# Date 2008-01-16 Time 03:14:03 PST -0800 (1200482043.57 s)
#phil __OFF__

Command line arguments: "../1153.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17662
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1153

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 46.93, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 2.00296
Completeness in resolution range: 0.952217
Completeness with d_max=infinity: 0.949355

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2939
                             d_min =   2.0030

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 2.00296
Completeness in resolution range: 0.952217
Completeness with d_max=infinity: 0.949355

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2943 -  4.2866 [2163/2188]  1944   219  10.1%
  bin  2:  4.2866 -  3.4148 [2072/2092]  1868   204   9.8%
  bin  3:  3.4148 -  2.9868 [2059/2078]  1852   207  10.1%
  bin  4:  2.9868 -  2.7154 [2022/2052]  1820   202  10.0%
  bin  5:  2.7154 -  2.5217 [2013/2032]  1816   197   9.8%
  bin  6:  2.5217 -  2.3736 [2014/2039]  1808   206  10.2%
  bin  7:  2.3736 -  2.2551 [1989/2017]  1788   201  10.1%
  bin  8:  2.2551 -  2.1572 [1989/2025]  1792   197   9.9%
  bin  9:  2.1572 -  2.0744 [1986/2028]  1791   195   9.8%
  bin 10:  2.0744 -  2.0030 [1282/2021]  1151   131  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1153/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2165
        3.04 -     3.66: 4566
        3.66 -     4.28: 8857
        4.28 -     4.90: 12181
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.997 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.376 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27774 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_1153/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1153/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 46.93 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4757   r_free= 0.4699   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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.277692                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.7813 0.99   1404  156 0.3932 0.3560      6.5991      6.5151|
|  2:  4.7813 -  3.8145 0.99   1346  151 0.3894 0.4173      6.7783       6.846|
|  3:  3.8145 -  3.3380 0.99   1326  143 0.4354 0.3939      6.6616       6.644|
|  4:  3.3380 -  3.0354 0.99   1326  153 0.4668 0.4250      6.5248      6.4271|
|  5:  3.0354 -  2.8193 0.99   1306  145 0.5038 0.5090      6.3653      6.4059|
|  6:  2.8193 -  2.6540 0.99   1301  141 0.4960 0.5318      6.2712       6.205|
|  7:  2.6540 -  2.5217 0.99   1291  140 0.5224 0.5324       6.246       6.238|
|  8:  2.5217 -  2.4124 0.98   1287  146 0.5364 0.4880       6.185      6.1522|
|  9:  2.4124 -  2.3198 0.98   1265  146 0.5006 0.5961       6.108      6.1837|
| 10:  2.3198 -  2.2400 1.00   1306  143 0.5326 0.5038      6.1109      6.0655|
| 11:  2.2400 -  2.1702 0.98   1276  138 0.5105 0.4970      6.0263      6.0635|
| 12:  2.1702 -  2.1083 0.98   1263  145 0.5152 0.4955       5.976      6.0025|
| 13:  2.1083 -  2.0529 0.99   1288  138 0.5324 0.5058      5.8765      5.7959|
| 14:  2.0529 -  2.0030 0.49    645   74 0.5295 0.4930        5.88      5.7923|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2943 -  4.7813  1404   156  0.72  32.76   0.79     0.75      66118.40|
|  2:  4.7813 -  3.8145  1346   151  0.73  32.95   0.87     0.78      96147.64|
|  3:  3.8145 -  3.3380  1326   143  0.64  40.91   0.82     0.73     102477.50|
|  4:  3.3380 -  3.0354  1326   153  0.54  48.68   0.79     0.62      92860.73|
|  5:  3.0354 -  2.8193  1306   145  0.45  56.12   0.73     0.53      78560.94|
|  6:  2.8193 -  2.6540  1301   141  0.40  60.13   0.72     0.45      71784.10|
|  7:  2.6540 -  2.5217  1291   140  0.35  63.72   0.72     0.40      67361.22|
|  8:  2.5217 -  2.4124  1287   146  0.32  65.67   0.70     0.37      61390.11|
|  9:  2.4124 -  2.3198  1265   146  0.33  64.95   0.73     0.38      56001.90|
| 10:  2.3198 -  2.2400  1306   143  0.35  64.08   0.73     0.40      49183.26|
| 11:  2.2400 -  2.1702  1276   138  0.36  62.77   0.76     0.43      45042.86|
| 12:  2.1702 -  2.1083  1263   145  0.39  61.10   0.73     0.46      40254.61|
| 13:  2.1083 -  2.0529  1288   138  0.37  62.72   0.68     0.45      34875.60|
