# Date 2008-01-16 Time 02:48:44 PST -0800 (1200480524.18 s)
#phil __OFF__

Command line arguments: "../983.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4808
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 983

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 45.9914, 85.9581, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.96366
Completeness in resolution range: 0.942731
Completeness with d_max=infinity: 0.940016

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9637

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.96366
Completeness in resolution range: 0.942731
Completeness with d_max=infinity: 0.940016

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2032 [2184/2211]  1967   217   9.9%
  bin  2:  4.2032 -  3.3481 [2089/2109]  1880   209  10.0%
  bin  3:  3.3481 -  2.9283 [2075/2094]  1864   211  10.2%
  bin  4:  2.9283 -  2.6622 [2033/2063]  1829   204  10.0%
  bin  5:  2.6622 -  2.4723 [2058/2077]  1859   199   9.7%
  bin  6:  2.4723 -  2.3270 [2013/2038]  1803   210  10.4%
  bin  7:  2.3270 -  2.2109 [2031/2059]  1829   202   9.9%
  bin  8:  2.2109 -  2.1149 [1993/2029]  1799   194   9.7%
  bin  9:  2.1149 -  2.0337 [2002/2044]  1801   201  10.0%
  bin 10:  2.0337 -  1.9637 [1111/2055]   999   112  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_983/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 32
        2.40 -     3.03: 2093
        3.03 -     3.65: 4695
        3.65 -     4.28: 9137
        4.28 -     4.90: 12471
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.776 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.838 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28423 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_983/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_983/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 45.9914 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4879   r_free= 0.4803   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.291130                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.6887 0.99   1417  159 0.4168 0.4198      6.6125      6.6511|
|  2:  4.6887 -  3.7401 0.99   1355  151 0.4130 0.3882      6.8263      6.7719|
|  3:  3.7401 -  3.2728 0.99   1335  142 0.4374 0.4146      6.6785        6.69|
|  4:  3.2728 -  2.9760 0.99   1334  155 0.4830 0.4697      6.5442      6.5013|
|  5:  2.9760 -  2.7641 0.99   1331  149 0.5147 0.5266      6.3759      6.3985|
|  6:  2.7641 -  2.6020 0.99   1316  141 0.5192 0.5155      6.2869      6.2211|
|  7:  2.6020 -  2.4723 0.99   1311  143 0.5343 0.4755      6.2558      6.1801|
|  8:  2.4723 -  2.3651 0.98   1290  146 0.5247 0.4636      6.1755      6.1675|
|  9:  2.3651 -  2.2743 0.98   1291  150 0.5231 0.5200      6.1294       6.176|
| 10:  2.2743 -  2.1961 1.00   1296  150 0.5277 0.5508      6.0973      6.0722|
| 11:  2.1961 -  2.1276 0.98   1307  132 0.5108 0.5196      6.0359      6.0495|
| 12:  2.1276 -  2.0669 0.98   1266  144 0.5300 0.5986      5.9536       6.016|
| 13:  2.0669 -  2.0127 0.96   1267  135 0.5556 0.5268      5.8829      5.8104|
| 14:  2.0127 -  1.9637 0.39    514   62 0.5646 0.4980      5.8842      5.8157|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1362 -  4.6887  1417   159  0.64  39.11   0.78     0.71      89673.86|
|  2:  4.6887 -  3.7401  1355   151  0.69  36.22   0.86     0.77     115189.90|
|  3:  3.7401 -  3.2728  1335   142  0.58  45.13   0.84     0.72     120633.72|
|  4:  3.2728 -  2.9760  1334   155  0.49  52.91   0.79     0.60     107965.71|
|  5:  2.9760 -  2.7641  1331   149  0.37  61.75   0.73     0.46      89663.94|
|  6:  2.7641 -  2.6020  1316   141  0.36  63.26   0.72     0.42      77053.92|
|  7:  2.6020 -  2.4723  1311   143  0.33  65.01   0.74     0.40      67860.31|
|  8:  2.4723 -  2.3651  1290   146  0.35  64.06   0.71     0.41      60457.31|
|  9:  2.3651 -  2.2743  1291   150  0.35  63.70   0.74     0.40      53706.41|
| 10:  2.2743 -  2.1961  1296   150  0.34  64.74   0.75     0.40      49681.92|
| 11:  2.1961 -  2.1276  1307   132  0.29  68.53   0.77     0.35      50182.42|
| 12:  2.1276 -  2.0669  1266   144  0.24  72.35   0.75     0.31      47852.16|
| 13:  2.0669 -  2.0127  1267   135  0.22  73.54   0.72     0.30      41383.49|
| 14:  2.0127 -  1.9637   514    62  0.32  66.12   0.71     0.35      29801.15|
|alpha:            min =        0.30 max =            0.77 mean =         0.48|
|beta:             min =    29801.15 max =       120633.72 mean =     73940.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.99 mean =        59.17|
|phase err.(test): min =        0.00 max =           89.94 mean =        59.34|
|-----------------------------------------------------------------------------|

