# Date 2008-01-16 Time 01:58:12 PST -0800 (1200477492.38 s)
#phil __OFF__

Command line arguments: "../641.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31612
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 641

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.4607, 85.5261, 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: 3.35, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98037
Completeness in resolution range: 0.976423
Completeness with d_max=infinity: 0.973415

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9804

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98037
Completeness in resolution range: 0.976423
Completeness with d_max=infinity: 0.973415

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.2373 [2099/2124]  1889   210  10.0%
  bin  2:  4.2373 -  3.3760 [2031/2051]  1828   203  10.0%
  bin  3:  3.3760 -  2.9530 [1998/2017]  1796   202  10.1%
  bin  4:  2.9530 -  2.6847 [1971/2001]  1777   194   9.8%
  bin  5:  2.6847 -  2.4932 [1980/1999]  1783   197   9.9%
  bin  6:  2.4932 -  2.3468 [1957/1982]  1762   195  10.0%
  bin  7:  2.3468 -  2.2297 [1943/1971]  1743   200  10.3%
  bin  8:  2.2297 -  2.1329 [1945/1981]  1752   193   9.9%
  bin  9:  2.1329 -  2.0510 [1933/1975]  1745   188   9.7%
  bin 10:  2.0510 -  1.9804 [1732/1961]  1555   177  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_641/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: 0.13 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: 23
        2.42 -     3.04: 2218
        3.04 -     3.66: 4757
        3.66 -     4.28: 9118
        4.28 -     4.90: 12448
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 110 " - " O   HOH Z 355 "  2.221 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.223 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  2.256 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28559 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_641/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_641/model_refine_001.geo

CPU time processing inputs: 9.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.4607 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4421   r_free= 0.4249   ksol= 0.00   Bsol= 0.00   scale= 0.823    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.237946                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7259 0.99   1372  152 0.3733 0.3732      6.5315      6.5161|
|  2:  4.7259 -  3.7709 0.99   1316  146 0.3442 0.3335      6.6834      6.6546|
|  3:  3.7709 -  3.3001 0.99   1286  144 0.3813 0.3572      6.5827      6.6216|
|  4:  3.3001 -  3.0010 0.99   1279  144 0.4153 0.3642      6.4745      6.3776|
|  5:  3.0010 -  2.7874 0.99   1279  141 0.4658 0.4695      6.3306      6.3417|
|  6:  2.7874 -  2.6240 0.99   1270  139 0.4621 0.5282      6.2542      6.2405|
|  7:  2.6240 -  2.4932 0.99   1271  140 0.4788 0.4308      6.2093      6.1826|
|  8:  2.4932 -  2.3851 0.98   1253  143 0.4994 0.4407      6.1785      6.1482|
|  9:  2.3851 -  2.2936 0.98   1245  134 0.4754 0.4757      6.0921      6.0952|
| 10:  2.2936 -  2.2147 1.00   1248  144 0.4916 0.4884      6.1144      6.0921|
| 11:  2.2147 -  2.1457 0.97   1259  136 0.5011 0.4117      6.0415      5.9629|
| 12:  2.1457 -  2.0845 0.98   1231  138 0.4919 0.4889      5.9799      5.9998|
| 13:  2.0845 -  2.0298 0.99   1247  142 0.5114 0.5288      5.8915       5.883|
| 14:  2.0298 -  1.9804 0.84   1074  116 0.5242 0.5059      5.8373      5.7624|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9533 -  4.7259  1372   152  0.71  33.65   0.81     0.75      67190.03|
|  2:  4.7259 -  3.7709  1316   146  0.76  29.76   0.91     0.83      81186.16|
|  3:  3.7709 -  3.3001  1286   144  0.69  36.29   0.89     0.80      83676.11|
|  4:  3.3001 -  3.0010  1279   144  0.63  41.38   0.84     0.71      75245.39|
|  5:  3.0010 -  2.7874  1279   141  0.52  50.33   0.77     0.61      67032.95|
|  6:  2.7874 -  2.6240  1270   139  0.50  52.19   0.76     0.56      60236.57|
|  7:  2.6240 -  2.4932  1271   140  0.48  53.49   0.75     0.55      55433.91|
|  8:  2.4932 -  2.3851  1253   143  0.49  53.27   0.76     0.56      49256.58|
|  9:  2.3851 -  2.2936  1245   134  0.51  51.12   0.75     0.57      42155.59|
| 10:  2.2936 -  2.2147  1248   144  0.52  50.68   0.78     0.59      37310.67|
| 11:  2.2147 -  2.1457  1259   136  0.50  52.30   0.78     0.59      35220.63|
| 12:  2.1457 -  2.0845  1231   138  0.45  56.44   0.80     0.54      36375.60|
| 13:  2.0845 -  2.0298  1247   142  0.37  62.34   0.76     0.44      34205.50|
| 14:  2.0298 -  1.9804  1074   116  0.32  65.84   0.73     0.35      29613.84|
|alpha:            min =        0.35 max =            0.83 mean =         0.61|
|beta:             min =    29613.84 max =        83676.11 mean =     54447.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           90.00 mean =        48.84|
|phase err.(test): min =        0.00 max =           89.91 mean =        48.89|
|-----------------------------------------------------------------------------|

