325
   mapped sites are within: 0.731 - 5.983

peak=    9.596 closest distance to " CB  VAL A 230 " =    1.469
peak=    5.778 closest distance to " O   HOH Z  82 " =    0.966
peak=    5.581 closest distance to " O   HOH Z 210 " =    1.178
peak=    5.417 closest distance to " CB  GLN A 223 " =    1.558
peak=    5.316 closest distance to " CD1AILE A 234 " =    1.141
peak=    5.260 closest distance to " CG  LEU A   5 " =    1.128
peak=    5.053 closest distance to " CG2 VAL A 296 " =    1.005
peak=    5.032 closest distance to " CG  LEU A 228 " =    1.245
peak=    5.031 closest distance to " O   HOH Z 425 " =    1.776
peak=    5.026 closest distance to " CZ  PHE A 218 " =    1.208
peak=    4.763 closest distance to " O   HOH Z 126 " =    1.785
peak=    4.751 closest distance to " NH1 ARG A 138 " =    1.056
peak=    4.730 closest distance to " O   HOH Z 369 " =    2.024
peak=    4.717 closest distance to " CB  VAL A 296 " =    1.107
peak=    4.712 closest distance to " O   HOH Z 232 " =    2.146
peak=    4.658 closest distance to " O   HOH Z 411 " =    3.540
peak=    4.610 closest distance to " OE1 GLN A  55 " =    1.189
peak=    4.561 closest distance to " CG1 VAL A 296 " =    1.282
peak=    4.560 closest distance to " CB  SER A  63 " =    1.357
peak=    4.530 closest distance to " O   HOH Z 207 " =    1.346
peak=    4.524 closest distance to " O   HOH Z 184 " =    1.709
peak=    4.514 closest distance to " O   HOH Z  49 " =    1.519
peak=    4.422 closest distance to " CA  TYR A  30 " =    1.032
peak=    4.410 closest distance to " O   HOH Z 102 " =    1.359
peak=    4.404 closest distance to " O   HOH Z  69 " =    0.908
peak=    4.343 closest distance to " NE2 GLN A  11 " =    1.021
peak=    4.329 closest distance to " CD2 LEU A   5 " =    1.119
peak=    4.328 closest distance to " CB  GLN A 183 " =    1.310
peak=    4.327 closest distance to " O   HOH Z 427 " =    3.075
peak=    4.325 closest distance to " CZ3 TRP A 266 " =    1.174
peak=    4.316 closest distance to " CA  ALA A  51 " =    1.047
peak=    4.278 closest distance to " O   HOH Z 290 " =    1.445
peak=    4.268 closest distance to " O   HOH Z 287 " =    1.864
peak=    4.262 closest distance to " O   PRO A 198 " =    1.572
peak=    4.261 closest distance to " CB  ASP A 124 " =    0.797
peak=    4.248 closest distance to " CA  ALA A 295 " =    1.143
peak=    4.221 closest distance to " O   HOH Z 261 " =    1.649
peak=    4.183 closest distance to " CB  TYR A 169 " =    0.779
peak=    4.170 closest distance to " CB  ARG A 190 " =    1.488
peak=    4.157 closest distance to " CG2 ILE A 234 " =    1.030
peak=    4.141 closest distance to " O   HOH Z 265 " =    1.916
peak=    4.141 closest distance to " O   HOH Z 359 " =    1.840
peak=    4.125 closest distance to " O   HOH Z 406 " =    1.581
peak=    4.114 closest distance to " NH1AARG A 145 " =    1.235
peak=    4.110 closest distance to " CA  ARG A 195 " =    1.285
peak=    4.101 closest distance to " CG  PRO A 198 " =    1.267
peak=    4.085 closest distance to " O   HOH Z 142 " =    1.721
peak=    4.067 closest distance to " CB  ASN A 148 " =    1.366
peak=    4.047 closest distance to " O   HOH Z 111 " =    1.929
peak=    4.032 closest distance to " CA  VAL A 230 " =    1.262
peak=    4.021 closest distance to " CB  GLU A 128 " =    1.161
peak=    4.004 closest distance to " CG2 THR A 221 " =    1.057
peak=    3.990 closest distance to " CB  ASN A 142 " =    1.096
peak=    3.987 closest distance to " O   HOH Z  76 " =    1.290
peak=    3.984 closest distance to " O   HOH Z 183 " =    1.563
peak=    3.981 closest distance to " CB  VAL A 202 " =    1.667
peak=    3.981 closest distance to " CB  GLN A  89 " =    1.164
peak=    3.955 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.939 closest distance to " CD  GLU A 152 " =    0.807
peak=    3.933 closest distance to " CB  GLU A 277 " =    3.776
peak=    3.931 closest distance to " CB  TRP A 266 " =    1.089
peak=    3.930 closest distance to " CA  GLY A 267 " =    0.787
peak=    3.925 closest distance to " O   HOH Z 303 " =    2.358
peak=    3.924 closest distance to " CD1 LEU A  96 " =    0.901
peak=    3.921 closest distance to " O   ASP A 200 " =    1.704
peak=    3.919 closest distance to " O   HOH Z 214 " =    1.505
peak=    3.905 closest distance to " CA  ARG A 139 " =    1.254
peak=    3.897 closest distance to " CG  MET A 185 " =    1.279
peak=    3.890 closest distance to " CD  ARG A  66 " =    2.373
peak=    3.879 closest distance to " O   HOH Z   9 " =    1.485
peak=    3.878 closest distance to " OE1 GLN A  88 " =    0.816
peak=    3.873 closest distance to " O   HOH Z   4 " =    1.831
peak=    3.865 closest distance to " CA  MET A 105 " =    1.039
peak=    3.865 closest distance to " CA  ALA A 160 " =    1.018
peak=    3.858 closest distance to " O   HOH Z 130 " =    1.099
peak=    3.854 closest distance to " CD ALYS A 290 " =    1.010
peak=    3.834 closest distance to " CD2 LEU A 228 " =    1.246
peak=    3.825 closest distance to " CG  PRO A 213 " =    1.219
peak=    3.818 closest distance to " O   HOH Z 188 " =    3.092
peak=    3.790 closest distance to " CB  SER A   3 " =    1.755
peak=    3.788 closest distance to " O   MET A 105 " =    1.605
peak=    3.786 closest distance to " O   HOH Z 368 " =    2.467
peak=    3.785 closest distance to " CD  ARG A 159 " =    0.743
peak=    3.782 closest distance to " O   HOH Z  80 " =    2.034
peak=    3.779 closest distance to " O   HOH Z 393 " =    3.993
peak=    3.772 closest distance to " O   HOH Z 316 " =    3.163
peak=    3.765 closest distance to " CA  TYR A  30 " =    1.085
peak=    3.757 closest distance to " O   ALA A 165 " =    1.456
