# Date 2008-01-16 Time 00:33:15 PST -0800 (1200472395.26 s)
#phil __OFF__

Command line arguments: "../49.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 = 31972
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 49

-------------------------------------------------------------------------------
  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: (68.4938, 46.6953, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.718 1.95076
Completeness in resolution range: 0.943593
Completeness with d_max=infinity: 0.940693

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7180
                             d_min =   1.9508

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: (68.4938, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.718 1.95076
Completeness in resolution range: 0.943593
Completeness with d_max=infinity: 0.940693

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7184 -  4.1738 [2184/2212]  1963   221  10.1%
  bin  2:  4.1738 -  3.3255 [2079/2099]  1871   208  10.0%
  bin  3:  3.3255 -  2.9088 [2079/2099]  1875   204   9.8%
  bin  4:  2.9088 -  2.6445 [2046/2070]  1838   208  10.2%
  bin  5:  2.6445 -  2.4559 [2019/2040]  1820   199   9.9%
  bin  6:  2.4559 -  2.3117 [2020/2066]  1816   204  10.1%
  bin  7:  2.3117 -  2.1963 [2015/2048]  1817   198   9.8%
  bin  8:  2.1963 -  2.1010 [2008/2042]  1798   210  10.5%
  bin  9:  2.1010 -  2.0203 [2008/2039]  1815   193   9.6%
  bin 10:  2.0203 -  1.9508 [1131/2045]  1017   114  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_49/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.31 -     2.03: 17
        2.03 -     2.75: 348
        2.75 -     3.47: 4689
        3.47 -     4.18: 9572
        4.18 -     4.90: 14217
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.314 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.358 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.510 3.040 -x+1,y-1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.557 3.120 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.585 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28838 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_49/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_49/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 68.49375 46.69535 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: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4621   r_free= 0.4549   ksol= 0.00   Bsol= 0.00   scale= 0.815    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.264311                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7184 -  4.6551 0.99   1414  158 0.3818 0.3789      6.5665      6.5842|
|  2:  4.6551 -  3.7144 0.99   1366  152 0.3665 0.3846       6.707      6.7486|
|  3:  3.7144 -  3.2507 0.99   1334  150 0.4202 0.4016      6.6279      6.6547|
|  4:  3.2507 -  2.9561 0.99   1332  139 0.4419 0.4541      6.4849      6.4785|
|  5:  2.9561 -  2.7457 0.99   1306  149 0.4905 0.4861      6.3497      6.3855|
|  6:  2.7457 -  2.5847 0.98   1310  147 0.4940 0.5263      6.2711      6.1946|
|  7:  2.5847 -  2.4559 0.99   1305  145 0.4912 0.4829      6.2265      6.1681|
|  8:  2.4559 -  2.3494 0.98   1301  146 0.4996 0.4744      6.1686      6.1648|
|  9:  2.3494 -  2.2593 0.98   1308  143 0.5081 0.5214      6.0945      6.1666|
| 10:  2.2593 -  2.1816 0.98   1286  141 0.5203 0.4997      6.1125      6.0525|
| 11:  2.1816 -  2.1136 0.99   1309  146 0.5315 0.4763      6.0425      6.0316|
| 12:  2.1136 -  2.0533 0.98   1281  145 0.5224 0.4894      5.9697      5.9837|
| 13:  2.0533 -  1.9994 0.97   1278  133 0.5283 0.4771      5.8869      5.8012|
| 14:  1.9994 -  1.9508 0.39    500   65 0.5267 0.5256      5.8841      5.7839|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7184 -  4.6551  1414   158  0.68  35.60   0.81     0.71      73903.92|
|  2:  4.6551 -  3.7144  1366   152  0.71  34.46   0.91     0.77      99580.17|
|  3:  3.7144 -  3.2507  1334   150  0.62  42.01   0.88     0.74     103769.06|
|  4:  3.2507 -  2.9561  1332   139  0.55  48.10   0.81     0.64      91994.73|
|  5:  2.9561 -  2.7457  1306   149  0.43  57.13   0.76     0.53      79427.26|
|  6:  2.7457 -  2.5847  1310   147  0.40  60.23   0.72     0.46      71756.54|
|  7:  2.5847 -  2.4559  1305   145  0.38  61.73   0.77     0.44      65836.22|
|  8:  2.4559 -  2.3494  1301   146  0.40  60.15   0.76     0.46      56162.74|
|  9:  2.3494 -  2.2593  1308   143  0.41  59.01   0.75     0.51      49641.18|
| 10:  2.2593 -  2.1816  1286   141  0.44  56.62   0.77     0.52      42312.88|
| 11:  2.1816 -  2.1136  1309   146  0.43  57.43   0.74     0.54      40635.05|
| 12:  2.1136 -  2.0533  1281   145  0.40  60.17   0.78     0.51      38966.33|
| 13:  2.0533 -  1.9994  1278   133  0.35  64.26   0.75     0.44      35694.98|
| 14:  1.9994 -  1.9508   500    65  0.31  66.63   0.76     0.33      29581.98|
|alpha:            min =        0.33 max =            0.77 mean =         0.56|
|beta:             min =    29581.98 max =       103769.06 mean =     64723.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.75|
|phase err.(test): min =        0.00 max =           89.99 mean =        54.01|
|-----------------------------------------------------------------------------|