============================== 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 = 8.363589              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.278   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.774146              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.515   (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:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      686 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1532 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2669 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3962 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5119 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6616 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7759 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.395 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.770 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4499   r_free= 0.4317   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.243107                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4330   r_free= 0.4156   ksol= 0.36   Bsol= 7.05   scale= 1.028    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.36,9.44,8.44,0.00,0.00,0.00); trace/3= 8.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.231405                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.636189              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.753   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.731468              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.979   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4330      final r-factor (work) = 0.3317          |
| start r-factor (free) = 0.4156      final r-factor (free) = 0.3546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.2476 = 7.64 * 0.50 * 6.2474 + 1.00 * 53.3946                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3969 = 7.64 * 0.50 * 6.0961 + 1.00 * 0.1213                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3317      final r-factor (work) = 0.2742          |
| start r-factor (free) = 0.3546      final r-factor (free) = 0.3139          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4738 = 0.73 * 1.00 * 6.0961 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3579 = 0.73 * 1.00 * 5.9406 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.40   11.08    None  None   None       |
|    all(noH): 2823   0      0.00    73.40   11.08    None  None   None       |
|    Sol.    : 438    0      0.00    63.22   27.12    None  None   None       |
|    Mac.    : 2385   0      0.00    73.40   8.13     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.340: 1425   |   5:    36.701 -  44.041:   71        |
|      1:     7.340 -  14.680:  714   |   6:    44.041 -  51.381:   34        |
|      2:    14.680 -  22.020:  262   |   7:    51.381 -  58.721:    7        |
|      3:    22.020 -  29.361:  183   |   8:    58.721 -  66.061:    5        |
|      4:    29.361 -  36.701:  121   |   9:    66.061 -  73.401:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2742 r_free = 0.3139             target_work(ml) = 5.891         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2737 r_free = 0.3139             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2737   r_free= 0.3139   ksol= 0.36   Bsol= 7.05   scale= 1.103    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.36,9.44,8.44,0.00,0.00,0.00); trace/3= 8.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.889811                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2679   r_free= 0.3070   ksol= 0.34   Bsol= 28.45   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,4.86,5.14,0.00,0.00,0.00); trace/3= 4.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.885198                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.325500              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.726   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.334449              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.860  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2679      final r-factor (work) = 0.1814          |
| start r-factor (free) = 0.3070      final r-factor (free) = 0.2265          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0086 = 3.33 * 0.50 * 5.9467 + 1.00 * 0.1207                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5426 = 3.33 * 0.50 * 5.7026 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1814      final r-factor (work) = 0.1637          |
| start r-factor (free) = 0.2265      final r-factor (free) = 0.2097          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9196 = 0.33 * 1.00 * 5.7026 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8477 = 0.33 * 1.00 * 5.4938 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.76   11.37    None  None   None       |
|    all(noH): 2823   0      0.00    74.76   11.37    None  None   None       |
|    Sol.    : 438    0      0.58    63.56   31.60    None  None   None       |
|    Mac.    : 2385   0      0.00    74.76   7.65     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.476: 1579   |   5:    37.379 -  44.854:  124        |
|      1:     7.476 -  14.952:  605   |   6:    44.854 -  52.330:   53        |
|      2:    14.952 -  22.427:  190   |   7:    52.330 -  59.806:    9        |
|      3:    22.427 -  29.903:  122   |   8:    59.806 -  67.282:    3        |
|      4:    29.903 -  37.379:  136   |   9:    67.282 -  74.757:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1637 r_free = 0.2097             target_work(ml) = 5.460         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1634 r_free = 0.2094             target_work(ml) = 5.459         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1634   r_free= 0.2094   ksol= 0.34   Bsol= 28.45   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,4.86,5.14,0.00,0.00,0.00); trace/3= 4.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.459383                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1632   r_free= 0.2088   ksol= 0.32   Bsol= 28.45   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.23,4.07,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.458318                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.056582              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.728  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.437389              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.393  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1632      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.2088      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2184 = 4.06 * 0.50 * 5.5011 + 1.00 * 0.0606                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9052 = 4.06 * 0.50 * 5.3427 + 1.00 * 0.0686                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6898 = 1.44 * 1.00 * 5.3427 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4825 = 1.44 * 1.00 * 5.1966 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.24   12.02    None  None   None       |
|    all(noH): 2823   0      0.00    86.24   12.02    None  None   None       |
|    Sol.    : 438    0      1.37    74.79   35.40    None  None   None       |
|    Mac.    : 2385   0      0.00    86.24   7.73     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 -   8.624: 1738   |   5:    43.118 -  51.742:   94        |
|      1:     8.624 -  17.247:  525   |   6:    51.742 -  60.366:   61        |
|      2:    17.247 -  25.871:  153   |   7:    60.366 -  68.989:   26        |
|      3:    25.871 -  34.495:  122   |   8:    68.989 -  77.613:    4        |
|      4:    34.495 -  43.118:   98   |   9:    77.613 -  86.237:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1174 r_free = 0.1627             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1173 r_free = 0.1626             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1626   ksol= 0.32   Bsol= 28.45   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.23,4.07,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175774                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1624   ksol= 0.32   Bsol= 34.84   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,2.98,3.93,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175882                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.236720              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.832  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.132275              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.607  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8803 = 2.24 * 0.50 * 5.1968 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8271 = 2.24 * 0.50 * 5.1577 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6951 = 0.13 * 1.00 * 5.1577 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6910 = 0.13 * 1.00 * 5.1551 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.93   11.38    None  None   None       |
|    all(noH): 2823   0      0.00    83.93   11.38    None  None   None       |
|    Sol.    : 438    0      1.47    70.69   32.45    None  None   None       |
|    Mac.    : 2385   0      0.00    83.93   7.52     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.394: 1752   |   5:    41.967 -  50.361:   85        |
