# Date 2008-01-16 Time 02:55:47 PST -0800 (1200480947.30 s)
#phil __OFF__

Command line arguments: "../1028.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13742
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1028

-------------------------------------------------------------------------------
  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, 46.93, 86.39, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00038
Completeness in resolution range: 0.971869
Completeness with d_max=infinity: 0.968889

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   2.0004

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, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00038
Completeness in resolution range: 0.971869
Completeness with d_max=infinity: 0.968889

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1573 -  4.2804 [2111/2136]  1901   210   9.9%
  bin  2:  4.2804 -  3.4102 [2037/2057]  1832   205  10.1%
  bin  3:  3.4102 -  2.9828 [2006/2025]  1803   203  10.1%
  bin  4:  2.9828 -  2.7118 [1988/2018]  1796   192   9.7%
  bin  5:  2.7118 -  2.5184 [1983/2002]  1786   197   9.9%
  bin  6:  2.5184 -  2.3705 [1964/1989]  1764   200  10.2%
  bin  7:  2.3705 -  2.2522 [1947/1975]  1747   200  10.3%
  bin  8:  2.2522 -  2.1544 [1959/1995]  1765   194   9.9%
  bin  9:  2.1544 -  2.0717 [1952/1994]  1762   190   9.7%
  bin 10:  2.0717 -  2.0004 [1642/1965]  1474   168  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1028/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2185
        3.04 -     3.66: 4603
        3.66 -     4.28: 9008
        4.28 -     4.90: 12263
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.948 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.304 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.318 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28063 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_1028/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1028/model_refine_001.geo

CPU time processing inputs: 9.27


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.93 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4239   r_free= 0.4115   ksol= 0.00   Bsol= 0.00   scale= 0.822    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.215685                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7741 0.99   1380  154 0.3620 0.3368      6.5228      6.4209|
|  2:  4.7741 -  3.8092 0.99   1324  145 0.3159 0.3239      6.6226      6.6427|
|  3:  3.8092 -  3.3335 0.99   1289  143 0.3599 0.3301      6.5293      6.5476|
|  4:  3.3335 -  3.0314 0.99   1283  147 0.3973 0.3521      6.4401      6.3405|
|  5:  3.0314 -  2.8156 0.99   1291  140 0.4421 0.4401      6.3034      6.3451|
|  6:  2.8156 -  2.6505 0.99   1274  142 0.4415 0.4618      6.2231      6.1749|
|  7:  2.6505 -  2.5184 0.99   1277  136 0.4882 0.4935      6.2084      6.2148|
|  8:  2.5184 -  2.4092 0.98   1254  147 0.4723 0.4370      6.1435      6.1178|
|  9:  2.4092 -  2.3168 0.98   1256  137 0.4538 0.4930       6.072      6.0985|
| 10:  2.3168 -  2.2371 1.00   1269  141 0.4853 0.4492      6.0844      6.0579|
| 11:  2.2371 -  2.1674 0.97   1248  137 0.4885 0.4370      6.0262       5.986|
| 12:  2.1674 -  2.1056 0.98   1242  142 0.4715 0.4909      5.9583      6.0144|
| 13:  2.1056 -  2.0503 1.00   1258  136 0.5049 0.5160      5.8898      5.8755|
| 14:  2.0503 -  2.0004 0.77    985  112 0.4877 0.4288      5.8457      5.6516|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7741  1380   154  0.75  30.13   0.81     0.77      55434.40|
|  2:  4.7741 -  3.8092  1324   145  0.80  26.73   0.91     0.83      67408.78|
|  3:  3.8092 -  3.3335  1289   143  0.73  32.63   0.87     0.81      69906.86|
|  4:  3.3335 -  3.0314  1283   147  0.67  37.97   0.84     0.74      64444.23|
|  5:  3.0314 -  2.8156  1291   140  0.57  46.50   0.77     0.65      59260.26|
|  6:  2.8156 -  2.6505  1274   142  0.54  49.21   0.78     0.59      55212.24|
|  7:  2.6505 -  2.5184  1277   136  0.50  52.38   0.74     0.55      52817.45|
|  8:  2.5184 -  2.4092  1254   147  0.48  53.40   0.76     0.55      48586.58|
|  9:  2.4092 -  2.3168  1256   137  0.51  51.72   0.75     0.56      42677.07|
| 10:  2.3168 -  2.2371  1269   141  0.51  51.16   0.78     0.57      37588.59|
| 11:  2.2371 -  2.1674  1248   137  0.50  52.07   0.77     0.56      34824.13|
| 12:  2.1674 -  2.1056  1242   142  0.49  53.47   0.79     0.56      34137.82|
| 13:  2.1056 -  2.0503  1258   136  0.48  53.66   0.75     0.56      28971.12|
| 14:  2.0503 -  2.0004   985   112  0.57  46.63   0.73     0.61      20261.91|
|alpha:            min =        0.55 max =            0.83 mean =         0.64|
|beta:             min =    20261.91 max =        69906.86 mean =     48628.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           90.00 mean =        45.32|
|phase err.(test): min =        0.00 max =           89.96 mean =        45.39|
|-----------------------------------------------------------------------------|