============================== 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 = 10.274235             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.241   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.927258              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.381   (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:        8 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       34 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      191 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      711 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1540 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2703 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4000 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5164 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6675 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7819 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.041 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.196 |       3.156 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4690   r_free= 0.4645   ksol= 0.00   Bsol= 0.00   scale= 0.782    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.266291                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4536   r_free= 0.4505   ksol= 0.36   Bsol= 9.70   scale= 1.018    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.97,8.17,8.00,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.254265                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.659074              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.847   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.977131              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.445   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4536      final r-factor (work) = 0.3650          |
| start r-factor (free) = 0.4505      final r-factor (free) = 0.3841          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.3115 = 9.66 * 0.50 * 6.2677 + 1.00 * 53.0414                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8795 = 9.66 * 0.50 * 6.1596 + 1.00 * 0.1313                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3650      final r-factor (work) = 0.3111          |
| start r-factor (free) = 0.3841      final r-factor (free) = 0.3584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0335 = 0.98 * 1.00 * 6.1596 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9190 = 0.98 * 1.00 * 6.0424 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    60.45   11.77    None  None   None       |
|    all(noH): 2823   0      0.00    60.45   11.77    None  None   None       |
|    Sol.    : 438    0      0.00    60.45   24.89    None  None   None       |
|    Mac.    : 2385   0      0.00    54.11   9.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.046: 1013   |   5:    30.227 -  36.273:   87        |
|      1:     6.046 -  12.091:  761   |   6:    36.273 -  42.318:   62        |
|      2:    12.091 -  18.136:  428   |   7:    42.318 -  48.364:   31        |
|      3:    18.136 -  24.182:  276   |   8:    48.364 -  54.409:    9        |
|      4:    24.182 -  30.227:  153   |   9:    54.409 -  60.455:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3111 r_free = 0.3584             target_work(ml) = 6.009         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3107 r_free = 0.3578             target_work(ml) = 6.008         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3107   r_free= 0.3578   ksol= 0.36   Bsol= 9.70   scale= 1.109    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.97,8.17,8.00,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.008207                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3061   r_free= 0.3522   ksol= 0.33   Bsol= 25.71   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.24,4.15,4.75,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.007063                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.237928              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.206   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.476601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.826  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3061      final r-factor (work) = 0.2279          |
| start r-factor (free) = 0.3522      final r-factor (free) = 0.2750          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9341 = 4.24 * 0.50 * 6.0423 + 1.00 * 0.1307                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5128 = 4.24 * 0.50 * 5.8711 + 1.00 * 0.0722                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2279      final r-factor (work) = 0.2058          |
| start r-factor (free) = 0.2750      final r-factor (free) = 0.2527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8172 = 0.48 * 1.00 * 5.8711 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7403 = 0.48 * 1.00 * 5.6984 + 1.00 * 0.0244                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.98   12.76    None  None   None       |
|    all(noH): 2823   0      0.00    85.98   12.76    None  None   None       |
|    Sol.    : 438    0      1.43    76.05   32.78    None  None   None       |
|    Mac.    : 2385   0      0.00    85.98   9.08     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 -   8.598: 1532   |   5:    42.992 -  51.590:   79        |
|      1:     8.598 -  17.197:  662   |   6:    51.590 -  60.189:   40        |
|      2:    17.197 -  25.795:  209   |   7:    60.189 -  68.787:   20        |
|      3:    25.795 -  34.394:  170   |   8:    68.787 -  77.385:    7        |
|      4:    34.394 -  42.992:  103   |   9:    77.385 -  85.984:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2058 r_free = 0.2527             target_work(ml) = 5.662         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2055 r_free = 0.2520             target_work(ml) = 5.661         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2055   r_free= 0.2520   ksol= 0.33   Bsol= 25.71   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.24,4.15,4.75,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.660539                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2033   r_free= 0.2511   ksol= 0.31   Bsol= 31.18   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,2.85,3.89,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.656517                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.768099              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.599  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.660384              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.222   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2033      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2511      final r-factor (free) = 0.1922          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9614 = 2.77 * 0.50 * 5.7001 + 1.00 * 0.0722                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7185 = 2.77 * 0.50 * 5.5330 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1518      final r-factor (work) = 0.1386          |
| start r-factor (free) = 0.1922      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6820 = 0.66 * 1.00 * 5.5330 + 1.00 * 0.0281                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5420 = 0.66 * 1.00 * 5.3444 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.12   13.27    None  None   None       |
|    all(noH): 2823   0      0.00    94.12   13.27    None  None   None       |
|    Sol.    : 438    0      1.61    81.64   37.05    None  None   None       |
|    Mac.    : 2385   0      0.00    94.12   8.91     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:     0.000 -   9.412: 1690   |   5:    47.061 -  56.473:   95        |
|      1:     9.412 -  18.824:  559   |   6:    56.473 -  65.885:   46        |
|      2:    18.824 -  28.236:  167   |   7:    65.885 -  75.297:   14        |
|      3:    28.236 -  37.648:  128   |   8:    75.297 -  84.709:    4        |
|      4:    37.648 -  47.061:  118   |   9:    84.709 -  94.121:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1386 r_free = 0.1813             target_work(ml) = 5.318         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1384 r_free = 0.1811             target_work(ml) = 5.317         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1384   r_free= 0.1811   ksol= 0.31   Bsol= 31.18   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,2.85,3.89,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.317060                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1379   r_free= 0.1814   ksol= 0.31   Bsol= 37.26   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.30,3.34,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.314907                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.111252              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.135  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.378567              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.758  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1379      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1814      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3814 = 3.11 * 0.50 * 5.3489 + 1.00 * 0.0605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2354 = 3.11 * 0.50 * 5.2506 + 1.00 * 0.0675                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1653      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0002 = 0.38 * 1.00 * 5.2506 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9752 = 0.38 * 1.00 * 5.1881 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.48   12.87    None  None   None       |