peak=    3.747 closest distance to " O   HOH Z 234 " =    3.704
peak=    3.740 closest distance to " O   HOH Z 103 " =    0.948
peak=    3.738 closest distance to " O   SER A  87 " =    2.384
peak=    3.736 closest distance to " O   HOH Z 422 " =    2.663
peak=    3.726 closest distance to " CD1 LEU A 300 " =    1.147
peak=    3.721 closest distance to " ND2 ASN A 249 " =    1.986
peak=    3.714 closest distance to " O   HOH Z 247 " =    1.436
peak=    3.714 closest distance to " CB  ARG A 275 " =    1.109
peak=    3.707 closest distance to " CD2 TRP A 179 " =    1.359
peak=    3.697 closest distance to " CG  PRO A 243 " =    1.119
peak=    3.697 closest distance to " O   HOH Z 346 " =    1.594
peak=    3.689 closest distance to " CB AVAL A  41 " =    1.235
peak=    3.689 closest distance to " CE3 TRP A  85 " =    1.018
peak=    3.688 closest distance to " O   HOH Z 213 " =    1.755
peak=    3.682 closest distance to " O   HOH Z 214 " =    2.904
peak=    3.679 closest distance to " NH1 ARG A  56 " =    1.215
peak=    3.666 closest distance to " O   HOH Z  56 " =    1.783
peak=    3.664 closest distance to " CA  LEU A 101 " =    1.232
peak=    3.662 closest distance to " O   HOH Z  99 " =    2.613
peak=    3.660 closest distance to " O   HOH Z  19 " =    2.385
peak=    3.658 closest distance to " O   HOH Z 227 " =    1.819
peak=    3.657 closest distance to " CG  GLU A  37 " =    1.000
peak=    3.654 closest distance to " CE1 HIS A  81 " =    1.720
peak=    3.651 closest distance to " CB  ARG A  79 " =    1.569
peak=    3.641 closest distance to " CA  ARG A 156 " =    1.176
peak=    3.640 closest distance to " O   HOH Z 158 " =    3.208
peak=    3.639 closest distance to " O   HOH Z 193 " =    2.251
peak=    3.637 closest distance to " CB  VAL A 265 " =    1.296
peak=    3.622 closest distance to " CA  ASP A 124 " =    0.810
peak=    3.620 closest distance to " CA  ALA A 291 " =    0.979
peak=    3.616 closest distance to " CG AARG A 275 " =    1.322
peak=    3.613 closest distance to " CG  LEU A 167 " =    1.167
peak=    3.610 closest distance to " CB  MET A  47 " =    0.967
peak=    3.607 closest distance to " O   ASP A 124 " =    1.225
peak=    3.606 closest distance to " O   HOH Z  88 " =    3.565
peak=    3.600 closest distance to " O   HOH Z 298 " =    2.224
peak=    3.586 closest distance to " OD1 ASN A 217 " =    1.584
peak=    3.585 closest distance to " O   ALA A 158 " =    1.372
peak=    3.581 closest distance to " CA  ASN A 127 " =    1.136
peak=    3.575 closest distance to " O   HOH Z 313 " =    1.788
peak=    3.561 closest distance to " O   HOH Z 258 " =    1.978
peak=    3.559 closest distance to " CB  SER A 216 " =    0.957
peak=    3.559 closest distance to " N   ALA A 256 " =    1.173
peak=    3.544 closest distance to " CA  TYR A 116 " =    1.427
peak=    3.544 closest distance to " O   HOH Z 403 " =    1.625
peak=    3.543 closest distance to " ND2 ASN A 187 " =    1.578
peak=    3.543 closest distance to " O   HOH Z 131 " =    2.239
peak=    3.535 closest distance to " CB  TYR A 116 " =    1.284
peak=    3.531 closest distance to " CA  ALA A 100 " =    0.940
peak=    3.529 closest distance to " OG  SER A 276 " =    1.423
peak=    3.529 closest distance to " O   HOH Z 420 " =    5.983
peak=    3.529 closest distance to " O   HOH Z 113 " =    1.722
peak=    3.528 closest distance to " CG1 VAL A 153 " =    1.099
peak=    3.526 closest distance to " CD  LYS A 166 " =    1.435
peak=    3.514 closest distance to " CD2 LEU A 255 " =    1.697
peak=    3.514 closest distance to " O   ASN A  74 " =    1.560
peak=    3.514 closest distance to " O   HOH Z 272 " =    1.258
peak=    3.511 closest distance to " O   HOH Z 154 " =    1.429
peak=    3.509 closest distance to " CA  ALA A 184 " =    1.170
peak=    3.508 closest distance to " CB  LEU A 143 " =    1.370
peak=    3.499 closest distance to " OG  SER A  62 " =    3.080
peak=    3.498 closest distance to " N   ARG A  66 " =    1.413
peak=    3.497 closest distance to " O   HOH Z 116 " =    1.933
peak=    3.494 closest distance to " CG2AVAL A 121 " =    2.095
peak=    3.491 closest distance to " O   HOH Z  57 " =    1.580
peak=    3.486 closest distance to " CA  LEU A 282 " =    1.095
peak=    3.486 closest distance to " N   PHE A 130 " =    1.306
peak=    3.485 closest distance to " O   HOH Z 155 " =    3.378
peak=    3.478 closest distance to " CD  ARG A 195 " =    1.024
peak=    3.474 closest distance to " O   THR A 251 " =    1.178
peak=    3.471 closest distance to " CD  LYS A  76 " =    2.072
peak=    3.468 closest distance to " CA  VAL A 125 " =    1.301
peak=    3.467 closest distance to " CA  GLU A 152 " =    0.880
peak=    3.462 closest distance to " N   TYR A  15 " =    1.031
peak=    3.459 closest distance to " CB  LEU A 228 " =    1.377
peak=    3.457 closest distance to " NE2 GLN A  58 " =    4.598
peak=    3.456 closest distance to " CD1 ILE A 199 " =    0.996
peak=    3.452 closest distance to " CB  THR A  52 " =    0.893
peak=    3.447 closest distance to " CG2 VAL A 197 " =    1.201
peak=    3.446 closest distance to " OD2 ASP A  65 " =    2.879
peak=    3.444 closest distance to " CB  SER A  62 " =    0.912
peak=    3.438 closest distance to " CB  PRO A  90 " =    1.304
peak=    3.438 closest distance to " N   SER A 271 " =    0.990
peak=    3.437 closest distance to " O   THR A 182 " =    1.412
peak=    3.436 closest distance to " O   HOH Z 402 " =    1.416
peak=    3.435 closest distance to " OD1 ASN A  69 " =    2.537
peak=    3.430 closest distance to " CD1 LEU A   5 " =    1.331
peak=    3.427 closest distance to " O   HOH Z 345 " =    3.979