============================== 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 = 18.792329             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.011   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.499943              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.678   (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:       33 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      697 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1529 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2659 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3953 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5084 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6583 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7745 |
|-----------------------------------------------------------------------------|
|-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 |       53.544 |
| 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 |       1.993 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    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 = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4921   r_free= 0.4827   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.292580                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4791   r_free= 0.4683   ksol= 0.38   Bsol= 20.00   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.92,9.62,6.93,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.285095                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.695310             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.065   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.415686              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.984   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4791      final r-factor (work) = 0.4042          |
| start r-factor (free) = 0.4683      final r-factor (free) = 0.4339          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 102.8791 = 15.70 * 0.50 * 6.2866 + 1.00 * 53.5438                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.9312 = 15.70 * 0.50 * 6.2161 + 1.00 * 0.1493                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4042      final r-factor (work) = 0.3642          |
| start r-factor (free) = 0.4339      final r-factor (free) = 0.4215          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8145 = 1.42 * 1.00 * 6.2161 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7272 = 1.42 * 1.00 * 6.1524 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    52.03   12.30    None  None   None       |
|    all(noH): 2823   0      0.00    52.03   12.30    None  None   None       |
|    Sol.    : 438    0      0.00    48.64   20.01    None  None   None       |
|    Mac.    : 2385   0      0.00    52.03   10.89    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 -   5.203:  679   |   5:    26.013 -  31.215:  138        |
|      1:     5.203 -  10.405:  715   |   6:    31.215 -  36.418:   69        |
|      2:    10.405 -  15.608:  583   |   7:    36.418 -  41.620:   34        |
|      3:    15.608 -  20.810:  374   |   8:    41.620 -  46.823:   22        |
|      4:    20.810 -  26.013:  207   |   9:    46.823 -  52.025:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3642 r_free = 0.4215             target_work(ml) = 6.141         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3640 r_free = 0.4212             target_work(ml) = 6.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3640   r_free= 0.4212   ksol= 0.38   Bsol= 20.00   scale= 1.083   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.92,9.62,6.93,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.140476                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3625   r_free= 0.4170   ksol= 0.37   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.60,5.66,4.26,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.141326                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.818419              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.568  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.830724              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.206  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3625      final r-factor (work) = 0.2934          |
| start r-factor (free) = 0.4170      final r-factor (free) = 0.3522          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1921 = 7.82 * 0.50 * 6.1503 + 1.00 * 0.1493                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7763 = 7.82 * 0.50 * 6.0598 + 1.00 * 0.0872                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2934      final r-factor (work) = 0.2723          |
| start r-factor (free) = 0.3522      final r-factor (free) = 0.3405          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0532 = 0.83 * 1.00 * 6.0598 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9581 = 0.83 * 1.00 * 5.9430 + 1.00 * 0.0211                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.50   13.07    None  None   None       |
|    all(noH): 2823   0      0.00    72.50   13.07    None  None   None       |
|    Sol.    : 438    0      0.00    61.07   27.00    None  None   None       |
|    Mac.    : 2385   0      0.00    72.50   10.52    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 -   7.250: 1083   |   5:    36.248 -  43.498:   92        |
|      1:     7.250 -  14.499:  751   |   6:    43.498 -  50.747:   29        |
|      2:    14.499 -  21.749:  436   |   7:    50.747 -  57.997:    9        |
|      3:    21.749 -  28.999:  268   |   8:    57.997 -  65.247:    3        |
|      4:    28.999 -  36.248:  150   |   9:    65.247 -  72.496:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2723 r_free = 0.3405             target_work(ml) = 5.924         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2721 r_free = 0.3403             target_work(ml) = 5.924         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2721   r_free= 0.3403   ksol= 0.37   Bsol= 50.00   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.60,5.66,4.26,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.924203                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2717   r_free= 0.3367   ksol= 0.35   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,3.45,3.59,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.922298                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.219644              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.612   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.330675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.525  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2717      final r-factor (work) = 0.1989          |
| start r-factor (free) = 0.3367      final r-factor (free) = 0.2622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5069 = 8.22 * 0.50 * 5.9418 + 1.00 * 0.0872                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9331 = 8.22 * 0.50 * 5.8002 + 1.00 * 0.0952                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1989      final r-factor (work) = 0.1774          |
| start r-factor (free) = 0.2622      final r-factor (free) = 0.2364          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9333 = 0.33 * 1.00 * 5.8002 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8696 = 0.33 * 1.00 * 5.6000 + 1.00 * 0.0178                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.24   12.81    None  None   None       |
|    all(noH): 2823   0      0.00    64.24   12.81    None  None   None       |
|    Sol.    : 438    0      2.41    64.24   30.63    None  None   None       |
|    Mac.    : 2385   0      0.00    63.06   9.54     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 -   6.425: 1027   |   5:    32.122 -  38.547:  139        |
|      1:     6.425 -  12.849:  873   |   6:    38.547 -  44.971:   87        |
|      2:    12.849 -  19.274:  320   |   7:    44.971 -  51.396:   30        |
|      3:    19.274 -  25.698:  191   |   8:    51.396 -  57.820:   10        |
|      4:    25.698 -  32.122:  141   |   9:    57.820 -  64.245:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1774 r_free = 0.2364             target_work(ml) = 5.543         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1771 r_free = 0.2354             target_work(ml) = 5.541         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1771   r_free= 0.2354   ksol= 0.35   Bsol= 50.00   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,3.45,3.59,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.541403                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1763   r_free= 0.2344   ksol= 0.35   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,1.69,2.81,0.00,0.00,0.00); trace/3= 2.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.539921                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.657830              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.294  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.623748              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.662   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1763      final r-factor (work) = 0.1460          |
| start r-factor (free) = 0.2344      final r-factor (free) = 0.2005          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3453 = 3.66 * 0.50 * 5.6045 + 1.00 * 0.0951                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0584 = 3.66 * 0.50 * 5.4646 + 1.00 * 0.0642                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1460      final r-factor (work) = 0.1339          |
| start r-factor (free) = 0.2005      final r-factor (free) = 0.1863          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4201 = 0.62 * 1.00 * 5.4646 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3484 = 0.62 * 1.00 * 5.3497 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.90   13.40    None  None   None       |
|    all(noH): 2823   0      0.00    75.90   13.40    None  None   None       |
|    Sol.    : 438    0      2.68    75.90   37.00    None  None   None       |
|    Mac.    : 2385   0      0.00    73.58   9.07     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 -   7.590: 1361   |   5:    37.949 -  45.539:  102        |
|      1:     7.590 -  15.180:  749   |   6:    45.539 -  53.128:   88        |
|      2:    15.180 -  22.769:  230   |   7:    53.128 -  60.718:   48        |
|      3:    22.769 -  30.359:  119   |   8:    60.718 -  68.308:   24        |
|      4:    30.359 -  37.949:   95   |   9:    68.308 -  75.898:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1339 r_free = 0.1863             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1338 r_free = 0.1860             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1338   r_free= 0.1860   ksol= 0.35   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,1.69,2.81,0.00,0.00,0.00); trace/3= 2.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.304964                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1342   r_free= 0.1855   ksol= 0.33   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,1.38,2.69,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.303227                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.843921              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.504  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.850073              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.408  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1342      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1855      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6709 = 2.84 * 0.50 * 5.3494 + 1.00 * 0.0642                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5566 = 2.84 * 0.50 * 5.2679 + 1.00 * 0.0658                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1720      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4896 = 0.85 * 1.00 * 5.2679 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4462 = 0.85 * 1.00 * 5.2156 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.32   13.43    None  None   None       |
|    all(noH): 2823   0      0.00    86.32   13.43    None  None   None       |
|    Sol.    : 438    0      2.25    86.32   38.14    None  None   None       |
|    Mac.    : 2385   0      0.00    85.19   8.89     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 -   8.633: 1568   |   5:    43.162 -  51.795:   93        |
|      1:     8.633 -  17.265:  654   |   6:    51.795 -  60.427:   68        |
|      2:    17.265 -  25.897:  175   |   7:    60.427 -  69.060:   35        |
|      3:    25.897 -  34.530:  115   |   8:    69.060 -  77.692:   15        |
|      4:    34.530 -  43.162:   94   |   9:    77.692 -  86.325:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1694             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1188 r_free = 0.1693             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1693   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,1.38,2.69,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206836                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.6887 0.99   1417  159 0.0992 0.1334       5.384      5.5976|
|  2:  4.6887 -  3.7401 0.99   1355  151 0.0881 0.1188      5.4782      5.6909|
|  3:  3.7401 -  3.2728 0.99   1335  142 0.1128 0.1584      5.5313      5.8891|
|  4:  3.2728 -  2.9760 0.99   1334  155 0.1337 0.1813      5.5256      5.6763|
|  5:  2.9760 -  2.7641 0.99   1331  149 0.1413 0.1813      5.3698      5.6102|
|  6:  2.7641 -  2.6020 0.99   1316  141 0.1291 0.1889       5.252      5.4815|
|  7:  2.6020 -  2.4723 0.99   1311  143 0.1347 0.1852      5.2227      5.4297|
|  8:  2.4723 -  2.3651 0.98   1290  146 0.1245 0.1974      5.1318      5.4544|
|  9:  2.3651 -  2.2743 0.98   1291  150 0.1272 0.1934      5.1081      5.3796|
| 10:  2.2743 -  2.1961 1.00   1296  150 0.1208 0.1792      5.0201      5.2334|
| 11:  2.1961 -  2.1276 0.98   1307  132 0.1206 0.2004      5.0178      5.3892|
| 12:  2.1276 -  2.0669 0.98   1266  144 0.1216 0.1758      4.9448      5.1829|
| 13:  2.0669 -  2.0127 0.96   1267  135 0.1206 0.1907      4.8446      5.1232|
| 14:  2.0127 -  1.9637 0.39    514   62 0.1023 0.1515      4.6807      4.8802|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1362 -  4.6887  1417   159  0.94   9.64   0.98     0.96       7593.83|
|  2:  4.6887 -  3.7401  1355   151  0.95   8.67   1.02     1.00      10166.97|
|  3:  3.7401 -  3.2728  1335   142  0.93  12.48   1.04     1.03      11877.66|
|  4:  3.2728 -  2.9760  1334   155  0.90  15.59   1.01     0.99      11965.07|
|  5:  2.9760 -  2.7641  1331   149  0.89  16.58   0.99     0.97       8927.03|
|  6:  2.7641 -  2.6020  1316   141  0.89  17.23   0.98     0.95       7795.00|
|  7:  2.6020 -  2.4723  1311   143  0.89  17.12   1.00     0.97       7127.43|
|  8:  2.4723 -  2.3651  1290   146  0.89  17.12   0.98     0.95       6163.78|
|  9:  2.3651 -  2.2743  1291   150  0.89  17.26   1.00     0.96       5983.52|
| 10:  2.2743 -  2.1961  1296   150  0.89  17.34   1.00     0.95       5141.24|
| 11:  2.1961 -  2.1276  1307   132  0.89  17.85   0.99     0.94       5182.94|
| 12:  2.1276 -  2.0669  1266   144  0.89  17.92   1.01     1.00       4778.97|
| 13:  2.0669 -  2.0127  1267   135  0.89  17.75   1.00     0.98       3851.32|
| 14:  2.0127 -  1.9637   514    62  0.91  15.56   0.98     0.95       2815.10|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2815.10 max =        11965.07 mean =      7335.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.51|
|phase err.(test): min =        0.00 max =           89.89 mean =        14.81|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1693   ksol= 0.32   Bsol= 47.90   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.05,-0.64,0.69,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206932                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1693   ksol= 0.32   Bsol= 47.90   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.05,-0.64,0.69,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206932                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.6887 0.99   1417  159 0.0989 0.1332      5.3825      5.5971|
|  2:  4.6887 -  3.7401 0.99   1355  151 0.0879 0.1185      5.4765      5.6877|
|  3:  3.7401 -  3.2728 0.99   1335  142 0.1127 0.1582      5.5301      5.8877|
|  4:  3.2728 -  2.9760 0.99   1334  155 0.1337 0.1815      5.5256      5.6767|
|  5:  2.9760 -  2.7641 0.99   1331  149 0.1414 0.1815      5.3704      5.6111|
|  6:  2.7641 -  2.6020 0.99   1316  141 0.1292 0.1890      5.2529      5.4819|
|  7:  2.6020 -  2.4723 0.99   1311  143 0.1348 0.1854      5.2237      5.4309|
|  8:  2.4723 -  2.3651 0.98   1290  146 0.1245 0.1977      5.1327      5.4556|
|  9:  2.3651 -  2.2743 0.98   1291  150 0.1272 0.1933      5.1088      5.3794|
| 10:  2.2743 -  2.1961 1.00   1296  150 0.1209 0.1794      5.0209      5.2344|
| 11:  2.1961 -  2.1276 0.98   1307  132 0.1206 0.2005      5.0182      5.3895|
| 12:  2.1276 -  2.0669 0.98   1266  144 0.1216 0.1759      4.9452      5.1832|
| 13:  2.0669 -  2.0127 0.96   1267  135 0.1207 0.1908       4.845      5.1234|
| 14:  2.0127 -  1.9637 0.39    514   62 0.1022 0.1516      4.6808       4.881|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1362 -  4.6887  1417   159  0.94   9.63   0.98     0.96       7585.78|
|  2:  4.6887 -  3.7401  1355   151  0.95   8.65   1.02     1.01      10136.57|
|  3:  3.7401 -  3.2728  1335   142  0.93  12.45   1.04     1.03      11831.17|
|  4:  3.2728 -  2.9760  1334   155  0.90  15.58   1.02     0.99      11955.25|
|  5:  2.9760 -  2.7641  1331   149  0.89  16.59   1.00     0.98       8935.59|
|  6:  2.7641 -  2.6020  1316   141  0.89  17.25   0.99     0.96       7810.73|
|  7:  2.6020 -  2.4723  1311   143  0.89  17.14   1.00     0.97       7145.62|
|  8:  2.4723 -  2.3651  1290   146  0.89  17.15   0.98     0.95       6176.76|
|  9:  2.3651 -  2.2743  1291   150  0.89  17.28   1.01     0.97       5993.13|
| 10:  2.2743 -  2.1961  1296   150  0.89  17.36   1.00     0.96       5147.39|
| 11:  2.1961 -  2.1276  1307   132  0.89  17.86   1.00     0.95       5188.92|
| 12:  2.1276 -  2.0669  1266   144  0.89  17.93   1.02     1.01       4784.56|
| 13:  2.0669 -  2.0127  1267   135  0.89  17.76   1.00     0.98       3855.32|
| 14:  2.0127 -  1.9637   514    62  0.91  15.57   0.99     0.96       2817.29|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2817.29 max =        11955.25 mean =      7334.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.51|
|phase err.(test): min =        0.00 max =           89.99 mean =        14.82|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.13    88.45   15.56    None  None   None       |
|    all(noH): 2823   0      2.13    88.45   15.56    None  None   None       |
|    Sol.    : 438    0      4.38    88.45   40.27    None  None   None       |
|    Mac.    : 2385   0      2.13    87.31   11.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.128 -  10.760: 1568   |   5:    45.290 -  53.922:   93        |
|      1:    10.760 -  19.393:  654   |   6:    53.922 -  62.555:   68        |
|      2:    19.393 -  28.025:  175   |   7:    62.555 -  71.187:   35        |
|      3:    28.025 -  36.658:  115   |   8:    71.187 -  79.820:   15        |
|      4:    36.658 -  45.290:   94   |   9:    79.820 -  88.452:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.303 - 5.886
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 335 from: 340
   mapped sites are within: 0.717 - 5.886