|    all(noH): 2823   0      0.00    94.48   12.87    None  None   None       |
|    Sol.    : 438    0      1.22    80.69   36.11    None  None   None       |
|    Mac.    : 2385   0      0.00    94.48   8.60     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.448: 1760   |   5:    47.240 -  56.688:   85        |
|      1:     9.448 -  18.896:  531   |   6:    56.688 -  66.136:   35        |
|      2:    18.896 -  28.344:  148   |   7:    66.136 -  75.584:   12        |
|      3:    28.344 -  37.792:  132   |   8:    75.584 -  85.032:    5        |
|      4:    37.792 -  47.240:  113   |   9:    85.032 -  94.480:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1610             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1610             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1610   ksol= 0.31   Bsol= 37.26   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.30,3.34,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171382                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1609   ksol= 0.32   Bsol= 37.28   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.30,3.34,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171567                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.030530              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.794  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.139937              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.996  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1155      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9284 = 3.03 * 0.50 * 5.1878 + 1.00 * 0.0675                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8783 = 3.03 * 0.50 * 5.1536 + 1.00 * 0.0692                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7324 = 0.14 * 1.00 * 5.1536 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7287 = 0.14 * 1.00 * 5.1458 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.41   12.09    None  None   None       |
|    all(noH): 2823   0      0.00    92.41   12.09    None  None   None       |
|    Sol.    : 438    0      2.10    75.92   32.63    None  None   None       |
|    Mac.    : 2385   0      0.00    92.41   8.32     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.242: 1753   |   5:    46.207 -  55.449:   52        |
|      1:     9.242 -  18.483:  560   |   6:    55.449 -  64.690:   15        |
|      2:    18.483 -  27.725:  146   |   7:    64.690 -  73.932:    7        |
|      3:    27.725 -  36.966:  165   |   8:    73.932 -  83.173:    3        |
|      4:    36.966 -  46.207:  120   |   9:    83.173 -  92.415:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1123 r_free = 0.1558             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1122 r_free = 0.1558             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1558   ksol= 0.32   Bsol= 37.28   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.30,3.34,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.142154                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7184 -  4.6551 0.99   1414  158 0.1047 0.1346      5.4289      5.5831|
|  2:  4.6551 -  3.7144 0.99   1366  152 0.0884 0.1141      5.4566      5.6428|
|  3:  3.7144 -  3.2507 0.99   1334  150 0.1060 0.1464      5.4616      5.7923|
|  4:  3.2507 -  2.9561 0.99   1332  139 0.1208 0.1612      5.4292      5.6029|
|  5:  2.9561 -  2.7457 0.99   1306  149 0.1304 0.1531        5.31      5.4905|
|  6:  2.7457 -  2.5847 0.98   1310  147 0.1199 0.2033      5.1803        5.48|
|  7:  2.5847 -  2.4559 0.99   1305  145 0.1235 0.1534      5.1563      5.3052|
|  8:  2.4559 -  2.3494 0.98   1301  146 0.1121 0.1587      5.0471      5.2879|
|  9:  2.3494 -  2.2593 0.98   1308  143 0.1198 0.1951      5.0183      5.3716|
| 10:  2.2593 -  2.1816 0.98   1286  141 0.1116 0.1531      4.9375      5.0866|
| 11:  2.1816 -  2.1136 0.99   1309  146 0.1128 0.1665      4.9131      5.2283|
| 12:  2.1136 -  2.0533 0.98   1281  145 0.1111 0.1677      4.8548       5.145|
| 13:  2.0533 -  1.9994 0.97   1278  133 0.1116 0.1704      4.7669      4.9687|
| 14:  1.9994 -  1.9508 0.39    500   65 0.1048 0.1715      4.6728      4.9351|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7184 -  4.6551  1414   158  0.94   9.53   0.99     0.96       7718.19|
|  2:  4.6551 -  3.7144  1366   152  0.95   8.19   1.03     1.01       9187.88|
|  3:  3.7144 -  3.2507  1334   150  0.93  11.32   1.04     1.03      10211.99|
|  4:  3.2507 -  2.9561  1332   139  0.92  13.09   1.02     1.01       9785.52|
|  5:  2.9561 -  2.7457  1306   149  0.90  15.81   1.00     0.97       8042.30|
|  6:  2.7457 -  2.5847  1310   147  0.90  15.88   0.98     0.95       6550.92|
|  7:  2.5847 -  2.4559  1305   145  0.91  15.19   0.99     0.95       5877.58|
|  8:  2.4559 -  2.3494  1301   146  0.91  14.44   1.01     1.00       5063.23|
|  9:  2.3494 -  2.2593  1308   143  0.91  15.33   1.02     1.00       4798.82|
| 10:  2.2593 -  2.1816  1286   141  0.90  15.35   1.02     0.98       4188.14|
| 11:  2.1816 -  2.1136  1309   146  0.90  16.02   1.02     0.99       4221.46|
| 12:  2.1136 -  2.0533  1281   145  0.91  15.27   1.03     1.03       3757.30|
| 13:  2.0533 -  1.9994  1278   133  0.91  15.60   1.02     1.01       3157.32|
| 14:  1.9994 -  1.9508   500    65  0.92  13.77   1.01     0.97       2473.02|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2473.02 max =        10211.99 mean =      6281.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.82 mean =        13.86|
|phase err.(test): min =        0.00 max =           89.84 mean =        13.36|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1555   ksol= 0.32   Bsol= 39.51   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,-0.13,1.05,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.141264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1555   ksol= 0.32   Bsol= 39.51   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,-0.13,1.05,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.141264                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7184 -  4.6551 0.99   1414  158 0.1023 0.1338      5.4214      5.5747|
|  2:  4.6551 -  3.7144 0.99   1366  152 0.0893 0.1126      5.4623      5.6436|
|  3:  3.7144 -  3.2507 0.99   1334  150 0.1059 0.1442      5.4611      5.7823|
|  4:  3.2507 -  2.9561 0.99   1332  139 0.1211 0.1614      5.4287      5.6047|
|  5:  2.9561 -  2.7457 0.99   1306  149 0.1304 0.1517      5.3082      5.4857|
|  6:  2.7457 -  2.5847 0.98   1310  147 0.1199 0.2028      5.1794       5.479|
|  7:  2.5847 -  2.4559 0.99   1305  145 0.1231 0.1544      5.1551      5.3065|
|  8:  2.4559 -  2.3494 0.98   1301  146 0.1121 0.1579      5.0447      5.2831|
|  9:  2.3494 -  2.2593 0.98   1308  143 0.1195 0.1950       5.016      5.3699|
| 10:  2.2593 -  2.1816 0.98   1286  141 0.1114 0.1536      4.9372      5.0869|
| 11:  2.1816 -  2.1136 0.99   1309  146 0.1127 0.1669       4.914      5.2305|
| 12:  2.1136 -  2.0533 0.98   1281  145 0.1108 0.1687      4.8546      5.1484|
| 13:  2.0533 -  1.9994 0.97   1278  133 0.1118 0.1694      4.7669      4.9641|
| 14:  1.9994 -  1.9508 0.39    500   65 0.1048 0.1717      4.6708      4.9375|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7184 -  4.6551  1414   158  0.94   9.58   0.99     0.96       7852.52|
|  2:  4.6551 -  3.7144  1366   152  0.95   8.24   1.02     1.01       9192.27|
|  3:  3.7144 -  3.2507  1334   150  0.93  11.32   1.03     1.03      10153.48|
|  4:  3.2507 -  2.9561  1332   139  0.92  13.01   1.01     1.00       9673.04|
|  5:  2.9561 -  2.7457  1306   149  0.90  15.79   1.00     0.96       8002.19|
|  6:  2.7457 -  2.5847  1310   147  0.90  15.87   0.98     0.95       6535.35|
|  7:  2.5847 -  2.4559  1305   145  0.91  15.15   0.99     0.94       5870.44|
|  8:  2.4559 -  2.3494  1301   146  0.91  14.41   1.00     0.99       5038.26|
|  9:  2.3494 -  2.2593  1308   143  0.91  15.26   1.01     1.00       4766.13|
| 10:  2.2593 -  2.1816  1286   141  0.90  15.38   1.01     0.97       4186.25|
| 11:  2.1816 -  2.1136  1309   146  0.90  16.06   1.01     0.98       4235.78|
| 12:  2.1136 -  2.0533  1281   145  0.91  15.31   1.02     1.01       3765.82|
| 13:  2.0533 -  1.9994  1278   133  0.91  15.59   1.01     1.00       3154.26|
| 14:  1.9994 -  1.9508   500    65  0.92  13.76   1.00     0.96       2469.63|
|alpha:            min =        0.94 max =            1.03 mean =         0.99|
|beta:             min =     2469.63 max =        10153.48 mean =      6271.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.86|
|phase err.(test): min =        0.00 max =           89.73 mean =        13.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.23    94.65   14.32    None  None   None       |
|    all(noH): 2823   0      2.23    94.65   14.32    None  None   None       |
|    Sol.    : 438    0      4.33    78.15   34.86    None  None   None       |
|    Mac.    : 2385   0      2.23    94.65   10.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.231 -  11.473: 1753   |   5:    48.439 -  57.680:   52        |
|      1:    11.473 -  20.714:  560   |   6:    57.680 -  66.922:   15        |
|      2:    20.714 -  29.956:  146   |   7:    66.922 -  76.163:    7        |
|      3:    29.956 -  39.197:  165   |   8:    76.163 -  85.405:    3        |
|      4:    39.197 -  48.439:  120   |   9:    85.405 -  94.646:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.425 - 4.682
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 286 from: 291
   mapped sites are within: 0.761 - 4.682