peak=    3.426 closest distance to " O   ASN A 209 " =    1.368
peak=    3.424 closest distance to " O   HOH Z 189 " =    3.489
peak=    3.423 closest distance to " N   TYR A 247 " =    1.295
peak=    3.418 closest distance to " O   HOH Z 176 " =    1.706
peak=    3.410 closest distance to " CH2 TRP A  70 " =    1.093
peak=    3.407 closest distance to " CB  SER A 141 " =    1.125
peak=    3.399 closest distance to " O   HOH Z  43 " =    2.058
peak=    3.399 closest distance to " CA  VAL A 112 " =    1.166
peak=    3.398 closest distance to " O   HOH Z  78 " =    2.027
peak=    3.396 closest distance to " OG  SER A 245 " =    1.761
peak=    3.388 closest distance to " CA  ALA A 158 " =    1.217
peak=    3.385 closest distance to " O   HOH Z 285 " =    2.209
peak=    3.383 closest distance to " CA  ARG A  36 " =    1.175
peak=    3.381 closest distance to " O   HOH Z 124 " =    2.258
peak=    3.379 closest distance to " CB  TRP A 179 " =    1.423
peak=    3.378 closest distance to " O  BHOH Z 338 " =    2.259
peak=    3.373 closest distance to " O   HOH Z 124 " =    1.920
peak=    3.369 closest distance to " CZ3 TRP A  85 " =    0.865
peak=    3.369 closest distance to " CB  ALA A  43 " =    1.043
peak=    3.364 closest distance to " O   HOH Z 112 " =    1.723
peak=    3.364 closest distance to " CE1 TYR A 186 " =    1.229
peak=    3.362 closest distance to " CB  SER A  26 " =    1.928
peak=    3.361 closest distance to " NZ  LYS A  48 " =    1.433
peak=    3.358 closest distance to " O   HOH Z 353 " =    2.619
peak=    3.354 closest distance to " CB  PRO A  54 " =    0.835
peak=    3.350 closest distance to " CB  GLN A  88 " =    1.346
peak=    3.349 closest distance to " O   HOH Z  54 " =    1.577
peak=    3.344 closest distance to " CA  ARG A 102 " =    1.153
peak=    3.339 closest distance to " CB  ALA A   9 " =    1.722
peak=    3.338 closest distance to " O   HOH Z 299 " =    4.390
peak=    3.334 closest distance to " O   HOH Z 281 " =    2.808
peak=    3.333 closest distance to " CB  ASN A  39 " =    0.882
peak=    3.330 closest distance to " O   HOH Z 433 " =    1.483
peak=    3.320 closest distance to " OG BSER A 164 " =    2.152
peak=    3.318 closest distance to " O   HOH Z 117 " =    1.190
peak=    3.317 closest distance to " CB  GLU A 236 " =    1.327
peak=    3.315 closest distance to " OE1 GLN A 240 " =    1.648
peak=    3.311 closest distance to " NH2 ARG A  56 " =    1.043
peak=    3.310 closest distance to " O   HOH Z 280 " =    2.938
peak=    3.305 closest distance to " O   HOH Z 361 " =    3.450
peak=    3.305 closest distance to " CB  ASP A 140 " =    0.822
peak=    3.302 closest distance to " CG  ARG A 269 " =    1.729
peak=    3.302 closest distance to " CB  SER A 212 " =    1.356
peak=    3.300 closest distance to " O   HOH Z 199 " =    1.574
peak=    3.299 closest distance to " O   HOH Z 368 " =    4.059
peak=    3.297 closest distance to " O   HOH Z 365 " =    3.002
peak=    3.297 closest distance to " CB  ALA A 104 " =    0.845
peak=    3.296 closest distance to " CB  TRP A 150 " =    1.394
peak=    3.296 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.295 closest distance to " O   HOH Z 133 " =    2.950
peak=    3.291 closest distance to " N   VAL A 126 " =    1.582
peak=    3.288 closest distance to " CA  ASP A 140 " =    1.449
peak=    3.288 closest distance to " O   HOH Z 357 " =    2.711
peak=    3.287 closest distance to " N   ASN A  39 " =    1.328
peak=    3.287 closest distance to " O   HOH Z 126 " =    2.182
peak=    3.287 closest distance to " CB  GLU A 152 " =    1.239
peak=    3.287 closest distance to " CG1AVAL A 121 " =    0.771
peak=    3.284 closest distance to " CB  GLU A  37 " =    0.926
peak=    3.283 closest distance to " O   HOH Z 109 " =    2.784
peak=    3.272 closest distance to " OG BSER A 134 " =    2.909
peak=    3.269 closest distance to " O   HOH Z  35 " =    4.787
peak=    3.268 closest distance to " CD2 LEU A  83 " =    1.403
peak=    3.267 closest distance to " O   HOH Z 171 " =    4.066
peak=    3.263 closest distance to " CB  GLU A  46 " =    0.980
peak=    3.255 closest distance to " O   HOH Z 298 " =    2.233
peak=    3.253 closest distance to " NZ  LYS A 117 " =    2.932
peak=    3.253 closest distance to " CB  PRO A 243 " =    1.135
peak=    3.252 closest distance to " O   HOH Z 163 " =    1.482
peak=    3.248 closest distance to " O   HOH Z 393 " =    3.147
peak=    3.248 closest distance to " CA  ALA A  21 " =    1.301
peak=    3.247 closest distance to " CA  LEU A 261 " =    1.496
peak=    3.245 closest distance to " O   HOH Z 145 " =    1.504
peak=    3.242 closest distance to " O   HOH Z 172 " =    3.902
peak=    3.240 closest distance to " CB  ALA A 248 " =    1.105
peak=    3.240 closest distance to " CB  THR A 235 " =    1.291
peak=    3.238 closest distance to " O   HOH Z 250 " =    1.172
peak=    3.238 closest distance to " CG  GLN A  89 " =    1.485
peak=    3.235 closest distance to " NE2 HIS A 207 " =    1.127
peak=    3.234 closest distance to " CG1 ILE A  49 " =    1.692
peak=    3.232 closest distance to " CA  MET A 105 " =    1.563
peak=    3.231 closest distance to " CA  ILE A 106 " =    0.835
peak=    3.227 closest distance to " C   PRO A  54 " =    0.815
peak=    3.227 closest distance to " O   PRO A  90 " =    1.493
peak=    3.226 closest distance to " O   PHE A 192 " =    1.475
peak=    3.225 closest distance to " O   HOH Z  88 " =    3.015
peak=    3.215 closest distance to " O  BHOH Z  74 " =    1.299
peak=    3.214 closest distance to " O   HOH Z 174 " =    2.416
peak=    3.211 closest distance to " CA  ILE A  33 " =    1.817