============================== 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 = 7.587105              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.746   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.552383              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.222   (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:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      679 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1501 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2595 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3894 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5017 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6545 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7661 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.085 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.614 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4317   r_free= 0.4195   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.221507                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4162   r_free= 0.4000   ksol= 0.33   Bsol= 18.29   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.99,7.90,8.00,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.211062                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.044157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.645   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.588787              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.099   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4162      final r-factor (work) = 0.3056          |
| start r-factor (free) = 0.4000      final r-factor (free) = 0.3300          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.0334 = 7.04 * 0.50 * 6.2316 + 1.00 * 54.0854                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4052 = 7.04 * 0.50 * 6.0450 + 1.00 * 0.1141                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3056      final r-factor (work) = 0.2396          |
| start r-factor (free) = 0.3300      final r-factor (free) = 0.2755          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5740 = 0.59 * 1.00 * 6.0450 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4608 = 0.59 * 1.00 * 5.8587 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    46.44   9.74     None  None   None       |
|    all(noH): 2823   0      0.00    46.44   9.74     None  None   None       |
|    Sol.    : 438    0      0.00    46.44   24.91    None  None   None       |
|    Mac.    : 2385   0      0.00    44.04   6.95     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 -   4.644: 1011   |   5:    23.219 -  27.863:  120        |
|      1:     4.644 -   9.288:  826   |   6:    27.863 -  32.507:   97        |
|      2:     9.288 -  13.932:  362   |   7:    32.507 -  37.151:   65        |
|      3:    13.932 -  18.575:  178   |   8:    37.151 -  41.794:   32        |
|      4:    18.575 -  23.219:  109   |   9:    41.794 -  46.438:   23        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2396 r_free = 0.2755             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2390 r_free = 0.2757             target_work(ml) = 5.780         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2390   r_free= 0.2757   ksol= 0.33   Bsol= 18.29   scale= 1.080   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.99,7.90,8.00,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.779808                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2339   r_free= 0.2689   ksol= 0.34   Bsol= 48.75   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.49,4.30,5.17,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.776528                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.526235              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.564   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.324108              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.925  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2339      final r-factor (work) = 0.1583          |
| start r-factor (free) = 0.2689      final r-factor (free) = 0.2033          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3929 = 4.53 * 0.50 * 5.8676 + 1.00 * 0.1138                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7556 = 4.53 * 0.50 * 5.6045 + 1.00 * 0.0719                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1583      final r-factor (work) = 0.1468          |
| start r-factor (free) = 0.2033      final r-factor (free) = 0.1931          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8809 = 0.32 * 1.00 * 5.6045 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9931 = 0.32 * 1.00 * 5.3920 + 1.00 * 0.2455                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.80   10.03    None  None   None       |
|    all(noH): 2823   0      0.00    77.80   10.03    None  None   None       |
|    Sol.    : 438    0      0.52    47.69   26.54    None  None   None       |
|    Mac.    : 2385   0      0.00    77.80   6.99     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 -   7.780: 1650   |   5:    38.899 -  46.679:   50        |
|      1:     7.780 -  15.560:  625   |   6:    46.679 -  54.459:    2        |
|      2:    15.560 -  23.340:  177   |   7:    54.459 -  62.239:    0        |
|      3:    23.340 -  31.119:  192   |   8:    62.239 -  70.019:    0        |
|      4:    31.119 -  38.899:  126   |   9:    70.019 -  77.798:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1468 r_free = 0.1931             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1467 r_free = 0.1930             target_work(ml) = 5.364         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1467   r_free= 0.1930   ksol= 0.34   Bsol= 48.75   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.49,4.30,5.17,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.364189                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1461   r_free= 0.1912   ksol= 0.34   Bsol= 48.75   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.75,3.47,4.46,0.00,0.00,0.00); trace/3= 3.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.363521                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.482448              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.438  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.168118              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.264   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1461      final r-factor (work) = 0.1299          |
| start r-factor (free) = 0.1912      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7735 = 2.48 * 0.50 * 5.3992 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6585 = 2.48 * 0.50 * 5.3105 + 1.00 * 0.0670                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1299      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1767      final r-factor (free) = 0.1674          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.4584 = 5.17 * 1.00 * 5.3105 + 1.00 * 0.0129                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.0757 = 5.17 * 1.00 * 5.2361 + 1.00 * 0.0148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.97   11.65    None  None   None       |
|    all(noH): 2823   0      0.00    80.97   11.65    None  None   None       |
|    Sol.    : 438    0      0.34    80.97   34.76    None  None   None       |
|    Mac.    : 2385   0      0.00    74.74   7.40     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 -   8.097: 1695   |   5:    40.485 -  48.582:   78        |
|      1:     8.097 -  16.194:  553   |   6:    48.582 -  56.679:   77        |
|      2:    16.194 -  24.291:  161   |   7:    56.679 -  64.777:   35        |
|      3:    24.291 -  32.388:  112   |   8:    64.777 -  72.874:   18        |
|      4:    32.388 -  40.485:   91   |   9:    72.874 -  80.971:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1200 r_free = 0.1674             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1200 r_free = 0.1674             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1674   ksol= 0.34   Bsol= 48.75   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.75,3.47,4.46,0.00,0.00,0.00); trace/3= 3.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207152                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1673   ksol= 0.32   Bsol= 48.75   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.55,3.37,4.39,0.00,0.00,0.00); trace/3= 3.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206265                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.256703              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.559  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.230718              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.678  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1673      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9743 = 2.26 * 0.50 * 5.2353 + 1.00 * 0.0670                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9206 = 2.26 * 0.50 * 5.1894 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2122 = 0.23 * 1.00 * 5.1894 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2067 = 0.23 * 1.00 * 5.1821 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.33   11.27    None  None   None       |