peak=   11.266 closest distance to " CB  VAL A 230 " =    1.458
peak=   10.917 closest distance to " CB  VAL A 296 " =    1.592
peak=    6.367 closest distance to " CG  LEU A   5 " =    1.216
peak=    5.639 closest distance to " CD2 LEU A   5 " =    1.157
peak=    5.630 closest distance to " O   HOH Z 142 " =    1.841
peak=    5.617 closest distance to " NE2 GLN A  11 " =    1.175
peak=    5.583 closest distance to " CB  ARG A 275 " =    0.923
peak=    5.354 closest distance to " O   HOH Z 209 " =    2.241
peak=    5.194 closest distance to " O   HOH Z 193 " =    1.723
peak=    5.185 closest distance to " O   HOH Z  85 " =    1.709
peak=    5.057 closest distance to " O   HOH Z 126 " =    1.848
peak=    5.039 closest distance to " O   HOH Z 124 " =    1.424
peak=    5.022 closest distance to " CG  LEU A 228 " =    1.204
peak=    4.979 closest distance to " O   HOH Z 346 " =    1.613
peak=    4.806 closest distance to " NH2 ARG A  56 " =    2.099
peak=    4.802 closest distance to " O   HOH Z 272 " =    1.878
peak=    4.802 closest distance to " O   HOH Z 126 " =    1.735
peak=    4.802 closest distance to " O   HOH Z 232 " =    2.317
peak=    4.720 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.711 closest distance to " CB  GLN A 223 " =    1.583
peak=    4.624 closest distance to " O   HOH Z 403 " =    1.749
peak=    4.532 closest distance to " O   SER A  87 " =    2.205
peak=    4.524 closest distance to " CB  ARG A  79 " =    1.355
peak=    4.491 closest distance to " CG  PRO A 243 " =    1.169
peak=    4.432 closest distance to " O   HOH Z 402 " =    1.446
peak=    4.389 closest distance to " CB  ALA A   9 " =    1.605
peak=    4.343 closest distance to " O   HOH Z  61 " =    1.639
peak=    4.322 closest distance to " O   HOH Z 248 " =    1.602
peak=    4.304 closest distance to " O   HOH Z 369 " =    2.140
peak=    4.294 closest distance to " O   HOH Z 250 " =    1.440
peak=    4.274 closest distance to " O   HOH Z  78 " =    1.766
peak=    4.269 closest distance to " O   HOH Z 298 " =    1.703
peak=    4.262 closest distance to " CG  PRO A 213 " =    1.211
peak=    4.258 closest distance to " OE1 GLU A   2 " =    2.246
peak=    4.241 closest distance to " O   HOH Z 427 " =    2.827
peak=    4.236 closest distance to " CB  VAL A 230 " =    1.196
peak=    4.220 closest distance to " O   HOH Z   3 " =    1.935
peak=    4.217 closest distance to " CB  SER A   3 " =    1.275
peak=    4.213 closest distance to " C   PRO A 198 " =    1.468
peak=    4.172 closest distance to " O   HOH Z 273 " =    2.719
peak=    4.164 closest distance to " O   HOH Z 406 " =    1.434
peak=    4.162 closest distance to " O   HOH Z  66 " =    2.299
peak=    4.156 closest distance to " ND2 ASN A 187 " =    1.556
peak=    4.155 closest distance to " O   HOH Z 117 " =    2.034
peak=    4.154 closest distance to " O   HOH Z 126 " =    1.473
peak=    4.151 closest distance to " O   HOH Z 423 " =    1.839
peak=    4.134 closest distance to " O   HOH Z  54 " =    1.661
peak=    4.134 closest distance to " CB  SER A  63 " =    1.213
peak=    4.130 closest distance to " O   HOH Z 368 " =    2.111
peak=    4.120 closest distance to " O   HOH Z 130 " =    1.125
peak=    4.116 closest distance to " O   HOH Z  44 " =    1.712
peak=    4.115 closest distance to " O   HOH Z 188 " =    2.843
peak=    4.088 closest distance to " CB  GLU A 152 " =    1.128
peak=    4.081 closest distance to " CB  VAL A 265 " =    1.317
peak=    4.069 closest distance to " CB  SER A  26 " =    1.703
peak=    4.039 closest distance to " CD2 TRP A 179 " =    1.378
peak=    4.025 closest distance to " O   HOH Z 261 " =    1.983
peak=    4.022 closest distance to " O   HOH Z  40 " =    1.597
peak=    4.011 closest distance to " CB  ASN A 148 " =    1.380
peak=    4.004 closest distance to " O   HOH Z 234 " =    3.540
peak=    4.002 closest distance to " O   HOH Z 287 " =    1.916
peak=    4.000 closest distance to " O   HOH Z 411 " =    3.749
peak=    3.975 closest distance to " O   HOH Z  59 " =    1.932
peak=    3.951 closest distance to " O   HOH Z 257 " =    2.186
peak=    3.944 closest distance to " O   HOH Z 303 " =    2.159
peak=    3.939 closest distance to " O   HOH Z 265 " =    2.254
peak=    3.931 closest distance to " O   HOH Z 130 " =    2.714
peak=    3.914 closest distance to " CB  ASN A 187 " =    1.320
peak=    3.889 closest distance to " O   HOH Z 286 " =    2.296
peak=    3.878 closest distance to " O   HOH Z 128 " =    2.043
peak=    3.876 closest distance to " CG AARG A 275 " =    1.273
peak=    3.866 closest distance to " CG  LEU A 167 " =    1.270
peak=    3.864 closest distance to " O   HOH Z 322 " =    2.142
peak=    3.862 closest distance to " O   HOH Z 118 " =    1.639
peak=    3.839 closest distance to " O   HOH Z  43 " =    2.172
peak=    3.832 closest distance to " O   HOH Z 261 " =    1.899
peak=    3.832 closest distance to " O   HOH Z 366 " =    2.687
peak=    3.823 closest distance to " O   HOH Z  97 " =    2.233
peak=    3.814 closest distance to " O   HOH Z  10 " =    1.725
peak=    3.804 closest distance to " O   HOH Z 118 " =    1.337
peak=    3.803 closest distance to " NH2AARG A 190 " =    1.872
peak=    3.803 closest distance to " CB  ARG A 139 " =    1.055
peak=    3.792 closest distance to " CB  VAL A 202 " =    1.526
peak=    3.783 closest distance to " CD  ARG A 269 " =    1.021
peak=    3.782 closest distance to " CB  GLN A  88 " =    1.183
peak=    3.779 closest distance to " OG ASER A 258 " =    2.902
peak=    3.771 closest distance to " CB  TRP A 266 " =    1.087
peak=    3.754 closest distance to " CA  ASN A 215 " =    1.018
peak=    3.752 closest distance to " CA  ALA A  51 " =    0.941
peak=    3.749 closest distance to " O   HOH Z 352 " =    1.285
peak=    3.731 closest distance to " O   HOH Z  43 " =    1.298
peak=    3.726 closest distance to " O   HOH Z 303 " =    1.678
peak=    3.720 closest distance to " O   HOH Z 145 " =    2.107
peak=    3.715 closest distance to " N   PHE A 130 " =    1.355
peak=    3.710 closest distance to " O   HOH Z 329 " =    3.840
peak=    3.705 closest distance to " N   ASN A  39 " =    1.199
peak=    3.702 closest distance to " O   HOH Z 128 " =    2.067
peak=    3.695 closest distance to " O   HOH Z 188 " =    2.480
peak=    3.695 closest distance to " CB  GLU A 277 " =    3.474
peak=    3.691 closest distance to " CB  ASN A  39 " =    0.825
peak=    3.690 closest distance to " O   HOH Z  15 " =    2.114
peak=    3.686 closest distance to " O   HOH Z 407 " =    2.418
peak=    3.678 closest distance to " CZ  PHE A 218 " =    1.160
peak=    3.678 closest distance to " O   HOH Z  88 " =    2.575
peak=    3.668 closest distance to " O  BHOH Z 338 " =    2.465
peak=    3.663 closest distance to " O   HOH Z  80 " =    1.566
peak=    3.663 closest distance to " O   HOH Z  95 " =    1.281
peak=    3.660 closest distance to " CG2 ILE A  20 " =    1.547
peak=    3.653 closest distance to " O   HOH Z  61 " =    1.508
peak=    3.653 closest distance to " O   HOH Z 392 " =    2.708
peak=    3.651 closest distance to " CD2 LEU A 228 " =    1.296
peak=    3.650 closest distance to " O   HOH Z 435 " =    1.946
peak=    3.641 closest distance to " O   HOH Z 188 " =    1.314
peak=    3.639 closest distance to " O   HOH Z 422 " =    2.360
peak=    3.633 closest distance to " CG  GLN A  88 " =    1.060
peak=    3.623 closest distance to " CD  LYS A 166 " =    1.298
peak=    3.621 closest distance to " O   HOH Z 371 " =    3.017
peak=    3.618 closest distance to " O   HOH Z 203 " =    1.538
peak=    3.612 closest distance to " CB  ALA A 248 " =    1.393
peak=    3.612 closest distance to " O   HOH Z 227 " =    2.222
peak=    3.604 closest distance to " CB  THR A  31 " =    1.603
peak=    3.598 closest distance to " CA  PHE A 283 " =    1.098
peak=    3.595 closest distance to " O   HOH Z 380 " =    1.855
peak=    3.587 closest distance to " O   HOH Z 238 " =    1.095
peak=    3.586 closest distance to " NZ  LYS A 117 " =    2.652
peak=    3.583 closest distance to " OG ASER A  99 " =    1.532
peak=    3.579 closest distance to " O   HOH Z 345 " =    3.071
peak=    3.569 closest distance to " OG BSER A 164 " =    2.049
peak=    3.563 closest distance to " NE  ARG A  56 " =    3.403
peak=    3.560 closest distance to " CG AARG A 275 " =    1.143
peak=    3.556 closest distance to " O   HOH Z 255 " =    1.685
peak=    3.555 closest distance to " O   HOH Z 251 " =    1.612
peak=    3.551 closest distance to " NH2BARG A 145 " =    1.999
peak=    3.550 closest distance to " O   ASP A 124 " =    1.362
peak=    3.546 closest distance to " O   HOH Z 327 " =    1.505
peak=    3.544 closest distance to " N   SER A 135 " =    1.342
peak=    3.537 closest distance to " CB  ASN A 142 " =    1.089
peak=    3.528 closest distance to " CB BVAL A  41 " =    1.087
peak=    3.515 closest distance to " CB  GLN A 278 " =    0.781
peak=    3.513 closest distance to " O   HOH Z 345 " =    1.602
peak=    3.513 closest distance to " N   ARG A 156 " =    1.308
peak=    3.510 closest distance to " CG BARG A 102 " =    1.729
peak=    3.510 closest distance to " N   ASP A 162 " =    1.190