|      1:     8.394 -  16.787:  550   |   6:    50.361 -  58.754:   42        |
|      2:    16.787 -  25.180:  143   |   7:    58.754 -  67.148:   18        |
|      3:    25.180 -  33.574:  124   |   8:    67.148 -  75.541:    2        |
|      4:    33.574 -  41.967:  104   |   9:    75.541 -  83.935:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1136 r_free = 0.1562             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1135 r_free = 0.1560             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1560   ksol= 0.32   Bsol= 34.84   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,2.98,3.93,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.142541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1560   ksol= 0.32   Bsol= 34.84   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,2.98,3.93,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.142699                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.533747              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.808  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.422187              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.492  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1135      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5895 = 2.53 * 0.50 * 5.1549 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5612 = 2.53 * 0.50 * 5.1270 + 1.00 * 0.0660                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1736 = 0.42 * 1.00 * 5.1270 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1708 = 0.42 * 1.00 * 5.1133 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.97   11.45    None  None   None       |
|    all(noH): 2823   0      0.00    84.97   11.45    None  None   None       |
|    Sol.    : 438    0      1.68    70.98   32.92    None  None   None       |
|    Mac.    : 2385   0      0.00    84.97   7.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.498: 1747   |   5:    42.487 -  50.985:   83        |
|      1:     8.498 -  16.995:  546   |   6:    50.985 -  59.482:   40        |
|      2:    16.995 -  25.492:  138   |   7:    59.482 -  67.980:   16        |
|      3:    25.492 -  33.990:  132   |   8:    67.980 -  76.477:    3        |
|      4:    33.990 -  42.487:  116   |   9:    76.477 -  84.975:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1085 r_free = 0.1549             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1548             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1548   ksol= 0.32   Bsol= 34.84   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,2.98,3.93,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.117442                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7259 0.99   1372  152 0.0993 0.1255      5.3721      5.4975|
|  2:  4.7259 -  3.7709 0.99   1316  146 0.0837 0.1127      5.4214      5.6289|
|  3:  3.7709 -  3.3001 0.99   1286  144 0.1040 0.1486       5.465      5.8286|
|  4:  3.3001 -  3.0010 0.99   1279  144 0.1189 0.1554      5.4434      5.5974|
|  5:  3.0010 -  2.7874 0.99   1279  141 0.1259 0.1695       5.304       5.547|
|  6:  2.7874 -  2.6240 0.99   1270  139 0.1137 0.1754      5.1805      5.4057|
|  7:  2.6240 -  2.4932 0.99   1271  140 0.1250 0.1598      5.1488      5.3788|
|  8:  2.4932 -  2.3851 0.98   1253  143 0.1124 0.1735      5.0501      5.3501|
|  9:  2.3851 -  2.2936 0.98   1245  134 0.1136 0.1607      5.0178      5.2121|
| 10:  2.2936 -  2.2147 1.00   1248  144 0.1050 0.1817      4.9307      5.2751|
| 11:  2.2147 -  2.1457 0.97   1259  136 0.1100 0.1678       4.925      5.2355|
| 12:  2.1457 -  2.0845 0.98   1231  138 0.1076 0.1755       4.852      5.2334|
| 13:  2.0845 -  2.0298 0.99   1247  142 0.1065 0.1661       4.767      5.0403|
| 14:  2.0298 -  1.9804 0.84   1074  116 0.1010 0.1617      4.6293      4.8598|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9533 -  4.7259  1372   152  0.94   8.64   0.99     0.96       6755.56|
|  2:  4.7259 -  3.7709  1316   146  0.96   7.59   1.03     1.02       8719.36|
|  3:  3.7709 -  3.3001  1286   144  0.94  10.95   1.03     1.02      10121.36|
|  4:  3.3001 -  3.0010  1279   144  0.92  13.26   1.01     1.00      10131.05|
|  5:  3.0010 -  2.7874  1279   141  0.90  15.51   1.00     0.96       8074.78|
|  6:  2.7874 -  2.6240  1270   139  0.91  15.11   0.99     0.96       6750.21|
|  7:  2.6240 -  2.4932  1271   140  0.90  15.62   0.99     0.96       6041.13|
|  8:  2.4932 -  2.3851  1253   143  0.91  14.74   1.00     0.98       5076.18|
|  9:  2.3851 -  2.2936  1245   134  0.91  14.88   1.01     0.99       4901.14|
| 10:  2.2936 -  2.2147  1248   144  0.91  14.57   1.01     0.98       4157.28|
| 11:  2.2147 -  2.1457  1259   136  0.90  16.32   1.01     0.98       4338.82|
| 12:  2.1457 -  2.0845  1231   138  0.92  14.57   1.02     1.01       3743.74|
| 13:  2.0845 -  2.0298  1247   142  0.91  15.07   1.02     1.01       3206.51|
| 14:  2.0298 -  1.9804  1074   116  0.92  13.88   1.00     0.97       2374.95|
|alpha:            min =        0.96 max =            1.02 mean =         0.99|
|beta:             min =     2374.95 max =        10131.05 mean =      6101.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.56|
|phase err.(test): min =        0.00 max =           89.47 mean =        13.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1548   ksol= 0.32   Bsol= 41.05   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.40,-0.31,0.71,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116937                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1548   ksol= 0.32   Bsol= 41.05   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.40,-0.31,0.71,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116937                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7259 0.99   1372  152 0.0994 0.1257      5.3724      5.4981|
|  2:  4.7259 -  3.7709 0.99   1316  146 0.0841 0.1132      5.4239      5.6318|
|  3:  3.7709 -  3.3001 0.99   1286  144 0.1042 0.1486      5.4665      5.8299|
|  4:  3.3001 -  3.0010 0.99   1279  144 0.1188 0.1554      5.4429      5.5964|
|  5:  3.0010 -  2.7874 0.99   1279  141 0.1258 0.1692      5.3025      5.5447|
|  6:  2.7874 -  2.6240 0.99   1270  139 0.1134 0.1750      5.1786       5.404|
|  7:  2.6240 -  2.4932 0.99   1271  140 0.1250 0.1599      5.1475      5.3788|
|  8:  2.4932 -  2.3851 0.98   1253  143 0.1123 0.1730      5.0491      5.3474|
|  9:  2.3851 -  2.2936 0.98   1245  134 0.1134 0.1609      5.0169       5.212|
| 10:  2.2936 -  2.2147 1.00   1248  144 0.1049 0.1816        4.93      5.2754|
| 11:  2.2147 -  2.1457 0.97   1259  136 0.1100 0.1675      4.9243      5.2347|
| 12:  2.1457 -  2.0845 0.98   1231  138 0.1074 0.1753      4.8511      5.2329|
| 13:  2.0845 -  2.0298 0.99   1247  142 0.1065 0.1660      4.7662      5.0396|
| 14:  2.0298 -  1.9804 0.84   1074  116 0.1011 0.1612      4.6278      4.8574|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9533 -  4.7259  1372   152  0.94   8.65   0.98     0.96       6766.44|
|  2:  4.7259 -  3.7709  1316   146  0.96   7.60   1.02     1.01       8746.06|
|  3:  3.7709 -  3.3001  1286   144  0.94  10.99   1.03     1.02      10155.17|
|  4:  3.3001 -  3.0010  1279   144  0.92  13.25   1.01     1.00      10118.94|
|  5:  3.0010 -  2.7874  1279   141  0.90  15.49   0.99     0.96       8048.95|
|  6:  2.7874 -  2.6240  1270   139  0.91  15.07   0.99     0.96       6724.96|
|  7:  2.6240 -  2.4932  1271   140  0.90  15.59   0.99     0.96       6019.31|
|  8:  2.4932 -  2.3851  1253   143  0.91  14.72   1.00     0.98       5063.44|
|  9:  2.3851 -  2.2936  1245   134  0.91  14.87   1.01     0.99       4895.87|
| 10:  2.2936 -  2.2147  1248   144  0.91  14.55   1.01     0.97       4151.07|
| 11:  2.2147 -  2.1457  1259   136  0.90  16.31   1.01     0.97       4333.89|
| 12:  2.1457 -  2.0845  1231   138  0.92  14.54   1.02     1.00       3735.78|
| 13:  2.0845 -  2.0298  1247   142  0.91  15.03   1.02     1.01       3197.53|
| 14:  2.0298 -  1.9804  1074   116  0.92  13.84   0.99     0.96       2364.99|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2364.99 max =        10155.17 mean =      6096.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.55|
|phase err.(test): min =        0.00 max =           89.40 mean =        13.11|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.17    88.15   14.63    None  None   None       |
|    all(noH): 2823   0      3.17    88.15   14.63    None  None   None       |
|    Sol.    : 438    0      4.86    74.15   36.09    None  None   None       |
|    Mac.    : 2385   0      3.17    88.15   10.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.171 -  11.669: 1747   |   5:    45.659 -  54.156:   83        |
|      1:    11.669 -  20.166:  546   |   6:    54.156 -  62.653:   40        |
|      2:    20.166 -  28.664:  138   |   7:    62.653 -  71.151:   16        |
|      3:    28.664 -  37.161:  132   |   8:    71.151 -  79.648:    3        |
|      4:    37.161 -  45.659:  116   |   9:    79.648 -  88.146:    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)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.410 - 5.564
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 301
   mapped sites are within: 0.705 - 5.564