|    all(noH): 2823   0      0.00    75.33   11.27    None  None   None       |
|    Sol.    : 438    0      1.00    75.33   33.27    None  None   None       |
|    Mac.    : 2385   0      0.00    73.75   7.23     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 -   7.533: 1680   |   5:    37.663 -  45.196:   68        |
|      1:     7.533 -  15.065:  555   |   6:    45.196 -  52.729:   80        |
|      2:    15.065 -  22.598:  163   |   7:    52.729 -  60.262:   40        |
|      3:    22.598 -  30.131:  109   |   8:    60.262 -  67.794:   11        |
|      4:    30.131 -  37.663:  107   |   9:    67.794 -  75.327:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1604             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1603             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1603   ksol= 0.32   Bsol= 48.75   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.55,3.37,4.39,0.00,0.00,0.00); trace/3= 3.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168737                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1602   ksol= 0.32   Bsol= 48.85   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,3.31,4.35,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168976                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.441802              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.541  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.330011              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.289  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1602      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8007 = 1.44 * 0.50 * 5.1818 + 1.00 * 0.0651                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7872 = 1.44 * 0.50 * 5.1740 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7185 = 0.33 * 1.00 * 5.1740 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7182 = 0.33 * 1.00 * 5.1716 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.10   11.23    None  None   None       |
|    all(noH): 2823   0      0.00    74.10   11.23    None  None   None       |
|    Sol.    : 438    0      1.10    73.16   33.08    None  None   None       |
|    Mac.    : 2385   0      0.00    74.10   7.22     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 -   7.410: 1663   |   5:    37.048 -  44.457:   73        |
|      1:     7.410 -  14.819:  556   |   6:    44.457 -  51.867:   80        |
|      2:    14.819 -  22.229:  167   |   7:    51.867 -  59.276:   38        |
|      3:    22.229 -  29.638:  114   |   8:    59.276 -  66.686:   11        |
|      4:    29.638 -  37.048:  111   |   9:    66.686 -  74.096:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1604             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1162 r_free = 0.1604             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1604   ksol= 0.32   Bsol= 48.85   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,3.31,4.35,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173502                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7741 0.99   1380  154 0.1022 0.1292      5.4046      5.5256|
|  2:  4.7741 -  3.8092 0.99   1324  145 0.0909 0.1131      5.4752       5.651|
|  3:  3.8092 -  3.3335 0.99   1289  143 0.1078 0.1524      5.4985      5.8504|
|  4:  3.3335 -  3.0314 0.99   1283  147 0.1232 0.1593      5.4766      5.6296|
|  5:  3.0314 -  2.8156 0.99   1291  140 0.1391 0.1752      5.3611      5.5694|
|  6:  2.8156 -  2.6505 0.99   1274  142 0.1234 0.1936      5.2359      5.4787|
|  7:  2.6505 -  2.5184 0.99   1277  136 0.1333 0.1594      5.2099      5.3817|
|  8:  2.5184 -  2.4092 0.98   1254  147 0.1238 0.1778      5.1131      5.3841|
|  9:  2.4092 -  2.3168 0.98   1256  137 0.1238 0.1772      5.0854      5.3159|
| 10:  2.3168 -  2.2371 1.00   1269  141 0.1187 0.1721      4.9939      5.2685|
| 11:  2.2371 -  2.1674 0.97   1248  137 0.1178 0.1710      4.9685      5.2328|
| 12:  2.1674 -  2.1056 0.98   1242  142 0.1168 0.1806      4.8993      5.2438|
| 13:  2.1056 -  2.0503 1.00   1258  136 0.1202 0.1768      4.8348      5.1067|
| 14:  2.0503 -  2.0004 0.77    985  112 0.1120 0.1788      4.7091      4.9396|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7741  1380   154  0.94   9.29   0.97     0.95       7294.80|
|  2:  4.7741 -  3.8092  1324   145  0.95   8.16   1.00     0.99       9256.94|
|  3:  3.8092 -  3.3335  1289   143  0.93  11.50   1.02     1.01      10878.73|
|  4:  3.3335 -  3.0314  1283   147  0.92  13.61   1.00     0.98      10503.17|
|  5:  3.0314 -  2.8156  1291   140  0.89  16.44   0.99     0.96       8685.01|
|  6:  2.8156 -  2.6505  1274   142  0.90  15.74   0.98     0.96       7361.88|
|  7:  2.6505 -  2.5184  1277   136  0.90  16.04   0.98     0.95       6523.54|
|  8:  2.5184 -  2.4092  1254   147  0.90  15.81   0.99     0.97       5695.19|
|  9:  2.4092 -  2.3168  1256   137  0.91  15.84   1.00     0.97       5401.81|
| 10:  2.3168 -  2.2371  1269   141  0.90  15.44   1.00     0.95       4429.28|
| 11:  2.2371 -  2.1674  1248   137  0.90  16.61   1.00     0.96       4522.97|
| 12:  2.1674 -  2.1056  1242   142  0.92  14.90   1.00     0.99       3973.48|
| 13:  2.1056 -  2.0503  1258   136  0.90  16.47   1.00     0.99       3605.88|
| 14:  2.0503 -  2.0004   985   112  0.91  15.27   0.97     0.94       2714.33|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2714.33 max =        10878.73 mean =      6584.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.29|
|phase err.(test): min =        0.00 max =           87.72 mean =        13.72|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1604   ksol= 0.32   Bsol= 52.54   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.38,0.66,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173502                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1604   ksol= 0.32   Bsol= 52.54   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.38,0.66,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173502                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7741 0.99   1380  154 0.1022 0.1292      5.4046      5.5256|
|  2:  4.7741 -  3.8092 0.99   1324  145 0.0909 0.1131      5.4752       5.651|
|  3:  3.8092 -  3.3335 0.99   1289  143 0.1078 0.1524      5.4985      5.8504|
|  4:  3.3335 -  3.0314 0.99   1283  147 0.1232 0.1593      5.4766      5.6296|
|  5:  3.0314 -  2.8156 0.99   1291  140 0.1391 0.1752      5.3611      5.5694|
|  6:  2.8156 -  2.6505 0.99   1274  142 0.1234 0.1936      5.2359      5.4787|
|  7:  2.6505 -  2.5184 0.99   1277  136 0.1333 0.1594      5.2099      5.3817|
|  8:  2.5184 -  2.4092 0.98   1254  147 0.1238 0.1778      5.1131      5.3841|
|  9:  2.4092 -  2.3168 0.98   1256  137 0.1238 0.1772      5.0854      5.3159|
| 10:  2.3168 -  2.2371 1.00   1269  141 0.1187 0.1721      4.9939      5.2685|
| 11:  2.2371 -  2.1674 0.97   1248  137 0.1178 0.1710      4.9685      5.2328|
| 12:  2.1674 -  2.1056 0.98   1242  142 0.1168 0.1806      4.8993      5.2438|
| 13:  2.1056 -  2.0503 1.00   1258  136 0.1202 0.1768      4.8348      5.1067|
| 14:  2.0503 -  2.0004 0.77    985  112 0.1120 0.1788      4.7091      4.9396|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7741  1380   154  0.94   9.29   0.97     0.95       7294.80|
|  2:  4.7741 -  3.8092  1324   145  0.95   8.16   1.00     0.99       9256.94|
|  3:  3.8092 -  3.3335  1289   143  0.93  11.50   1.02     1.01      10878.73|
|  4:  3.3335 -  3.0314  1283   147  0.92  13.61   1.00     0.98      10503.17|
|  5:  3.0314 -  2.8156  1291   140  0.89  16.44   0.99     0.96       8685.01|
|  6:  2.8156 -  2.6505  1274   142  0.90  15.74   0.98     0.96       7361.88|
|  7:  2.6505 -  2.5184  1277   136  0.90  16.04   0.98     0.95       6523.54|
|  8:  2.5184 -  2.4092  1254   147  0.90  15.81   0.99     0.97       5695.19|
|  9:  2.4092 -  2.3168  1256   137  0.91  15.84   1.00     0.97       5401.81|
| 10:  2.3168 -  2.2371  1269   141  0.90  15.44   1.00     0.95       4429.28|
| 11:  2.2371 -  2.1674  1248   137  0.90  16.61   1.00     0.96       4522.97|
| 12:  2.1674 -  2.1056  1242   142  0.92  14.90   1.00     0.99       3973.48|
| 13:  2.1056 -  2.0503  1258   136  0.90  16.47   1.00     0.99       3605.88|
| 14:  2.0503 -  2.0004   985   112  0.91  15.27   0.97     0.94       2714.33|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2714.33 max =        10878.73 mean =      6584.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.29|
|phase err.(test): min =        0.00 max =           87.72 mean =        13.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.69    77.79   14.92    None  None   None       |
|    all(noH): 2823   0      3.69    77.79   14.92    None  None   None       |
|    Sol.    : 438    0      4.79    76.85   36.77    None  None   None       |
|    Mac.    : 2385   0      3.69    77.79   10.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.691 -  11.101: 1663   |   5:    40.739 -  48.148:   73        |
|      1:    11.101 -  18.510:  556   |   6:    48.148 -  55.558:   80        |
|      2:    18.510 -  25.920:  167   |   7:    55.558 -  62.967:   38        |
|      3:    25.920 -  33.329:  114   |   8:    62.967 -  70.377:   11        |
|      4:    33.329 -  40.739:  111   |   9:    70.377 -  77.787:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.327 - 4.746
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 320
   mapped sites are within: 0.707 - 4.746