peak=    3.211 closest distance to " O   HOH Z 343 " =    2.785
peak=    3.204 closest distance to " O   HOH Z 272 " =    1.815
peak=    3.204 closest distance to " O   THR A 220 " =    1.214
peak=    3.203 closest distance to " CA  GLY A 211 " =    1.400
peak=    3.201 closest distance to " CD1 ILE A  33 " =    1.673
peak=    3.197 closest distance to " CB  TYR A 247 " =    1.027
peak=    3.197 closest distance to " OE2 GLU A  53 " =    1.913
peak=    3.194 closest distance to " CZ  PHE A  38 " =    1.249
peak=    3.180 closest distance to " CB  SER A 288 " =    1.367
peak=    3.177 closest distance to " C   ALA A 299 " =    0.919
peak=    3.176 closest distance to " O   HOH Z 201 " =    2.759
peak=    3.175 closest distance to " O   HOH Z 305 " =    3.480
peak=    3.175 closest distance to " O   HOH Z 203 " =    1.802
peak=    3.169 closest distance to " CB  ASN A 215 " =    1.296
peak=    3.168 closest distance to " CB  ASN A 285 " =    0.969
peak=    3.168 closest distance to " CB  TYR A  30 " =    1.135
peak=    3.154 closest distance to " CA  GLU A  46 " =    0.731
peak=    3.154 closest distance to " OG BSER A 258 " =    3.218
peak=    3.152 closest distance to " CB  ALA A 227 " =    1.172
peak=    3.151 closest distance to " CB  THR A  31 " =    1.424
peak=    3.150 closest distance to " O   HOH Z 185 " =    2.040
peak=    3.150 closest distance to " CG1 VAL A 174 " =    1.148
peak=    3.146 closest distance to " CE3 TRP A 150 " =    1.138
peak=    3.144 closest distance to " CB  ALA A 242 " =    0.788
peak=    3.140 closest distance to " O   HOH Z 148 " =    3.402
peak=    3.135 closest distance to " O   HOH Z 132 " =    2.705
peak=    3.131 closest distance to " CB  ALA A 291 " =    1.279
peak=    3.130 closest distance to " CG1 ILE A  33 " =    1.220
peak=    3.129 closest distance to " CE3 TRP A  85 " =    0.947
peak=    3.128 closest distance to " O   HOH Z  78 " =    1.101
peak=    3.120 closest distance to " CB  LYS A 193 " =    1.039
peak=    3.116 closest distance to " O   HOH Z  68 " =    1.704
peak=    3.113 closest distance to " O   HOH Z  59 " =    2.092
peak=    3.112 closest distance to " O   HOH Z 156 " =    2.726
peak=    3.111 closest distance to " O   HOH Z 211 " =    1.526
peak=    3.110 closest distance to " OG  SER A 271 " =    2.153
peak=    3.105 closest distance to " NE2 HIS A 115 " =    1.000
peak=    3.095 closest distance to " CG  MET A 113 " =    1.697
peak=    3.094 closest distance to " O   HOH Z 423 " =    1.690
peak=    3.093 closest distance to " O   HOH Z  42 " =    2.126
peak=    3.091 closest distance to " O   HOH Z 128 " =    2.074
peak=    3.091 closest distance to " CA  VAL A 153 " =    1.014
peak=    3.090 closest distance to " N   ASN A 127 " =    1.356
peak=    3.088 closest distance to " CB  LEU A  83 " =    0.739
peak=    3.082 closest distance to " O   HOH Z 301 " =    1.605
peak=    3.082 closest distance to " CZ  PHE A 192 " =    0.973
peak=    3.081 closest distance to " CG1 ILE A  20 " =    1.339
peak=    3.075 closest distance to " O   ASP A 124 " =    1.818
peak=    3.072 closest distance to " CG  ARG A 159 " =    0.957
peak=    3.065 closest distance to " O   HOH Z 394 " =    1.908
peak=    3.063 closest distance to " CD  LYS A  76 " =    1.341
peak=    3.060 closest distance to " CA  LYS A 117 " =    1.232
peak=    3.052 closest distance to " CZ3 TRP A  92 " =    1.362
peak=    3.041 closest distance to " CZ3 TRP A  85 " =    1.024
peak=    3.021 closest distance to " O   HOH Z 377 " =    1.392

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.499 - 5.826
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 218
   mapped sites are within: 0.754 - 5.826

peak=   -5.086 closest distance to " CG1 VAL A 250 " =    2.674
peak=   -4.571 closest distance to " CG2 VAL A 230 " =    0.879
peak=   -4.542 closest distance to " O   HOH Z 103 " =    1.009
peak=   -4.259 closest distance to " CG1 VAL A 296 " =    1.115
peak=   -4.240 closest distance to " O   HOH Z 216 " =    1.092
peak=   -4.234 closest distance to " O   HOH Z 162 " =    2.827
peak=   -4.181 closest distance to " CD  ARG A  14 " =    3.303
peak=   -4.179 closest distance to " CD  ARG A 156 " =    2.102
peak=   -4.160 closest distance to " CG2 ILE A  49 " =    2.918
peak=   -4.108 closest distance to " CD1 PHE A  59 " =    2.053
peak=   -4.069 closest distance to " CD2 TYR A 293 " =    1.923
peak=   -4.067 closest distance to " O   HOH Z  10 " =    1.670
peak=   -4.053 closest distance to " O   HOH Z 166 " =    1.545
peak=   -4.035 closest distance to " O   HOH Z 231 " =    2.174
peak=   -4.023 closest distance to " OE1 GLN A 223 " =    2.358
peak=   -4.021 closest distance to " CD  GLN A  58 " =    0.901
peak=   -4.015 closest distance to " CE3 TRP A  70 " =    1.865
peak=   -4.006 closest distance to " O   HOH Z 411 " =    5.233
peak=   -3.986 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.953 closest distance to " O   VAL A  67 " =    2.758
peak=   -3.919 closest distance to " O   HOH Z 255 " =    0.937
peak=   -3.899 closest distance to " CG  GLN A  88 " =    0.920
peak=   -3.872 closest distance to " CG2 VAL A 189 " =    2.078
peak=   -3.871 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -3.867 closest distance to " O   HOH Z  73 " =    2.630
peak=   -3.837 closest distance to " C   ALA A 158 " =    1.289
peak=   -3.819 closest distance to " CG  ARG A 269 " =    2.380
peak=   -3.801 closest distance to " O   HOH Z  37 " =    2.157
peak=   -3.800 closest distance to " OD1 ASN A 148 " =    1.562
peak=   -3.798 closest distance to " O   SER A 271 " =    2.057
peak=   -3.795 closest distance to " O   HOH Z 196 " =    2.501