peak=    3.501 closest distance to " NE2 GLN A 223 " =    1.936
peak=    3.500 closest distance to " CB  ASN A 110 " =    1.073
peak=    3.499 closest distance to " CG2 ILE A 120 " =    1.279
peak=    3.492 closest distance to " O   HOH Z 337 " =    1.683
peak=    3.490 closest distance to " CA  TYR A  30 " =    0.986
peak=    3.487 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.484 closest distance to " CB  GLU A 128 " =    0.906
peak=    3.482 closest distance to " CG  MET A 185 " =    1.158
peak=    3.473 closest distance to " O   TRP A 274 " =    1.920
peak=    3.472 closest distance to " OG BSER A 210 " =    1.439
peak=    3.465 closest distance to " CG1 ILE A  49 " =    1.378
peak=    3.458 closest distance to " CG  PRO A 198 " =    1.305
peak=    3.442 closest distance to " CB  TRP A 179 " =    1.194
peak=    3.439 closest distance to " O   HOH Z 236 " =    1.510
peak=    3.434 closest distance to " O   HOH Z 359 " =    1.844
peak=    3.434 closest distance to " CG  LYS A  76 " =    1.686
peak=    3.433 closest distance to " CB  PRO A  90 " =    1.142
peak=    3.431 closest distance to " CG1 ILE A  33 " =    1.335
peak=    3.429 closest distance to " O   HOH Z 214 " =    2.222
peak=    3.428 closest distance to " CB  ASN A 148 " =    1.892
peak=    3.427 closest distance to " CB  PRO A  54 " =    0.801
peak=    3.423 closest distance to " O   HOH Z 158 " =    3.108
peak=    3.422 closest distance to " O   HOH Z 263 " =    1.710
peak=    3.416 closest distance to " CB  ARG A 156 " =    1.255
peak=    3.412 closest distance to " O   HOH Z 337 " =    3.367
peak=    3.411 closest distance to " NH1 ARG A 138 " =    1.308
peak=    3.408 closest distance to " CA  LYS A 117 " =    1.166
peak=    3.406 closest distance to " O   HOH Z 143 " =    1.518
peak=    3.403 closest distance to " O   HOH Z 299 " =    4.120
peak=    3.402 closest distance to " O   HOH Z 425 " =    1.958
peak=    3.401 closest distance to " CA  ASP A 162 " =    0.967
peak=    3.393 closest distance to " CD2 TYR A 186 " =    1.076
peak=    3.389 closest distance to " CD2 LEU A 297 " =    1.028
peak=    3.388 closest distance to " O   HOH Z 388 " =    2.075
peak=    3.386 closest distance to " O   ASN A  74 " =    1.544
peak=    3.386 closest distance to " CG  LYS A 119 " =    1.124
peak=    3.385 closest distance to " O   HOH Z 389 " =    1.365
peak=    3.379 closest distance to " OG1 THR A 294 " =    2.365
peak=    3.377 closest distance to " O   HOH Z 245 " =    1.499
peak=    3.375 closest distance to " CA  ALA A  21 " =    1.065
peak=    3.373 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.373 closest distance to " O   HOH Z 438 " =    2.414
peak=    3.368 closest distance to " O   HOH Z 123 " =    1.275
peak=    3.362 closest distance to " O   HOH Z  21 " =    1.846
peak=    3.360 closest distance to " O   HOH Z 137 " =    1.460
peak=    3.358 closest distance to " CG2 VAL A 257 " =    0.859
peak=    3.356 closest distance to " O   HOH Z 109 " =    1.280
peak=    3.355 closest distance to " O   HOH Z 244 " =    1.661
peak=    3.350 closest distance to " O   HOH Z  99 " =    1.875
peak=    3.349 closest distance to " O   HOH Z 132 " =    2.464
peak=    3.347 closest distance to " OD1BASN A 224 " =    2.232
peak=    3.335 closest distance to " O   GLY A  91 " =    1.614
peak=    3.335 closest distance to " CA  ASN A 176 " =    1.020
peak=    3.333 closest distance to " O   ARG A  56 " =    2.884
peak=    3.330 closest distance to " CG2 THR A 294 " =    1.597
peak=    3.329 closest distance to " CG1BVAL A  72 " =    1.478
peak=    3.319 closest distance to " CB  ALA A  10 " =    1.375
peak=    3.318 closest distance to " O   HOH Z  41 " =    1.985
peak=    3.315 closest distance to " O   HOH Z 173 " =    2.156
peak=    3.307 closest distance to " CE1 TYR A 186 " =    1.346
peak=    3.301 closest distance to " CA  VAL A  41 " =    0.799
peak=    3.301 closest distance to " OD1 ASN A  69 " =    2.522
peak=    3.299 closest distance to " O   HOH Z 253 " =    1.337
peak=    3.298 closest distance to " OG  SER A  62 " =    2.760
peak=    3.293 closest distance to " CA  ALA A 129 " =    1.602
peak=    3.287 closest distance to " O   HOH Z 389 " =    1.634
peak=    3.285 closest distance to " O   HOH Z 412 " =    2.111
peak=    3.284 closest distance to " O   HOH Z 419 " =    1.792
peak=    3.283 closest distance to " CB  PHE A 204 " =    0.761
peak=    3.280 closest distance to " O   HOH Z 357 " =    1.846
peak=    3.275 closest distance to " O   HOH Z 421 " =    1.240
peak=    3.270 closest distance to " O   HOH Z  40 " =    2.650
peak=    3.267 closest distance to " CA  GLY A 267 " =    0.938
peak=    3.266 closest distance to " O   HOH Z 425 " =    1.379
peak=    3.255 closest distance to " O   HOH Z 141 " =    1.583
peak=    3.254 closest distance to " O   HOH Z 417 " =    1.792
peak=    3.252 closest distance to " CZ2 TRP A 150 " =    1.130
peak=    3.252 closest distance to " N   VAL A 126 " =    1.295
peak=    3.247 closest distance to " OH  TYR A 116 " =    1.147
peak=    3.240 closest distance to " CB  ARG A 219 " =    1.326
peak=    3.235 closest distance to " CE AMET A  47 " =    1.448
peak=    3.235 closest distance to " OE2 GLU A  53 " =    2.108
peak=    3.234 closest distance to " NZ  LYS A  48 " =    1.221
peak=    3.233 closest distance to " CA  SER A  87 " =    0.929
peak=    3.226 closest distance to " O   HOH Z  88 " =    3.136
peak=    3.225 closest distance to " O   HOH Z 234 " =    2.143
peak=    3.224 closest distance to " O   HOH Z 272 " =    2.267
peak=    3.221 closest distance to " OG1 THR A 221 " =    1.332
peak=    3.217 closest distance to " CA  LYS A 290 " =    1.205
peak=    3.216 closest distance to " O   HOH Z 414 " =    1.435
peak=    3.215 closest distance to " O   HOH Z  89 " =    1.972
peak=    3.214 closest distance to " O   HOH Z 344 " =    2.794
peak=    3.213 closest distance to " CA  ALA A  84 " =    1.233
peak=    3.213 closest distance to " NH2BARG A 190 " =    1.739
peak=    3.206 closest distance to " O   HOH Z 109 " =    2.087
peak=    3.204 closest distance to " O   HOH Z 254 " =    1.466
peak=    3.198 closest distance to " O   HOH Z 199 " =    2.216
peak=    3.196 closest distance to " O   HOH Z 284 " =    3.016
peak=    3.194 closest distance to " O   HOH Z 250 " =    1.464
peak=    3.191 closest distance to " CA  THR A  52 " =    1.182
peak=    3.191 closest distance to " O   HOH Z 301 " =    1.742
peak=    3.190 closest distance to " O   HOH Z 417 " =    3.516
peak=    3.187 closest distance to " CG1 ILE A 120 " =    1.216
peak=    3.186 closest distance to " CA  GLN A 194 " =    1.245
peak=    3.185 closest distance to " O   HOH Z 183 " =    1.780
peak=    3.185 closest distance to " O   ALA A   1 " =    1.719
peak=    3.185 closest distance to " CG  MET A 113 " =    0.954
peak=    3.185 closest distance to " O   HOH Z 367 " =    3.847
peak=    3.184 closest distance to " O   HOH Z 383 " =    1.809
peak=    3.179 closest distance to " CB  GLU A  46 " =    1.034
peak=    3.179 closest distance to " O   HOH Z  94 " =    1.944
peak=    3.161 closest distance to " O   HOH Z 426 " =    1.648
peak=    3.160 closest distance to " CB  VAL A 268 " =    0.818
peak=    3.160 closest distance to " CG  GLN A  77 " =    2.193
peak=    3.158 closest distance to " O   HOH Z 324 " =    1.395
peak=    3.155 closest distance to " O   HOH Z  59 " =    1.914
peak=    3.155 closest distance to " O   HOH Z 353 " =    2.491
peak=    3.149 closest distance to " O   SER A 164 " =    1.142
peak=    3.146 closest distance to " CB  ALA A 114 " =    1.413
peak=    3.139 closest distance to " O   HOH Z 299 " =    2.281
peak=    3.138 closest distance to " O   HOH Z 433 " =    1.921
peak=    3.134 closest distance to " O   HOH Z  80 " =    2.133
peak=    3.128 closest distance to " O   HOH Z 438 " =    1.839
peak=    3.128 closest distance to " O   HOH Z 226 " =    1.624
peak=    3.125 closest distance to " O   HOH Z 251 " =    1.514
peak=    3.119 closest distance to " CG  LYS A  76 " =    0.921
peak=    3.119 closest distance to " O   HOH Z 327 " =    1.759
peak=    3.113 closest distance to " O   HOH Z 249 " =    1.204
peak=    3.108 closest distance to " CZ2 TRP A 274 " =    1.640
peak=    3.107 closest distance to " O   HOH Z 344 " =    1.426
peak=    3.088 closest distance to " O   HOH Z 409 " =    1.327
peak=    3.087 closest distance to " O   HOH Z 196 " =    1.403
peak=    3.077 closest distance to " O   HOH Z 172 " =    3.775
peak=    3.072 closest distance to " O   HOH Z  47 " =    1.778
peak=    3.071 closest distance to " CZ3 TRP A  85 " =    0.895
peak=    3.070 closest distance to " CB  ARG A 190 " =    1.752
peak=    3.068 closest distance to " CA  ASP A 149 " =    1.035
peak=    3.057 closest distance to " CB  ALA A   1 " =    4.682
peak=    3.057 closest distance to " CD  LYS A 119 " =    1.993
peak=    3.053 closest distance to " CE BMET A  47 " =    1.169
peak=    3.050 closest distance to " O  BHOH Z  74 " =    1.417
peak=    3.028 closest distance to " CG  ARG A  66 " =    0.975
peak=    3.027 closest distance to " O   HOH Z  85 " =    1.491