peak=   11.358 closest distance to " CB  VAL A 230 " =    1.460
peak=    6.369 closest distance to " CG2 VAL A 296 " =    1.080
peak=    6.356 closest distance to " CG  LEU A   5 " =    1.179
peak=    5.965 closest distance to " NE2 GLN A  11 " =    1.210
peak=    5.729 closest distance to " CB  VAL A 296 " =    1.116
peak=    5.677 closest distance to " CD2 LEU A   5 " =    1.250
peak=    5.514 closest distance to " NH2 ARG A  56 " =    2.112
peak=    5.425 closest distance to " CG  LEU A 228 " =    1.134
peak=    5.349 closest distance to " CG  PRO A  54 " =    1.238
peak=    5.228 closest distance to " O   HOH Z 144 " =    1.761
peak=    5.156 closest distance to " CB  GLN A 183 " =    1.230
peak=    5.005 closest distance to " O   HOH Z 126 " =    1.898
peak=    4.994 closest distance to " CB  GLN A 223 " =    1.515
peak=    4.952 closest distance to " CB  SER A  63 " =    1.249
peak=    4.828 closest distance to " O   HOH Z 427 " =    2.731
peak=    4.816 closest distance to " O   HOH Z 232 " =    2.418
peak=    4.801 closest distance to " O   HOH Z 193 " =    1.772
peak=    4.788 closest distance to " C   PRO A 198 " =    1.495
peak=    4.776 closest distance to " O   HOH Z 209 " =    2.267
peak=    4.688 closest distance to " CB  ARG A 275 " =    0.903
peak=    4.644 closest distance to " CB  VAL A 230 " =    1.148
peak=    4.601 closest distance to " CB  GLU A 152 " =    1.222
peak=    4.516 closest distance to " CB  PRO A  54 " =    0.942
peak=    4.482 closest distance to " OD1 ASN A  69 " =    2.632
peak=    4.482 closest distance to " CB  SER A   3 " =    1.319
peak=    4.482 closest distance to " O   HOH Z 272 " =    1.845
peak=    4.465 closest distance to " O   HOH Z 203 " =    1.667
peak=    4.458 closest distance to " CG  PRO A 213 " =    1.196
peak=    4.436 closest distance to " O   SER A  87 " =    2.336
peak=    4.430 closest distance to " O   HOH Z 236 " =    1.927
peak=    4.353 closest distance to " O   HOH Z  78 " =    1.894
peak=    4.325 closest distance to " O   HOH Z 346 " =    1.605
peak=    4.322 closest distance to " CD2 LEU A 228 " =    1.153
peak=    4.308 closest distance to " CB  ARG A  79 " =    1.406
peak=    4.301 closest distance to " O   HOH Z  61 " =    1.678
peak=    4.265 closest distance to " CB  ASN A 148 " =    1.397
peak=    4.263 closest distance to " O   HOH Z 263 " =    1.622
peak=    4.248 closest distance to " O   HOH Z 316 " =    3.024
peak=    4.238 closest distance to " CB  VAL A 265 " =    1.332
peak=    4.225 closest distance to " CB  ARG A 139 " =    0.992
peak=    4.207 closest distance to " O   HOH Z 124 " =    1.394
peak=    4.201 closest distance to " O   HOH Z 303 " =    2.060
peak=    4.182 closest distance to " O   HOH Z 158 " =    3.151
peak=    4.161 closest distance to " O   HOH Z 298 " =    1.745
peak=    4.123 closest distance to " CB  ASN A 187 " =    1.276
peak=    4.111 closest distance to " O   HOH Z 368 " =    2.041
peak=    4.104 closest distance to " ND2 ASN A 187 " =    1.524
peak=    4.095 closest distance to " O   HOH Z   9 " =    2.171
peak=    4.052 closest distance to " O   HOH Z 265 " =    2.413
peak=    4.044 closest distance to " O   HOH Z 403 " =    1.661
peak=    4.029 closest distance to " O   HOH Z 371 " =    2.884
peak=    4.019 closest distance to " CB  TYR A 169 " =    0.727
peak=    3.992 closest distance to " OG BSER A 164 " =    2.139
peak=    3.992 closest distance to " O   HOH Z 369 " =    2.119
peak=    3.981 closest distance to " CB  TRP A 266 " =    0.988
peak=    3.973 closest distance to " CA  ASN A 215 " =    1.136
peak=    3.972 closest distance to " N   PHE A 130 " =    1.282
peak=    3.957 closest distance to " O   HOH Z 389 " =    1.930
peak=    3.947 closest distance to " CG2AVAL A  72 " =    1.583
peak=    3.908 closest distance to " O   HOH Z 144 " =    2.266
peak=    3.907 closest distance to " O   HOH Z  97 " =    1.936
peak=    3.904 closest distance to " O   HOH Z 248 " =    1.645
peak=    3.899 closest distance to " CA  TYR A  30 " =    0.974
peak=    3.892 closest distance to " O   HOH Z 392 " =    3.211
peak=    3.888 closest distance to " CB  TRP A 179 " =    1.356
peak=    3.882 closest distance to " CG  ARG A  66 " =    2.657
peak=    3.881 closest distance to " O   HOH Z 128 " =    1.983
peak=    3.858 closest distance to " CG2 VAL A 257 " =    0.872
peak=    3.843 closest distance to " O   HOH Z  43 " =    2.006
peak=    3.835 closest distance to " CG  PRO A 243 " =    1.118
peak=    3.820 closest distance to " O   HOH Z 147 " =    1.709
peak=    3.817 closest distance to " O   HOH Z 411 " =    3.796
peak=    3.815 closest distance to " CB  ASN A  39 " =    0.874
peak=    3.807 closest distance to " O   HOH Z  66 " =    2.230
peak=    3.807 closest distance to " O   HOH Z 273 " =    2.654
peak=    3.803 closest distance to " O   HOH Z 234 " =    3.482
peak=    3.802 closest distance to " OD2 ASP A 286 " =    2.749
peak=    3.777 closest distance to " CB  GLU A 128 " =    0.933
peak=    3.775 closest distance to " O   HOH Z 322 " =    2.008
peak=    3.761 closest distance to " O   HOH Z 189 " =    2.680
peak=    3.755 closest distance to " O   HOH Z 193 " =    1.796
peak=    3.754 closest distance to " CB  SER A 216 " =    0.745
peak=    3.739 closest distance to " O   HOH Z  93 " =    2.460
peak=    3.735 closest distance to " O   HOH Z  10 " =    1.781
peak=    3.720 closest distance to " O   HOH Z  44 " =    1.713
peak=    3.716 closest distance to " CB  ASP A 140 " =    0.870
peak=    3.701 closest distance to " O   HOH Z 425 " =    2.127
peak=    3.693 closest distance to " O   HOH Z 402 " =    1.430
peak=    3.692 closest distance to " O   HOH Z  40 " =    1.910
peak=    3.685 closest distance to " CB  GLU A 277 " =    3.506
peak=    3.682 closest distance to " O   HOH Z 344 " =    2.900
peak=    3.676 closest distance to " O   HOH Z 280 " =    2.960
peak=    3.648 closest distance to " CA  ALA A  51 " =    0.997
peak=    3.648 closest distance to " CB  LEU A 143 " =    1.142
peak=    3.644 closest distance to " O   HOH Z 286 " =    2.401
peak=    3.626 closest distance to " CD BLYS A 290 " =    1.236
peak=    3.623 closest distance to " CA  ALA A  21 " =    1.163
peak=    3.623 closest distance to " NH2 ARG A 156 " =    1.087
peak=    3.619 closest distance to " O   HOH Z   1 " =    1.782
peak=    3.612 closest distance to " CA  ALA A 158 " =    1.184
peak=    3.607 closest distance to " O   HOH Z 426 " =    1.560
peak=    3.605 closest distance to " CB BVAL A  41 " =    1.099
peak=    3.604 closest distance to " O   HOH Z 425 " =    1.322
peak=    3.597 closest distance to " O   HOH Z 180 " =    2.137
peak=    3.596 closest distance to " O   HOH Z 245 " =    1.380
peak=    3.594 closest distance to " O   HOH Z 407 " =    2.271
peak=    3.593 closest distance to " O   HOH Z  88 " =    3.101
peak=    3.593 closest distance to " O   HOH Z  54 " =    1.584
peak=    3.592 closest distance to " O   HOH Z 130 " =    2.243
peak=    3.592 closest distance to " O   HOH Z 422 " =    2.605
peak=    3.591 closest distance to " CD1 ILE A 106 " =    1.097
peak=    3.591 closest distance to " O   HOH Z 175 " =    2.043
peak=    3.590 closest distance to " O   HOH Z  30 " =    1.341
peak=    3.584 closest distance to " O   HOH Z   3 " =    1.935
peak=    3.574 closest distance to " CB  VAL A 202 " =    1.585
peak=    3.569 closest distance to " O   HOH Z 419 " =    1.937
peak=    3.563 closest distance to " CB  ASN A 142 " =    1.008
peak=    3.562 closest distance to " O   HOH Z 227 " =    2.172
peak=    3.560 closest distance to " O   HOH Z 250 " =    1.326
peak=    3.559 closest distance to " CZ  PHE A 218 " =    1.064
peak=    3.559 closest distance to " O   HOH Z 145 " =    1.944
peak=    3.555 closest distance to " CG  LEU A 167 " =    1.216
peak=    3.554 closest distance to " O   HOH Z  61 " =    1.541
peak=    3.554 closest distance to " CG1 ILE A  33 " =    1.269
peak=    3.549 closest distance to " O   HOH Z 214 " =    2.034
peak=    3.546 closest distance to " O   HOH Z 227 " =    1.770
peak=    3.546 closest distance to " NZ  LYS A 117 " =    3.198
peak=    3.544 closest distance to " CA  PHE A 283 " =    1.164
peak=    3.530 closest distance to " CB  SER A  26 " =    1.621
peak=    3.530 closest distance to " O   HOH Z   9 " =    1.167
peak=    3.526 closest distance to " CD2 TRP A 179 " =    1.347
peak=    3.521 closest distance to " O   HOH Z 193 " =    1.804
peak=    3.511 closest distance to " CB  THR A 157 " =    1.115
peak=    3.506 closest distance to " CB  THR A  82 " =    1.347
peak=    3.502 closest distance to " O   HOH Z 145 " =    3.454
peak=    3.501 closest distance to " O   HOH Z 329 " =    3.831
peak=    3.501 closest distance to " O   HOH Z   1 " =    1.700
peak=    3.501 closest distance to " CA  THR A 264 " =    0.807
peak=    3.499 closest distance to " N   ARG A 156 " =    1.285
peak=    3.496 closest distance to " O   HOH Z 423 " =    2.729
peak=    3.490 closest distance to " O   HOH Z   2 " =    1.570
peak=    3.485 closest distance to " CB  GLN A  88 " =    1.275
peak=    3.480 closest distance to " O   HOH Z  59 " =    1.829
peak=    3.468 closest distance to " O   HOH Z 213 " =    2.104
peak=    3.460 closest distance to " CG2 THR A 221 " =    1.254
peak=    3.454 closest distance to " O   HOH Z 291 " =    1.530
peak=    3.450 closest distance to " OG  SER A  22 " =    2.786
peak=    3.447 closest distance to " CD1 LEU A 228 " =    1.994
peak=    3.445 closest distance to " O   HOH Z 132 " =    2.540