peak=    9.935 closest distance to " CB  VAL A 230 " =    1.446
peak=    7.808 closest distance to " O   HOH Z 130 " =    1.539
peak=    6.485 closest distance to " CD2 LEU A   5 " =    1.276
peak=    6.421 closest distance to " CG  ARG A 138 " =    1.075
peak=    6.362 closest distance to " O   HOH Z  65 " =    1.331
peak=    6.279 closest distance to " CG2 VAL A 296 " =    1.046
peak=    6.132 closest distance to " NE2 GLN A  11 " =    1.208
peak=    5.656 closest distance to " O   HOH Z 222 " =    1.419
peak=    5.542 closest distance to " NH2 ARG A  56 " =    2.098
peak=    5.434 closest distance to " O   HOH Z   7 " =    1.747
peak=    5.366 closest distance to " CD1AILE A 234 " =    1.056
peak=    5.185 closest distance to " CB  VAL A 296 " =    1.168
peak=    5.062 closest distance to " O   HOH Z   9 " =    1.508
peak=    4.942 closest distance to " O   HOH Z 425 " =    1.749
peak=    4.935 closest distance to " CG  LEU A 228 " =    1.116
peak=    4.911 closest distance to " CB  GLN A 183 " =    1.215
peak=    4.899 closest distance to " CG  LEU A   5 " =    1.187
peak=    4.886 closest distance to " CB  PRO A  54 " =    1.056
peak=    4.868 closest distance to " O   HOH Z 232 " =    2.173
peak=    4.851 closest distance to " CB  VAL A 230 " =    1.195
peak=    4.842 closest distance to " O   HOH Z 139 " =    1.579
peak=    4.811 closest distance to " CG  PRO A  54 " =    1.366
peak=    4.797 closest distance to " O   HOH Z 410 " =    1.552
peak=    4.778 closest distance to " CB  SER A   3 " =    1.500
peak=    4.770 closest distance to " O   HOH Z 369 " =    1.989
peak=    4.703 closest distance to " O   HOH Z 126 " =    2.073
peak=    4.642 closest distance to " O   HOH Z 144 " =    1.842
peak=    4.589 closest distance to " NH1 ARG A 138 " =    1.017
peak=    4.585 closest distance to " O   HOH Z 427 " =    2.484
peak=    4.534 closest distance to " CB  GLN A 223 " =    1.512
peak=    4.487 closest distance to " O   HOH Z 193 " =    1.747
peak=    4.478 closest distance to " CB  SER A  63 " =    1.308
peak=    4.471 closest distance to " CG  PRO A 213 " =    1.249
peak=    4.449 closest distance to " O   HOH Z 287 " =    1.820
peak=    4.434 closest distance to " CG  PRO A 198 " =    1.243
peak=    4.414 closest distance to " O   HOH Z 298 " =    1.974
peak=    4.382 closest distance to " O   HOH Z   2 " =    1.883
peak=    4.362 closest distance to " CD2 LEU A 228 " =    1.193
peak=    4.348 closest distance to " O   HOH Z 147 " =    1.411
peak=    4.345 closest distance to " O   HOH Z 371 " =    2.664
peak=    4.334 closest distance to " O   HOH Z 361 " =    1.466
peak=    4.312 closest distance to " CB  ASN A 148 " =    1.379
peak=    4.299 closest distance to " CG  LEU A 167 " =    1.241
peak=    4.281 closest distance to " O   HOH Z 427 " =    1.210
peak=    4.279 closest distance to " CB  ASP A 124 " =    0.784
peak=    4.274 closest distance to " O   HOH Z  61 " =    1.597
peak=    4.261 closest distance to " O   HOH Z  63 " =    1.581
peak=    4.259 closest distance to " O   HOH Z  78 " =    1.589
peak=    4.237 closest distance to " CB  SER A 216 " =    0.978
peak=    4.235 closest distance to " O   HOH Z 132 " =    1.225
peak=    4.231 closest distance to " O   PRO A 198 " =    1.263
peak=    4.225 closest distance to " CB  VAL A 202 " =    1.618
peak=    4.216 closest distance to " O   HOH Z 225 " =    1.475
peak=    4.194 closest distance to " O   HOH Z 414 " =    1.292
peak=    4.178 closest distance to " O   HOH Z 124 " =    1.419
peak=    4.172 closest distance to " O   HOH Z 380 " =    1.798
peak=    4.167 closest distance to " O   HOH Z 424 " =    1.182
peak=    4.142 closest distance to " OD2 ASP A 286 " =    2.767
peak=    4.135 closest distance to " O   HOH Z 217 " =    2.470
peak=    4.123 closest distance to " NH1AARG A 145 " =    1.037
peak=    4.108 closest distance to " O   HOH Z 417 " =    1.325
peak=    4.090 closest distance to " O   HOH Z 236 " =    1.682
peak=    4.080 closest distance to " O   HOH Z 234 " =    3.754
peak=    4.078 closest distance to " CD  ARG A 138 " =    1.216
peak=    4.071 closest distance to " O   HOH Z 209 " =    2.436
peak=    4.054 closest distance to " O   HOH Z  59 " =    2.064
peak=    4.040 closest distance to " O   HOH Z 133 " =    1.675
peak=    4.021 closest distance to " O   HOH Z  58 " =    1.933
peak=    4.018 closest distance to " O   HOH Z 316 " =    3.045
peak=    4.011 closest distance to " CB  ARG A 275 " =    0.929
peak=    4.006 closest distance to " CB  ASN A  39 " =    0.955
peak=    4.005 closest distance to " O   HOH Z 272 " =    1.831
peak=    4.004 closest distance to " O   HOH Z 419 " =    1.927
peak=    3.994 closest distance to " O   HOH Z 193 " =    1.767
peak=    3.992 closest distance to " O   SER A  87 " =    2.302
peak=    3.988 closest distance to " O   HOH Z 392 " =    1.312
peak=    3.972 closest distance to " CB  GLU A 128 " =    1.177
peak=    3.960 closest distance to " O   HOH Z 374 " =    1.115
peak=    3.946 closest distance to " CA  SER A  87 " =    0.986
peak=    3.938 closest distance to " O   HOH Z 411 " =    3.304
peak=    3.935 closest distance to " ND1 HIS A  86 " =    1.819
peak=    3.932 closest distance to " OG BSER A 258 " =    0.791
peak=    3.910 closest distance to " O   HOH Z 183 " =    1.440
peak=    3.851 closest distance to " CD  GLN A 240 " =    1.656
peak=    3.845 closest distance to " CG  LYS A  76 " =    1.555
peak=    3.823 closest distance to " CG  GLN A  88 " =    1.180
peak=    3.815 closest distance to " O   HOH Z  78 " =    2.053
peak=    3.802 closest distance to " O   HOH Z 195 " =    1.602
peak=    3.798 closest distance to " CB  TRP A 266 " =    1.070
peak=    3.790 closest distance to " CB  MET A  40 " =    0.836
peak=    3.789 closest distance to " CD2 TRP A 179 " =    2.199
peak=    3.777 closest distance to " CA  GLY A 267 " =    1.130
peak=    3.764 closest distance to " CB  GLU A 277 " =    3.601
peak=    3.757 closest distance to " CA  ASN A 215 " =    1.287
peak=    3.737 closest distance to " O   HOH Z 158 " =    2.748
peak=    3.730 closest distance to " CB  LEU A 237 " =    0.869
peak=    3.729 closest distance to " CB BVAL A  41 " =    1.227
peak=    3.727 closest distance to " O   HOH Z 133 " =    2.316
peak=    3.725 closest distance to " O   HOH Z 352 " =    1.550
peak=    3.724 closest distance to " O   HOH Z 122 " =    2.109
peak=    3.721 closest distance to " CG2 VAL A 257 " =    0.885
peak=    3.719 closest distance to " CG1 ILE A  33 " =    1.266
peak=    3.716 closest distance to " O   HOH Z 184 " =    1.467
peak=    3.714 closest distance to " CG  PRO A 280 " =    0.892
peak=    3.713 closest distance to " CB  VAL A 265 " =    1.280
peak=    3.710 closest distance to " O   HOH Z  30 " =    1.938
peak=    3.704 closest distance to " O   HOH Z  44 " =    2.682
peak=    3.700 closest distance to " OG BSER A  99 " =    2.171
peak=    3.690 closest distance to " O   HOH Z 359 " =    1.373
peak=    3.688 closest distance to " O   HOH Z 148 " =    1.457
peak=    3.684 closest distance to " O   HOH Z   9 " =    1.700
peak=    3.684 closest distance to " CG1 ILE A 151 " =    1.040