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.325 - 5.938
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 217
   mapped sites are within: 0.713 - 5.938

peak=   -4.959 closest distance to " O   HOH Z 290 " =    0.906
peak=   -4.639 closest distance to " CG  GLN A  58 " =    0.988
peak=   -4.484 closest distance to " CD  ARG A 156 " =    2.049
peak=   -4.479 closest distance to " O   HOH Z 100 " =    0.888
peak=   -4.438 closest distance to " CD  ARG A  14 " =    3.111
peak=   -4.405 closest distance to " OG BSER A 134 " =    1.180
peak=   -4.296 closest distance to " CG2 ILE A  20 " =    2.863
peak=   -4.266 closest distance to " C   HIS A 108 " =    1.229
peak=   -4.082 closest distance to " CG  GLN A 223 " =    1.919
peak=   -4.078 closest distance to " O   HOH Z 387 " =    2.524
peak=   -4.068 closest distance to " OXT GLY A 302 " =    2.771
peak=   -4.053 closest distance to " NE2 GLN A  88 " =    0.989
peak=   -4.049 closest distance to " CE2 TYR A  30 " =    2.774
peak=   -4.005 closest distance to " O   VAL A  67 " =    2.457
peak=   -3.996 closest distance to " O   HOH Z 429 " =    1.811
peak=   -3.989 closest distance to " CD1 LEU A 255 " =    2.658
peak=   -3.968 closest distance to " O   PRO A 163 " =    2.062
peak=   -3.936 closest distance to " O   HOH Z 351 " =    1.491
peak=   -3.932 closest distance to " N   HIS A 115 " =    2.146
peak=   -3.930 closest distance to " N   GLN A  58 " =    2.047
peak=   -3.928 closest distance to " N   ALA A 248 " =    1.637
peak=   -3.894 closest distance to " O   HOH Z  11 " =    1.883
peak=   -3.875 closest distance to " O   PRO A 198 " =    1.120
peak=   -3.837 closest distance to " CB  ASP A 132 " =    2.334
peak=   -3.786 closest distance to " CD1 LEU A 101 " =    2.234
peak=   -3.776 closest distance to " O   HOH Z 238 " =    0.797
peak=   -3.773 closest distance to " C   GLN A 205 " =    1.845
peak=   -3.765 closest distance to " O   HOH Z 211 " =    1.570
peak=   -3.754 closest distance to " O   HOH Z 266 " =    4.945
peak=   -3.752 closest distance to " CB  ALA A 248 " =    2.363
peak=   -3.736 closest distance to " CZ  TYR A 169 " =    1.748
peak=   -3.734 closest distance to " OD1 ASN A 301 " =    1.940
peak=   -3.731 closest distance to " O   HOH Z 394 " =    1.473
peak=   -3.726 closest distance to " O   HOH Z 313 " =    1.646
peak=   -3.718 closest distance to " O   ALA A 161 " =    1.662
peak=   -3.709 closest distance to " CG1 VAL A 112 " =    2.730
peak=   -3.697 closest distance to " O   HOH Z 103 " =    1.779
peak=   -3.687 closest distance to " CA  GLY A 241 " =    2.328
peak=   -3.657 closest distance to " CG  ASP A 231 " =    0.784
peak=   -3.634 closest distance to " CG1 VAL A 230 " =    1.832
peak=   -3.626 closest distance to " CB  PHE A 192 " =    1.977
peak=   -3.609 closest distance to " CB  ALA A 248 " =    2.203
peak=   -3.602 closest distance to " CB  ALA A 291 " =    2.162
peak=   -3.599 closest distance to " O   HOH Z 114 " =    3.149
peak=   -3.592 closest distance to " ND2 ASN A 187 " =    1.689
peak=   -3.591 closest distance to " CB  PRO A 163 " =    2.543
peak=   -3.582 closest distance to " CB  ALA A 161 " =    2.396
peak=   -3.573 closest distance to " C   MET A 188 " =    1.569
peak=   -3.566 closest distance to " CD2 TYR A 293 " =    2.039
peak=   -3.566 closest distance to " CG  GLU A 152 " =    1.021
peak=   -3.562 closest distance to " CB  SER A 210 " =    1.337
peak=   -3.561 closest distance to " CB  ALA A  51 " =    1.911
peak=   -3.558 closest distance to " CD2 LEU A 300 " =    2.533
peak=   -3.556 closest distance to " O   HOH Z 406 " =    0.844
peak=   -3.552 closest distance to " ND2 ASN A  39 " =    1.089
peak=   -3.548 closest distance to " O   HOH Z  97 " =    1.213
peak=   -3.524 closest distance to " N   ALA A 226 " =    1.974
peak=   -3.521 closest distance to " O   GLY A 196 " =    1.217
peak=   -3.513 closest distance to " O   HOH Z 421 " =    3.188
peak=   -3.500 closest distance to " O   HOH Z 193 " =    1.613
peak=   -3.497 closest distance to " CG  PHE A 283 " =    2.607
peak=   -3.497 closest distance to " CZ  TYR A 172 " =    1.769
peak=   -3.490 closest distance to " O   ASN A 187 " =    1.580
peak=   -3.489 closest distance to " CG  LEU A 228 " =    0.911
peak=   -3.488 closest distance to " O   HOH Z 187 " =    1.762
peak=   -3.487 closest distance to " O   HOH Z 133 " =    3.040
peak=   -3.485 closest distance to " NH2 ARG A  79 " =    1.947
peak=   -3.483 closest distance to " NE2 GLN A  88 " =    1.766
peak=   -3.483 closest distance to " CB  ASP A 132 " =    2.186
peak=   -3.477 closest distance to " O   ALA A 292 " =    2.232
peak=   -3.473 closest distance to " O   HOH Z 185 " =    2.323
peak=   -3.469 closest distance to " N   THR A 157 " =    1.438
peak=   -3.467 closest distance to " CG2 VAL A 296 " =    0.713
peak=   -3.465 closest distance to " CB  ASN A  39 " =    2.204
peak=   -3.446 closest distance to " O   PHE A 218 " =    1.732
peak=   -3.441 closest distance to " CG2 VAL A 202 " =    2.678
peak=   -3.430 closest distance to " CD1 ILE A 199 " =    2.320
peak=   -3.423 closest distance to " O   PRO A 198 " =    1.169
peak=   -3.423 closest distance to " O   HOH Z 165 " =    2.000
peak=   -3.415 closest distance to " O   HOH Z 196 " =    2.281
peak=   -3.415 closest distance to " ND2 ASN A  45 " =    1.111
peak=   -3.414 closest distance to " CD1 ILE A 263 " =    2.747
peak=   -3.413 closest distance to " OD2 ASP A 191 " =    1.316
peak=   -3.409 closest distance to " O   HOH Z 174 " =    4.059
peak=   -3.404 closest distance to " CB  ALA A  64 " =    2.619
peak=   -3.402 closest distance to " CG2 THR A  18 " =    2.783
peak=   -3.401 closest distance to " CG2 ILE A 263 " =    2.218
peak=   -3.394 closest distance to " O   HOH Z 140 " =    1.237
peak=   -3.393 closest distance to " O   ALA A   8 " =    1.710
peak=   -3.390 closest distance to " O   HOH Z 393 " =    3.556
peak=   -3.388 closest distance to " O   HOH Z 362 " =    5.938
peak=   -3.386 closest distance to " CE1 TYR A 247 " =    2.564
peak=   -3.386 closest distance to " CA  ASP A 298 " =    1.107
peak=   -3.374 closest distance to " N   MET A 188 " =    1.871
peak=   -3.360 closest distance to " O   HOH Z 131 " =    4.117
peak=   -3.359 closest distance to " CG  LEU A   5 " =    0.891
peak=   -3.358 closest distance to " O   HOH Z 166 " =    2.025
peak=   -3.358 closest distance to " O   ALA A  51 " =    1.220
peak=   -3.349 closest distance to " O   HOH Z 249 " =    0.943
peak=   -3.348 closest distance to " CD  GLU A 277 " =    1.071
peak=   -3.342 closest distance to " O   HOH Z 426 " =    1.586
peak=   -3.338 closest distance to " CD  ARG A 139 " =    1.579
peak=   -3.329 closest distance to " O   HOH Z 394 " =    1.260