peak=    3.444 closest distance to " CD1 LEU A 300 " =    1.291
peak=    3.443 closest distance to " O   HOH Z 207 " =    1.762
peak=    3.441 closest distance to " O   HOH Z 133 " =    1.547
peak=    3.437 closest distance to " O   HOH Z 234 " =    1.843
peak=    3.433 closest distance to " O   HOH Z 359 " =    3.683
peak=    3.432 closest distance to " CG  PRO A 198 " =    1.239
peak=    3.430 closest distance to " O   HOH Z 299 " =    4.218
peak=    3.428 closest distance to " CB  SER A 212 " =    1.180
peak=    3.426 closest distance to " O   HOH Z 148 " =    3.317
peak=    3.425 closest distance to " O   HOH Z 371 " =    1.709
peak=    3.424 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.422 closest distance to " CD1 ILE A  33 " =    1.655
peak=    3.414 closest distance to " CG  MET A 185 " =    1.194
peak=    3.414 closest distance to " CA  VAL A 126 " =    0.872
peak=    3.411 closest distance to " NH2AARG A 190 " =    1.834
peak=    3.409 closest distance to " CB  ASN A 110 " =    1.124
peak=    3.407 closest distance to " CB  ALA A 291 " =    1.490
peak=    3.407 closest distance to " NH2BARG A 145 " =    2.000
peak=    3.406 closest distance to " O   HOH Z 423 " =    1.766
peak=    3.405 closest distance to " CE  LYS A  76 " =    0.939
peak=    3.403 closest distance to " CG  GLN A  77 " =    2.157
peak=    3.403 closest distance to " O   TRP A 274 " =    1.844
peak=    3.403 closest distance to " CB  ILE A  20 " =    1.439
peak=    3.394 closest distance to " O   HOH Z 222 " =    2.438
peak=    3.394 closest distance to " CE1 TYR A 186 " =    1.336
peak=    3.389 closest distance to " O   HOH Z 305 " =    3.405
peak=    3.388 closest distance to " CA  ASP A 162 " =    1.036
peak=    3.385 closest distance to " CB  ALA A   9 " =    1.613
peak=    3.382 closest distance to " O   HOH Z 374 " =    2.594
peak=    3.375 closest distance to " O   HOH Z 163 " =    1.859
peak=    3.370 closest distance to " CB  ASN A 224 " =    1.036
peak=    3.370 closest distance to " O   GLN A 278 " =    1.336
peak=    3.368 closest distance to " O   MET A 105 " =    1.837
peak=    3.366 closest distance to " CA  LYS A 117 " =    1.243
peak=    3.366 closest distance to " CG  GLN A  88 " =    1.042
peak=    3.358 closest distance to " ND1 HIS A  86 " =    1.765
peak=    3.358 closest distance to " CB  LEU A 228 " =    1.277
peak=    3.355 closest distance to " O   HOH Z 303 " =    1.766
peak=    3.353 closest distance to " CA  VAL A  41 " =    0.877
peak=    3.353 closest distance to " O  BHOH Z 338 " =    2.413
peak=    3.346 closest distance to " CB  MET A  40 " =    0.843
peak=    3.344 closest distance to " N   ASN A  39 " =    1.143
peak=    3.344 closest distance to " NH1AARG A 145 " =    1.056
peak=    3.343 closest distance to " CD  ARG A 159 " =    0.733
peak=    3.341 closest distance to " CB  ARG A 190 " =    1.620
peak=    3.337 closest distance to " CA  ALA A 248 " =    1.402
peak=    3.330 closest distance to " OE2 GLU A  53 " =    2.033
peak=    3.326 closest distance to " O   HOH Z 433 " =    1.753
peak=    3.326 closest distance to " CD  LYS A 119 " =    1.461
peak=    3.323 closest distance to " O   HOH Z 126 " =    1.524
peak=    3.322 closest distance to " CG1 ILE A 151 " =    1.009
peak=    3.322 closest distance to " O   HOH Z 128 " =    2.176
peak=    3.318 closest distance to " O   HOH Z 112 " =    1.615
peak=    3.309 closest distance to " O   HOH Z 366 " =    2.888
peak=    3.301 closest distance to " O   HOH Z 437 " =    2.025
peak=    3.299 closest distance to " O   HOH Z 116 " =    1.658
peak=    3.296 closest distance to " CB  SER A 273 " =    0.855
peak=    3.295 closest distance to " CB  HIS A 108 " =    0.833
peak=    3.290 closest distance to " O   HOH Z 108 " =    2.336
peak=    3.286 closest distance to " CB  GLN A 278 " =    0.855
peak=    3.283 closest distance to " O   HOH Z  89 " =    2.351
peak=    3.281 closest distance to " CB  LYS A 117 " =    1.184
peak=    3.280 closest distance to " CA  SER A 146 " =    1.792
peak=    3.279 closest distance to " CG  MET A 185 " =    1.031
peak=    3.270 closest distance to " O   HOH Z 417 " =    3.338
peak=    3.264 closest distance to " CG2 ILE A  20 " =    1.521
peak=    3.264 closest distance to " CA  ALA A 233 " =    1.115
peak=    3.260 closest distance to " O   HOH Z  50 " =    1.637
peak=    3.260 closest distance to " CB  LEU A 255 " =    0.766
peak=    3.259 closest distance to " CA  ALA A 299 " =    0.954
peak=    3.254 closest distance to " CA  LYS A 290 " =    1.259
peak=    3.254 closest distance to " N   SER A 135 " =    1.293
peak=    3.253 closest distance to " O   HOH Z 251 " =    1.647
peak=    3.252 closest distance to " CB  ALA A  71 " =    1.415
peak=    3.252 closest distance to " O   GLN A  58 " =    1.509
peak=    3.251 closest distance to " N   VAL A 126 " =    1.284
peak=    3.248 closest distance to " O   HOH Z 128 " =    1.903
peak=    3.247 closest distance to " CA  THR A 221 " =    0.961
peak=    3.246 closest distance to " CA  ALA A 291 " =    0.972
peak=    3.245 closest distance to " CG BARG A 102 " =    1.850
peak=    3.244 closest distance to " CD  LYS A 166 " =    1.304
peak=    3.241 closest distance to " CB  ALA A  34 " =    0.999
peak=    3.239 closest distance to " CA  ARG A  36 " =    1.039
peak=    3.239 closest distance to " CA  ASN A  74 " =    1.201
peak=    3.239 closest distance to " O   HOH Z 189 " =    2.723
peak=    3.237 closest distance to " CG1 VAL A 153 " =    0.958
peak=    3.234 closest distance to " O   HOH Z 172 " =    3.448
peak=    3.233 closest distance to " O   HOH Z  48 " =    1.623
peak=    3.228 closest distance to " O   HOH Z  64 " =    1.908
peak=    3.226 closest distance to " O   HOH Z   1 " =    4.619
peak=    3.225 closest distance to " O   HOH Z  71 " =    2.252
peak=    3.215 closest distance to " O   LYS A 290 " =    2.412
peak=    3.215 closest distance to " O   HOH Z 255 " =    1.687
peak=    3.214 closest distance to " OG BSER A  99 " =    2.189
peak=    3.211 closest distance to " CA  SER A  87 " =    0.978
peak=    3.208 closest distance to " OG  SER A 206 " =    1.258
peak=    3.207 closest distance to " OG BSER A 134 " =    3.163
peak=    3.201 closest distance to " CB  TRP A 150 " =    1.490
peak=    3.200 closest distance to " OE1 GLU A   2 " =    2.107
peak=    3.200 closest distance to " CD2 LEU A 255 " =    1.524
peak=    3.199 closest distance to " CB  ALA A 233 " =    1.390
peak=    3.198 closest distance to " CB  GLN A 205 " =    1.191
peak=    3.194 closest distance to " CD1 ILE A 263 " =    1.270
peak=    3.189 closest distance to " O   HOH Z 271 " =    2.003
peak=    3.189 closest distance to " O   HOH Z  21 " =    1.729
peak=    3.185 closest distance to " N   ASN A 127 " =    1.271
peak=    3.183 closest distance to " O   HOH Z 345 " =    3.348
peak=    3.179 closest distance to " OG  SER A  62 " =    2.914
peak=    3.178 closest distance to " O   HOH Z 411 " =    1.739
peak=    3.170 closest distance to " NH1 ARG A 138 " =    1.148
peak=    3.170 closest distance to " O   ALA A   1 " =    1.759
peak=    3.170 closest distance to " O   HOH Z 334 " =    1.448
peak=    3.168 closest distance to " NZ  LYS A  76 " =    1.275
peak=    3.164 closest distance to " CE BLYS A 290 " =    1.143
peak=    3.161 closest distance to " O   HOH Z   7 " =    1.511
peak=    3.159 closest distance to " CA  GLY A 267 " =    0.890
peak=    3.154 closest distance to " O   HOH Z 409 " =    3.099
peak=    3.153 closest distance to " N   GLN A 278 " =    1.134
peak=    3.152 closest distance to " O   HOH Z 350 " =    1.549
peak=    3.149 closest distance to " CA  GLN A 194 " =    1.304
peak=    3.147 closest distance to " O   HOH Z 380 " =    1.661
peak=    3.143 closest distance to " CD2 LEU A   5 " =    0.705
peak=    3.140 closest distance to " O   HOH Z 383 " =    1.819
peak=    3.139 closest distance to " O   HOH Z  85 " =    1.422
peak=    3.137 closest distance to " O   HOH Z  88 " =    2.528
peak=    3.133 closest distance to " OG  SER A  62 " =    5.368
peak=    3.131 closest distance to " O   HOH Z 432 " =    1.491
peak=    3.129 closest distance to " CA  LEU A 282 " =    1.153
peak=    3.129 closest distance to " CB  ILE A 120 " =    1.296
peak=    3.129 closest distance to " CG  GLN A  89 " =    1.472
peak=    3.129 closest distance to " CB  ASN A 215 " =    1.138
peak=    3.129 closest distance to " N   ASP A 162 " =    1.286
peak=    3.123 closest distance to " CD  ARG A 195 " =    3.550
peak=    3.122 closest distance to " CB  THR A  31 " =    1.661
peak=    3.118 closest distance to " O   HOH Z  85 " =    2.145
peak=    3.118 closest distance to " O   HOH Z 327 " =    1.625
peak=    3.117 closest distance to " O   HOH Z 172 " =    5.564
peak=    3.117 closest distance to " ND1 HIS A  81 " =    1.666
peak=    3.112 closest distance to " O   THR A  31 " =    1.563
peak=    3.109 closest distance to " CB  MET A  47 " =    1.280
peak=    3.082 closest distance to " CB  VAL A 268 " =    0.853
peak=    3.063 closest distance to " O   HOH Z 367 " =    3.563
peak=    3.058 closest distance to " O   HOH Z 154 " =    2.193
peak=    3.052 closest distance to " O   HOH Z 175 " =    2.094
peak=    3.038 closest distance to " O   HOH Z 353 " =    2.543
peak=    3.031 closest distance to " NZ  LYS A  48 " =    2.216
peak=    3.029 closest distance to " O   HOH Z  49 " =    2.308
peak=    3.027 closest distance to " O   HOH Z  88 " =    2.586
peak=    3.021 closest distance to " O   HOH Z   9 " =    1.871