| 14:  2.0529 -  2.0030   645    74  0.38  61.28   0.72     0.41      28897.95|
|alpha:            min =        0.37 max =            0.78 mean =         0.52|
|beta:             min =    28897.95 max =       102477.50 mean =     65239.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.98 mean =        55.07|
|phase err.(test): min =        0.00 max =           89.78 mean =        55.03|
|-----------------------------------------------------------------------------|

============================== 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 = 13.802041             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.111   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.186244              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.935   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      158 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      679 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1478 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2559 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3863 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4990 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6424 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7574 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.588 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.621 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.353)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.353)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4811   r_free= 0.4759   ksol= 0.00   Bsol= 0.00   scale= 0.753    |
|                                                                             |
| 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: 6.278875                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4678   r_free= 0.4617   ksol= 0.33   Bsol= 50.00   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.47,6.28,10.56,0.00,0.00,0.00); trace/3= 8.44                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.271797                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.458515             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.057   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.046396              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.629   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4678      final r-factor (work) = 0.3786          |
| start r-factor (free) = 0.4617      final r-factor (free) = 0.4039          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.6808 = 12.46 * 0.50 * 6.2757 + 1.00 * 54.5877                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.6102 = 12.46 * 0.50 * 6.1743 + 1.00 * 0.1486                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3786      final r-factor (work) = 0.3307          |
| start r-factor (free) = 0.4039      final r-factor (free) = 0.3788          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4753 = 1.05 * 1.00 * 6.1743 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3763 = 1.05 * 1.00 * 6.0785 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.353)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.79   12.50    None  None   None       |
|    all(noH): 2823   0      0.00    71.79   12.50    None  None   None       |
|    Sol.    : 438    0      0.00    71.79   27.13    None  None   None       |
|    Mac.    : 2385   0      0.00    63.25   9.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.179: 1179   |   5:    35.894 -  43.073:   76        |
|      1:     7.179 -  14.358:  738   |   6:    43.073 -  50.251:   47        |
|      2:    14.358 -  21.536:  401   |   7:    50.251 -  57.430:   19        |
|      3:    21.536 -  28.715:  215   |   8:    57.430 -  64.609:   13        |