peak=   10.172 closest distance to " CG2 VAL A 230 " =    1.344
peak=    7.287 closest distance to " CG2 VAL A 296 " =    1.129
peak=    5.980 closest distance to " CG  LEU A   5 " =    1.263
peak=    5.931 closest distance to " O   HOH Z 111 " =    2.277
peak=    5.870 closest distance to " CB  GLN A 223 " =    1.447
peak=    5.654 closest distance to " CD2 LEU A   5 " =    1.215
peak=    5.153 closest distance to " CG  LEU A 228 " =    1.181
peak=    4.981 closest distance to " CB  VAL A 230 " =    1.216
peak=    4.934 closest distance to " CG  PRO A 213 " =    1.227
peak=    4.881 closest distance to " CG  PRO A 198 " =    1.248
peak=    4.855 closest distance to " CB  GLN A 183 " =    1.246
peak=    4.799 closest distance to " O   HOH Z 232 " =    2.283
peak=    4.797 closest distance to " CB  SER A  63 " =    1.307
peak=    4.681 closest distance to " CG  PRO A 243 " =    1.152
peak=    4.634 closest distance to " O   HOH Z 126 " =    1.924
peak=    4.616 closest distance to " NE2 GLN A  11 " =    1.108
peak=    4.600 closest distance to " CB  VAL A 296 " =    1.100
peak=    4.556 closest distance to " O   HOH Z 369 " =    2.003
peak=    4.556 closest distance to " CB  ASN A 148 " =    1.357
peak=    4.462 closest distance to " O   HOH Z 142 " =    1.663
peak=    4.445 closest distance to " CB  ARG A 275 " =    0.852
peak=    4.431 closest distance to " O   HOH Z 368 " =    2.153
peak=    4.392 closest distance to " C   PRO A 198 " =    1.549
peak=    4.385 closest distance to " CZ  PHE A 218 " =    1.049
peak=    4.380 closest distance to " O   HOH Z 298 " =    1.774
peak=    4.375 closest distance to " CB  ASP A 124 " =    0.789
peak=    4.364 closest distance to " O   HOH Z 427 " =    3.106
peak=    4.347 closest distance to " CB  GLU A 128 " =    1.015
peak=    4.304 closest distance to " CB  TRP A 266 " =    0.938
peak=    4.294 closest distance to " CB  SER A   3 " =    1.324
peak=    4.290 closest distance to " O   HOH Z 316 " =    3.112
peak=    4.286 closest distance to " CB  GLU A 152 " =    1.214
peak=    4.227 closest distance to " CB  VAL A 265 " =    1.280
peak=    4.218 closest distance to " O   HOH Z 425 " =    1.474
peak=    4.212 closest distance to " CD2 LEU A 228 " =    1.159
peak=    4.159 closest distance to " O   HOH Z 236 " =    1.961
peak=    4.152 closest distance to " O   HOH Z 209 " =    2.278
peak=    4.146 closest distance to " OD1 ASN A  69 " =    2.606
peak=    4.143 closest distance to " NH1AARG A 145 " =    1.143
peak=    4.127 closest distance to " O   HOH Z 272 " =    1.894
peak=    4.108 closest distance to " ND2 ASN A 187 " =    1.494
peak=    4.101 closest distance to " O   HOH Z  63 " =    1.857
peak=    4.088 closest distance to " O   HOH Z 403 " =    1.810
peak=    4.082 closest distance to " CB  LEU A 143 " =    1.185
peak=    4.077 closest distance to " O   HOH Z  54 " =    2.384
peak=    4.076 closest distance to " CB  ASP A 140 " =    0.867
peak=    4.074 closest distance to " O   HOH Z  78 " =    1.724
peak=    4.070 closest distance to " O   HOH Z  43 " =    1.952
peak=    4.054 closest distance to " CB  ASN A  39 " =    0.884
peak=    4.018 closest distance to " O   HOH Z  15 " =    2.155
peak=    4.014 closest distance to " O   HOH Z 158 " =    3.093
peak=    4.013 closest distance to " CB  ASN A 187 " =    1.176
peak=    4.001 closest distance to " CA  ALA A  51 " =    1.014
peak=    3.993 closest distance to " O   HOH Z 261 " =    1.974
peak=    3.990 closest distance to " CD  ARG A 159 " =    0.794
peak=    3.987 closest distance to " CB  PRO A  54 " =    0.809
peak=    3.983 closest distance to " CA  THR A 264 " =    0.743
peak=    3.974 closest distance to " O   HOH Z 303 " =    2.107
peak=    3.966 closest distance to " O   HOH Z  68 " =    2.136
peak=    3.960 closest distance to " O   HOH Z 234 " =    3.785
peak=    3.941 closest distance to " CB  SER A 216 " =    0.848
peak=    3.887 closest distance to " O   HOH Z 346 " =    1.644
peak=    3.886 closest distance to " CA  TYR A  30 " =    0.962
peak=    3.877 closest distance to " CG1 VAL A 153 " =    0.975
peak=    3.859 closest distance to " CD1 LEU A 300 " =    1.142
peak=    3.848 closest distance to " CZ  PHE A 192 " =    0.977
peak=    3.848 closest distance to " CB  GLU A 277 " =    3.647
peak=    3.842 closest distance to " CG2 VAL A 257 " =    0.941
peak=    3.831 closest distance to " CA  SER A  87 " =    0.968
peak=    3.821 closest distance to " O   SER A  87 " =    2.236
peak=    3.807 closest distance to " O   HOH Z 189 " =    2.944
peak=    3.799 closest distance to " O   HOH Z  88 " =    3.242
peak=    3.792 closest distance to " O   HOH Z 411 " =    3.610
peak=    3.788 closest distance to " CD BLYS A 290 " =    1.009
peak=    3.785 closest distance to " CB  ARG A  79 " =    1.477
peak=    3.779 closest distance to " CA  ASN A 215 " =    1.199
peak=    3.778 closest distance to " CB  ALA A   9 " =    1.595
peak=    3.773 closest distance to " O   HOH Z  61 " =    1.667
peak=    3.766 closest distance to " CD  ARG A  66 " =    2.526
peak=    3.765 closest distance to " CB  LEU A 228 " =    1.221
peak=    3.762 closest distance to " CA  LEU A 282 " =    1.000
peak=    3.761 closest distance to " ND2 ASN A 249 " =    1.891
peak=    3.757 closest distance to " CB  MET A  40 " =    0.797
peak=    3.749 closest distance to " CG2 THR A 221 " =    1.035
peak=    3.742 closest distance to " CB  ARG A 190 " =    1.584
peak=    3.733 closest distance to " NH2 ARG A 156 " =    1.138
peak=    3.733 closest distance to " CG1 VAL A 296 " =    1.228
peak=    3.729 closest distance to " CB  ALA A 291 " =    1.395
peak=    3.728 closest distance to " CD  LYS A 166 " =    1.323
peak=    3.718 closest distance to " CG  MET A 185 " =    1.190
peak=    3.705 closest distance to " OD2 ASP A 286 " =    2.893
peak=    3.704 closest distance to " O   MET A 105 " =    1.793
peak=    3.696 closest distance to " CB  ASN A 142 " =    1.030
peak=    3.692 closest distance to " N   ASN A  39 " =    1.148
peak=    3.687 closest distance to " CG1 ILE A  33 " =    1.316
peak=    3.683 closest distance to " CB  SER A 212 " =    1.237
peak=    3.681 closest distance to " O   HOH Z 248 " =    1.730
peak=    3.675 closest distance to " O   HOH Z 273 " =    2.646
peak=    3.672 closest distance to " O   HOH Z 203 " =    1.754
peak=    3.670 closest distance to " O   HOH Z 437 " =    1.767
peak=    3.670 closest distance to " O   HOH Z 112 " =    1.645
peak=    3.664 closest distance to " CB  VAL A 202 " =    1.624
peak=    3.661 closest distance to " CD  ARG A 269 " =    0.971
peak=    3.658 closest distance to " O   ASP A 124 " =    0.961
peak=    3.637 closest distance to " CG  LEU A 167 " =    1.202
peak=    3.620 closest distance to " CB  ALA A 104 " =    0.763
peak=    3.611 closest distance to " O   HOH Z 280 " =    3.011
peak=    3.605 closest distance to " O   HOH Z 263 " =    1.644
peak=    3.604 closest distance to " CB  THR A  82 " =    1.384
peak=    3.604 closest distance to " CB  ILE A 120 " =    1.279
peak=    3.601 closest distance to " O   HOH Z 423 " =    1.668
peak=    3.589 closest distance to " O   HOH Z  92 " =    2.477
peak=    3.585 closest distance to " O   HOH Z 135 " =    1.906
peak=    3.576 closest distance to " O   HOH Z 128 " =    2.107
peak=    3.574 closest distance to " O   HOH Z 344 " =    3.042
peak=    3.574 closest distance to " CG1BVAL A  72 " =    1.622
peak=    3.573 closest distance to " CD1 LEU A   5 " =    1.353
peak=    3.572 closest distance to " O   HOH Z 247 " =    1.323
peak=    3.568 closest distance to " O   HOH Z 290 " =    1.163
peak=    3.565 closest distance to " O   HOH Z 193 " =    1.947
peak=    3.565 closest distance to " CE1 TYR A 186 " =    1.319
peak=    3.561 closest distance to " CB BVAL A  41 " =    1.199
peak=    3.560 closest distance to " CB  ALA A 248 " =    1.361
peak=    3.536 closest distance to " CB  GLU A  46 " =    0.950
peak=    3.536 closest distance to " O   HOH Z  97 " =    2.016
peak=    3.533 closest distance to " O   HOH Z 214 " =    2.061
peak=    3.530 closest distance to " N   PHE A 130 " =    1.193
peak=    3.530 closest distance to " CB  ALA A 161 " =    0.886
peak=    3.521 closest distance to " ND1 HIS A  81 " =    1.694
peak=    3.520 closest distance to " ND1 HIS A  86 " =    1.707
peak=    3.519 closest distance to " NH1 ARG A  56 " =    0.929
peak=    3.518 closest distance to " CB  TRP A 179 " =    1.496
peak=    3.515 closest distance to " O   HOH Z 171 " =    3.896
peak=    3.514 closest distance to " NZ  LYS A 117 " =    3.233
peak=    3.510 closest distance to " CG  GLN A  88 " =    1.059
peak=    3.510 closest distance to " CA  ARG A 195 " =    1.227
peak=    3.500 closest distance to " CE  LYS A  76 " =    0.872
peak=    3.500 closest distance to " CA  THR A 221 " =    0.887
peak=    3.498 closest distance to " CA  ALA A 295 " =    1.093
peak=    3.495 closest distance to " CB  THR A 157 " =    1.116
peak=    3.489 closest distance to " O   TRP A 274 " =    1.873
peak=    3.488 closest distance to " O   HOH Z 193 " =    1.886
peak=    3.486 closest distance to " O   HOH Z 227 " =    1.690
peak=    3.484 closest distance to " N   VAL A 126 " =    1.321
peak=    3.483 closest distance to " O   HOH Z 128 " =    2.224
peak=    3.481 closest distance to " CA  LYS A 117 " =    1.203
peak=    3.480 closest distance to " CB  HIS A 108 " =    0.808
peak=    3.474 closest distance to " CB  VAL A 268 " =    0.834
peak=    3.468 closest distance to " CA  ARG A  36 " =    1.139
peak=    3.467 closest distance to " O   HOH Z 368 " =    3.541
peak=    3.466 closest distance to " OG  SER A 206 " =    1.201
peak=    3.465 closest distance to " O   HOH Z 133 " =    1.740
peak=    3.464 closest distance to " O   HOH Z 132 " =    2.609
peak=    3.462 closest distance to " O   HOH Z 180 " =    2.128
peak=    3.462 closest distance to " O   HOH Z 193 " =    1.689
peak=    3.458 closest distance to " O   HOH Z 250 " =    1.324