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.531 - 5.424
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 207
   mapped sites are within: 0.751 - 5.424

peak=   -5.555 closest distance to " CG2 VAL A 230 " =    0.761
peak=   -4.553 closest distance to " CD  ARG A 156 " =    2.013
peak=   -4.503 closest distance to " SG  CYS A 254 " =    3.227
peak=   -4.454 closest distance to " CB  PRO A 243 " =    2.616
peak=   -4.339 closest distance to " O   HOH Z 435 " =    2.834
peak=   -4.311 closest distance to " OG BSER A 134 " =    1.222
peak=   -4.285 closest distance to " O   HOH Z 290 " =    1.105
peak=   -4.235 closest distance to " C   HIS A 108 " =    1.206
peak=   -4.212 closest distance to " O   HOH Z 266 " =    4.789
peak=   -4.167 closest distance to " CG2 VAL A 296 " =    1.160
peak=   -4.102 closest distance to " CB  ALA A 248 " =    2.045
peak=   -4.060 closest distance to " CG  GLN A 223 " =    1.883
peak=   -4.029 closest distance to " O   VAL A  67 " =    2.748
peak=   -3.951 closest distance to " N   GLN A  58 " =    1.685
peak=   -3.946 closest distance to " CE2 TYR A  30 " =    2.823
peak=   -3.936 closest distance to " CG  ASP A 231 " =    0.766
peak=   -3.934 closest distance to " O   HOH Z  11 " =    1.928
peak=   -3.908 closest distance to " CE  MET A 105 " =    2.232
peak=   -3.892 closest distance to " NH2 ARG A  79 " =    1.870
peak=   -3.881 closest distance to " O   PRO A 198 " =    1.232
peak=   -3.844 closest distance to " O   HOH Z 231 " =    1.904
peak=   -3.818 closest distance to " O   HOH Z 389 " =    1.914
peak=   -3.814 closest distance to " O   ARG A 145 " =    1.594
peak=   -3.808 closest distance to " CB  PRO A 163 " =    2.508
peak=   -3.790 closest distance to " CE2 PHE A 218 " =    2.557
peak=   -3.789 closest distance to " O   ILE A 109 " =    2.556
peak=   -3.764 closest distance to " CZ  PHE A  59 " =    1.465
peak=   -3.756 closest distance to " CB  ALA A 291 " =    2.347
peak=   -3.756 closest distance to " O   HOH Z 211 " =    1.609
peak=   -3.754 closest distance to " N   THR A 157 " =    1.467
peak=   -3.748 closest distance to " O   HOH Z 114 " =    2.960
peak=   -3.725 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.725 closest distance to " OG  SER A   3 " =    1.652
peak=   -3.718 closest distance to " ND2 ASN A  45 " =    1.649
peak=   -3.717 closest distance to " CB  PHE A 192 " =    1.850
peak=   -3.716 closest distance to " CB  ASP A 132 " =    2.341
peak=   -3.710 closest distance to " O   VAL A  67 " =    2.641
peak=   -3.700 closest distance to " O   HOH Z 166 " =    1.448
peak=   -3.655 closest distance to " CB  PRO A 280 " =    2.081
peak=   -3.654 closest distance to " O   HOH Z 407 " =    3.028
peak=   -3.653 closest distance to " CZ3 TRP A 179 " =    1.224
peak=   -3.652 closest distance to " OXT GLY A 302 " =    2.891
peak=   -3.630 closest distance to " O   HOH Z 185 " =    2.163
peak=   -3.630 closest distance to " O   SER A  22 " =    2.245
peak=   -3.620 closest distance to " CD  GLN A  58 " =    1.103
peak=   -3.617 closest distance to " O   HOH Z 103 " =    1.774
peak=   -3.617 closest distance to " CG1 VAL A 112 " =    2.713
peak=   -3.607 closest distance to " CD2 LEU A 237 " =    2.688
peak=   -3.606 closest distance to " OG BSER A 134 " =    1.622
peak=   -3.604 closest distance to " CZ  TYR A 169 " =    1.615
peak=   -3.601 closest distance to " O   HOH Z 134 " =    2.814
peak=   -3.599 closest distance to " O   PRO A 163 " =    1.994
peak=   -3.598 closest distance to " O   HOH Z 313 " =    1.731
peak=   -3.591 closest distance to " CD2 LEU A 300 " =    2.836
peak=   -3.583 closest distance to " N   ALA A 248 " =    1.603
peak=   -3.583 closest distance to " CD1 PHE A  59 " =    1.983
peak=   -3.570 closest distance to " OG  SER A  87 " =    1.348
peak=   -3.554 closest distance to " N   HIS A 115 " =    2.045
peak=   -3.549 closest distance to " O   HOH Z  60 " =    2.202
peak=   -3.546 closest distance to " NZ  LYS A 119 " =    3.387
peak=   -3.545 closest distance to " OD1 ASN A 148 " =    1.487
peak=   -3.541 closest distance to " CB  VAL A 296 " =    1.193
peak=   -3.537 closest distance to " CG2 THR A 178 " =    2.171
peak=   -3.505 closest distance to " CG  LEU A 228 " =    1.019
peak=   -3.502 closest distance to " O   ALA A 161 " =    1.604
peak=   -3.501 closest distance to " CD  ARG A 139 " =    1.572
peak=   -3.501 closest distance to " O   HOH Z 309 " =    2.582
peak=   -3.499 closest distance to " O   HOH Z  43 " =    1.880
peak=   -3.496 closest distance to " C   LEU A 222 " =    0.751
peak=   -3.488 closest distance to " N   ALA A 226 " =    2.007
peak=   -3.479 closest distance to " C   ALA A 158 " =    1.311
peak=   -3.473 closest distance to " O   HOH Z 102 " =    1.560
peak=   -3.470 closest distance to " CD  LYS A 289 " =    2.495
peak=   -3.470 closest distance to " CD1 LEU A 228 " =    2.123
peak=   -3.467 closest distance to " CA  GLY A  98 " =    1.832
peak=   -3.458 closest distance to " O   HOH Z 198 " =    1.391
peak=   -3.445 closest distance to " O   MET A  40 " =    2.690
peak=   -3.444 closest distance to " CG  PHE A 283 " =    2.702
peak=   -3.442 closest distance to " O   PRO A 198 " =    1.289
peak=   -3.441 closest distance to " O   GLY A  80 " =    2.487
peak=   -3.440 closest distance to " O   HOH Z 191 " =    5.424
peak=   -3.438 closest distance to " CB  ALA A 248 " =    2.408
peak=   -3.429 closest distance to " N   PHE A  59 " =    2.143
peak=   -3.427 closest distance to " CG1 VAL A 296 " =    1.291
peak=   -3.426 closest distance to " C   MET A 188 " =    1.417
peak=   -3.412 closest distance to " CG  TRP A 266 " =    1.876
peak=   -3.408 closest distance to " CB  ASN A  39 " =    2.139
peak=   -3.406 closest distance to " NH2AARG A 275 " =    5.140
peak=   -3.399 closest distance to " ND2 ASN A 187 " =    1.532
peak=   -3.396 closest distance to " NE2 GLN A  88 " =    1.956
peak=   -3.394 closest distance to " O   VAL A 189 " =    2.541
peak=   -3.388 closest distance to " ND2 ASN A 249 " =    2.354
peak=   -3.383 closest distance to " N   ALA A  43 " =    2.412
peak=   -3.380 closest distance to " O   HOH Z 140 " =    1.622
peak=   -3.376 closest distance to " OG1 THR A 178 " =    1.193
peak=   -3.376 closest distance to " NH2BARG A 275 " =    1.560
peak=   -3.371 closest distance to " CB  TYR A  15 " =    2.152
peak=   -3.371 closest distance to " O   HOH Z 394 " =    1.496
peak=   -3.369 closest distance to " CB  ALA A  43 " =    2.342
peak=   -3.368 closest distance to " O   HOH Z  56 " =    2.403
peak=   -3.364 closest distance to " O   SER A 135 " =    1.439