|      4:    28.715 -  35.894:  133   |   9:    64.609 -  71.788:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3307 r_free = 0.3788             target_work(ml) = 6.052         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3304 r_free = 0.3800             target_work(ml) = 6.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3304   r_free= 0.3800   ksol= 0.33   Bsol= 50.00   scale= 1.070   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.47,6.28,10.56,0.00,0.00,0.00); trace/3= 8.44                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.051601                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3289   r_free= 0.3775   ksol= 0.32   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.53,3.85,7.55,0.00,0.00,0.00); trace/3= 5.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.053401                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.461954              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.899   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.538777              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.909  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3289      final r-factor (work) = 0.2371          |
| start r-factor (free) = 0.3775      final r-factor (free) = 0.2905          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.7724 = 6.46 * 0.50 * 6.0736 + 1.00 * 0.1486                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2238 = 6.46 * 0.50 * 5.9245 + 1.00 * 0.0819                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2371      final r-factor (work) = 0.2186          |
| start r-factor (free) = 0.2905      final r-factor (free) = 0.2729          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2320 = 0.54 * 1.00 * 5.9245 + 1.00 * 0.0401                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1987 = 0.54 * 1.00 * 5.7377 + 1.00 * 0.1074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.353)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.45   12.60    None  None   None       |
|    all(noH): 2823   0      0.00    87.45   12.60    None  None   None       |
|    Sol.    : 438    0      0.00    72.49   29.80    None  None   None       |
|    Mac.    : 2385   0      0.00    87.45   9.44     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 -   8.745: 1384   |   5:    43.724 -  52.469:   51        |
|      1:     8.745 -  17.490:  768   |   6:    52.469 -  61.213:   25        |
|      2:    17.490 -  26.234:  304   |   7:    61.213 -  69.958:    4        |
|      3:    26.234 -  34.979:  184   |   8:    69.958 -  78.703:    1        |
|      4:    34.979 -  43.724:  101   |   9:    78.703 -  87.448:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2186 r_free = 0.2729             target_work(ml) = 5.710         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2183 r_free = 0.2726             target_work(ml) = 5.709         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2183   r_free= 0.2726   ksol= 0.32   Bsol= 50.00   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.53,3.85,7.55,0.00,0.00,0.00); trace/3= 5.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.709081                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2164   r_free= 0.2711   ksol= 0.32   Bsol= 61.78   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,2.64,4.72,0.00,0.00,0.00); trace/3= 3.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.710499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.185012              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.871   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.287264              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.538   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2164      final r-factor (work) = 0.1685          |
| start r-factor (free) = 0.2711      final r-factor (free) = 0.2182          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1008 = 4.19 * 0.50 * 5.7438 + 1.00 * 0.0819                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8108 = 4.19 * 0.50 * 5.6073 + 1.00 * 0.0776                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1685      final r-factor (work) = 0.1460          |
| start r-factor (free) = 0.2182      final r-factor (free) = 0.1986          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.8407 = 2.29 * 1.00 * 5.6073 + 1.00 * 0.0155                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.4206 = 2.29 * 1.00 * 5.4231 + 1.00 * 0.0165                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.353)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.77   13.89    None  None   None       |
|    all(noH): 2823   0      0.00    97.77   13.89    None  None   None       |
|    Sol.    : 438    0      0.00    97.77   39.69    None  None   None       |