peak=    3.455 closest distance to " O   HOH Z 197 " =    3.135
peak=    3.452 closest distance to " CA  ASP A 191 " =    0.726
peak=    3.452 closest distance to " C   TYR A 214 " =    1.597
peak=    3.451 closest distance to " CB  GLN A  88 " =    1.245
peak=    3.450 closest distance to " CD2 LEU A 255 " =    1.691
peak=    3.449 closest distance to " O   HOH Z 371 " =    3.031
peak=    3.448 closest distance to " CB  TRP A 150 " =    1.413
peak=    3.446 closest distance to " O   GLN A 278 " =    1.318
peak=    3.444 closest distance to " N   ARG A 156 " =    1.370
peak=    3.438 closest distance to " CA  ALA A  21 " =    1.164
peak=    3.437 closest distance to " O   HOH Z  97 " =    2.718
peak=    3.435 closest distance to " NE2 HIS A 207 " =    1.318
peak=    3.434 closest distance to " CA  ALA A 158 " =    1.149
peak=    3.429 closest distance to " CD2 TRP A 179 " =    1.383
peak=    3.429 closest distance to " CB  ALA A 137 " =    1.046
peak=    3.429 closest distance to " N   SER A 135 " =    1.419
peak=    3.428 closest distance to " O   HOH Z 313 " =    1.786
peak=    3.427 closest distance to " CB  MET A  47 " =    1.053
peak=    3.424 closest distance to " CB  ASN A 110 " =    1.159
peak=    3.422 closest distance to " CA  GLY A 267 " =    0.858
peak=    3.421 closest distance to " O   HOH Z 295 " =    1.558
peak=    3.408 closest distance to " CB  PRO A 198 " =    0.996
peak=    3.405 closest distance to " O   HOH Z 147 " =    1.715
peak=    3.404 closest distance to " CG1 ILE A  49 " =    1.443
peak=    3.399 closest distance to " O   HOH Z 245 " =    1.365
peak=    3.398 closest distance to " CB  ALA A  34 " =    0.863
peak=    3.397 closest distance to " CA  MET A  40 " =    1.100
peak=    3.394 closest distance to " CB  LEU A  83 " =    0.707
peak=    3.386 closest distance to " CG1 ILE A 151 " =    1.050
peak=    3.382 closest distance to " O   HOH Z 305 " =    3.554
peak=    3.377 closest distance to " O   HOH Z 102 " =    1.296
peak=    3.372 closest distance to " CA  VAL A  41 " =    0.835
peak=    3.369 closest distance to " O   ALA A 158 " =    1.410
peak=    3.368 closest distance to " O   HOH Z 327 " =    2.368
peak=    3.364 closest distance to " O   HOH Z 313 " =    1.742
peak=    3.360 closest distance to " CG BARG A 275 " =    1.492
peak=    3.359 closest distance to " CA  ALA A 154 " =    1.087
peak=    3.354 closest distance to " O   HOH Z 141 " =    1.673
peak=    3.348 closest distance to " CB  SER A 210 " =    0.849
peak=    3.347 closest distance to " O   HOH Z 353 " =    2.676
peak=    3.346 closest distance to " CB  ALA A   1 " =    4.746
peak=    3.343 closest distance to " CA  TYR A  30 " =    1.075
peak=    3.343 closest distance to " O   HOH Z 285 " =    3.047
peak=    3.341 closest distance to " O   HOH Z 350 " =    1.638
peak=    3.341 closest distance to " CD  ARG A 219 " =    1.094
peak=    3.335 closest distance to " O   HOH Z  21 " =    1.711
peak=    3.333 closest distance to " CB  ALA A 242 " =    0.805
peak=    3.332 closest distance to " CA  ASN A 127 " =    1.020
peak=    3.329 closest distance to " O   HOH Z 422 " =    2.631
peak=    3.325 closest distance to " O   HOH Z 163 " =    1.542
peak=    3.324 closest distance to " O   HOH Z 184 " =    1.403
peak=    3.320 closest distance to " O   HOH Z 185 " =    2.297
peak=    3.314 closest distance to " CB  ARG A 139 " =    0.836
peak=    3.313 closest distance to " CA  LYS A 290 " =    1.290
peak=    3.312 closest distance to " CG2 THR A 220 " =    0.936
peak=    3.311 closest distance to " CD1 TRP A 266 " =    1.170
peak=    3.310 closest distance to " O   HOH Z 172 " =    3.749
peak=    3.305 closest distance to " O   HOH Z 435 " =    2.053
peak=    3.303 closest distance to " N   SER A 146 " =    1.656
peak=    3.301 closest distance to " O   HOH Z  40 " =    1.908
peak=    3.296 closest distance to " O   HOH Z  10 " =    1.743
peak=    3.292 closest distance to " CD1 ILE A  33 " =    1.657
peak=    3.291 closest distance to " CG  MET A 185 " =    0.995
peak=    3.291 closest distance to " OG1 THR A 294 " =    1.700
peak=    3.290 closest distance to " OG1 THR A 279 " =    1.506
peak=    3.290 closest distance to " O   HOH Z  80 " =    1.626
peak=    3.289 closest distance to " CG  ARG A 159 " =    1.067
peak=    3.285 closest distance to " CB  SER A 273 " =    0.883
peak=    3.285 closest distance to " CA  LYS A 181 " =    1.053
peak=    3.282 closest distance to " O   HOH Z  48 " =    1.635
peak=    3.281 closest distance to " O   HOH Z 381 " =    1.786
peak=    3.280 closest distance to " O   HOH Z 216 " =    2.789
peak=    3.279 closest distance to " NH1 ARG A 138 " =    1.081
peak=    3.276 closest distance to " CB  ALA A 248 " =    1.114
peak=    3.275 closest distance to " O   HOH Z 402 " =    1.441
peak=    3.275 closest distance to " O   HOH Z 145 " =    1.845
peak=    3.267 closest distance to " O   HOH Z 108 " =    2.625
peak=    3.265 closest distance to " O   HOH Z 291 " =    1.623
peak=    3.263 closest distance to " NH1 ARG A  14 " =    0.909
peak=    3.263 closest distance to " CA  ILE A 106 " =    0.779
peak=    3.261 closest distance to " O   HOH Z 392 " =    1.943
peak=    3.259 closest distance to " CA  ASP A 140 " =    1.280
peak=    3.251 closest distance to " C   ALA A 299 " =    0.976
peak=    3.250 closest distance to " C   ASN A  39 " =    1.054
peak=    3.249 closest distance to " CA  ASP A 162 " =    0.983
peak=    3.247 closest distance to " OG  SER A  22 " =    2.870
peak=    3.243 closest distance to " O   HOH Z 345 " =    3.500
peak=    3.242 closest distance to " O   HOH Z  62 " =    2.290
peak=    3.240 closest distance to " O   HOH Z 383 " =    2.130
peak=    3.239 closest distance to " O   HOH Z 329 " =    3.898
peak=    3.236 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.235 closest distance to " CA  ILE A 234 " =    0.865
peak=    3.232 closest distance to " NZ  LYS A  48 " =    1.407
peak=    3.230 closest distance to " O   HOH Z 133 " =    2.441
peak=    3.221 closest distance to " OH  TYR A 214 " =    1.243
peak=    3.219 closest distance to " N   ALA A 256 " =    1.127
peak=    3.211 closest distance to " O   HOH Z 173 " =    2.164
peak=    3.211 closest distance to " O   GLY A 203 " =    1.460
peak=    3.210 closest distance to " O   HOH Z 126 " =    1.621
peak=    3.209 closest distance to " N   GLN A 278 " =    1.072
peak=    3.207 closest distance to " OG BSER A 134 " =    2.920
peak=    3.206 closest distance to " O   HOH Z 109 " =    2.610
peak=    3.200 closest distance to " CA  ALA A 233 " =    1.359
peak=    3.196 closest distance to " CB  PHE A  16 " =    1.112
peak=    3.194 closest distance to " CG2AVAL A 121 " =    2.380
peak=    3.193 closest distance to " O   HOH Z 409 " =    3.168
peak=    3.193 closest distance to " NH2AARG A 275 " =    3.647
peak=    3.193 closest distance to " CA  ALA A 291 " =    0.936
peak=    3.187 closest distance to " O   HOH Z 294 " =    1.589
peak=    3.182 closest distance to " CA  ALA A 248 " =    1.218
peak=    3.177 closest distance to " CD1 ILE A 106 " =    0.952
peak=    3.177 closest distance to " N   ASN A 127 " =    1.217
peak=    3.170 closest distance to " O   HOH Z 166 " =    3.524
peak=    3.169 closest distance to " O   HOH Z 417 " =    1.948
peak=    3.167 closest distance to " N   TYR A  15 " =    0.778
peak=    3.167 closest distance to " O   HOH Z   4 " =    1.727
peak=    3.165 closest distance to " O   HOH Z 426 " =    1.610
peak=    3.162 closest distance to " CA  GLY A 211 " =    1.325
peak=    3.160 closest distance to " CB  ALA A  10 " =    0.938
peak=    3.158 closest distance to " O   THR A 251 " =    1.259
peak=    3.157 closest distance to " O   HOH Z 148 " =    3.330
peak=    3.152 closest distance to " O   HOH Z 302 " =    1.937
peak=    3.152 closest distance to " O   HOH Z   1 " =    1.972
peak=    3.151 closest distance to " CB  PRO A  54 " =    1.302
peak=    3.151 closest distance to " CB  PRO A 243 " =    1.491
peak=    3.150 closest distance to " O   HOH Z 329 " =    2.782
peak=    3.143 closest distance to " O   HOH Z 201 " =    3.127
peak=    3.138 closest distance to " CD  LYS A 119 " =    1.484
peak=    3.137 closest distance to " CB  GLN A  89 " =    1.155
peak=    3.129 closest distance to " CA  TYR A 116 " =    1.452
peak=    3.128 closest distance to " CG1 VAL A 174 " =    1.040
peak=    3.125 closest distance to " OG BSER A 164 " =    2.226
peak=    3.125 closest distance to " CA  MET A 105 " =    0.965
peak=    3.122 closest distance to " O   HOH Z 410 " =    1.398
peak=    3.111 closest distance to " CB  ALA A 114 " =    1.220
peak=    3.110 closest distance to " CZ  PHE A  38 " =    1.126
peak=    3.106 closest distance to " O   HOH Z  20 " =    1.653
peak=    3.105 closest distance to " O   ALA A 292 " =    1.750
peak=    3.103 closest distance to " CG BARG A 102 " =    1.829
peak=    3.102 closest distance to " ND2 ASN A 110 " =    1.628
peak=    3.101 closest distance to " O   TYR A 116 " =    1.275
peak=    3.098 closest distance to " O   HOH Z 183 " =    1.315
peak=    3.097 closest distance to " CB  ASN A 224 " =    0.999
peak=    3.097 closest distance to " OG BSER A 212 " =    2.444
peak=    3.092 closest distance to " O   HOH Z 403 " =    1.387
peak=    3.088 closest distance to " CB  GLN A 103 " =    1.017
peak=    3.085 closest distance to " CE2 TYR A 186 " =    0.892
peak=    3.084 closest distance to " CA  GLY A  80 " =    1.088
peak=    3.073 closest distance to " CD1 ILE A 199 " =    0.775
peak=    3.072 closest distance to " CB  TYR A 116 " =    0.824
peak=    3.066 closest distance to " OE2 GLU A  53 " =    2.068
peak=    3.062 closest distance to " O   HOH Z 148 " =    2.062
peak=    3.060 closest distance to " O   HOH Z 151 " =    1.709
peak=    3.048 closest distance to " O   HOH Z 213 " =    2.012
peak=    3.039 closest distance to " CB  ILE A  20 " =    1.440
peak=    3.026 closest distance to " O   HOH Z 124 " =    1.870
peak=    3.021 closest distance to " O   HOH Z  49 " =    2.729