peak=   -3.776 closest distance to " ND2 ASN A  45 " =    2.448
peak=   -3.769 closest distance to " CB  VAL A 230 " =    1.061
peak=   -3.756 closest distance to " O   HOH Z  52 " =    1.624
peak=   -3.756 closest distance to " CG  PRO A 163 " =    2.162
peak=   -3.754 closest distance to " CE2 TYR A  30 " =    2.589
peak=   -3.728 closest distance to " CD1 LEU A   5 " =    2.462
peak=   -3.726 closest distance to " O   HOH Z 295 " =    1.613
peak=   -3.722 closest distance to " O   HOH Z 426 " =    1.883
peak=   -3.710 closest distance to " O   PRO A 198 " =    1.360
peak=   -3.710 closest distance to " CD2 HIS A 207 " =    2.201
peak=   -3.706 closest distance to " O   HOH Z 115 " =    1.623
peak=   -3.703 closest distance to " CD  LYS A 289 " =    2.295
peak=   -3.693 closest distance to " ND2 ASN A  69 " =    1.815
peak=   -3.691 closest distance to " CD2 PHE A  61 " =    2.094
peak=   -3.675 closest distance to " O   VAL A 189 " =    2.655
peak=   -3.670 closest distance to " OG  SER A  97 " =    2.243
peak=   -3.668 closest distance to " O   TYR A 186 " =    1.919
peak=   -3.643 closest distance to " O   HOH Z  43 " =    1.654
peak=   -3.629 closest distance to " O   PHE A 218 " =    1.533
peak=   -3.617 closest distance to " OG  SER A  62 " =    4.449
peak=   -3.615 closest distance to " O   GLY A 203 " =    2.352
peak=   -3.602 closest distance to " O   HOH Z 251 " =    4.920
peak=   -3.596 closest distance to " ND2BASN A 224 " =    1.964
peak=   -3.595 closest distance to " OE1 GLN A  88 " =    1.196
peak=   -3.594 closest distance to " O   HOH Z 232 " =    1.838
peak=   -3.592 closest distance to " OG BSER A 134 " =    1.598
peak=   -3.591 closest distance to " CA  GLY A 203 " =    2.460
peak=   -3.586 closest distance to " CH2 TRP A 179 " =    1.167
peak=   -3.584 closest distance to " OD2 ASP A 171 " =    1.895
peak=   -3.584 closest distance to " O   HOH Z   9 " =    1.609
peak=   -3.576 closest distance to " CA  SER A  62 " =    2.829
peak=   -3.573 closest distance to " CA  GLY A 133 " =    2.390
peak=   -3.568 closest distance to " O   HOH Z  17 " =    1.476
peak=   -3.555 closest distance to " CD1 LEU A 282 " =    2.696
peak=   -3.551 closest distance to " O   HOH Z 236 " =    1.508
peak=   -3.544 closest distance to " O   HOH Z 100 " =    1.202
peak=   -3.543 closest distance to " O   HOH Z 359 " =    3.106
peak=   -3.542 closest distance to " O   HOH Z 177 " =    1.756
peak=   -3.533 closest distance to " O   HOH Z 198 " =    2.553
peak=   -3.532 closest distance to " O   HOH Z  19 " =    1.909
peak=   -3.530 closest distance to " CG1 VAL A 125 " =    1.895
peak=   -3.528 closest distance to " O   HOH Z 407 " =    3.199
peak=   -3.524 closest distance to " CA  GLY A 241 " =    3.149
peak=   -3.522 closest distance to " O   HOH Z 183 " =    1.237
peak=   -3.522 closest distance to " O   HOH Z 394 " =    1.521
peak=   -3.521 closest distance to " CE2 TRP A  70 " =    2.425
peak=   -3.517 closest distance to " O   HOH Z 174 " =    2.508
peak=   -3.511 closest distance to " CE1 PHE A  59 " =    2.050
peak=   -3.507 closest distance to " O   HOH Z 145 " =    0.754
peak=   -3.498 closest distance to " O   HOH Z 357 " =    2.082
peak=   -3.498 closest distance to " NH1 ARG A 195 " =    0.986
peak=   -3.489 closest distance to " CB  ALA A 161 " =    2.693
peak=   -3.467 closest distance to " O   SER A 276 " =    1.695
peak=   -3.461 closest distance to " CD  GLN A  55 " =    1.197
peak=   -3.460 closest distance to " O   HOH Z 259 " =    3.931
peak=   -3.457 closest distance to " OG  SER A  87 " =    1.633
peak=   -3.453 closest distance to " CG2BVAL A  41 " =    1.883
peak=   -3.450 closest distance to " O   HOH Z  70 " =    1.926
peak=   -3.449 closest distance to " CB  HIS A  86 " =    1.116
peak=   -3.449 closest distance to " CE3 TRP A 150 " =    2.371
peak=   -3.442 closest distance to " O   HOH Z   6 " =    1.653
peak=   -3.442 closest distance to " C   GLY A  17 " =    1.298
peak=   -3.433 closest distance to " O   HOH Z 193 " =    1.449
peak=   -3.425 closest distance to " CE  LYS A  76 " =    2.587
peak=   -3.418 closest distance to " CG  MET A 105 " =    1.004
peak=   -3.416 closest distance to " CZ  PHE A  38 " =    2.540
peak=   -3.409 closest distance to " CG2 THR A 178 " =    2.331
peak=   -3.406 closest distance to " C   HIS A 108 " =    1.279
peak=   -3.405 closest distance to " O   HOH Z 431 " =    1.918
peak=   -3.404 closest distance to " CG1 VAL A 112 " =    2.859
peak=   -3.399 closest distance to " N   ALA A  43 " =    2.846
peak=   -3.398 closest distance to " O   HOH Z 177 " =    1.319
peak=   -3.385 closest distance to " O   HOH Z 275 " =    1.700
peak=   -3.380 closest distance to " CA  ASN A 127 " =    1.047
peak=   -3.378 closest distance to " C   LEU A 143 " =    1.298
peak=   -3.377 closest distance to " O   HOH Z 191 " =    5.826
peak=   -3.377 closest distance to " O   SER A 210 " =    1.825
peak=   -3.366 closest distance to " O   HOH Z  32 " =    2.134
peak=   -3.361 closest distance to " CA  GLY A  98 " =    2.196
peak=   -3.358 closest distance to " CB  ALA A  10 " =    2.305
peak=   -3.357 closest distance to " OG1 THR A  82 " =    1.540
peak=   -3.352 closest distance to " O   HOH Z 285 " =    1.988
peak=   -3.351 closest distance to " OG1 THR A  82 " =    1.829
peak=   -3.348 closest distance to " O   HOH Z 166 " =    1.827
peak=   -3.338 closest distance to " CD2 LEU A 167 " =    1.800
peak=   -3.338 closest distance to " O   GLN A 240 " =    2.560
peak=   -3.336 closest distance to " N   ILE A 120 " =    1.123
peak=   -3.332 closest distance to " O   HOH Z 231 " =    1.293