|    Mac.    : 2385   0      0.00    85.99   9.16     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 -   9.777: 1667   |   5:    48.883 -  58.659:   84        |
|      1:     9.777 -  19.553:  597   |   6:    58.659 -  68.436:   57        |
|      2:    19.553 -  29.330:  170   |   7:    68.436 -  78.212:   25        |
|      3:    29.330 -  39.106:  114   |   8:    78.212 -  87.989:    6        |
|      4:    39.106 -  48.883:   99   |   9:    87.989 -  97.765:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1460 r_free = 0.1986             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1459 r_free = 0.1986             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1986   ksol= 0.32   Bsol= 61.78   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,2.64,4.72,0.00,0.00,0.00); trace/3= 3.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.380524                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1986   ksol= 0.33   Bsol= 76.37   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.23,1.90,3.80,0.00,0.00,0.00); trace/3= 2.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.380354                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.328560              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.879  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.236365              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.152  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1459      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1986      final r-factor (free) = 0.1812          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8255 = 4.33 * 0.50 * 5.4281 + 1.00 * 0.0776                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6144 = 4.33 * 0.50 * 5.3237 + 1.00 * 0.0923                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1260      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1812      final r-factor (free) = 0.1734          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2747 = 0.24 * 1.00 * 5.3237 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2599 = 0.24 * 1.00 * 5.2675 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.353)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.90   13.03    None  None   None       |
|    all(noH): 2823   0      0.00    92.90   13.03    None  None   None       |
|    Sol.    : 438    0      1.65    92.90   36.62    None  None   None       |
|    Mac.    : 2385   0      0.00    76.33   8.70     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 -   9.291: 1678   |   5:    46.452 -  55.743:   88        |
|      1:     9.291 -  18.581:  605   |   6:    55.743 -  65.033:   43        |
|      2:    18.581 -  27.871:  162   |   7:    65.033 -  74.324:   17        |
|      3:    27.871 -  37.162:  125   |   8:    74.324 -  83.614:    5        |
|      4:    37.162 -  46.452:   96   |   9:    83.614 -  92.904:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1242 r_free = 0.1734             target_work(ml) = 5.242         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1241 r_free = 0.1734             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1241   r_free= 0.1734   ksol= 0.33   Bsol= 76.37   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.23,1.90,3.80,0.00,0.00,0.00); trace/3= 2.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.241354                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1734   ksol= 0.32   Bsol= 65.63   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,1.92,3.64,0.00,0.00,0.00); trace/3= 2.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.241050                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.707930              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.869  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.352443              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.851   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1240      final r-factor (work) = 0.1263          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5898 = 1.71 * 0.50 * 5.2667 + 1.00 * 0.0923                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5471 = 1.71 * 0.50 * 5.2520 + 1.00 * 0.0621                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1263      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1724          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8638 = 0.35 * 1.00 * 5.2520 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8814 = 0.35 * 1.00 * 5.2465 + 1.00 * 0.0323                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.353)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.61   12.93    None  None   None       |