peak=    3.673 closest distance to " O   HOH Z 368 " =    2.005
peak=    3.671 closest distance to " O   HOH Z 438 " =    2.372
peak=    3.666 closest distance to " O   HOH Z 193 " =    1.906
peak=    3.665 closest distance to " O   HOH Z 207 " =    2.328
peak=    3.650 closest distance to " OG  SER A  62 " =    3.163
peak=    3.649 closest distance to " CG2 THR A 221 " =    1.240
peak=    3.648 closest distance to " CG  GLN A  11 " =    2.134
peak=    3.643 closest distance to " CB  LEU A 228 " =    1.298
peak=    3.639 closest distance to " OG  SER A  62 " =    2.842
peak=    3.633 closest distance to " CD  ARG A 159 " =    0.772
peak=    3.629 closest distance to " OD1 ASN A  69 " =    2.655
peak=    3.626 closest distance to " O   HOH Z 384 " =    1.451
peak=    3.623 closest distance to " O   HOH Z 181 " =    2.269
peak=    3.617 closest distance to " O   ASN A 209 " =    1.525
peak=    3.611 closest distance to " O   HOH Z 389 " =    1.886
peak=    3.609 closest distance to " CB  ILE A 234 " =    1.077
peak=    3.607 closest distance to " CB  GLU A 152 " =    1.451
peak=    3.607 closest distance to " CD BLYS A 290 " =    1.068
peak=    3.606 closest distance to " O   HOH Z 334 " =    1.585
peak=    3.594 closest distance to " CB  ASN A 142 " =    0.954
peak=    3.592 closest distance to " CD1 ILE A  33 " =    1.716
peak=    3.590 closest distance to " CA  TYR A  30 " =    0.978
peak=    3.588 closest distance to " O   HOH Z 313 " =    1.843
peak=    3.584 closest distance to " O   HOH Z 108 " =    2.182
peak=    3.576 closest distance to " O   HOH Z 222 " =    1.951
peak=    3.576 closest distance to " CA  ALA A 299 " =    0.987
peak=    3.572 closest distance to " OG BSER A 212 " =    2.838
peak=    3.569 closest distance to " O   HOH Z 109 " =    2.337
peak=    3.564 closest distance to " N   PHE A 130 " =    1.305
peak=    3.563 closest distance to " O   HOH Z  88 " =    3.677
peak=    3.562 closest distance to " OE2 GLU A   2 " =    1.803
peak=    3.560 closest distance to " CD  ARG A  66 " =    2.443
peak=    3.560 closest distance to " CA  TYR A 116 " =    1.487
peak=    3.559 closest distance to " CB  LEU A 143 " =    1.035
peak=    3.557 closest distance to " ND1 HIS A  81 " =    1.762
peak=    3.557 closest distance to " CB  THR A 157 " =    1.099
peak=    3.555 closest distance to " O   HOH Z 425 " =    2.015
peak=    3.553 closest distance to " CD1 LEU A 300 " =    1.231
peak=    3.544 closest distance to " O   HOH Z   1 " =    1.899
peak=    3.543 closest distance to " O   PRO A 198 " =    1.495
peak=    3.533 closest distance to " O   HOH Z  55 " =    1.795
peak=    3.527 closest distance to " O   HOH Z 418 " =    0.968
peak=    3.525 closest distance to " CA  ASN A 127 " =    1.070
peak=    3.518 closest distance to " N   TYR A  15 " =    0.936
peak=    3.509 closest distance to " CA  LEU A 101 " =    1.513
peak=    3.508 closest distance to " O   HOH Z 217 " =    1.820
peak=    3.506 closest distance to " O   HOH Z 305 " =    3.482
peak=    3.505 closest distance to " OD1 ASN A 217 " =    1.574
peak=    3.504 closest distance to " O   HOH Z  20 " =    1.651
peak=    3.502 closest distance to " NH2BARG A 145 " =    2.130
peak=    3.502 closest distance to " O   HOH Z 145 " =    3.529
peak=    3.499 closest distance to " NZ BLYS A 290 " =    0.931
peak=    3.495 closest distance to " O   HOH Z 119 " =    1.481
peak=    3.493 closest distance to " NH1 ARG A  56 " =    1.093
peak=    3.481 closest distance to " O   HOH Z 422 " =    2.728
peak=    3.479 closest distance to " O   HOH Z 258 " =    2.116
peak=    3.476 closest distance to " O   HOH Z 371 " =    1.965
peak=    3.475 closest distance to " CG2 ILE A 234 " =    0.860
peak=    3.474 closest distance to " N   SER A 271 " =    0.980
peak=    3.471 closest distance to " O   HOH Z 346 " =    1.726
peak=    3.470 closest distance to " N   ASN A 127 " =    1.425
peak=    3.468 closest distance to " O   HOH Z 134 " =    1.408
peak=    3.464 closest distance to " O   HOH Z 132 " =    2.288
peak=    3.459 closest distance to " O   HOH Z  48 " =    1.507
peak=    3.457 closest distance to " O   HOH Z 214 " =    1.317
peak=    3.454 closest distance to " CB  TRP A 179 " =    1.480
peak=    3.451 closest distance to " O   HOH Z  32 " =    2.225
peak=    3.450 closest distance to " NE AARG A 275 " =    1.361
peak=    3.448 closest distance to " CG1BVAL A  72 " =    0.852
peak=    3.446 closest distance to " O   HOH Z  40 " =    2.103
peak=    3.444 closest distance to " CG1 ILE A 120 " =    1.340
peak=    3.433 closest distance to " CB  HIS A 108 " =    0.804
peak=    3.423 closest distance to " N   GLN A 278 " =    1.155
peak=    3.417 closest distance to " NH1 ARG A  14 " =    0.927
peak=    3.416 closest distance to " CA  ILE A 234 " =    1.006
peak=    3.416 closest distance to " O   HOH Z 171 " =    2.798
peak=    3.415 closest distance to " CG1 ILE A 263 " =    1.289
peak=    3.413 closest distance to " CA  ALA A 160 " =    0.920
peak=    3.409 closest distance to " O   HOH Z  59 " =    1.600
peak=    3.408 closest distance to " O   HOH Z 356 " =    1.394
peak=    3.407 closest distance to " O   HOH Z 156 " =    3.049
peak=    3.407 closest distance to " CG  GLN A  89 " =    1.421
peak=    3.406 closest distance to " CB  MET A  47 " =    1.087
peak=    3.404 closest distance to " O   HOH Z  10 " =    1.760
peak=    3.402 closest distance to " CH2 TRP A 266 " =    1.125
peak=    3.400 closest distance to " O   HOH Z 145 " =    2.080
peak=    3.399 closest distance to " O   HOH Z 405 " =    1.594
peak=    3.398 closest distance to " CE1 TYR A 186 " =    1.330
peak=    3.388 closest distance to " ND2 ASN A 187 " =    1.695
peak=    3.384 closest distance to " O   HOH Z 115 " =    1.520
peak=    3.379 closest distance to " CB  ASN A 148 " =    1.914
peak=    3.376 closest distance to " CE3 TRP A 150 " =    1.009
peak=    3.376 closest distance to " CZ  PHE A 192 " =    0.963
peak=    3.375 closest distance to " CB  ASN A 187 " =    1.051
peak=    3.375 closest distance to " O   HOH Z 175 " =    2.078
peak=    3.373 closest distance to " CB  SER A 276 " =    1.099
peak=    3.372 closest distance to " O   MET A 105 " =    1.676
peak=    3.372 closest distance to " CG BARG A 102 " =    1.990
peak=    3.372 closest distance to " CB  SER A 212 " =    1.342
peak=    3.369 closest distance to " OG BSER A 210 " =    1.119
peak=    3.363 closest distance to " O   HOH Z  49 " =    1.589
peak=    3.357 closest distance to " O   HOH Z 334 " =    2.953
peak=    3.356 closest distance to " CA  LYS A 117 " =    1.155
peak=    3.354 closest distance to " CA  ALA A  51 " =    1.038
peak=    3.353 closest distance to " O   HOH Z  22 " =    2.132
peak=    3.349 closest distance to " O   HOH Z 180 " =    2.070
peak=    3.348 closest distance to " O   HOH Z 213 " =    2.291
peak=    3.347 closest distance to " O   HOH Z 146 " =    1.726
peak=    3.346 closest distance to " O   HOH Z 368 " =    3.621
peak=    3.345 closest distance to " O   HOH Z  44 " =    2.046
peak=    3.341 closest distance to " CG  PRO A 243 " =    1.120