peak=   -3.330 closest distance to " O   HOH Z 377 " =    1.918
peak=   -3.329 closest distance to " O   HOH Z 118 " =    4.920
peak=   -3.321 closest distance to " O   HOH Z 113 " =    2.399
peak=   -3.319 closest distance to " O   HOH Z  68 " =    1.883
peak=   -3.318 closest distance to " O   PRO A 163 " =    2.101
peak=   -3.317 closest distance to " NE2 GLN A 103 " =    1.810
peak=   -3.317 closest distance to " O   HOH Z 185 " =    2.449
peak=   -3.311 closest distance to " CZ  TYR A 169 " =    1.854
peak=   -3.308 closest distance to " CG2AVAL A  41 " =    2.735
peak=   -3.303 closest distance to " CG1BVAL A  72 " =    2.572
peak=   -3.297 closest distance to " CG  GLU A  53 " =    1.518
peak=   -3.297 closest distance to " ND2 ASN A  60 " =    1.342
peak=   -3.296 closest distance to " N   PHE A  59 " =    1.912
peak=   -3.294 closest distance to " O   GLY A 262 " =    2.392
peak=   -3.293 closest distance to " CG  TRP A 266 " =    1.760
peak=   -3.292 closest distance to " CB  GLU A 277 " =    1.448
peak=   -3.283 closest distance to " O   HOH Z 131 " =    4.049
peak=   -3.282 closest distance to " O   HOH Z 155 " =    1.908
peak=   -3.278 closest distance to " OG  SER A 141 " =    1.699
peak=   -3.274 closest distance to " CA  GLY A 241 " =    2.312
peak=   -3.270 closest distance to " O   HOH Z 340 " =    1.609
peak=   -3.268 closest distance to " O   HOH Z 325 " =    1.748
peak=   -3.263 closest distance to " N   VAL A  67 " =    1.240
peak=   -3.258 closest distance to " O   HOH Z 298 " =    2.741
peak=   -3.258 closest distance to " NH2 ARG A  79 " =    2.228
peak=   -3.257 closest distance to " O   HOH Z 243 " =    1.618
peak=   -3.253 closest distance to " O   HOH Z 411 " =    1.749
peak=   -3.253 closest distance to " N   LYS A 166 " =    1.997
peak=   -3.249 closest distance to " CG  LEU A 281 " =    1.968
peak=   -3.248 closest distance to " O   HOH Z 107 " =    0.907
peak=   -3.247 closest distance to " O   GLY A 211 " =    1.471
peak=   -3.246 closest distance to " CD1 TRP A 274 " =    1.058
peak=   -3.244 closest distance to " O   HOH Z 140 " =    1.845
peak=   -3.244 closest distance to " CB  HIS A  81 " =    1.057
peak=   -3.243 closest distance to " O   HOH Z 317 " =    2.036
peak=   -3.241 closest distance to " CB  VAL A 189 " =    2.336
peak=   -3.238 closest distance to " C   ARG A  79 " =    2.662
peak=   -3.235 closest distance to " O   HOH Z 147 " =    2.228
peak=   -3.235 closest distance to " NE2 GLN A 194 " =    2.001
peak=   -3.235 closest distance to " O   HOH Z 368 " =    1.490
peak=   -3.234 closest distance to " NE2 GLN A  55 " =    2.476
peak=   -3.226 closest distance to " CB  PHE A 130 " =    1.272
peak=   -3.223 closest distance to " ND2 ASN A  60 " =    4.196
peak=   -3.222 closest distance to " CE2 PHE A  61 " =    2.561
peak=   -3.217 closest distance to " O   HOH Z  93 " =    2.124
peak=   -3.216 closest distance to " OD1 ASN A 173 " =    1.308
peak=   -3.215 closest distance to " O   HOH Z 353 " =    2.262
peak=   -3.214 closest distance to " O   HOH Z 364 " =    2.926
peak=   -3.214 closest distance to " CD2 PHE A 225 " =    1.231
peak=   -3.211 closest distance to " O   HOH Z 350 " =    1.813
peak=   -3.209 closest distance to " CB  ALA A 248 " =    2.148
peak=   -3.209 closest distance to " O   HOH Z 341 " =    1.196
peak=   -3.202 closest distance to " O   ALA A 180 " =    1.483
peak=   -3.196 closest distance to " CG1 VAL A  78 " =    2.524
peak=   -3.192 closest distance to " CD  GLN A 223 " =    1.348
peak=   -3.188 closest distance to " O   HOH Z 348 " =    2.139
peak=   -3.185 closest distance to " O   HOH Z  64 " =    1.917
peak=   -3.183 closest distance to " O   HOH Z 110 " =    1.377
peak=   -3.182 closest distance to " CD1 LEU A 101 " =    2.468
peak=   -3.181 closest distance to " O   HOH Z 438 " =    3.070
peak=   -3.177 closest distance to " OG ASER A 134 " =    1.332
peak=   -3.173 closest distance to " O   HOH Z 106 " =    2.151
peak=   -3.173 closest distance to " CG  ARG A 259 " =    1.467
peak=   -3.167 closest distance to " O   HOH Z  60 " =    2.187
peak=   -3.166 closest distance to " CZ2 TRP A 274 " =    1.092
peak=   -3.165 closest distance to " CD1 ILE A 109 " =    2.862
peak=   -3.163 closest distance to " CB  SER A  63 " =    3.369
peak=   -3.160 closest distance to " ND2 ASN A 249 " =    2.496
peak=   -3.152 closest distance to " CB  PRO A 163 " =    2.560
peak=   -3.147 closest distance to " CA  ASN A 110 " =    1.079
peak=   -3.133 closest distance to " CG  LYS A 166 " =    2.031
peak=   -3.130 closest distance to " O   HOH Z 428 " =    1.931
peak=   -3.128 closest distance to " O   HOH Z 351 " =    1.794
peak=   -3.124 closest distance to " CA  VAL A  67 " =    2.703
peak=   -3.123 closest distance to " CG2 THR A  52 " =    2.809
peak=   -3.122 closest distance to " CG  ARG A  24 " =    1.968
peak=   -3.119 closest distance to " OD1 ASP A 171 " =    1.628
peak=   -3.118 closest distance to " CB  ALA A  43 " =    2.796
peak=   -3.110 closest distance to " CE  MET A  93 " =    1.697
peak=   -3.109 closest distance to " O   HOH Z 250 " =    1.669
peak=   -3.108 closest distance to " C   MET A 188 " =    1.444
peak=   -3.102 closest distance to " O   HOH Z 174 " =    2.973
peak=   -3.101 closest distance to " O   HOH Z 100 " =    1.152
peak=   -3.096 closest distance to " SD  MET A  40 " =    2.061
peak=   -3.090 closest distance to " OE1 GLN A  88 " =    1.069
peak=   -3.090 closest distance to " O   HOH Z 257 " =    1.497
peak=   -3.090 closest distance to " O   HOH Z 312 " =    1.569
peak=   -3.089 closest distance to " O   HOH Z 326 " =    4.818