|    all(noH): 2823   0      0.00    93.61   12.93    None  None   None       |
|    Sol.    : 438    0      1.96    93.61   36.33    None  None   None       |
|    Mac.    : 2385   0      0.00    78.13   8.63     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 -   9.361: 1705   |   5:    46.803 -  56.164:   94        |
|      1:     9.361 -  18.721:  573   |   6:    56.164 -  65.524:   39        |
|      2:    18.721 -  28.082:  167   |   7:    65.524 -  74.885:   13        |
|      3:    28.082 -  37.442:  132   |   8:    74.885 -  84.245:    5        |
|      4:    37.442 -  46.803:   91   |   9:    84.245 -  93.606:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1252 r_free = 0.1724             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1251 r_free = 0.1725             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1725   ksol= 0.32   Bsol= 65.63   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,1.92,3.64,0.00,0.00,0.00); trace/3= 2.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248277                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.7813 0.99   1404  156 0.1063 0.1377      5.4392      5.5904|
|  2:  4.7813 -  3.8145 0.99   1346  151 0.0919 0.1231      5.5004      5.7007|
|  3:  3.8145 -  3.3380 0.99   1326  143 0.1157 0.1546      5.5518      5.8623|
|  4:  3.3380 -  3.0354 0.99   1326  153 0.1340 0.1830      5.5254      5.7043|
|  5:  3.0354 -  2.8193 0.99   1306  145 0.1533 0.1890      5.4423      5.6399|
|  6:  2.8193 -  2.6540 0.99   1301  141 0.1380 0.2319      5.3146      5.6231|
|  7:  2.6540 -  2.5217 0.99   1291  140 0.1451 0.1673      5.2907      5.3973|
|  8:  2.5217 -  2.4124 0.98   1287  146 0.1339 0.1772       5.196      5.4091|
|  9:  2.4124 -  2.3198 0.98   1265  146 0.1352 0.2026      5.1569      5.4225|
| 10:  2.3198 -  2.2400 1.00   1306  143 0.1312 0.1860       5.074      5.2825|
| 11:  2.2400 -  2.1702 0.98   1276  138 0.1306 0.1927      5.0493      5.3201|
| 12:  2.1702 -  2.1083 0.98   1263  145 0.1241 0.1954       4.955      5.3094|
| 13:  2.1083 -  2.0529 0.99   1288  138 0.1305 0.1823      4.8941      5.0975|
| 14:  2.0529 -  2.0030 0.49    645   74 0.1185 0.1730      4.8126      5.0274|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2943 -  4.7813  1404   156  0.94   9.53   0.96     0.94       7866.12|
|  2:  4.7813 -  3.8145  1346   151  0.95   8.65   0.99     0.98      10058.98|
|  3:  3.8145 -  3.3380  1326   143  0.93  12.42   1.01     1.01      12036.26|
|  4:  3.3380 -  3.0354  1326   153  0.91  14.83   1.00     0.98      11578.21|
|  5:  3.0354 -  2.8193  1306   145  0.88  17.82   0.99     0.97      10245.18|
|  6:  2.8193 -  2.6540  1301   141  0.88  18.28   0.97     0.94       8759.21|
|  7:  2.6540 -  2.5217  1291   140  0.89  17.69   0.98     0.95       7805.20|
|  8:  2.5217 -  2.4124  1287   146  0.89  17.62   0.98     0.96       6852.30|
|  9:  2.4124 -  2.3198  1265   146  0.89  17.67   0.99     0.93       6314.69|
| 10:  2.3198 -  2.2400  1306   143  0.88  18.11   0.99     0.95       5503.15|
| 11:  2.2400 -  2.1702  1276   138  0.89  17.57   0.98     0.92       5155.31|
| 12:  2.1702 -  2.1083  1263   145  0.90  16.86   0.99     0.98       4653.99|
| 13:  2.1083 -  2.0529  1288   138  0.88  18.85   0.98     0.96       4217.62|
| 14:  2.0529 -  2.0030   645    74  0.89  17.01   0.96     0.93       3499.09|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3499.09 max =        12036.26 mean =      7651.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.81|
|phase err.(test): min =        0.00 max =           88.08 mean =        15.19|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1719   ksol= 0.33   Bsol= 68.20   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,-0.65,1.07,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247370                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1719   ksol= 0.33   Bsol= 68.20   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,-0.65,1.07,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247370                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.7813 0.99   1404  156 0.1067 0.1325      5.4302      5.5666|