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.496 - 5.477
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 205
   mapped sites are within: 0.761 - 5.477

peak=   -5.480 closest distance to " CG2 VAL A 230 " =    0.792
peak=   -4.273 closest distance to " CB  PRO A 243 " =    2.618
peak=   -4.244 closest distance to " CD  ARG A 156 " =    2.022
peak=   -4.095 closest distance to " O   HOH Z 290 " =    1.208
peak=   -4.092 closest distance to " O   HOH Z 231 " =    1.770
peak=   -4.082 closest distance to " CD  ARG A  14 " =    3.253
peak=   -4.054 closest distance to " CG  GLN A 223 " =    2.097
peak=   -4.049 closest distance to " O   HOH Z 351 " =    1.449
peak=   -4.037 closest distance to " C   ALA A 158 " =    1.337
peak=   -4.022 closest distance to " O   HOH Z 266 " =    5.248
peak=   -3.972 closest distance to " CA  ASN A 110 " =    2.596
peak=   -3.966 closest distance to " CG2 VAL A 296 " =    1.401
peak=   -3.957 closest distance to " CG2BVAL A  41 " =    2.642
peak=   -3.940 closest distance to " CG  ASP A 231 " =    0.761
peak=   -3.929 closest distance to " CE2 TYR A  30 " =    2.833
peak=   -3.892 closest distance to " CD  GLN A  58 " =    0.992
peak=   -3.881 closest distance to " O   HOH Z 166 " =    1.873
peak=   -3.877 closest distance to " CG1 VAL A 112 " =    2.604
peak=   -3.861 closest distance to " N   ALA A 226 " =    2.177
peak=   -3.842 closest distance to " CG1 VAL A 296 " =    1.367
peak=   -3.828 closest distance to " CZ3 TRP A 179 " =    1.155
peak=   -3.800 closest distance to " O   HOH Z 118 " =    3.184
peak=   -3.791 closest distance to " CG2 THR A   4 " =    1.976
peak=   -3.788 closest distance to " O   HOH Z 394 " =    1.481
peak=   -3.746 closest distance to " O   HOH Z 185 " =    2.293
peak=   -3.737 closest distance to " O   HOH Z 179 " =    2.313
peak=   -3.723 closest distance to " NH2AARG A 275 " =    5.429
peak=   -3.720 closest distance to " O   PRO A 163 " =    2.067
peak=   -3.717 closest distance to " O   VAL A  67 " =    2.695
peak=   -3.711 closest distance to " O   GLY A 203 " =    2.378
peak=   -3.708 closest distance to " O   HOH Z 196 " =    2.276
peak=   -3.701 closest distance to " O   HOH Z  10 " =    1.537
peak=   -3.697 closest distance to " OG BSER A 134 " =    1.127
peak=   -3.692 closest distance to " O   HOH Z 435 " =    2.802
peak=   -3.690 closest distance to " O   HOH Z  19 " =    2.474
peak=   -3.689 closest distance to " OE1 GLN A  88 " =    0.965
peak=   -3.681 closest distance to " O   HOH Z 231 " =    1.262
peak=   -3.660 closest distance to " O   HOH Z  52 " =    1.613
peak=   -3.655 closest distance to " O   HOH Z 211 " =    1.491
peak=   -3.649 closest distance to " C   HIS A 108 " =    1.179
peak=   -3.623 closest distance to " O   PRO A 198 " =    1.218
peak=   -3.622 closest distance to " CG1 VAL A 265 " =    2.393
peak=   -3.621 closest distance to " CB  PRO A 163 " =    2.561
peak=   -3.619 closest distance to " CD2 LEU A 300 " =    2.776
peak=   -3.617 closest distance to " CA  GLY A 241 " =    3.082
peak=   -3.607 closest distance to " CD1 LEU A 101 " =    2.772
peak=   -3.601 closest distance to " NH2 ARG A  79 " =    1.980
peak=   -3.591 closest distance to " N   THR A 157 " =    1.498
peak=   -3.587 closest distance to " O   HOH Z 241 " =    1.207
peak=   -3.586 closest distance to " CD1 LEU A 228 " =    2.429
peak=   -3.584 closest distance to " OG  SER A  97 " =    2.274
peak=   -3.581 closest distance to " O   GLY A 211 " =    1.325
peak=   -3.576 closest distance to " CB  ALA A  43 " =    2.564
peak=   -3.573 closest distance to " N   ALA A  43 " =    2.468
peak=   -3.567 closest distance to " CB  VAL A 230 " =    1.008
peak=   -3.565 closest distance to " O   HOH Z 426 " =    1.743
peak=   -3.563 closest distance to " O   HOH Z  13 " =    1.426
peak=   -3.562 closest distance to " O   HOH Z 389 " =    1.983
peak=   -3.561 closest distance to " CG  TRP A 266 " =    1.835
peak=   -3.553 closest distance to " CG1 VAL A 112 " =    3.083
peak=   -3.542 closest distance to " CA  GLY A 241 " =    2.312
peak=   -3.531 closest distance to " OD1 ASN A 148 " =    1.425
peak=   -3.519 closest distance to " CA  ASP A 298 " =    1.094
peak=   -3.508 closest distance to " O   HOH Z  43 " =    1.729
peak=   -3.506 closest distance to " CG  PHE A 283 " =    2.843
peak=   -3.505 closest distance to " O   HOH Z  73 " =    2.198
peak=   -3.500 closest distance to " CE3 TRP A 150 " =    2.026
peak=   -3.495 closest distance to " O   HOH Z  38 " =    1.543
peak=   -3.494 closest distance to " CE  MET A 105 " =    2.206
peak=   -3.489 closest distance to " O   GLY A 196 " =    1.213
peak=   -3.477 closest distance to " CG  MET A 105 " =    0.985
peak=   -3.476 closest distance to " OG  SER A  87 " =    1.542
peak=   -3.464 closest distance to " O   HOH Z  44 " =    2.125
peak=   -3.461 closest distance to " OD1 ASN A 187 " =    1.607
peak=   -3.457 closest distance to " O   GLY A  80 " =    2.485
peak=   -3.456 closest distance to " CB  ALA A 248 " =    2.125
peak=   -3.449 closest distance to " NZ  LYS A 119 " =    3.500
peak=   -3.448 closest distance to " O   VAL A 189 " =    2.608
peak=   -3.447 closest distance to " CB  PHE A 192 " =    1.864
peak=   -3.444 closest distance to " O   HOH Z 113 " =    1.879
peak=   -3.441 closest distance to " CG2 VAL A 112 " =    2.545
peak=   -3.437 closest distance to " O   HOH Z 275 " =    1.504
peak=   -3.436 closest distance to " OXT GLY A 302 " =    2.958
peak=   -3.429 closest distance to " N   THR A  18 " =    1.358
peak=   -3.424 closest distance to " O   HOH Z 377 " =    1.971
peak=   -3.423 closest distance to " CD2 LEU A 237 " =    2.746
peak=   -3.423 closest distance to " CD2 TYR A 293 " =    2.072
peak=   -3.418 closest distance to " O   HOH Z 222 " =    1.539
peak=   -3.405 closest distance to " CD  ARG A 139 " =    1.643
peak=   -3.402 closest distance to " CD  LYS A 289 " =    2.566
peak=   -3.399 closest distance to " O   HOH Z 388 " =    2.084
peak=   -3.398 closest distance to " CE BMET A  47 " =    1.700
peak=   -3.398 closest distance to " CG  HIS A  86 " =    1.065
peak=   -3.397 closest distance to " OG  SER A 206 " =    1.732
peak=   -3.393 closest distance to " O   HOH Z 102 " =    1.634
peak=   -3.392 closest distance to " ND2 ASN A  45 " =    1.310
peak=   -3.388 closest distance to " CD2 LEU A 167 " =    1.791
peak=   -3.384 closest distance to " O   HOH Z 103 " =    1.877
peak=   -3.379 closest distance to " O   VAL A 121 " =    1.198
peak=   -3.379 closest distance to " O   HOH Z 407 " =    3.145