peak=   -3.086 closest distance to " CH2 TRP A 150 " =    1.183
peak=   -3.083 closest distance to " C   ASN A 176 " =    1.419
peak=   -3.076 closest distance to " O   PRO A 243 " =    1.903
peak=   -3.071 closest distance to " O   HOH Z 357 " =    2.138
peak=   -3.065 closest distance to " CD2 LEU A 237 " =    2.535
peak=   -3.057 closest distance to " CG  PRO A 243 " =    1.709
peak=   -3.032 closest distance to " CB  GLN A  11 " =    1.677
peak=   -3.030 closest distance to " N   SER A 276 " =    1.444
peak=   -3.010 closest distance to " O   HOH Z 165 " =    1.985
peak=   -3.001 closest distance to " CB  ALA A 227 " =    2.448

================= 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    :  0.5000 0.4920   6.297875e+00   6.286275e+00
   1_bss:  0.4932 0.4827   6.293552e+00   6.280353e+00
   1_xyz:  0.4210 0.4477   6.210866e+00   6.234271e+00
   1_adp:  0.3802 0.4348   6.150896e+00   6.215394e+00
   1_occ:  0.3798 0.4359   6.150628e+00   6.216937e+00
   2_bss:  0.3792 0.4344   6.152208e+00   6.216949e+00
   2_xyz:  0.3010 0.3626   5.966369e+00   6.095556e+00
   2_adp:  0.2751 0.3384   5.900061e+00   6.047038e+00
   2_occ:  0.2749 0.3381   5.899472e+00   6.046750e+00
   3_bss:  0.2730 0.3361   5.901020e+00   6.045839e+00
   3_xyz:  0.2020 0.2627   5.648576e+00   5.838387e+00
   3_adp:  0.1749 0.2354   5.533790e+00   5.752271e+00
   3_occ:  0.1747 0.2356   5.533537e+00   5.752464e+00
   4_bss:  0.1745 0.2351   5.531464e+00   5.749947e+00
   4_xyz:  0.1503 0.2066   5.408384e+00   5.639752e+00
   4_adp:  0.1423 0.1985   5.366484e+00   5.600675e+00
   4_occ:  0.1421 0.1986   5.366232e+00   5.600487e+00
   5_bss:  0.1423 0.1988   5.366728e+00   5.600594e+00
   5_xyz:  0.1283 0.1856   5.286685e+00   5.533964e+00
   5_adp:  0.1252 0.1818   5.265348e+00   5.513447e+00
   5_occ:  0.1251 0.1817   5.264926e+00   5.512964e+00
   5_bss:  0.1251 0.1816   5.264705e+00   5.512763e+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:  0.300  50.000   7.387   6.897  10.469   0.000   0.000   0.000
   1_xyz:  0.300  50.000   7.387   6.897  10.469   0.000   0.000   0.000
   1_adp:  0.300  50.000   7.387   6.897  10.469   0.000   0.000   0.000
   1_occ:  0.300  50.000   7.387   6.897  10.469   0.000   0.000   0.000
   2_bss:  0.309  50.000   4.924   4.752   7.651   0.000   0.000   0.000
   2_xyz:  0.309  50.000   4.924   4.752   7.651   0.000   0.000   0.000
   2_adp:  0.309  50.000   4.924   4.752   7.651   0.000   0.000   0.000
   2_occ:  0.309  50.000   4.924   4.752   7.651   0.000   0.000   0.000
   3_bss:  0.310  50.000   2.529   2.716   4.673   0.000   0.000   0.000
   3_xyz:  0.310  50.000   2.529   2.716   4.673   0.000   0.000   0.000
   3_adp:  0.310  50.000   2.529   2.716   4.673   0.000   0.000   0.000
   3_occ:  0.310  50.000   2.529   2.716   4.673   0.000   0.000   0.000
   4_bss:  0.334  83.407   1.572   1.645   3.286   0.000   0.000   0.000
   4_xyz:  0.334  83.407   1.572   1.645   3.286   0.000   0.000   0.000
   4_adp:  0.334  83.407   1.572   1.645   3.286   0.000   0.000   0.000
   4_occ:  0.334  83.407   1.572   1.645   3.286   0.000   0.000   0.000
   5_bss:  0.336  86.469   1.584   1.679   3.271   0.000   0.000   0.000
   5_xyz:  0.336  86.469   1.584   1.679   3.271   0.000   0.000   0.000
   5_adp:  0.336  86.469   1.584   1.679   3.271   0.000   0.000   0.000
   5_occ:  0.336  86.469   1.584   1.679   3.271   0.000   0.000   0.000
   5_bss:  0.325  81.947  -0.527  -0.531   1.057   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.017 0.3535  0.3994    74967.987
   1_bss:  60.924 0.3808  0.5458    73533.968
   1_xyz:  53.844 0.4703  0.6585    59134.829
   1_adp:  51.111 0.5052  0.7604    55103.615
   1_occ:  51.284 0.5030  0.7549    55363.072
   2_bss:  51.235 0.5036  0.6977    55316.430
   2_xyz:  39.096 0.6527  0.9051    36155.432
   2_adp:  35.569 0.6947  0.9588    30973.506
   2_occ:  35.600 0.6942  0.9573    30922.905
   3_bss:  35.531 0.6950  0.8790    30881.811
   3_xyz:  26.153 0.7989  0.9731    17801.642
   3_adp:  23.004 0.8318  0.9818    14237.265
   3_occ:  23.012 0.8317  0.9812    14222.622
   4_bss:  22.906 0.8327  0.9435    14088.299
   4_xyz:  19.809 0.8632  0.9601    10926.213
   4_adp:  18.823 0.8728  0.9505    10062.191
   4_occ:  18.825 0.8727  0.9503    10052.606
   5_bss:  18.835 0.8727  0.9504    10064.194
   5_xyz:  17.265 0.8870  0.9605     8625.169
   5_adp:  16.720 0.8922  0.9517     8301.025
   5_occ:  16.710 0.8922  0.9516     8286.970
   5_bss:  16.707 0.8923  0.9589     8282.773
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4851e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4851e+01
   1_xyz:   1.824  0.015  0.115 18.506  0.007  4.111   1.6255e-01
   1_adp:   1.824  0.015  0.115 18.506  0.007  4.111   1.6255e-01
   1_occ:   1.824  0.015  0.115 18.506  0.007  4.111   1.6255e-01
   2_bss:   1.824  0.015  0.115 18.506  0.007  4.111   1.6255e-01
   2_xyz:   1.348  0.010  0.089 17.357  0.005  4.112   1.0657e-01
   2_adp:   1.348  0.010  0.089 17.357  0.005  4.112   1.0657e-01
   2_occ:   1.348  0.010  0.089 17.357  0.005  4.112   1.0657e-01
   3_bss:   1.348  0.010  0.089 17.357  0.005  4.112   1.0657e-01
   3_xyz:   1.231  0.011  0.088 16.567  0.005  4.143   1.0122e-01
   3_adp:   1.231  0.011  0.088 16.567  0.005  4.143   1.0122e-01
   3_occ:   1.231  0.011  0.088 16.567  0.005  4.143   1.0122e-01
   4_bss:   1.231  0.011  0.088 16.567  0.005  4.143   1.0122e-01
   4_xyz:   1.125  0.010  0.084 16.136  0.004  4.119   7.7487e-02
   4_adp:   1.125  0.010  0.084 16.136  0.004  4.119   7.7487e-02
   4_occ:   1.125  0.010  0.084 16.136  0.004  4.119   7.7487e-02
   5_bss:   1.125  0.010  0.084 16.136  0.004  4.119   7.7487e-02