|  2:  4.7813 -  3.8145 0.99   1346  151 0.0923 0.1219      5.4983      5.6983|
|  3:  3.8145 -  3.3380 0.99   1326  143 0.1158 0.1551      5.5501      5.8657|
|  4:  3.3380 -  3.0354 0.99   1326  153 0.1338 0.1836      5.5259      5.7076|
|  5:  3.0354 -  2.8193 0.99   1306  145 0.1532 0.1888      5.4427      5.6395|
|  6:  2.8193 -  2.6540 0.99   1301  141 0.1379 0.2319      5.3144      5.6241|
|  7:  2.6540 -  2.5217 0.99   1291  140 0.1452 0.1673      5.2913      5.3973|
|  8:  2.5217 -  2.4124 0.98   1287  146 0.1338 0.1773      5.1962      5.4098|
|  9:  2.4124 -  2.3198 0.98   1265  146 0.1352 0.2025      5.1569      5.4226|
| 10:  2.3198 -  2.2400 1.00   1306  143 0.1312 0.1859      5.0741      5.2824|
| 11:  2.2400 -  2.1702 0.98   1276  138 0.1305 0.1928      5.0492      5.3205|
| 12:  2.1702 -  2.1083 0.98   1263  145 0.1241 0.1955      4.9551      5.3099|
| 13:  2.1083 -  2.0529 0.99   1288  138 0.1305 0.1823      4.8941      5.0973|
| 14:  2.0529 -  2.0030 0.49    645   74 0.1184 0.1730      4.8125      5.0271|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2943 -  4.7813  1404   156  0.94   9.50   0.96     0.94       7608.57|
|  2:  4.7813 -  3.8145  1346   151  0.95   8.52   0.99     0.98       9863.06|
|  3:  3.8145 -  3.3380  1326   143  0.93  12.41   1.01     1.01      11991.02|
|  4:  3.3380 -  3.0354  1326   153  0.91  14.87   1.00     0.98      11609.88|
|  5:  3.0354 -  2.8193  1306   145  0.88  17.85   0.99     0.97      10274.15|
|  6:  2.8193 -  2.6540  1301   141  0.88  18.28   0.97     0.94       8759.99|
|  7:  2.6540 -  2.5217  1291   140  0.89  17.70   0.98     0.95       7811.35|
|  8:  2.5217 -  2.4124  1287   146  0.89  17.62   0.98     0.96       6861.77|
|  9:  2.4124 -  2.3198  1265   146  0.89  17.67   0.99     0.93       6314.15|
| 10:  2.3198 -  2.2400  1306   143  0.88  18.12   0.99     0.95       5506.02|
| 11:  2.2400 -  2.1702  1276   138  0.89  17.58   0.98     0.92       5158.38|
| 12:  2.1702 -  2.1083  1263   145  0.90  16.87   0.99     0.98       4656.32|
| 13:  2.1083 -  2.0529  1288   138  0.88  18.85   0.98     0.96       4217.81|
| 14:  2.0529 -  2.0030   645    74  0.89  17.01   0.96     0.93       3497.33|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3497.33 max =        11991.02 mean =      7618.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.80|
|phase err.(test): min =        0.00 max =           88.36 mean =        15.18|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.353)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.57    96.18   15.50    None  None   None       |
|    all(noH): 2823   0      2.57    96.18   15.50    None  None   None       |
|    Sol.    : 438    0      4.54    96.18   38.90    None  None   None       |
|    Mac.    : 2385   0      2.57    80.70   11.20    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:     2.571 -  11.932: 1705   |   5:    49.374 -  58.734:   94        |
|      1:    11.932 -  21.292:  573   |   6:    58.734 -  68.095:   39        |
|      2:    21.292 -  30.653:  167   |   7:    68.095 -  77.456:   13        |
|      3:    30.653 -  40.013:  132   |   8:    77.456 -  86.816:    5        |
|      4:    40.013 -  49.374:   91   |   9:    86.816 -  96.177:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.408 - 4.857
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 341
   mapped sites are within: 0.712 - 4.857

peak=   10.072 closest distance to " CB  VAL A 230 " =    1.489
peak=    7.568 closest distance to " CG2 VAL A 296 " =    1.225
peak=    5.870 closest distance to " CB  GLN A 223 " =    1.449
peak=    5.786 closest distance to " CG  LEU A   5 " =    1.222
peak=    5.606 closest distance to " NH1 ARG A 138 " =    1.053
peak=    5.296 closest distance to " O   HOH Z 232 " =    2.207
peak=    5.193 closest distance to " CD2 LEU A   5 " =    1.149
peak=    4.964 closest distance to " CZ  PHE A 218 " =    1.092
peak=    4.909 closest distance to " O   HOH Z 111 " =    2.072
peak=    4.841 closest distance to " CG  LEU A 228 " =    1.210
peak=    4.731 closest distance to " CG  PRO A 198 " =    1.295
peak=    4.726 closest distance to " O   HOH Z 102 " =    1.395