peak=    3.341 closest distance to " CB  VAL A 250 " =    1.075
peak=    3.341 closest distance to " CA  PHE A 283 " =    1.293
peak=    3.340 closest distance to " NE2 GLN A  58 " =    3.569
peak=    3.339 closest distance to " O   ALA A  10 " =    1.597
peak=    3.339 closest distance to " O   HOH Z 153 " =    3.690
peak=    3.336 closest distance to " NH2BARG A 190 " =    1.591
peak=    3.334 closest distance to " CB  GLU A 236 " =    1.156
peak=    3.334 closest distance to " O   HOH Z 329 " =    3.882
peak=    3.330 closest distance to " O   HOH Z 128 " =    1.912
peak=    3.329 closest distance to " OG  SER A  22 " =    2.946
peak=    3.328 closest distance to " O   HOH Z  64 " =    2.157
peak=    3.326 closest distance to " NE  ARG A  56 " =    3.528
peak=    3.325 closest distance to " CB  GLN A  88 " =    1.403
peak=    3.325 closest distance to " O   HOH Z 424 " =    2.794
peak=    3.319 closest distance to " O   HOH Z 362 " =    2.238
peak=    3.319 closest distance to " CA  LEU A 282 " =    1.027
peak=    3.318 closest distance to " O   HOH Z 345 " =    3.361
peak=    3.317 closest distance to " O   ALA A 233 " =    1.848
peak=    3.306 closest distance to " O   HOH Z  97 " =    1.395
peak=    3.302 closest distance to " O   HOH Z 263 " =    1.542
peak=    3.296 closest distance to " O   HOH Z 233 " =    1.578
peak=    3.293 closest distance to " O   HOH Z  55 " =    1.791
peak=    3.290 closest distance to " N   ALA A   1 " =    1.387
peak=    3.290 closest distance to " CB  GLN A  89 " =    1.164
peak=    3.288 closest distance to " OH  TYR A 186 " =    0.995
peak=    3.287 closest distance to " O   HOH Z 214 " =    1.887
peak=    3.286 closest distance to " O   HOH Z 261 " =    2.246
peak=    3.274 closest distance to " N   ALA A   1 " =    2.349
peak=    3.274 closest distance to " O   HOH Z 144 " =    2.473
peak=    3.269 closest distance to " O   HOH Z 409 " =    2.463
peak=    3.266 closest distance to " O   HOH Z  61 " =    1.570
peak=    3.265 closest distance to " O   HOH Z 350 " =    1.518
peak=    3.265 closest distance to " O   HOH Z 273 " =    2.740
peak=    3.263 closest distance to " O   HOH Z 244 " =    1.574
peak=    3.262 closest distance to " NZ  LYS A 117 " =    1.203
peak=    3.261 closest distance to " CA  MET A  47 " =    1.137
peak=    3.260 closest distance to " CA  THR A 221 " =    0.933
peak=    3.257 closest distance to " NE2 GLN A  58 " =    5.693
peak=    3.256 closest distance to " CB  ARG A 190 " =    1.776
peak=    3.247 closest distance to " O   GLY A 302 " =    2.135
peak=    3.246 closest distance to " O   HOH Z  64 " =    2.178
peak=    3.245 closest distance to " O   HOH Z 207 " =    1.778
peak=    3.244 closest distance to " O   HOH Z 373 " =    1.478
peak=    3.243 closest distance to " CB  ARG A  79 " =    1.323
peak=    3.238 closest distance to " O   HOH Z 215 " =    1.294
peak=    3.230 closest distance to " OE2 GLU A  53 " =    2.018
peak=    3.229 closest distance to " CA  ALA A 248 " =    1.262
peak=    3.229 closest distance to " CB  ASN A 110 " =    1.159
peak=    3.226 closest distance to " N   ALA A 154 " =    0.717
peak=    3.223 closest distance to " O   HOH Z 323 " =    1.594
peak=    3.219 closest distance to " CE3 TRP A 274 " =    1.268
peak=    3.219 closest distance to " O   HOH Z 281 " =    4.554
peak=    3.219 closest distance to " N   ALA A 256 " =    0.997
peak=    3.216 closest distance to " CB  THR A 235 " =    1.011
peak=    3.215 closest distance to " CG  ARG A 159 " =    0.994
peak=    3.211 closest distance to " O   HOH Z 185 " =    1.915
peak=    3.210 closest distance to " CG  GLN A 278 " =    1.251
peak=    3.209 closest distance to " CB  ALA A 114 " =    1.573
peak=    3.205 closest distance to " CB  ASP A 140 " =    0.944
peak=    3.203 closest distance to " CB  ARG A 139 " =    1.043
peak=    3.202 closest distance to " N   GLY A 196 " =    1.211
peak=    3.201 closest distance to " O   HOH Z 415 " =    5.886
peak=    3.189 closest distance to " CA  ALA A 295 " =    0.941
peak=    3.187 closest distance to " O   HOH Z  21 " =    1.570
peak=    3.182 closest distance to " CD  ARG A 269 " =    0.999
peak=    3.176 closest distance to " O   HOH Z  68 " =    1.959
peak=    3.170 closest distance to " CB  PHE A 225 " =    1.502
peak=    3.169 closest distance to " ND2 ASN A 249 " =    0.763
peak=    3.166 closest distance to " O   HOH Z 375 " =    0.894
peak=    3.164 closest distance to " O   HOH Z 110 " =    1.730
peak=    3.162 closest distance to " O   HOH Z 271 " =    2.024
peak=    3.159 closest distance to " CB  ALA A  10 " =    0.940
peak=    3.156 closest distance to " CA  ALA A 158 " =    1.112
peak=    3.154 closest distance to " O   HOH Z 402 " =    1.373
peak=    3.153 closest distance to " O   HOH Z  80 " =    1.482
peak=    3.147 closest distance to " O   HOH Z 367 " =    2.259
peak=    3.147 closest distance to " O   HOH Z  97 " =    1.810
peak=    3.142 closest distance to " N   ILE A  33 " =    1.067
peak=    3.142 closest distance to " CA  ALA A 233 " =    0.921
peak=    3.142 closest distance to " CA  THR A 264 " =    0.735
peak=    3.141 closest distance to " CA  ARG A 195 " =    1.350
peak=    3.136 closest distance to " CG1 ILE A  49 " =    1.245
peak=    3.135 closest distance to " O   HOH Z 357 " =    1.244
peak=    3.135 closest distance to " CA  TYR A 186 " =    1.563
peak=    3.134 closest distance to " CA  ALA A 291 " =    0.929
peak=    3.134 closest distance to " O   HOH Z 406 " =    1.623
peak=    3.133 closest distance to " CZ  PHE A 218 " =    1.061
peak=    3.128 closest distance to " O   ALA A 165 " =    1.343
peak=    3.123 closest distance to " O   HOH Z 133 " =    2.123
peak=    3.121 closest distance to " NZ  LYS A  48 " =    1.902
peak=    3.120 closest distance to " O   HOH Z 145 " =    1.657
peak=    3.120 closest distance to " OH  TYR A 116 " =    1.159
peak=    3.114 closest distance to " CB  ARG A 138 " =    1.311
peak=    3.112 closest distance to " O   HOH Z 130 " =    2.923
peak=    3.111 closest distance to " CG1 VAL A 296 " =    1.205
peak=    3.107 closest distance to " CB  SER A 210 " =    0.908
peak=    3.106 closest distance to " CB  LYS A 117 " =    1.199
peak=    3.097 closest distance to " O   THR A 294 " =    1.080
peak=    3.097 closest distance to " CB  THR A  82 " =    1.226
peak=    3.096 closest distance to " O   HOH Z 172 " =    2.454
peak=    3.094 closest distance to " CD  LYS A 166 " =    1.430
peak=    3.090 closest distance to " CB  LEU A 143 " =    0.888
peak=    3.081 closest distance to " O   HOH Z 152 " =    2.387
peak=    3.081 closest distance to " CZ3 TRP A  92 " =    1.227
peak=    3.077 closest distance to " O   HOH Z 128 " =    2.054
peak=    3.076 closest distance to " O   HOH Z 303 " =    2.855
peak=    3.076 closest distance to " O   ALA A 158 " =    1.446
peak=    3.071 closest distance to " CB  GLU A 152 " =    1.426
peak=    3.063 closest distance to " O   HOH Z 344 " =    2.993
peak=    3.061 closest distance to " OG BSER A 164 " =    2.286
peak=    3.047 closest distance to " CD2 LEU A 255 " =    1.557
peak=    3.013 closest distance to " O   HOH Z 115 " =    1.948