peak=   -3.329 closest distance to " O   HOH Z 359 " =    3.217
peak=   -3.324 closest distance to " O   HOH Z 300 " =    1.211
peak=   -3.317 closest distance to " CZ  ARG A 259 " =    0.865
peak=   -3.313 closest distance to " OG  SER A  87 " =    1.335
peak=   -3.308 closest distance to " O   HOH Z 139 " =    4.951
peak=   -3.306 closest distance to " CE BMET A  47 " =    1.476
peak=   -3.304 closest distance to " O   HOH Z 281 " =    3.067
peak=   -3.303 closest distance to " N   ASP A 286 " =    2.150
peak=   -3.303 closest distance to " O   HOH Z 191 " =    5.229
peak=   -3.302 closest distance to " O   HOH Z 139 " =    3.352
peak=   -3.301 closest distance to " OG ASER A 134 " =    1.437
peak=   -3.299 closest distance to " O   SER A 210 " =    1.922
peak=   -3.295 closest distance to " CB  ALA A  43 " =    2.237
peak=   -3.294 closest distance to " CD2 LEU A 237 " =    2.764
peak=   -3.290 closest distance to " ND2 ASN A 173 " =    1.317
peak=   -3.279 closest distance to " CZ3 TRP A 179 " =    1.301
peak=   -3.278 closest distance to " C   LEU A 222 " =    1.214
peak=   -3.272 closest distance to " O   HOH Z 183 " =    1.467
peak=   -3.269 closest distance to " CE3 TRP A 150 " =    1.956
peak=   -3.267 closest distance to " O   HOH Z 423 " =    2.014
peak=   -3.265 closest distance to " CE  MET A 105 " =    2.055
peak=   -3.261 closest distance to " CE3 TRP A 274 " =    2.187
peak=   -3.260 closest distance to " N   PRO A 163 " =    1.555
peak=   -3.259 closest distance to " O   HOH Z 372 " =    2.325
peak=   -3.259 closest distance to " OG  SER A  97 " =    2.186
peak=   -3.258 closest distance to " C   ASP A 231 " =    2.388
peak=   -3.255 closest distance to " O   HOH Z 193 " =    1.802
peak=   -3.254 closest distance to " CD1 LEU A 228 " =    2.046
peak=   -3.253 closest distance to " O   HOH Z  89 " =    2.670
peak=   -3.253 closest distance to " O   SER A   3 " =    1.033
peak=   -3.251 closest distance to " O   ILE A 106 " =    2.020
peak=   -3.250 closest distance to " O   HOH Z  47 " =    1.614
peak=   -3.249 closest distance to " OE2 GLU A   2 " =    1.081
peak=   -3.243 closest distance to " CA  GLY A  98 " =    1.815
peak=   -3.241 closest distance to " CZ  ARG A  66 " =    1.075
peak=   -3.241 closest distance to " OE1 GLN A 183 " =    1.443
peak=   -3.238 closest distance to " N   ALA A 244 " =    1.600
peak=   -3.238 closest distance to " CG  ARG A 219 " =    2.530
peak=   -3.234 closest distance to " O   HOH Z  91 " =    1.596
peak=   -3.234 closest distance to " CB  ASN A  69 " =    1.089
peak=   -3.230 closest distance to " O   HOH Z  56 " =    2.479
peak=   -3.229 closest distance to " O   HOH Z 313 " =    1.112
peak=   -3.228 closest distance to " O   TRP A  70 " =    1.514
peak=   -3.228 closest distance to " C   LEU A 143 " =    1.021
peak=   -3.222 closest distance to " O   ALA A   1 " =    1.781
peak=   -3.219 closest distance to " OG  SER A  62 " =    1.026
peak=   -3.215 closest distance to " O   TRP A  92 " =    1.844
peak=   -3.213 closest distance to " C   GLY A  91 " =    1.275
peak=   -3.212 closest distance to " O   HOH Z 389 " =    1.982
peak=   -3.207 closest distance to " CG1 VAL A 197 " =    2.114
peak=   -3.204 closest distance to " OD2 ASP A 171 " =    2.132
peak=   -3.203 closest distance to " O   HOH Z 407 " =    2.740
peak=   -3.202 closest distance to " NE2 GLN A 278 " =    1.856
peak=   -3.202 closest distance to " CG  TRP A 266 " =    1.901
peak=   -3.201 closest distance to " CD  PRO A 243 " =    2.091
peak=   -3.201 closest distance to " O   GLN A  77 " =    1.698
peak=   -3.200 closest distance to " CA  GLY A 133 " =    1.895
peak=   -3.199 closest distance to " CG1 VAL A 296 " =    1.974
peak=   -3.197 closest distance to " OG  SER A   3 " =    1.261
peak=   -3.196 closest distance to " O   HOH Z  69 " =    1.967
peak=   -3.193 closest distance to " O   HOH Z 427 " =    1.398
peak=   -3.192 closest distance to " O   HOH Z 137 " =    1.640
peak=   -3.189 closest distance to " O   HOH Z 345 " =    1.550
peak=   -3.184 closest distance to " O   HOH Z 194 " =    0.849
peak=   -3.182 closest distance to " O   HOH Z 344 " =    2.496
peak=   -3.181 closest distance to " O   HOH Z 243 " =    1.877
peak=   -3.173 closest distance to " CB  TYR A  15 " =    2.147
peak=   -3.164 closest distance to " CD2 PHE A  61 " =    2.034
peak=   -3.161 closest distance to " O   HOH Z 414 " =    2.314
peak=   -3.161 closest distance to " O   ARG A  24 " =    1.790
peak=   -3.158 closest distance to " O   HOH Z 250 " =    1.378
peak=   -3.148 closest distance to " O   HOH Z 339 " =    1.685
peak=   -3.144 closest distance to " CZ2 TRP A 274 " =    1.072
peak=   -3.144 closest distance to " O   SER A  22 " =    2.255
peak=   -3.140 closest distance to " NE2 GLN A 194 " =    1.741
peak=   -3.139 closest distance to " O   HOH Z 174 " =    2.201
peak=   -3.138 closest distance to " OD1 ASN A 176 " =    1.353
peak=   -3.137 closest distance to " C   ILE A 239 " =    2.085
peak=   -3.136 closest distance to " O   VAL A 174 " =    2.201
peak=   -3.131 closest distance to " OD2 ASP A 140 " =    0.995
peak=   -3.128 closest distance to " O   HOH Z 198 " =    0.978
peak=   -3.125 closest distance to " N   SER A 276 " =    1.214
peak=   -3.125 closest distance to " O   HOH Z  33 " =    2.123
peak=   -3.120 closest distance to " O   GLY A  80 " =    2.545
peak=   -3.117 closest distance to " CB  PHE A 208 " =    2.293
peak=   -3.110 closest distance to " CD  GLN A 278 " =    2.041
peak=   -3.110 closest distance to " CG  MET A 105 " =    0.869
peak=   -3.105 closest distance to " CD1 TYR A 247 " =    2.552
peak=   -3.102 closest distance to " O   HOH Z 221 " =    0.984
peak=   -3.102 closest distance to " CB  PRO A 243 " =    2.523
peak=   -3.094 closest distance to " CE1 PHE A 208 " =    2.257
peak=   -3.094 closest distance to " OE2 GLU A 152 " =    1.307
peak=   -3.090 closest distance to " CA  GLY A  23 " =    1.766
peak=   -3.086 closest distance to " C   ALA A 158 " =    1.304
peak=   -3.082 closest distance to " O   HOH Z  13 " =    1.766
peak=   -3.073 closest distance to " O   HOH Z 111 " =    4.701
peak=   -3.068 closest distance to " N   THR A 220 " =    2.162
peak=   -3.068 closest distance to " CD2 PHE A 225 " =    1.085
peak=   -3.058 closest distance to " CG1 VAL A 268 " =    2.430
peak=   -3.051 closest distance to " N   ARG A  36 " =    1.906
peak=   -3.049 closest distance to " O   HOH Z 216 " =    1.563
peak=   -3.038 closest distance to " CE1 HIS A  81 " =    1.637
peak=   -3.035 closest distance to " ND2 ASN A  60 " =    1.317
peak=   -3.032 closest distance to " O   HOH Z 389 " =    1.396
peak=   -3.021 closest distance to " CB  ALA A  84 " =    2.605