peak=    4.703 closest distance to " CB  ASP A 124 " =    0.833
peak=    4.693 closest distance to " O   HOH Z 369 " =    2.104
peak=    4.671 closest distance to " O   HOH Z 265 " =    2.127
peak=    4.627 closest distance to " NE2 GLN A  11 " =    1.100
peak=    4.592 closest distance to " CB  GLN A 183 " =    1.250
peak=    4.563 closest distance to " CB  SER A  63 " =    1.296
peak=    4.549 closest distance to " O   HOH Z 142 " =    1.857
peak=    4.538 closest distance to " CA  VAL A 230 " =    1.235
peak=    4.511 closest distance to " CB  ASN A 148 " =    1.337
peak=    4.404 closest distance to " O   HOH Z 145 " =    2.033
peak=    4.383 closest distance to " CB  TRP A 266 " =    0.978
peak=    4.381 closest distance to " O   HOH Z 303 " =    2.150
peak=    4.370 closest distance to " O   HOH Z 368 " =    2.150
peak=    4.336 closest distance to " O   HOH Z 298 " =    2.082
peak=    4.300 closest distance to " CG  PRO A 243 " =    1.130
peak=    4.292 closest distance to " CD  LYS A 166 " =    1.337
peak=    4.260 closest distance to " CB  ASN A 142 " =    0.952
peak=    4.260 closest distance to " O   HOH Z 287 " =    2.117
peak=    4.230 closest distance to " O   HOH Z 222 " =    1.297
peak=    4.201 closest distance to " O   HOH Z 183 " =    1.353
peak=    4.189 closest distance to " O   PRO A 198 " =    1.553
peak=    4.175 closest distance to " O   HOH Z 425 " =    1.513
peak=    4.162 closest distance to " CD  ARG A 159 " =    0.779
peak=    4.137 closest distance to " O   HOH Z 427 " =    3.112
peak=    4.124 closest distance to " NH1AARG A 145 " =    1.188
peak=    4.117 closest distance to " NE2 HIS A 207 " =    1.121
peak=    4.086 closest distance to " CG  PRO A 213 " =    1.273
peak=    4.071 closest distance to " CB  ASN A  39 " =    0.925
peak=    4.053 closest distance to " ND2 ASN A 187 " =    1.538
peak=    4.051 closest distance to " O   SER A  87 " =    2.387
peak=    4.017 closest distance to " CA  ALA A  51 " =    0.996
peak=    4.013 closest distance to " CB  TYR A 169 " =    0.714
peak=    4.002 closest distance to " CG  LEU A 167 " =    1.219
peak=    3.985 closest distance to " O   HOH Z 188 " =    3.080
peak=    3.983 closest distance to " O   HOH Z 184 " =    1.570
peak=    3.982 closest distance to " O   HOH Z 193 " =    2.072
peak=    3.961 closest distance to " O   HOH Z 359 " =    1.547
peak=    3.961 closest distance to " O   HOH Z 290 " =    1.398
peak=    3.961 closest distance to " CB  VAL A 265 " =    1.282
peak=    3.955 closest distance to " CA  SER A  87 " =    0.917
peak=    3.949 closest distance to " CZ3 TRP A 266 " =    1.156
peak=    3.932 closest distance to " CB  GLU A 128 " =    0.983
peak=    3.931 closest distance to " CZ  PHE A 192 " =    1.002
peak=    3.925 closest distance to " O   HOH Z   9 " =    1.563
peak=    3.923 closest distance to " CD  ARG A 269 " =    0.900
peak=    3.919 closest distance to " O   HOH Z 214 " =    2.091
peak=    3.917 closest distance to " CA  ARG A 195 " =    1.259
peak=    3.913 closest distance to " O   HOH Z 411 " =    3.636
peak=    3.905 closest distance to " CG2 THR A 221 " =    1.040
peak=    3.895 closest distance to " N   PHE A 130 " =    1.265
peak=    3.892 closest distance to " CD1 LEU A 300 " =    1.157
peak=    3.889 closest distance to " CD2 LEU A 228 " =    1.205
peak=    3.882 closest distance to " CG  MET A 185 " =    1.261
peak=    3.864 closest distance to " CG  GLU A  37 " =    0.935
peak=    3.861 closest distance to " CB  ARG A 275 " =    0.939
peak=    3.858 closest distance to " CB  LEU A  83 " =    0.779
peak=    3.858 closest distance to " O   HOH Z 346 " =    1.636
peak=    3.850 closest distance to " CB  ARG A 190 " =    1.551
peak=    3.845 closest distance to " CB  SER A   3 " =    1.446
peak=    3.831 closest distance to " CG1 VAL A 153 " =    0.994
peak=    3.828 closest distance to " CB  GLU A 277 " =    3.744
peak=    3.821 closest distance to " CD1AILE A 234 " =    1.006
peak=    3.819 closest distance to " CB  SER A 210 " =    0.877
peak=    3.814 closest distance to " CB  SER A 212 " =    1.300
peak=    3.806 closest distance to " CA  TYR A  30 " =    1.008
peak=    3.801 closest distance to " CB  ARG A  79 " =    1.556
peak=    3.800 closest distance to " CB  VAL A 202 " =    1.637
peak=    3.793 closest distance to " CB  SER A 216 " =    0.910