   5_xyz:   1.245  0.013  0.094 15.890  0.004  4.132   9.5051e-02
   5_adp:   1.245  0.013  0.094 15.890  0.004  4.132   9.5051e-02
   5_occ:   1.245  0.013  0.094 15.890  0.004  4.132   9.5051e-02
   5_bss:   1.245  0.013  0.094 15.890  0.004  4.132   9.5051e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.1122e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.1122e+00
   1_xyz:  15.261  0.182  0.478 86.810  0.045  2.215   1.1720e-01
   1_adp:  15.261  0.182  0.478 86.810  0.045  2.215   1.1720e-01
   1_occ:  15.261  0.182  0.478 86.810  0.045  2.215   1.1720e-01
   2_bss:  15.261  0.182  0.478 86.810  0.045  2.215   1.1720e-01
   2_xyz:   8.618  0.092  0.287 83.671  0.025  1.948   6.6841e-02
   2_adp:   8.618  0.092  0.287 83.671  0.025  1.948   6.6841e-02
   2_occ:   8.618  0.092  0.287 83.671  0.025  1.948   6.6841e-02
   3_bss:   8.618  0.092  0.287 83.671  0.025  1.948   6.6841e-02
   3_xyz:   8.688  0.070  0.286 85.790  0.040  2.243   2.1269e-01
   3_adp:   8.688  0.070  0.286 85.790  0.040  2.243   2.1269e-01
   3_occ:   8.688  0.070  0.286 85.790  0.040  2.243   2.1269e-01
   4_bss:   8.688  0.070  0.286 85.790  0.040  2.243   2.1269e-01
   4_xyz:   8.359  0.054  0.332 85.312  0.038  2.324   4.2803e-02
   4_adp:   8.359  0.054  0.332 85.312  0.038  2.324   4.2803e-02
   4_occ:   8.359  0.054  0.332 85.312  0.038  2.324   4.2803e-02
   5_bss:   8.359  0.054  0.332 85.312  0.038  2.324   4.2803e-02
   5_xyz:   8.115  0.076  0.455 83.952  0.043  2.193   8.9865e-02
   5_adp:   8.115  0.076  0.455 83.952  0.043  2.193   8.9865e-02
   5_occ:   8.115  0.076  0.455 83.952  0.043  2.193   8.9865e-02
   5_bss:   8.115  0.076  0.455 83.952  0.043  2.193   8.9865e-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:  96.64   0.00  15.71  80.96   0.00  13.42  96.64   0.00  28.19
   1_occ:  96.64   0.00  15.71  80.96   0.00  13.42  96.64   0.00  28.19
   2_bss:  96.64   0.00  15.71  80.96   0.00  13.42  96.64   0.00  28.19
   2_xyz:  96.64   0.00  15.71  80.96   0.00  13.42  96.64   0.00  28.19
   2_adp:  98.80   0.00  15.06  79.14   0.00  11.71  98.80   0.00  33.31
   2_occ:  98.80   0.00  15.06  79.14   0.00  11.71  98.80   0.00  33.31
   3_bss:  98.80   0.00  15.06  79.14   0.00  11.71  98.80   0.00  33.31
   3_xyz:  98.80   0.00  15.06  79.14   0.00  11.71  98.80   0.00  33.31
   3_adp:  97.75   0.00  15.68  93.74   0.00  10.73  97.75   0.00  42.66
   3_occ:  97.75   0.00  15.68  93.74   0.00  10.73  97.75   0.00  42.66
   4_bss:  97.75   0.00  15.68  93.74   0.00  10.73  97.75   0.00  42.66
   4_xyz:  97.75   0.00  15.68  93.74   0.00  10.73  97.75   0.00  42.66
   4_adp: 109.00   0.00  15.59 102.65   0.00  10.12 109.00   0.00  45.37
   4_occ: 109.00   0.00  15.59 102.65   0.00  10.12 109.00   0.00  45.37
   5_bss: 109.00   0.00  15.59 102.65   0.00  10.12 109.00   0.00  45.37
   5_xyz: 109.00   0.00  15.59 102.65   0.00  10.12 109.00   0.00  45.37
   5_adp: 116.38   0.00  15.10  99.31   0.00   9.72 116.38   0.00  44.43
   5_occ: 116.38   0.00  15.10  99.31   0.00   9.72 116.38   0.00  44.43
   5_bss: 118.78   2.40  17.50 101.71   2.40  12.11 118.78   2.40  46.83
------------------------------------------------------------------------
 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:    1.291    0.026    0.418
   1_adp:    1.291    0.026    0.418
   1_occ:    1.291    0.026    0.418
   2_bss:    1.291    0.026    0.418
   2_xyz:    1.837    0.033    0.621
   2_adp:    1.837    0.033    0.621
   2_occ:    1.837    0.033    0.621
   3_bss:    1.837    0.033    0.621
   3_xyz:    1.738    0.062    0.735
   3_adp:    1.738    0.062    0.735
   3_occ:    1.738    0.062    0.735
   4_bss:    1.738    0.062    0.735
   4_xyz:    1.842    0.046    0.787
   4_adp:    1.842    0.046    0.787
   4_occ:    1.842    0.046    0.787
   5_bss:    1.842    0.046    0.787
   5_xyz:    1.915    0.064    0.817
   5_adp:    1.915    0.064    0.817
   5_occ:    1.915    0.064    0.817
   5_bss:    1.915    0.064    0.817
------------------------------------------------------------------------

CPU time actual refinement: 348.40


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1176/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_1176/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1176/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1176/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1176/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.24 
  Macro-tasks:
    bulk solvent and scale       = 47.91  
    individual site refinement   = 144.88 
    weights calculation          = 32.18  
    collect and process          = 6.58   
    model show statistics        = 0.17   
    TOTAL for macro-tasks        = 231.72 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 105.26 
    alpha_beta                      = 8.65   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 116.54 
    fmodel                         = 8.23   
    r_factors                      = 0.37   
    phase_errors                   = 10.15  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 253.06 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.857 micro seconds
Total CPU time: 6.03 minutes
from_scatterers_fft:    651 calls, 105.05 s
gradients_fft:          596 calls, 102.87 s

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

# Date 2008-01-16 Time 03:23:09 PST -0800 (1200482589.69 s)
Start R-work = 0.5000, R-free = 0.4920 (no bulk solvent and anisotropic scale)
Final R-work = 0.1407, R-free = 0.1954 (no bulk solvent and anisotropic scale)

Start R-work = 0.4932, R-free = 0.4827
Final R-work = 0.1251, R-free = 0.1816