================= 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    :  0.4621 0.4549   6.264311e+00   6.254353e+00
   1_bss:  0.4536 0.4505   6.254265e+00   6.244984e+00
   1_xyz:  0.3650 0.3841   6.120032e+00   6.163550e+00
   1_adp:  0.3111 0.3584   6.009016e+00   6.105720e+00
   1_occ:  0.3107 0.3578   6.008207e+00   6.106370e+00
   2_bss:  0.3061 0.3522   6.007063e+00   6.104316e+00
   2_xyz:  0.2279 0.2750   5.750082e+00   5.907184e+00
   2_adp:  0.2058 0.2527   5.662027e+00   5.836915e+00
   2_occ:  0.2055 0.2520   5.660539e+00   5.835068e+00
   3_bss:  0.2033 0.2511   5.656517e+00   5.832306e+00
   3_xyz:  0.1518 0.1922   5.389730e+00   5.584787e+00
   3_adp:  0.1386 0.1813   5.317565e+00   5.530137e+00
   3_occ:  0.1384 0.1811   5.317060e+00   5.529850e+00
   4_bss:  0.1379 0.1814   5.314907e+00   5.526203e+00
   4_xyz:  0.1184 0.1653   5.198571e+00   5.435168e+00
   4_adp:  0.1156 0.1610   5.172296e+00   5.406253e+00
   4_occ:  0.1155 0.1610   5.171382e+00   5.405406e+00
   5_bss:  0.1155 0.1609   5.171567e+00   5.405605e+00
   5_xyz:  0.1107 0.1563   5.137484e+00   5.379193e+00
   5_adp:  0.1123 0.1558   5.142903e+00   5.375257e+00
   5_occ:  0.1122 0.1558   5.142154e+00   5.374548e+00
   5_bss:  0.1119 0.1555   5.141264e+00   5.372678e+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:  0.355   9.700   8.969   8.172   8.001   0.000   0.000   0.000
   1_xyz:  0.355   9.700   8.969   8.172   8.001   0.000   0.000   0.000
   1_adp:  0.355   9.700   8.969   8.172   8.001   0.000   0.000   0.000
   1_occ:  0.355   9.700   8.969   8.172   8.001   0.000   0.000   0.000
   2_bss:  0.330  25.705   5.235   4.152   4.751   0.000   0.000   0.000
   2_xyz:  0.330  25.705   5.235   4.152   4.751   0.000   0.000   0.000
   2_adp:  0.330  25.705   5.235   4.152   4.751   0.000   0.000   0.000
   2_occ:  0.330  25.705   5.235   4.152   4.751   0.000   0.000   0.000
   3_bss:  0.313  31.184   2.713   2.847   3.892   0.000   0.000   0.000
   3_xyz:  0.313  31.184   2.713   2.847   3.892   0.000   0.000   0.000
   3_adp:  0.313  31.184   2.713   2.847   3.892   0.000   0.000   0.000
   3_occ:  0.313  31.184   2.713   2.847   3.892   0.000   0.000   0.000
   4_bss:  0.313  37.256   1.605   2.304   3.339   0.000   0.000   0.000
   4_xyz:  0.313  37.256   1.605   2.304   3.339   0.000   0.000   0.000
   4_adp:  0.313  37.256   1.605   2.304   3.339   0.000   0.000   0.000
   4_occ:  0.313  37.256   1.605   2.304   3.339   0.000   0.000   0.000
   5_bss:  0.319  37.281   1.605   2.304   3.339   0.000   0.000   0.000
   5_xyz:  0.319  37.281   1.605   2.304   3.339   0.000   0.000   0.000
   5_adp:  0.319  37.281   1.605   2.304   3.339   0.000   0.000   0.000
   5_occ:  0.319  37.281   1.605   2.304   3.339   0.000   0.000   0.000
   5_bss:  0.324  39.512  -0.918  -0.128   1.046   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.772 0.4744  0.5554    64713.991
   1_bss:  54.054 0.4688  0.7063    62277.624
   1_xyz:  43.572 0.5990  0.8789    43732.179
   1_adp:  38.058 0.6662  0.9951    36035.394
   1_occ:  38.057 0.6663  0.9941    36016.904
   2_bss:  37.673 0.6707  0.8771    35536.304
   2_xyz:  28.400 0.7744  0.9821    20308.446
   2_adp:  25.288 0.8084  1.0167    17002.346
   2_occ:  25.216 0.8092  1.0168    16909.480
   3_bss:  25.085 0.8106  0.9614    16805.503
   3_xyz:  18.338 0.8773  1.0075     9543.174
   3_adp:  17.046 0.8896  1.0139     8645.839
   3_occ:  17.040 0.8896  1.0138     8632.288
   4_bss:  16.954 0.8903  0.9872     8553.950
   4_xyz:  15.123 0.9057  0.9915     7077.282
   4_adp:  14.505 0.9110  0.9901     6713.593
   4_occ:  14.485 0.9111  0.9901     6696.206
   5_bss:  14.491 0.9111  0.9901     6702.565
   5_xyz:  13.948 0.9155  0.9923     6306.146
   5_adp:  13.829 0.9166  0.9923     6294.296
   5_occ:  13.812 0.9167  0.9922     6279.874
   5_bss:  13.808 0.9167  0.9851     6270.410
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.3041e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.3041e+01
   1_xyz:   1.596  0.012  0.103 18.152  0.006  4.117   1.3130e-01
   1_adp:   1.596  0.012  0.103 18.152  0.006  4.117   1.3130e-01
   1_occ:   1.596  0.012  0.103 18.152  0.006  4.117   1.3130e-01
   2_bss:   1.596  0.012  0.103 18.152  0.006  4.117   1.3130e-01
   2_xyz:   1.066  0.007  0.077 16.178  0.005  4.117   7.2205e-02
   2_adp:   1.066  0.007  0.077 16.178  0.005  4.117   7.2205e-02
   2_occ:   1.066  0.007  0.077 16.178  0.005  4.117   7.2205e-02
   3_bss:   1.066  0.007  0.077 16.178  0.005  4.117   7.2205e-02
   3_xyz:   0.998  0.006  0.073 15.823  0.003  4.111   6.0544e-02
   3_adp:   0.998  0.006  0.073 15.823  0.003  4.111   6.0544e-02
   3_occ:   0.998  0.006  0.073 15.823  0.003  4.111   6.0544e-02
   4_bss:   0.998  0.006  0.073 15.823  0.003  4.111   6.0544e-02
   4_xyz:   1.073  0.007  0.078 15.910  0.004  4.114   6.7489e-02
   4_adp:   1.073  0.007  0.078 15.910  0.004  4.114   6.7489e-02
   4_occ:   1.073  0.007  0.078 15.910  0.004  4.114   6.7489e-02
   5_bss:   1.073  0.007  0.078 15.910  0.004  4.114   6.7489e-02
   5_xyz:   1.088  0.008  0.081 15.881  0.004  4.109   6.9205e-02
   5_adp:   1.088  0.008  0.081 15.881  0.004  4.109   6.9205e-02
   5_occ:   1.088  0.008  0.081 15.881  0.004  4.109   6.9205e-02
   5_bss:   1.088  0.008  0.081 15.881  0.004  4.109   6.9205e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8657e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8657e+00
   1_xyz:  13.842  0.149  0.437 86.682  0.032  2.212   9.1352e-02
   1_adp:  13.842  0.149  0.437 86.682  0.032  2.212   9.1352e-02
   1_occ:  13.842  0.149  0.437 86.682  0.032  2.212   9.1352e-02
   2_bss:  13.842  0.149  0.437 86.682  0.032  2.212   9.1352e-02
   2_xyz:   6.348  0.109  0.342 80.546  0.041  2.313   6.0269e-02
   2_adp:   6.348  0.109  0.342 80.546  0.041  2.313   6.0269e-02
   2_occ:   6.348  0.109  0.342 80.546  0.041  2.313   6.0269e-02
   3_bss:   6.348  0.109  0.342 80.546  0.041  2.313   6.0269e-02
   3_xyz:   7.472  0.040  0.298 86.481  0.024  2.327   4.4357e-02
   3_adp:   7.472  0.040  0.298 86.481  0.024  2.327   4.4357e-02
   3_occ:   7.472  0.040  0.298 86.481  0.024  2.327   4.4357e-02
   4_bss:   7.472  0.040  0.298 86.481  0.024  2.327   4.4357e-02
   4_xyz:   7.558  0.046  0.290 84.644  0.033  2.328   5.1211e-02
   4_adp:   7.558  0.046  0.290 84.644  0.033  2.328   5.1211e-02
   4_occ:   7.558  0.046  0.290 84.644  0.033  2.328   5.1211e-02
   5_bss:   7.558  0.046  0.290 84.644  0.033  2.328   5.1211e-02
   5_xyz:   7.320  0.051  0.308 84.020  0.034  2.314   5.1275e-02
   5_adp:   7.320  0.051  0.308 84.020  0.034  2.314   5.1275e-02
   5_occ:   7.320  0.051  0.308 84.020  0.034  2.314   5.1275e-02
   5_bss:   7.320  0.051  0.308 84.020  0.034  2.314   5.1275e-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:  60.45   0.00  11.77  54.11   0.00   9.36  60.45   0.00  24.89
   1_occ:  60.45   0.00  11.77  54.11   0.00   9.36  60.45   0.00  24.89
   2_bss:  60.45   0.00  11.77  54.11   0.00   9.36  60.45   0.00  24.89
   2_xyz:  60.45   0.00  11.77  54.11   0.00   9.36  60.45   0.00  24.89
   2_adp:  85.98   0.00  12.76  85.98   0.00   9.08  76.05   1.43  32.78
   2_occ:  85.98   0.00  12.76  85.98   0.00   9.08  76.05   1.43  32.78
   3_bss:  85.98   0.00  12.76  85.98   0.00   9.08  76.05   1.43  32.78
   3_xyz:  85.98   0.00  12.76  85.98   0.00   9.08  76.05   1.43  32.78
   3_adp:  94.12   0.00  13.27  94.12   0.00   8.91  81.64   1.61  37.05
   3_occ:  94.12   0.00  13.27  94.12   0.00   8.91  81.64   1.61  37.05
   4_bss:  94.12   0.00  13.27  94.12   0.00   8.91  81.64   1.61  37.05
   4_xyz:  94.12   0.00  13.27  94.12   0.00   8.91  81.64   1.61  37.05
   4_adp:  94.48   0.00  12.87  94.48   0.00   8.60  80.69   1.22  36.11
   4_occ:  94.48   0.00  12.87  94.48   0.00   8.60  80.69   1.22  36.11
   5_bss:  94.48   0.00  12.87  94.48   0.00   8.60  80.69   1.22  36.11
   5_xyz:  94.48   0.00  12.87  94.48   0.00   8.60  80.69   1.22  36.11
   5_adp:  92.41   0.00  12.09  92.41   0.00   8.32  75.92   2.10  32.63
   5_occ:  92.41   0.00  12.09  92.41   0.00   8.32  75.92   2.10  32.63
   5_bss:  94.65   2.23  14.32  94.65   2.23  10.55  78.15   4.33  34.86
------------------------------------------------------------------------
 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:    1.225    0.020    0.406
   1_adp:    1.225    0.020    0.406
   1_occ:    1.225    0.020    0.406
   2_bss:    1.225    0.020    0.406
   2_xyz:    1.574    0.047    0.541
   2_adp:    1.574    0.047    0.541
   2_occ:    1.574    0.047    0.541
   3_bss:    1.574    0.047    0.541
   3_xyz:    1.517    0.041    0.604
   3_adp:    1.517    0.041    0.604
   3_occ:    1.517    0.041    0.604
   4_bss:    1.517    0.041    0.604
   4_xyz:    1.596    0.062    0.641
   4_adp:    1.596    0.062    0.641
   4_occ:    1.596    0.062    0.641
   5_bss:    1.596    0.062    0.641
   5_xyz:    1.642    0.046    0.652
   5_adp:    1.642    0.046    0.652
   5_occ:    1.642    0.046    0.652
   5_bss:    1.642    0.046    0.652
------------------------------------------------------------------------

CPU time actual refinement: 335.95


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_49/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_49/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_49/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_49/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_49/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.79 
  Macro-tasks:
    bulk solvent and scale       = 42.95  
    individual site refinement   = 138.40 
    weights calculation          = 33.02  
    collect and process          = 6.63   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 221.12 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 102.75 
    alpha_beta                      = 8.31   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 112.88 
    fmodel                         = 7.07   
    r_factors                      = 0.27   
    phase_errors                   = 10.72  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 245.82 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.760 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    629 calls, 102.49 s
gradients_fft:          574 calls,  99.88 s

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

# Date 2008-01-16 Time 00:39:07 PST -0800 (1200472747.02 s)
Start R-work = 0.4621, R-free = 0.4549 (no bulk solvent and anisotropic scale)
Final R-work = 0.1304, R-free = 0.1726 (no bulk solvent and anisotropic scale)

Start R-work = 0.4536, R-free = 0.4505
Final R-work = 0.1119, R-free = 0.1555