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.588 - 5.543
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 218
   mapped sites are within: 0.770 - 5.543

peak=   -4.801 closest distance to " CG2 VAL A 230 " =    0.851
peak=   -4.498 closest distance to " CD  ARG A  14 " =    3.107
peak=   -4.388 closest distance to " CG  ARG A 138 " =    1.004
peak=   -4.247 closest distance to " OG  SER A  87 " =    1.359
peak=   -4.173 closest distance to " OG BSER A 134 " =    1.505
peak=   -4.154 closest distance to " CB  PRO A 243 " =    2.595
peak=   -4.128 closest distance to " O   HOH Z 198 " =    2.457
peak=   -4.062 closest distance to " O   HOH Z 266 " =    4.763
peak=   -4.042 closest distance to " O   HOH Z  52 " =    1.454
peak=   -4.031 closest distance to " CD  ARG A 156 " =    1.991
peak=   -4.006 closest distance to " CD  LYS A 289 " =    2.404
peak=   -3.986 closest distance to " OE1 GLU A 277 " =    2.343
peak=   -3.979 closest distance to " O   HOH Z 185 " =    2.280
peak=   -3.938 closest distance to " O   HOH Z 377 " =    1.719
peak=   -3.912 closest distance to " O   HOH Z 290 " =    1.262
peak=   -3.898 closest distance to " O   HOH Z  43 " =    1.749
peak=   -3.870 closest distance to " O   PRO A 198 " =    1.271
peak=   -3.848 closest distance to " N   THR A 157 " =    1.521
peak=   -3.840 closest distance to " CD1 LEU A 255 " =    2.994
peak=   -3.829 closest distance to " CB  ASP A  27 " =    2.394
peak=   -3.812 closest distance to " O   HOH Z 350 " =    1.797
peak=   -3.803 closest distance to " CB  ALA A 248 " =    2.003
peak=   -3.803 closest distance to " O   SER A  22 " =    2.601
peak=   -3.764 closest distance to " O   HOH Z 359 " =    1.634
peak=   -3.762 closest distance to " O   SER A 135 " =    1.580
peak=   -3.757 closest distance to " N   ALA A  43 " =    2.581
peak=   -3.746 closest distance to " CG1 VAL A 296 " =    1.325
peak=   -3.744 closest distance to " O   HOH Z 131 " =    4.017
peak=   -3.736 closest distance to " CB  ALA A 227 " =    2.326
peak=   -3.731 closest distance to " NH2 ARG A  79 " =    1.957
peak=   -3.720 closest distance to " CG  MET A 105 " =    0.972
peak=   -3.715 closest distance to " CB  ALA A  43 " =    2.415
peak=   -3.713 closest distance to " CB  ASP A 132 " =    2.346
peak=   -3.708 closest distance to " O   HOH Z  13 " =    1.801
peak=   -3.705 closest distance to " CD  GLN A 223 " =    2.415
peak=   -3.655 closest distance to " O   HOH Z 211 " =    1.428
peak=   -3.653 closest distance to " C   HIS A 108 " =    1.144
peak=   -3.645 closest distance to " CD1 LEU A 101 " =    2.347
peak=   -3.644 closest distance to " CG2 VAL A 296 " =    1.299
peak=   -3.641 closest distance to " O   ALA A   1 " =    1.159
peak=   -3.641 closest distance to " OE1 GLN A  88 " =    1.032
peak=   -3.640 closest distance to " CB  ASN A  39 " =    2.077
peak=   -3.635 closest distance to " CA  GLY A 133 " =    2.037
peak=   -3.631 closest distance to " CE2 TYR A  30 " =    2.552
peak=   -3.615 closest distance to " CG  TRP A 266 " =    1.724
peak=   -3.603 closest distance to " CE2 PHE A 218 " =    2.502
peak=   -3.593 closest distance to " O   HOH Z 134 " =    2.793
peak=   -3.585 closest distance to " CG  PRO A 163 " =    2.508
peak=   -3.578 closest distance to " O   HOH Z 407 " =    3.255
peak=   -3.575 closest distance to " CD  ARG A 138 " =    1.392
peak=   -3.573 closest distance to " O   VAL A 197 " =    1.735
peak=   -3.571 closest distance to " O   HOH Z 166 " =    1.399
peak=   -3.568 closest distance to " CB  PRO A 163 " =    2.391
peak=   -3.563 closest distance to " CA  GLY A  98 " =    1.843
peak=   -3.531 closest distance to " O   HOH Z 298 " =    1.074
peak=   -3.528 closest distance to " O   ASN A 301 " =    1.272
peak=   -3.526 closest distance to " CD1 ILE A 239 " =    2.470
peak=   -3.519 closest distance to " CB  ALA A   9 " =    2.480
peak=   -3.516 closest distance to " O   HOH Z 231 " =    1.799
peak=   -3.516 closest distance to " OG ASER A 134 " =    1.109
peak=   -3.509 closest distance to " O   HOH Z 275 " =    1.577
peak=   -3.482 closest distance to " O   GLY A 211 " =    1.211
peak=   -3.481 closest distance to " C   LEU A 143 " =    1.233
peak=   -3.478 closest distance to " O   HOH Z 111 " =    0.925
peak=   -3.477 closest distance to " O   GLY A 203 " =    2.462
peak=   -3.473 closest distance to " O   TYR A  30 " =    2.724
peak=   -3.471 closest distance to " CA  GLY A 241 " =    2.137
peak=   -3.467 closest distance to " C   ALA A 158 " =    1.303
peak=   -3.449 closest distance to " CD  GLN A  58 " =    0.953
peak=   -3.439 closest distance to " C   ASN A 285 " =    2.177
peak=   -3.439 closest distance to " O   HOH Z 352 " =    1.912
peak=   -3.437 closest distance to " CD2 LEU A   5 " =    0.945
peak=   -3.435 closest distance to " NH2AARG A 275 " =    5.543
peak=   -3.422 closest distance to " O   ILE A  49 " =    1.750
peak=   -3.420 closest distance to " C   ARG A 269 " =    1.396
peak=   -3.418 closest distance to " O   HOH Z  53 " =    1.749
peak=   -3.404 closest distance to " O   ASP A 191 " =    1.900
peak=   -3.403 closest distance to " O   HOH Z 350 " =    2.537
peak=   -3.402 closest distance to " OG  SER A  97 " =    2.148
peak=   -3.398 closest distance to " O   HOH Z 426 " =    1.639
peak=   -3.397 closest distance to " O   HOH Z 388 " =    2.290
peak=   -3.394 closest distance to " O   HOH Z 348 " =    1.897
peak=   -3.393 closest distance to " O   HOH Z 111 " =    2.255
peak=   -3.390 closest distance to " O   HOH Z  90 " =    3.019
peak=   -3.389 closest distance to " O   HOH Z 415 " =    1.181
peak=   -3.382 closest distance to " CB  PHE A 130 " =    1.254
peak=   -3.375 closest distance to " O   PRO A 163 " =    1.949
peak=   -3.373 closest distance to " CG2 THR A  18 " =    2.819
peak=   -3.364 closest distance to " CB  PHE A 192 " =    1.597
peak=   -3.364 closest distance to " O   HOH Z  39 " =    1.143
peak=   -3.363 closest distance to " CB  PRO A  54 " =    2.458
peak=   -3.363 closest distance to " O   HOH Z  11 " =    1.959
peak=   -3.359 closest distance to " O   GLN A  11 " =    1.505
peak=   -3.357 closest distance to " N   PRO A 163 " =    1.557
peak=   -3.357 closest distance to " ND2 ASN A  60 " =    1.582
peak=   -3.354 closest distance to " CD2 TYR A 293 " =    1.877
peak=   -3.354 closest distance to " O   GLY A  80 " =    2.491
peak=   -3.351 closest distance to " CD  LYS A 166 " =    2.352
peak=   -3.346 closest distance to " O   ALA A  84 " =    1.825
peak=   -3.344 closest distance to " ND2 ASN A 209 " =    1.922
peak=   -3.344 closest distance to " O   HOH Z 122 " =    2.157
peak=   -3.343 closest distance to " O   HOH Z  60 " =    2.056
peak=   -3.342 closest distance to " O   HOH Z  65 " =    1.249
peak=   -3.338 closest distance to " O   HOH Z 414 " =    1.902
peak=   -3.333 closest distance to " O   HOH Z 193 " =    2.026
peak=   -3.333 closest distance to " O   HOH Z 292 " =    1.657