peak=   -3.376 closest distance to " CB  ALA A 291 " =    2.215
peak=   -3.376 closest distance to " CB  ALA A 291 " =    2.218
peak=   -3.360 closest distance to " C   LEU A 222 " =    0.885
peak=   -3.357 closest distance to " CG  LEU A 101 " =    2.458
peak=   -3.348 closest distance to " OD2 ASP A  50 " =    2.362
peak=   -3.338 closest distance to " C   MET A 188 " =    1.457
peak=   -3.338 closest distance to " SD BMET A  47 " =    0.959
peak=   -3.337 closest distance to " O   HOH Z 396 " =    1.848
peak=   -3.335 closest distance to " CD  GLN A  88 " =    0.832
peak=   -3.333 closest distance to " NH1 ARG A 195 " =    2.544
peak=   -3.330 closest distance to " O   HOH Z 353 " =    2.130
peak=   -3.327 closest distance to " OG BSER A 134 " =    1.806
peak=   -3.325 closest distance to " CD2 PHE A  61 " =    2.479
peak=   -3.323 closest distance to " O   MET A  40 " =    2.725
peak=   -3.322 closest distance to " O   HOH Z 417 " =    2.893
peak=   -3.320 closest distance to " NH2 ARG A  66 " =    2.041
peak=   -3.316 closest distance to " C   ASP A 231 " =    2.655
peak=   -3.314 closest distance to " C   ASN A 285 " =    2.494
peak=   -3.313 closest distance to " CA  GLY A 203 " =    2.462
peak=   -3.303 closest distance to " C   ASN A 187 " =    1.834
peak=   -3.299 closest distance to " O   HOH Z  63 " =    1.248
peak=   -3.297 closest distance to " OG  SER A  26 " =    1.300
peak=   -3.287 closest distance to " CE1 TYR A 169 " =    2.474
peak=   -3.286 closest distance to " O   HOH Z  98 " =    2.143
peak=   -3.275 closest distance to " N   GLN A  58 " =    1.910
peak=   -3.274 closest distance to " CZ  PHE A 192 " =    2.871
peak=   -3.274 closest distance to " CD1 TYR A 247 " =    2.793
peak=   -3.271 closest distance to " CB  ALA A 248 " =    2.529
peak=   -3.270 closest distance to " O   HOH Z 372 " =    2.434
peak=   -3.270 closest distance to " O   HOH Z 113 " =    2.079
peak=   -3.267 closest distance to " O   SER A  22 " =    2.153
peak=   -3.266 closest distance to " C   PHE A  59 " =    1.258
peak=   -3.260 closest distance to " O   HOH Z 191 " =    5.477
peak=   -3.258 closest distance to " O   HOH Z 423 " =    2.064
peak=   -3.257 closest distance to " O   HOH Z 292 " =    4.639
peak=   -3.253 closest distance to " CB  ASN A  69 " =    1.229
peak=   -3.251 closest distance to " O   HOH Z  60 " =    2.333
peak=   -3.251 closest distance to " O   HOH Z  51 " =    1.314
peak=   -3.249 closest distance to " O   HOH Z 166 " =    1.598
peak=   -3.248 closest distance to " CE  LYS A  76 " =    2.595
peak=   -3.246 closest distance to " CB  VAL A 296 " =    1.240
peak=   -3.239 closest distance to " CG  GLU A 277 " =    1.186
peak=   -3.238 closest distance to " CB  ASN A  39 " =    2.227
peak=   -3.233 closest distance to " N   SER A 212 " =    1.711
peak=   -3.229 closest distance to " O   HOH Z 295 " =    1.436
peak=   -3.227 closest distance to " N   ALA A 248 " =    1.790
peak=   -3.227 closest distance to " CB  TYR A  15 " =    2.254
peak=   -3.226 closest distance to " O   HOH Z 140 " =    1.498
peak=   -3.223 closest distance to " O   HOH Z 308 " =    1.719
peak=   -3.218 closest distance to " NE2 GLN A  88 " =    1.035
peak=   -3.214 closest distance to " C   LEU A 143 " =    1.114
peak=   -3.211 closest distance to " CG1 VAL A 197 " =    2.351
peak=   -3.208 closest distance to " CG  ARG A 269 " =    2.404
peak=   -3.206 closest distance to " N   VAL A 230 " =    1.124
peak=   -3.199 closest distance to " CB  ASP A 132 " =    2.297
peak=   -3.198 closest distance to " CE2 PHE A 218 " =    2.558
peak=   -3.196 closest distance to " O   LEU A 167 " =    1.479
peak=   -3.196 closest distance to " CB  ASP A 132 " =    2.334
peak=   -3.193 closest distance to " N   SER A 276 " =    1.277
peak=   -3.187 closest distance to " O   HOH Z 111 " =    2.324
peak=   -3.178 closest distance to " OXT GLY A 302 " =    3.543
peak=   -3.177 closest distance to " O   HOH Z 298 " =    1.239
peak=   -3.171 closest distance to " O   HOH Z 174 " =    2.537
peak=   -3.166 closest distance to " O   HOH Z 177 " =    1.644
peak=   -3.166 closest distance to " OG1 THR A 246 " =    1.433
peak=   -3.163 closest distance to " C   ASP A 270 " =    1.235
peak=   -3.160 closest distance to " CZ  TYR A 169 " =    1.623
peak=   -3.158 closest distance to " CG1 VAL A 125 " =    1.982
peak=   -3.156 closest distance to " NH2 ARG A  79 " =    1.560
peak=   -3.153 closest distance to " O   THR A  18 " =    1.550
peak=   -3.151 closest distance to " NH2BARG A 275 " =    1.915
peak=   -3.147 closest distance to " CB  ALA A 114 " =    2.555
peak=   -3.146 closest distance to " O   HOH Z 165 " =    1.853
peak=   -3.146 closest distance to " ND2 ASN A  60 " =    1.498
peak=   -3.141 closest distance to " O   HOH Z 359 " =    1.600
peak=   -3.136 closest distance to " O   HOH Z 310 " =    1.999
peak=   -3.131 closest distance to " ND2 ASN A  60 " =    1.752
peak=   -3.131 closest distance to " O   HOH Z 216 " =    1.783
peak=   -3.131 closest distance to " NE2 GLN A 103 " =    1.800
peak=   -3.130 closest distance to " O   HOH Z  90 " =    1.591
peak=   -3.128 closest distance to " O   HOH Z 253 " =    4.080
peak=   -3.123 closest distance to " O   HOH Z 184 " =    1.426
peak=   -3.115 closest distance to " N   SER A   3 " =    1.986
peak=   -3.107 closest distance to " N   VAL A 296 " =    2.617
peak=   -3.107 closest distance to " O   HOH Z 281 " =    2.566
peak=   -3.104 closest distance to " CD  PRO A 213 " =    2.166
peak=   -3.100 closest distance to " OG  SER A  62 " =    1.733
peak=   -3.099 closest distance to " CD1 ILE A 151 " =    2.373
peak=   -3.099 closest distance to " NE2 GLN A 278 " =    2.068
peak=   -3.095 closest distance to " O   HOH Z 128 " =    2.549
peak=   -3.093 closest distance to " CD1 ILE A 199 " =    2.638
peak=   -3.088 closest distance to " O   HOH Z 298 " =    2.898
peak=   -3.087 closest distance to " CA  SER A 135 " =    1.322
peak=   -3.081 closest distance to " CD  ARG A 195 " =    5.113
peak=   -3.069 closest distance to " CD  PRO A 243 " =    2.130
peak=   -3.065 closest distance to " CE3 TRP A  70 " =    1.841
peak=   -3.063 closest distance to " CB  TRP A  85 " =    2.486
peak=   -3.054 closest distance to " CG2 THR A 178 " =    2.235
peak=   -3.053 closest distance to " O   VAL A 125 " =    2.314
peak=   -3.049 closest distance to " OD1 ASN A 249 " =    2.172
peak=   -3.048 closest distance to " O   HOH Z 176 " =    0.968
peak=   -3.019 closest distance to " O   PRO A 198 " =    1.328