peak=   -3.353 closest distance to " N   SER A 276 " =    1.262
peak=   -3.351 closest distance to " CE BMET A  47 " =    1.735
peak=   -3.350 closest distance to " O   HOH Z 281 " =    3.198
peak=   -3.349 closest distance to " CG  PRO A 163 " =    2.608
peak=   -3.347 closest distance to " OD1 ASP A 191 " =    1.470
peak=   -3.346 closest distance to " N   GLN A  77 " =    1.707
peak=   -3.345 closest distance to " OG  SER A  62 " =    1.442
peak=   -3.344 closest distance to " C   ASN A 187 " =    1.844
peak=   -3.344 closest distance to " CG  GLU A 277 " =    1.234
peak=   -3.343 closest distance to " CD1 ILE A 239 " =    2.556
peak=   -3.342 closest distance to " O   HOH Z 417 " =    2.759
peak=   -3.339 closest distance to " CA  GLY A 133 " =    2.013
peak=   -3.339 closest distance to " O   HOH Z 369 " =    1.986
peak=   -3.336 closest distance to " O   HOH Z 359 " =    3.283
peak=   -3.335 closest distance to " CD1 LEU A 101 " =    2.848
peak=   -3.333 closest distance to " N   THR A 235 " =    1.335
peak=   -3.333 closest distance to " CG1 VAL A 112 " =    2.629
peak=   -3.321 closest distance to " O   HOH Z 244 " =    2.081
peak=   -3.319 closest distance to " O   HOH Z 385 " =    1.940
peak=   -3.319 closest distance to " O   HOH Z 348 " =    1.865
peak=   -3.310 closest distance to " O   HOH Z 111 " =    4.635
peak=   -3.310 closest distance to " OD2 ASP A 191 " =    1.363
peak=   -3.306 closest distance to " O   HOH Z 198 " =    2.189
peak=   -3.306 closest distance to " O   HOH Z 423 " =    2.103
peak=   -3.302 closest distance to " OG  SER A 206 " =    1.704
peak=   -3.300 closest distance to " CA  GLY A 203 " =    2.203
peak=   -3.300 closest distance to " O   HOH Z 281 " =    2.810
peak=   -3.299 closest distance to " O   LYS A 117 " =    1.725
peak=   -3.297 closest distance to " C   LEU A 143 " =    1.022
peak=   -3.296 closest distance to " CG1 VAL A 197 " =    2.192
peak=   -3.286 closest distance to " O   HOH Z 234 " =    3.937
peak=   -3.285 closest distance to " O   GLY A 196 " =    1.110
peak=   -3.284 closest distance to " CA  GLY A 241 " =    2.252
peak=   -3.281 closest distance to " O   HOH Z 388 " =    2.146
peak=   -3.280 closest distance to " O   HOH Z  90 " =    2.699
peak=   -3.279 closest distance to " CB  ALA A 244 " =    2.050
peak=   -3.274 closest distance to " OG  SER A  26 " =    1.148
peak=   -3.271 closest distance to " O   ALA A  51 " =    1.370
peak=   -3.270 closest distance to " O   HOH Z  38 " =    1.842
peak=   -3.270 closest distance to " O   PHE A 218 " =    1.671
peak=   -3.269 closest distance to " O   HOH Z  52 " =    1.499
peak=   -3.268 closest distance to " O   HOH Z  13 " =    1.491
peak=   -3.267 closest distance to " CB  ASP A 132 " =    2.277
peak=   -3.264 closest distance to " O   HOH Z 166 " =    2.153
peak=   -3.263 closest distance to " OXT GLY A 302 " =    3.497
peak=   -3.260 closest distance to " OH  TYR A 214 " =    1.195
peak=   -3.255 closest distance to " O   HOH Z 423 " =    1.111
peak=   -3.249 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.249 closest distance to " C   GLN A 205 " =    1.903
peak=   -3.245 closest distance to " CG  GLU A 152 " =    1.309
peak=   -3.245 closest distance to " CG1 VAL A 230 " =    1.852
peak=   -3.239 closest distance to " O   HOH Z 131 " =    4.070
peak=   -3.237 closest distance to " CD2 TYR A 293 " =    2.031
peak=   -3.232 closest distance to " NH1 ARG A  56 " =    2.529
peak=   -3.228 closest distance to " CG  LYS A 193 " =    2.410
peak=   -3.218 closest distance to " O   HOH Z 385 " =    1.803
peak=   -3.217 closest distance to " OE1 GLN A  73 " =    2.486
peak=   -3.216 closest distance to " CA  TYR A  30 " =    2.869
peak=   -3.215 closest distance to " OG  SER A  97 " =    2.177
peak=   -3.214 closest distance to " CA  GLY A 133 " =    2.194
peak=   -3.213 closest distance to " O   HOH Z 295 " =    1.553
peak=   -3.202 closest distance to " O   HOH Z 150 " =    1.930
peak=   -3.202 closest distance to " C   ASN A 285 " =    2.425
peak=   -3.199 closest distance to " CA  SER A 146 " =    2.350
peak=   -3.197 closest distance to " C   ASP A 231 " =    2.544
peak=   -3.195 closest distance to " N   ALA A 248 " =    2.201
peak=   -3.192 closest distance to " CB  GLN A  11 " =    1.919
peak=   -3.187 closest distance to " NH1AARG A 275 " =    1.840
peak=   -3.177 closest distance to " O   HOH Z 275 " =    1.457
peak=   -3.173 closest distance to " CG1 VAL A 250 " =    2.746
peak=   -3.171 closest distance to " O   HOH Z 436 " =    1.432
peak=   -3.168 closest distance to " O   HOH Z 152 " =    4.913
peak=   -3.167 closest distance to " O   HOH Z 175 " =    4.303
peak=   -3.166 closest distance to " O   HOH Z 350 " =    1.899
peak=   -3.157 closest distance to " OG ASER A 216 " =    1.066
peak=   -3.151 closest distance to " O   HOH Z 139 " =    2.979
peak=   -3.149 closest distance to " O   LYS A 289 " =    3.037
peak=   -3.144 closest distance to " CA  GLY A 241 " =    3.048
peak=   -3.140 closest distance to " N   VAL A  72 " =    1.599
peak=   -3.138 closest distance to " CG  GLN A 278 " =    2.079
peak=   -3.133 closest distance to " OD1 ASP A 171 " =    1.638
peak=   -3.130 closest distance to " O   HOH Z 210 " =    1.104
peak=   -3.128 closest distance to " O   SER A 210 " =    1.976
peak=   -3.115 closest distance to " CD  GLN A  88 " =    0.893
peak=   -3.114 closest distance to " N   ASP A 171 " =    2.348
peak=   -3.105 closest distance to " CD1 TYR A 247 " =    2.673
peak=   -3.104 closest distance to " CE  LYS A  76 " =    2.942
peak=   -3.102 closest distance to " O   HOH Z 250 " =    1.435
peak=   -3.098 closest distance to " O   HOH Z   9 " =    1.506
peak=   -3.097 closest distance to " O   GLN A 240 " =    1.829
peak=   -3.096 closest distance to " CG  ASP A  50 " =    2.266
peak=   -3.096 closest distance to " CG  MET A 105 " =    0.905
peak=   -3.087 closest distance to " O   VAL A 174 " =    2.067
peak=   -3.086 closest distance to " O   HOH Z 222 " =    1.598
peak=   -3.081 closest distance to " O   HOH Z 313 " =    1.056
peak=   -3.068 closest distance to " O   HOH Z  51 " =    1.268
peak=   -3.068 closest distance to " O   HOH Z 407 " =    3.269
peak=   -3.066 closest distance to " CG2 THR A 157 " =    2.154
peak=   -3.066 closest distance to " O   HOH Z 134 " =    3.449
peak=   -3.065 closest distance to " CE3 TRP A 274 " =    2.407
peak=   -3.053 closest distance to " OD1 ASN A 301 " =    1.962
peak=   -3.048 closest distance to " CD1 ILE A 199 " =    2.441
peak=   -3.013 closest distance to " O   HOH Z 128 " =    4.137