peak=   -3.330 closest distance to " O   THR A  42 " =    2.492
peak=   -3.327 closest distance to " CG2 ILE A 151 " =    2.520
peak=   -3.327 closest distance to " OG  SER A 206 " =    1.787
peak=   -3.324 closest distance to " N   SER A 276 " =    1.253
peak=   -3.318 closest distance to " CB  PRO A  90 " =    1.500
peak=   -3.317 closest distance to " CB  ALA A 248 " =    2.409
peak=   -3.317 closest distance to " OG  SER A 141 " =    1.796
peak=   -3.315 closest distance to " CB  VAL A 230 " =    1.019
peak=   -3.314 closest distance to " O   HOH Z 353 " =    1.610
peak=   -3.310 closest distance to " O   HOH Z 389 " =    1.998
peak=   -3.310 closest distance to " O   HOH Z 191 " =    5.409
peak=   -3.308 closest distance to " CZ3 TRP A 179 " =    1.236
peak=   -3.307 closest distance to " CZ  PHE A  59 " =    1.522
peak=   -3.306 closest distance to " O   ARG A 145 " =    1.419
peak=   -3.299 closest distance to " N   THR A 235 " =    1.203
peak=   -3.299 closest distance to " CZ2 TRP A 274 " =    0.840
peak=   -3.298 closest distance to " CH2 TRP A 123 " =    2.266
peak=   -3.297 closest distance to " CD1 PHE A  59 " =    2.043
peak=   -3.295 closest distance to " CE3 TRP A 123 " =    1.394
peak=   -3.293 closest distance to " O   VAL A  67 " =    2.896
peak=   -3.292 closest distance to " ND2 ASN A 285 " =    2.108
peak=   -3.291 closest distance to " O   HOH Z 427 " =    1.785
peak=   -3.281 closest distance to " CE2 TYR A 116 " =    3.081
peak=   -3.280 closest distance to " OG  SER A  87 " =    1.658
peak=   -3.279 closest distance to " O   VAL A 189 " =    2.565
peak=   -3.278 closest distance to " NE2 GLN A 223 " =    1.504
peak=   -3.277 closest distance to " O   HOH Z 359 " =    3.499
peak=   -3.273 closest distance to " OG  SER A  26 " =    1.068
peak=   -3.269 closest distance to " OH  TYR A 214 " =    1.164
peak=   -3.269 closest distance to " O   HOH Z 207 " =    1.926
peak=   -3.268 closest distance to " O   HOH Z 102 " =    1.515
peak=   -3.262 closest distance to " O   HOH Z 389 " =    1.444
peak=   -3.261 closest distance to " CG  GLN A  88 " =    0.839
peak=   -3.260 closest distance to " O   TYR A 247 " =    2.818
peak=   -3.259 closest distance to " C   LEU A 222 " =    0.770
peak=   -3.251 closest distance to " O   HOH Z 298 " =    2.636
peak=   -3.249 closest distance to " CD  ARG A 139 " =    1.739
peak=   -3.246 closest distance to " OG  SER A  62 " =    4.454
peak=   -3.246 closest distance to " N   GLN A  58 " =    1.944
peak=   -3.244 closest distance to " CB  ALA A 291 " =    2.049
peak=   -3.239 closest distance to " O   HOH Z 143 " =    1.139
peak=   -3.236 closest distance to " N   ARG A 138 " =    1.501
peak=   -3.236 closest distance to " N   VAL A 232 " =    2.197
peak=   -3.236 closest distance to " O   HOH Z 216 " =    2.087
peak=   -3.235 closest distance to " OE1 GLN A  58 " =    2.964
peak=   -3.234 closest distance to " O   HOH Z 435 " =    2.192
peak=   -3.233 closest distance to " CG  ASN A 301 " =    1.946
peak=   -3.229 closest distance to " CG2 VAL A 202 " =    2.754
peak=   -3.228 closest distance to " O   HOH Z 377 " =    0.941
peak=   -3.228 closest distance to " CB  ALA A 114 " =    2.383
peak=   -3.225 closest distance to " CD1 LEU A 228 " =    2.355
peak=   -3.219 closest distance to " O   HOH Z  60 " =    2.150
peak=   -3.218 closest distance to " N   PHE A  59 " =    1.995
peak=   -3.217 closest distance to " O   HOH Z 351 " =    1.530
peak=   -3.216 closest distance to " O   HOH Z 189 " =    2.742
peak=   -3.215 closest distance to " CB  TRP A  85 " =    2.588
peak=   -3.213 closest distance to " CG  GLU A 152 " =    2.147
peak=   -3.211 closest distance to " C   MET A 188 " =    1.600
peak=   -3.208 closest distance to " O   HOH Z 108 " =    1.920
peak=   -3.207 closest distance to " C   LYS A  76 " =    1.263
peak=   -3.203 closest distance to " O   HOH Z 394 " =    1.527
peak=   -3.198 closest distance to " OD1 ASN A 148 " =    1.583
peak=   -3.190 closest distance to " ND2 ASN A 252 " =    1.962
peak=   -3.188 closest distance to " CG2 THR A 178 " =    2.147
peak=   -3.183 closest distance to " NE BARG A 102 " =    2.236
peak=   -3.179 closest distance to " OE1 GLN A  77 " =    1.807
peak=   -3.179 closest distance to " O   HOH Z 420 " =    3.218
peak=   -3.178 closest distance to " CE  LYS A  76 " =    2.745
peak=   -3.177 closest distance to " OE2 GLU A 152 " =    1.014
peak=   -3.176 closest distance to " O   SER A 271 " =    2.169
peak=   -3.176 closest distance to " O   HOH Z 357 " =    1.936
peak=   -3.175 closest distance to " OD2 ASP A  50 " =    2.021
peak=   -3.175 closest distance to " OD2 ASP A  50 " =    1.593
peak=   -3.174 closest distance to " O   VAL A  67 " =    2.422
peak=   -3.168 closest distance to " NH2 ARG A 219 " =    1.818
peak=   -3.163 closest distance to " O   HOH Z 423 " =    1.260
peak=   -3.162 closest distance to " N   VAL A  72 " =    1.522
peak=   -3.161 closest distance to " O   HOH Z 389 " =    4.595
peak=   -3.150 closest distance to " CB  ALA A 161 " =    2.573
peak=   -3.150 closest distance to " O   HOH Z 368 " =    2.466
peak=   -3.144 closest distance to " O   HOH Z 238 " =    0.896
peak=   -3.144 closest distance to " CB  CYS A 254 " =    1.946
peak=   -3.143 closest distance to " O   HOH Z 424 " =    1.212
peak=   -3.141 closest distance to " O   HOH Z 255 " =    2.453
peak=   -3.134 closest distance to " CB  SER A  63 " =    3.222
peak=   -3.133 closest distance to " CB  TYR A  15 " =    2.061
peak=   -3.133 closest distance to " O   HOH Z  52 " =    1.873
peak=   -3.133 closest distance to " CG1 VAL A 250 " =    2.683
peak=   -3.130 closest distance to " O   HOH Z 266 " =    3.209
peak=   -3.129 closest distance to " O   HOH Z 186 " =    1.438
peak=   -3.125 closest distance to " O   HOH Z 426 " =    2.159
peak=   -3.123 closest distance to " CB  CYS A 201 " =    2.173
peak=   -3.122 closest distance to " N   VAL A 125 " =    0.938
peak=   -3.112 closest distance to " O   VAL A 125 " =    2.317
peak=   -3.108 closest distance to " CE BMET A  47 " =    1.618
peak=   -3.105 closest distance to " CG  PHE A 283 " =    2.588
peak=   -3.093 closest distance to " ND2 ASN A 215 " =    2.193
peak=   -3.092 closest distance to " CB  CYS A 201 " =    2.487
peak=   -3.091 closest distance to " OD1 ASN A 187 " =    1.564
peak=   -3.086 closest distance to " OG ASER A 216 " =    1.219
peak=   -3.081 closest distance to " O   HOH Z 318 " =    1.833
peak=   -3.069 closest distance to " O   HOH Z 243 " =    1.809
peak=   -3.066 closest distance to " CE2 TRP A  70 " =    2.413
peak=   -3.063 closest distance to " CD  GLU A 277 " =    1.137
peak=   -3.061 closest distance to " CD1 LEU A 297 " =    2.278
peak=   -3.060 closest distance to " CB  ALA A 100 " =    2.342
peak=   -3.044 closest distance to " O   HOH Z 200 " =    3.503
peak=   -3.023 closest distance to " CZ BARG A 275 " =    1.589
peak=   -3.011 closest distance to " O   HOH Z 353 " =    1.896