================= 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    :  0.4239 0.4115   6.215685e+00   6.189827e+00
   1_bss:  0.4162 0.4000   6.211062e+00   6.177945e+00
   1_xyz:  0.3056 0.3300   5.985154e+00   6.043856e+00
   1_adp:  0.2396 0.2755   5.781126e+00   5.907204e+00
   1_occ:  0.2390 0.2757   5.779808e+00   5.908327e+00
   2_bss:  0.2339 0.2689   5.776528e+00   5.901171e+00
   2_xyz:  0.1583 0.2033   5.430623e+00   5.624927e+00
   2_adp:  0.1468 0.1931   5.364532e+00   5.573142e+00
   2_occ:  0.1467 0.1930   5.364189e+00   5.573237e+00
   3_bss:  0.1461 0.1912   5.363521e+00   5.570598e+00
   3_xyz:  0.1299 0.1767   5.271177e+00   5.499454e+00
   3_adp:  0.1200 0.1674   5.206941e+00   5.446968e+00
   3_occ:  0.1200 0.1674   5.207152e+00   5.447363e+00
   4_bss:  0.1200 0.1673   5.206265e+00   5.446872e+00
   4_xyz:  0.1150 0.1640   5.177654e+00   5.427930e+00
   4_adp:  0.1155 0.1604   5.168984e+00   5.407420e+00
   4_occ:  0.1155 0.1603   5.168737e+00   5.407236e+00
   5_bss:  0.1157 0.1602   5.168976e+00   5.406391e+00
   5_xyz:  0.1168 0.1603   5.173949e+00   5.406187e+00
   5_adp:  0.1163 0.1604   5.173728e+00   5.409078e+00
   5_occ:  0.1162 0.1604   5.173502e+00   5.408858e+00
   5_bss:  0.1162 0.1604   5.173502e+00   5.408858e+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:  0.333  18.290   8.992   7.897   8.000   0.000   0.000   0.000
   1_xyz:  0.333  18.290   8.992   7.897   8.000   0.000   0.000   0.000
   1_adp:  0.333  18.290   8.992   7.897   8.000   0.000   0.000   0.000
   1_occ:  0.333  18.290   8.992   7.897   8.000   0.000   0.000   0.000
   2_bss:  0.341  48.748   5.487   4.303   5.169   0.000   0.000   0.000
   2_xyz:  0.341  48.748   5.487   4.303   5.169   0.000   0.000   0.000
   2_adp:  0.341  48.748   5.487   4.303   5.169   0.000   0.000   0.000
   2_occ:  0.341  48.748   5.487   4.303   5.169   0.000   0.000   0.000
   3_bss:  0.337  48.748   3.748   3.465   4.458   0.000   0.000   0.000
   3_xyz:  0.337  48.748   3.748   3.465   4.458   0.000   0.000   0.000
   3_adp:  0.337  48.748   3.748   3.465   4.458   0.000   0.000   0.000
   3_occ:  0.337  48.748   3.748   3.465   4.458   0.000   0.000   0.000
   4_bss:  0.321  48.749   3.551   3.370   4.390   0.000   0.000   0.000
   4_xyz:  0.321  48.749   3.551   3.370   4.390   0.000   0.000   0.000
   4_adp:  0.321  48.749   3.551   3.370   4.390   0.000   0.000   0.000
   4_occ:  0.321  48.749   3.551   3.370   4.390   0.000   0.000   0.000
   5_bss:  0.324  48.849   3.408   3.311   4.354   0.000   0.000   0.000
   5_xyz:  0.324  48.849   3.408   3.311   4.354   0.000   0.000   0.000
   5_adp:  0.324  48.849   3.408   3.311   4.354   0.000   0.000   0.000
   5_occ:  0.324  48.849   3.408   3.311   4.354   0.000   0.000   0.000
   5_bss:  0.324  52.540  -0.283  -0.380   0.663   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.330 0.5800  0.6402    48626.518
   1_bss:  45.291 0.5787  0.8207    46700.839
   1_xyz:  35.750 0.6919  0.9520    30292.674
   1_adp:  28.007 0.7805  1.0385    20388.902
   1_occ:  28.032 0.7801  1.0378    20416.733
   2_bss:  27.721 0.7834  0.9245    19976.156
   2_xyz:  19.283 0.8685  0.9939    10358.206
   2_adp:  17.865 0.8821  1.0100     9326.792
   2_occ:  17.865 0.8821  1.0098     9329.030
   3_bss:  17.827 0.8824  0.9699     9286.538
   3_xyz:  16.211 0.8968  0.9746     7999.744
   3_adp:  15.166 0.9055  0.9756     7136.447
   3_occ:  15.174 0.9055  0.9755     7140.001
   4_bss:  15.159 0.9056  0.9711     7125.765
   4_xyz:  14.717 0.9093  0.9727     6850.002
   4_adp:  14.219 0.9136  0.9743     6607.209
   4_occ:  14.216 0.9136  0.9742     6600.742
   5_bss:  14.214 0.9135  0.9706     6571.184
   5_xyz:  14.179 0.9139  0.9700     6552.886
   5_adp:  14.241 0.9135  0.9688     6586.107
   5_occ:  14.234 0.9135  0.9688     6583.990
   5_bss:  14.234 0.9135  0.9688     6583.990
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4085e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4085e+01
   1_xyz:   1.476  0.011  0.099 17.942  0.006  4.124   1.1408e-01
   1_adp:   1.476  0.011  0.099 17.942  0.006  4.124   1.1408e-01
   1_occ:   1.476  0.011  0.099 17.942  0.006  4.124   1.1408e-01
   2_bss:   1.476  0.011  0.099 17.942  0.006  4.124   1.1408e-01
   2_xyz:   1.078  0.008  0.080 16.448  0.004  4.130   7.1857e-02
   2_adp:   1.078  0.008  0.080 16.448  0.004  4.130   7.1857e-02
   2_occ:   1.078  0.008  0.080 16.448  0.004  4.130   7.1857e-02
   3_bss:   1.078  0.008  0.080 16.448  0.004  4.130   7.1857e-02
   3_xyz:   1.041  0.008  0.083 16.262  0.003  4.137   6.6974e-02
   3_adp:   1.041  0.008  0.083 16.262  0.003  4.137   6.6974e-02
   3_occ:   1.041  0.008  0.083 16.262  0.003  4.137   6.6974e-02
   4_bss:   1.041  0.008  0.083 16.262  0.003  4.137   6.6974e-02
   4_xyz:   1.018  0.008  0.084 15.854  0.004  4.141   6.5130e-02
   4_adp:   1.018  0.008  0.084 15.854  0.004  4.141   6.5130e-02
   4_occ:   1.018  0.008  0.084 15.854  0.004  4.141   6.5130e-02
   5_bss:   1.018  0.008  0.084 15.854  0.004  4.141   6.5130e-02
   5_xyz:   0.945  0.007  0.077 15.633  0.003  4.114   5.7266e-02
   5_adp:   0.945  0.007  0.077 15.633  0.003  4.114   5.7266e-02
   5_occ:   0.945  0.007  0.077 15.633  0.003  4.114   5.7266e-02
   5_bss:   0.945  0.007  0.077 15.633  0.003  4.114   5.7266e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0132e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0132e+00
   1_xyz:  12.229  0.133  0.388 87.780  0.040  2.281   8.5621e-02
   1_adp:  12.229  0.133  0.388 87.780  0.040  2.281   8.5621e-02
   1_occ:  12.229  0.133  0.388 87.780  0.040  2.281   8.5621e-02
   2_bss:  12.229  0.133  0.388 87.780  0.040  2.281   8.5621e-02
   2_xyz:   7.654  0.076  0.368 82.286  0.041  2.351   5.5573e-02
   2_adp:   7.654  0.076  0.368 82.286  0.041  2.351   5.5573e-02
   2_occ:   7.654  0.076  0.368 82.286  0.041  2.351   5.5573e-02
   3_bss:   7.654  0.076  0.368 82.286  0.041  2.351   5.5573e-02
   3_xyz:   8.901  0.056  0.512 81.954  0.037  2.360   4.2680e-02
   3_adp:   8.901  0.056  0.512 81.954  0.037  2.360   4.2680e-02
   3_occ:   8.901  0.056  0.512 81.954  0.037  2.360   4.2680e-02
   4_bss:   8.901  0.056  0.512 81.954  0.037  2.360   4.2680e-02
   4_xyz:   7.652  0.040  0.548 82.537  0.040  2.326   4.2219e-02
   4_adp:   7.652  0.040  0.548 82.537  0.040  2.326   4.2219e-02
   4_occ:   7.652  0.040  0.548 82.537  0.040  2.326   4.2219e-02
   5_bss:   7.652  0.040  0.548 82.537  0.040  2.326   4.2219e-02
   5_xyz:   7.649  0.039  0.477 83.032  0.037  2.392   3.2187e-02
   5_adp:   7.649  0.039  0.477 83.032  0.037  2.392   3.2187e-02
   5_occ:   7.649  0.039  0.477 83.032  0.037  2.392   3.2187e-02
   5_bss:   7.649  0.039  0.477 83.032  0.037  2.392   3.2187e-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:  46.44   0.00   9.74  44.04   0.00   6.95  46.44   0.00  24.91
   1_occ:  46.44   0.00   9.74  44.04   0.00   6.95  46.44   0.00  24.91
   2_bss:  46.44   0.00   9.74  44.04   0.00   6.95  46.44   0.00  24.91
   2_xyz:  46.44   0.00   9.74  44.04   0.00   6.95  46.44   0.00  24.91
   2_adp:  77.80   0.00  10.03  77.80   0.00   6.99  47.69   0.52  26.54
   2_occ:  77.80   0.00  10.03  77.80   0.00   6.99  47.69   0.52  26.54
   3_bss:  77.80   0.00  10.03  77.80   0.00   6.99  47.69   0.52  26.54
   3_xyz:  77.80   0.00  10.03  77.80   0.00   6.99  47.69   0.52  26.54
   3_adp:  80.97   0.00  11.65  74.74   0.00   7.40  80.97   0.34  34.76
   3_occ:  80.97   0.00  11.65  74.74   0.00   7.40  80.97   0.34  34.76
   4_bss:  80.97   0.00  11.65  74.74   0.00   7.40  80.97   0.34  34.76
   4_xyz:  80.97   0.00  11.65  74.74   0.00   7.40  80.97   0.34  34.76
   4_adp:  75.33   0.00  11.27  73.75   0.00   7.23  75.33   1.00  33.27
   4_occ:  75.33   0.00  11.27  73.75   0.00   7.23  75.33   1.00  33.27
   5_bss:  75.33   0.00  11.27  73.75   0.00   7.23  75.33   1.00  33.27
   5_xyz:  75.33   0.00  11.27  73.75   0.00   7.23  75.33   1.00  33.27
   5_adp:  74.10   0.00  11.23  74.10   0.00   7.22  73.16   1.10  33.08
   5_occ:  74.10   0.00  11.23  74.10   0.00   7.22  73.16   1.10  33.08
   5_bss:  77.79   3.69  14.92  77.79   3.69  10.91  76.85   4.79  36.77
------------------------------------------------------------------------
 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:    1.167    0.015    0.400
   1_adp:    1.167    0.015    0.400
   1_occ:    1.167    0.015    0.400
   2_bss:    1.167    0.015    0.400
   2_xyz:    1.377    0.020    0.504
   2_adp:    1.377    0.020    0.504
   2_occ:    1.377    0.020    0.504
   3_bss:    1.377    0.020    0.504
   3_xyz:    1.358    0.028    0.525
   3_adp:    1.358    0.028    0.525
   3_occ:    1.358    0.028    0.525
   4_bss:    1.358    0.028    0.525
   4_xyz:    1.518    0.063    0.538
   4_adp:    1.518    0.063    0.538
   4_occ:    1.518    0.063    0.538
   5_bss:    1.518    0.063    0.538
   5_xyz:    1.554    0.035    0.541
   5_adp:    1.554    0.035    0.541
   5_occ:    1.554    0.035    0.541
   5_bss:    1.554    0.035    0.541
------------------------------------------------------------------------

CPU time actual refinement: 327.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1028/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_1028/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1028/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1028/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1028/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.44 
  Macro-tasks:
    bulk solvent and scale       = 41.45  
    individual site refinement   = 130.64 
    weights calculation          = 32.83  
    collect and process          = 6.81   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 211.87 
  Micro-tasks:
    mask                            = 1.69   
    f_calc                          = 98.77  
    alpha_beta                      = 8.32   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 109.23 
    fmodel                         = 7.58   
    r_factors                      = 0.20   
    phase_errors                   = 11.11  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 238.33 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.627 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    643 calls, 98.34 s
gradients_fft:          588 calls, 95.87 s

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

# Date 2008-01-16 Time 03:01:28 PST -0800 (1200481288.10 s)
Start R-work = 0.4239, R-free = 0.4115 (no bulk solvent and anisotropic scale)
Final R-work = 0.1331, R-free = 0.1762 (no bulk solvent and anisotropic scale)

Start R-work = 0.4162, R-free = 0.4000
Final R-work = 0.1162, R-free = 0.1604