================= 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    :  0.4421 0.4249   6.237946e+00   6.215960e+00
   1_bss:  0.4330 0.4156   6.231405e+00   6.203189e+00
   1_xyz:  0.3317 0.3546   6.047776e+00   6.083505e+00
   1_adp:  0.2742 0.3139   5.891024e+00   5.990765e+00
   1_occ:  0.2737 0.3139   5.889811e+00   5.991632e+00
   2_bss:  0.2679 0.3070   5.885198e+00   5.983919e+00
   2_xyz:  0.1814 0.2265   5.547873e+00   5.722096e+00
   2_adp:  0.1637 0.2097   5.460137e+00   5.655830e+00
   2_occ:  0.1634 0.2094   5.459383e+00   5.654874e+00
   3_bss:  0.1632 0.2088   5.458318e+00   5.652259e+00
   3_xyz:  0.1246 0.1685   5.223684e+00   5.455021e+00
   3_adp:  0.1174 0.1627   5.175990e+00   5.416928e+00
   3_occ:  0.1173 0.1626   5.175774e+00   5.416571e+00
   4_bss:  0.1176 0.1624   5.175882e+00   5.415393e+00
   4_xyz:  0.1120 0.1583   5.145903e+00   5.396770e+00
   4_adp:  0.1136 0.1562   5.143311e+00   5.379374e+00
   4_occ:  0.1135 0.1560   5.142541e+00   5.378153e+00
   5_bss:  0.1135 0.1560   5.142699e+00   5.378327e+00
   5_xyz:  0.1100 0.1544   5.120909e+00   5.367827e+00
   5_adp:  0.1085 0.1549   5.117713e+00   5.373652e+00
   5_occ:  0.1085 0.1548   5.117442e+00   5.373229e+00
   5_bss:  0.1084 0.1548   5.116937e+00   5.372760e+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:  0.357   7.049   7.362   9.443   8.442   0.000   0.000   0.000
   1_xyz:  0.357   7.049   7.362   9.443   8.442   0.000   0.000   0.000
   1_adp:  0.357   7.049   7.362   9.443   8.442   0.000   0.000   0.000
   1_occ:  0.357   7.049   7.362   9.443   8.442   0.000   0.000   0.000
   2_bss:  0.338  28.449   3.683   4.857   5.139   0.000   0.000   0.000
   2_xyz:  0.338  28.449   3.683   4.857   5.139   0.000   0.000   0.000
   2_adp:  0.338  28.449   3.683   4.857   5.139   0.000   0.000   0.000
   2_occ:  0.338  28.449   3.683   4.857   5.139   0.000   0.000   0.000
   3_bss:  0.321  28.449   2.806   3.233   4.073   0.000   0.000   0.000
   3_xyz:  0.321  28.449   2.806   3.233   4.073   0.000   0.000   0.000
   3_adp:  0.321  28.449   2.806   3.233   4.073   0.000   0.000   0.000
   3_occ:  0.321  28.449   2.806   3.233   4.073   0.000   0.000   0.000
   4_bss:  0.316  34.843   2.801   2.982   3.926   0.000   0.000   0.000
   4_xyz:  0.316  34.843   2.801   2.982   3.926   0.000   0.000   0.000
   4_adp:  0.316  34.843   2.801   2.982   3.926   0.000   0.000   0.000
   4_occ:  0.316  34.843   2.801   2.982   3.926   0.000   0.000   0.000
   5_bss:  0.321  34.843   2.801   2.982   3.926   0.000   0.000   0.000
   5_xyz:  0.321  34.843   2.801   2.982   3.926   0.000   0.000   0.000
   5_adp:  0.321  34.843   2.801   2.982   3.926   0.000   0.000   0.000
   5_occ:  0.321  34.843   2.801   2.982   3.926   0.000   0.000   0.000
   5_bss:  0.323  41.046  -0.399  -0.311   0.709   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.843 0.5363  0.6085    54449.653
   1_bss:  48.880 0.5334  0.7724    51587.915
   1_xyz:  38.125 0.6644  0.9426    34374.805
   1_adp:  31.253 0.7451  1.0511    25532.662
   1_occ:  31.315 0.7444  1.0493    25530.732
   2_bss:  30.917 0.7483  0.9179    24857.647
   2_xyz:  21.918 0.8427  0.9960    12792.590
   2_adp:  19.899 0.8632  1.0088    11131.900
   2_occ:  19.867 0.8635  1.0087    11091.614
   3_bss:  19.775 0.8641  0.9665    10983.878
   3_xyz:  15.423 0.9026  0.9888     7151.918
   3_adp:  14.601 0.9097  0.9894     6669.765
   3_occ:  14.593 0.9098  0.9893     6663.498
   4_bss:  14.569 0.9100  0.9845     6665.629
   4_xyz:  14.048 0.9147  0.9852     6361.401
   4_adp:  13.620 0.9183  0.9873     6185.745
   4_occ:  13.603 0.9184  0.9872     6166.224
   5_bss:  13.606 0.9184  0.9872     6170.501
   5_xyz:  13.408 0.9198  0.9878     6055.218
   5_adp:  13.528 0.9190  0.9853     6106.313
   5_occ:  13.520 0.9190  0.9852     6101.603
   5_bss:  13.507 0.9191  0.9831     6096.901
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3395e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3395e+01
   1_xyz:   1.551  0.012  0.101 17.939  0.006  4.118   1.2131e-01
   1_adp:   1.551  0.012  0.101 17.939  0.006  4.118   1.2131e-01
   1_occ:   1.551  0.012  0.101 17.939  0.006  4.118   1.2131e-01
   2_bss:   1.551  0.012  0.101 17.939  0.006  4.118   1.2131e-01
   2_xyz:   0.968  0.006  0.070 15.859  0.004  4.116   6.0595e-02
   2_adp:   0.968  0.006  0.070 15.859  0.004  4.116   6.0595e-02
   2_occ:   0.968  0.006  0.070 15.859  0.004  4.116   6.0595e-02
   3_bss:   0.968  0.006  0.070 15.859  0.004  4.116   6.0595e-02
   3_xyz:   1.071  0.007  0.084 16.004  0.004  4.120   6.8616e-02
   3_adp:   1.071  0.007  0.084 16.004  0.004  4.120   6.8616e-02
   3_occ:   1.071  0.007  0.084 16.004  0.004  4.120   6.8616e-02
   4_bss:   1.071  0.007  0.084 16.004  0.004  4.120   6.8616e-02
   4_xyz:   0.970  0.006  0.079 15.611  0.004  4.112   5.8911e-02
   4_adp:   0.970  0.006  0.079 15.611  0.004  4.112   5.8911e-02
   4_occ:   0.970  0.006  0.079 15.611  0.004  4.112   5.8911e-02
   5_bss:   0.970  0.006  0.079 15.611  0.004  4.112   5.8911e-02
   5_xyz:   1.045  0.007  0.086 15.671  0.004  4.112   6.6040e-02
   5_adp:   1.045  0.007  0.086 15.671  0.004  4.112   6.6040e-02
   5_occ:   1.045  0.007  0.086 15.671  0.004  4.112   6.6040e-02
   5_bss:   1.045  0.007  0.086 15.671  0.004  4.112   6.6040e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9224e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9224e+00
   1_xyz:  12.358  0.153  0.414 88.641  0.036  2.257   8.9204e-02
   1_adp:  12.358  0.153  0.414 88.641  0.036  2.257   8.9204e-02
   1_occ:  12.358  0.153  0.414 88.641  0.036  2.257   8.9204e-02
   2_bss:  12.358  0.153  0.414 88.641  0.036  2.257   8.9204e-02
   2_xyz:   6.143  0.062  0.294 88.429  0.040  2.331   4.4929e-02
   2_adp:   6.143  0.062  0.294 88.429  0.040  2.331   4.4929e-02
   2_occ:   6.143  0.062  0.294 88.429  0.040  2.331   4.4929e-02
   3_bss:   6.143  0.062  0.294 88.429  0.040  2.331   4.4929e-02
   3_xyz:   8.982  0.056  0.520 83.641  0.033  2.248   6.0297e-02
   3_adp:   8.982  0.056  0.520 83.641  0.033  2.248   6.0297e-02
   3_occ:   8.982  0.056  0.520 83.641  0.033  2.248   6.0297e-02
   4_bss:   8.982  0.056  0.520 83.641  0.033  2.248   6.0297e-02
   4_xyz:   6.942  0.046  0.546 83.792  0.037  2.336   4.1875e-02
   4_adp:   6.942  0.046  0.546 83.792  0.037  2.336   4.1875e-02
   4_occ:   6.942  0.046  0.546 83.792  0.037  2.336   4.1875e-02
   5_bss:   6.942  0.046  0.546 83.792  0.037  2.336   4.1875e-02
   5_xyz:   6.465  0.043  0.641 83.513  0.038  2.211   4.8813e-02
   5_adp:   6.465  0.043  0.641 83.513  0.038  2.211   4.8813e-02
   5_occ:   6.465  0.043  0.641 83.513  0.038  2.211   4.8813e-02
   5_bss:   6.465  0.043  0.641 83.513  0.038  2.211   4.8813e-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:  73.40   0.00  11.08  73.40   0.00   8.13  63.22   0.00  27.12
   1_occ:  73.40   0.00  11.08  73.40   0.00   8.13  63.22   0.00  27.12
   2_bss:  73.40   0.00  11.08  73.40   0.00   8.13  63.22   0.00  27.12
   2_xyz:  73.40   0.00  11.08  73.40   0.00   8.13  63.22   0.00  27.12
   2_adp:  74.76   0.00  11.37  74.76   0.00   7.65  63.56   0.58  31.60
   2_occ:  74.76   0.00  11.37  74.76   0.00   7.65  63.56   0.58  31.60
   3_bss:  74.76   0.00  11.37  74.76   0.00   7.65  63.56   0.58  31.60
   3_xyz:  74.76   0.00  11.37  74.76   0.00   7.65  63.56   0.58  31.60
   3_adp:  86.24   0.00  12.02  86.24   0.00   7.73  74.79   1.37  35.40
   3_occ:  86.24   0.00  12.02  86.24   0.00   7.73  74.79   1.37  35.40
   4_bss:  86.24   0.00  12.02  86.24   0.00   7.73  74.79   1.37  35.40
   4_xyz:  86.24   0.00  12.02  86.24   0.00   7.73  74.79   1.37  35.40
   4_adp:  83.93   0.00  11.38  83.93   0.00   7.52  70.69   1.47  32.45
   4_occ:  83.93   0.00  11.38  83.93   0.00   7.52  70.69   1.47  32.45
   5_bss:  83.93   0.00  11.38  83.93   0.00   7.52  70.69   1.47  32.45
   5_xyz:  83.93   0.00  11.38  83.93   0.00   7.52  70.69   1.47  32.45
   5_adp:  84.97   0.00  11.45  84.97   0.00   7.51  70.98   1.68  32.92
   5_occ:  84.97   0.00  11.45  84.97   0.00   7.51  70.98   1.68  32.92
   5_bss:  88.15   3.17  14.63  88.15   3.17  10.68  74.15   4.86  36.09
------------------------------------------------------------------------
 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:    1.187    0.017    0.403
   1_adp:    1.187    0.017    0.403
   1_occ:    1.187    0.017    0.403
   2_bss:    1.187    0.017    0.403
   2_xyz:    1.373    0.042    0.518
   2_adp:    1.373    0.042    0.518
   2_occ:    1.373    0.042    0.518
   3_bss:    1.373    0.042    0.518
   3_xyz:    1.493    0.024    0.572
   3_adp:    1.493    0.024    0.572
   3_occ:    1.493    0.024    0.572
   4_bss:    1.493    0.024    0.572
   4_xyz:    1.645    0.029    0.585
   4_adp:    1.645    0.029    0.585
   4_occ:    1.645    0.029    0.585
   5_bss:    1.645    0.029    0.585
   5_xyz:    1.687    0.017    0.596
   5_adp:    1.687    0.017    0.596
   5_occ:    1.687    0.017    0.596
   5_bss:    1.687    0.017    0.596
------------------------------------------------------------------------

CPU time actual refinement: 323.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_641/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_641/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_641/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_641/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_641/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.37 
  Macro-tasks:
    bulk solvent and scale       = 43.89  
    individual site refinement   = 124.61 
    weights calculation          = 32.87  
    collect and process          = 6.68   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 208.16 
  Micro-tasks:
    mask                            = 1.61   
    f_calc                          = 98.61  
    alpha_beta                      = 8.34   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 103.60 
    fmodel                         = 7.59   
    r_factors                      = 0.23   
    phase_errors                   = 11.75  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 233.20 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.621 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    635 calls, 98.26 s
gradients_fft:          580 calls, 92.67 s

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

# Date 2008-01-16 Time 02:03:49 PST -0800 (1200477829.21 s)
Start R-work = 0.4421, R-free = 0.4249 (no bulk solvent and anisotropic scale)
Final R-work = 0.1261, R-free = 0.1713 (no bulk solvent and anisotropic scale)

Start R-work = 0.4330, R-free = 0.4156
Final R-work = 0.1084, R-free = 0.1548