================= 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    :  0.4879 0.4803   6.291130e+00   6.278503e+00
   1_bss:  0.4791 0.4683   6.285095e+00   6.270768e+00
   1_xyz:  0.4042 0.4339   6.193937e+00   6.225724e+00
   1_adp:  0.3642 0.4215   6.141256e+00   6.215899e+00
   1_occ:  0.3640 0.4212   6.140476e+00   6.215635e+00
   2_bss:  0.3625 0.4170   6.141326e+00   6.213904e+00
   2_xyz:  0.2934 0.3522   5.973636e+00   6.093877e+00
   2_adp:  0.2723 0.3405   5.924375e+00   6.064868e+00
   2_occ:  0.2721 0.3403   5.924203e+00   6.065195e+00
   3_bss:  0.2717 0.3367   5.922298e+00   6.061478e+00
   3_xyz:  0.1989 0.2622   5.650783e+00   5.847484e+00
   3_adp:  0.1774 0.2364   5.543493e+00   5.755614e+00
   3_occ:  0.1771 0.2354   5.541403e+00   5.753697e+00
   4_bss:  0.1763 0.2344   5.539921e+00   5.750848e+00
   4_xyz:  0.1460 0.2005   5.385485e+00   5.620657e+00
   4_adp:  0.1339 0.1863   5.305943e+00   5.544694e+00
   4_occ:  0.1338 0.1860   5.304964e+00   5.543272e+00
   5_bss:  0.1342 0.1855   5.303227e+00   5.541822e+00
   5_xyz:  0.1219 0.1720   5.225126e+00   5.473132e+00
   5_adp:  0.1188 0.1694   5.207325e+00   5.458111e+00
   5_occ:  0.1188 0.1693   5.206836e+00   5.457330e+00
   5_bss:  0.1187 0.1693   5.206932e+00   5.457382e+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:  0.379  20.000   7.920   9.616   6.932   0.000   0.000   0.000
   1_xyz:  0.379  20.000   7.920   9.616   6.932   0.000   0.000   0.000
   1_adp:  0.379  20.000   7.920   9.616   6.932   0.000   0.000   0.000
   1_occ:  0.379  20.000   7.920   9.616   6.932   0.000   0.000   0.000
   2_bss:  0.372  50.000   4.601   5.661   4.264   0.000   0.000   0.000
   2_xyz:  0.372  50.000   4.601   5.661   4.264   0.000   0.000   0.000
   2_adp:  0.372  50.000   4.601   5.661   4.264   0.000   0.000   0.000
   2_occ:  0.372  50.000   4.601   5.661   4.264   0.000   0.000   0.000
   3_bss:  0.347  50.001   3.339   3.451   3.593   0.000   0.000   0.000
   3_xyz:  0.347  50.001   3.339   3.451   3.593   0.000   0.000   0.000
   3_adp:  0.347  50.001   3.339   3.451   3.593   0.000   0.000   0.000
   3_occ:  0.347  50.001   3.339   3.451   3.593   0.000   0.000   0.000
   4_bss:  0.347  50.001   2.148   1.693   2.813   0.000   0.000   0.000
   4_xyz:  0.347  50.001   2.148   1.693   2.813   0.000   0.000   0.000
   4_adp:  0.347  50.001   2.148   1.693   2.813   0.000   0.000   0.000
   4_occ:  0.347  50.001   2.148   1.693   2.813   0.000   0.000   0.000
   5_bss:  0.327  50.001   1.961   1.382   2.687   0.000   0.000   0.000
   5_xyz:  0.327  50.001   1.961   1.382   2.687   0.000   0.000   0.000
   5_adp:  0.327  50.001   1.961   1.382   2.687   0.000   0.000   0.000
   5_occ:  0.327  50.001   1.961   1.382   2.687   0.000   0.000   0.000
   5_bss:  0.319  47.905  -0.051  -0.642   0.692  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.183 0.4045  0.4811    73934.088
   1_bss:  58.740 0.4092  0.6158    71932.665
   1_xyz:  52.190 0.4916  0.7242    58199.444
   1_adp:  49.838 0.5215  0.8075    55438.474
   1_occ:  49.846 0.5214  0.8070    55467.953
   2_bss:  49.483 0.5258  0.7269    54779.514
   2_xyz:  39.018 0.6531  0.8805    36077.476
   2_adp:  36.478 0.6838  0.9213    32721.541
   2_occ:  36.505 0.6834  0.9204    32741.443
   3_bss:  36.164 0.6871  0.8802    32168.758
   3_xyz:  26.457 0.7950  0.9833    17805.485
   3_adp:  23.153 0.8302  1.0071    14364.833
   3_occ:  23.090 0.8307  1.0066    14248.743
   4_bss:  22.998 0.8315  0.9633    14137.229
   4_xyz:  19.435 0.8668  0.9773    10534.075
   4_adp:  17.555 0.8846  0.9774     8987.574
   4_occ:  17.524 0.8849  0.9773     8952.652
   5_bss:  17.479 0.8851  0.9697     8886.309
   5_xyz:  15.865 0.8992  0.9772     7589.279
   5_adp:  15.450 0.9031  0.9725     7349.308
   5_occ:  15.437 0.9032  0.9725     7335.574
   5_bss:  15.444 0.9031  0.9764     7334.809
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3544e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3544e+01
   1_xyz:   1.734  0.014  0.108 18.375  0.007  4.107   1.4927e-01
   1_adp:   1.734  0.014  0.108 18.375  0.007  4.107   1.4927e-01
   1_occ:   1.734  0.014  0.108 18.375  0.007  4.107   1.4927e-01
   2_bss:   1.734  0.014  0.108 18.375  0.007  4.107   1.4927e-01
   2_xyz:   1.152  0.009  0.082 16.328  0.006  4.104   8.7208e-02
   2_adp:   1.152  0.009  0.082 16.328  0.006  4.104   8.7208e-02
   2_occ:   1.152  0.009  0.082 16.328  0.006  4.104   8.7208e-02
   3_bss:   1.152  0.009  0.082 16.328  0.006  4.104   8.7208e-02
   3_xyz:   1.283  0.010  0.092 16.036  0.005  4.122   9.5218e-02
   3_adp:   1.283  0.010  0.092 16.036  0.005  4.122   9.5218e-02
   3_occ:   1.283  0.010  0.092 16.036  0.005  4.122   9.5218e-02
   4_bss:   1.283  0.010  0.092 16.036  0.005  4.122   9.5218e-02
   4_xyz:   1.024  0.007  0.077 15.568  0.004  4.116   6.4180e-02
   4_adp:   1.024  0.007  0.077 15.568  0.004  4.116   6.4180e-02
   4_occ:   1.024  0.007  0.077 15.568  0.004  4.116   6.4180e-02
   5_bss:   1.024  0.007  0.077 15.568  0.004  4.116   6.4180e-02
   5_xyz:   1.045  0.007  0.082 15.557  0.004  4.108   6.5805e-02
   5_adp:   1.045  0.007  0.082 15.557  0.004  4.108   6.5805e-02
   5_occ:   1.045  0.007  0.082 15.557  0.004  4.108   6.5805e-02
   5_bss:   1.045  0.007  0.082 15.557  0.004  4.108   6.5805e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9402e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9402e+00
   1_xyz:  13.823  0.191  0.456 87.136  0.043  2.193   1.0533e-01
   1_adp:  13.823  0.191  0.456 87.136  0.043  2.193   1.0533e-01
   1_occ:  13.823  0.191  0.456 87.136  0.043  2.193   1.0533e-01
   2_bss:  13.823  0.191  0.456 87.136  0.043  2.193   1.0533e-01
   2_xyz:   7.151  0.088  0.303 76.667  0.057  2.173   9.0803e-02
   2_adp:   7.151  0.088  0.303 76.667  0.057  2.173   9.0803e-02
   2_occ:   7.151  0.088  0.303 76.667  0.057  2.173   9.0803e-02
   3_bss:   7.151  0.088  0.303 76.667  0.057  2.173   9.0803e-02
   3_xyz:   8.733  0.115  0.456 78.952  0.051  2.073   9.1992e-02
   3_adp:   8.733  0.115  0.456 78.952  0.051  2.073   9.1992e-02
   3_occ:   8.733  0.115  0.456 78.952  0.051  2.073   9.1992e-02
   4_bss:   8.733  0.115  0.456 78.952  0.051  2.073   9.1992e-02
   4_xyz:   7.772  0.055  0.431 82.461  0.035  2.279   4.5845e-02
   4_adp:   7.772  0.055  0.431 82.461  0.035  2.279   4.5845e-02
   4_occ:   7.772  0.055  0.431 82.461  0.035  2.279   4.5845e-02
   5_bss:   7.772  0.055  0.431 82.461  0.035  2.279   4.5845e-02
   5_xyz:   8.702  0.055  0.540 82.715  0.033  2.315   5.0696e-02
   5_adp:   8.702  0.055  0.540 82.715  0.033  2.315   5.0696e-02
   5_occ:   8.702  0.055  0.540 82.715  0.033  2.315   5.0696e-02
   5_bss:   8.702  0.055  0.540 82.715  0.033  2.315   5.0696e-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:  52.03   0.00  12.30  52.03   0.00  10.89  48.64   0.00  20.01
   1_occ:  52.03   0.00  12.30  52.03   0.00  10.89  48.64   0.00  20.01
   2_bss:  52.03   0.00  12.30  52.03   0.00  10.89  48.64   0.00  20.01
   2_xyz:  52.03   0.00  12.30  52.03   0.00  10.89  48.64   0.00  20.01
   2_adp:  72.50   0.00  13.07  72.50   0.00  10.52  61.07   0.00  27.00
   2_occ:  72.50   0.00  13.07  72.50   0.00  10.52  61.07   0.00  27.00
   3_bss:  72.50   0.00  13.07  72.50   0.00  10.52  61.07   0.00  27.00
   3_xyz:  72.50   0.00  13.07  72.50   0.00  10.52  61.07   0.00  27.00
   3_adp:  64.24   0.00  12.81  63.06   0.00   9.54  64.24   2.41  30.63
   3_occ:  64.24   0.00  12.81  63.06   0.00   9.54  64.24   2.41  30.63
   4_bss:  64.24   0.00  12.81  63.06   0.00   9.54  64.24   2.41  30.63
   4_xyz:  64.24   0.00  12.81  63.06   0.00   9.54  64.24   2.41  30.63
   4_adp:  75.90   0.00  13.40  73.58   0.00   9.07  75.90   2.68  37.00
   4_occ:  75.90   0.00  13.40  73.58   0.00   9.07  75.90   2.68  37.00
   5_bss:  75.90   0.00  13.40  73.58   0.00   9.07  75.90   2.68  37.00
   5_xyz:  75.90   0.00  13.40  73.58   0.00   9.07  75.90   2.68  37.00
   5_adp:  86.32   0.00  13.43  85.19   0.00   8.89  86.32   2.25  38.14
   5_occ:  86.32   0.00  13.43  85.19   0.00   8.89  86.32   2.25  38.14
   5_bss:  88.45   2.13  15.56  87.31   2.13  11.02  88.45   4.38  40.27
------------------------------------------------------------------------
 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:    1.245    0.033    0.416
   1_adp:    1.245    0.033    0.416
   1_occ:    1.245    0.033    0.416
   2_bss:    1.245    0.033    0.416
   2_xyz:    1.494    0.043    0.587
   2_adp:    1.494    0.043    0.587
   2_occ:    1.494    0.043    0.587
   3_bss:    1.494    0.043    0.587
   3_xyz:    1.785    0.070    0.731
   3_adp:    1.785    0.070    0.731
   3_occ:    1.785    0.070    0.731
   4_bss:    1.785    0.070    0.731
   4_xyz:    2.067    0.033    0.776
   4_adp:    2.067    0.033    0.776
   4_occ:    2.067    0.033    0.776
   5_bss:    2.067    0.033    0.776
   5_xyz:    2.131    0.031    0.799
   5_adp:    2.131    0.031    0.799
   5_occ:    2.131    0.031    0.799
   5_bss:    2.131    0.031    0.799
------------------------------------------------------------------------

CPU time actual refinement: 354.06


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_983/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_983/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_983/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_983/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_983/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.90 
  Macro-tasks:
    bulk solvent and scale       = 41.36  
    individual site refinement   = 151.93 
    weights calculation          = 32.93  
    collect and process          = 6.45   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 232.80 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 111.91 
    alpha_beta                      = 8.21   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 122.83 
    fmodel                         = 7.15   
    r_factors                      = 0.27   
    phase_errors                   = 10.35  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 264.54 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.929 micro seconds
Total CPU time: 6.13 minutes
from_scatterers_fft:    650 calls, 111.53 s
gradients_fft:          595 calls, 109.01 s

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

# Date 2008-01-16 Time 02:54:50 PST -0800 (1200480890.60 s)
Start R-work = 0.4879, R-free = 0.4803 (no bulk solvent and anisotropic scale)
Final R-work = 0.1349, R-free = 0.1840 (no bulk solvent and anisotropic scale)

Start R-work = 0.4791, R-free = 0.4683
Final R-work = 0.1187, R-free = 0.1693