peak=    3.792 closest distance to " O   HOH Z 207 " =    1.237
peak=    3.787 closest distance to " CB  ALA A 104 " =    0.826
peak=    3.774 closest distance to " CB  PRO A  54 " =    0.879
peak=    3.768 closest distance to " O   HOH Z 171 " =    3.982
peak=    3.767 closest distance to " CG2 VAL A 257 " =    0.917
peak=    3.764 closest distance to " CB  GLU A 152 " =    1.185
peak=    3.756 closest distance to " O   HOH Z 316 " =    3.126
peak=    3.738 closest distance to " CA  VAL A 296 " =    1.085
peak=    3.734 closest distance to " O   HOH Z 423 " =    1.572
peak=    3.734 closest distance to " CB  LEU A 228 " =    1.226
peak=    3.731 closest distance to " CD ALYS A 290 " =    1.019
peak=    3.724 closest distance to " O   HOH Z 126 " =    1.967
peak=    3.722 closest distance to " O   HOH Z  43 " =    1.982
peak=    3.709 closest distance to " CB  LEU A 143 " =    1.264
peak=    3.705 closest distance to " O   HOH Z 313 " =    1.858
peak=    3.701 closest distance to " CB  ILE A 120 " =    1.270
peak=    3.699 closest distance to " CA  ALA A 184 " =    1.108
peak=    3.697 closest distance to " O   HOH Z  88 " =    3.241
peak=    3.692 closest distance to " CA  ALA A 295 " =    1.167
peak=    3.691 closest distance to " OG  SER A 276 " =    1.379
peak=    3.687 closest distance to " O   HOH Z 234 " =    3.878
peak=    3.685 closest distance to " O   HOH Z 158 " =    3.161
peak=    3.682 closest distance to " CB  ASP A 140 " =    0.807
peak=    3.672 closest distance to " CD1 LEU A   5 " =    1.346
peak=    3.667 closest distance to " O   HOH Z  78 " =    1.677
peak=    3.665 closest distance to " CG2 ILE A 234 " =    0.879
peak=    3.665 closest distance to " CB  GLN A  89 " =    1.169
peak=    3.663 closest distance to " O  BHOH Z  74 " =    1.258
peak=    3.653 closest distance to " CB  GLU A  46 " =    0.937
peak=    3.651 closest distance to " N   SER A 135 " =    1.420
peak=    3.650 closest distance to " CA  ARG A  36 " =    1.175
peak=    3.637 closest distance to " NH2AARG A 145 " =    1.226
peak=    3.634 closest distance to " CD  ARG A  66 " =    2.231
peak=    3.625 closest distance to " O   ASP A 124 " =    1.102
peak=    3.623 closest distance to " CZ  PHE A  38 " =    1.190
peak=    3.622 closest distance to " O   HOH Z 211 " =    1.277
peak=    3.619 closest distance to " O   HOH Z 213 " =    1.841
peak=    3.615 closest distance to " CB  PRO A 243 " =    1.219
peak=    3.594 closest distance to " CA  ARG A 139 " =    1.131
peak=    3.594 closest distance to " CG1 ILE A 151 " =    1.231
peak=    3.586 closest distance to " CA  ALA A 160 " =    1.106
peak=    3.584 closest distance to " CB  THR A  82 " =    1.350
peak=    3.572 closest distance to " CE  LYS A  76 " =    0.891
peak=    3.569 closest distance to " O   HOH Z 272 " =    1.858
peak=    3.567 closest distance to " O   HOH Z  10 " =    1.844
peak=    3.563 closest distance to " O   HOH Z 353 " =    2.598
peak=    3.561 closest distance to " CA  TYR A 116 " =    1.445
peak=    3.556 closest distance to " CB  ALA A 242 " =    0.802
peak=    3.549 closest distance to " N   ASN A  39 " =    1.224
peak=    3.545 closest distance to " O   HOH Z 406 " =    1.576
peak=    3.541 closest distance to " CA  ASN A 127 " =    1.050
peak=    3.526 closest distance to " O   HOH Z  80 " =    1.808
peak=    3.516 closest distance to " CE3 TRP A 150 " =    1.068
peak=    3.512 closest distance to " O   HOH Z 227 " =    1.794
peak=    3.510 closest distance to " O   ASP A 200 " =    1.667
peak=    3.505 closest distance to " NH1 ARG A  14 " =    0.996
peak=    3.505 closest distance to " CG  ARG A 269 " =    1.697
peak=    3.505 closest distance to " OH  TYR A 247 " =    1.125
peak=    3.504 closest distance to " OG1 THR A 264 " =    0.728
peak=    3.504 closest distance to " N   ALA A 256 " =    1.131
peak=    3.495 closest distance to " O   HOH Z  92 " =    2.482
peak=    3.495 closest distance to " CG  PHE A 204 " =    0.989
peak=    3.488 closest distance to " O   HOH Z 126 " =    1.577
peak=    3.487 closest distance to " CG  GLN A  88 " =    1.092
peak=    3.484 closest distance to " CB  ALA A 291 " =    1.192
peak=    3.482 closest distance to " O   HOH Z  57 " =    1.405
peak=    3.482 closest distance to " CB  ASN A 187 " =    1.080
peak=    3.474 closest distance to " CD1 LEU A  96 " =    0.807
peak=    3.473 closest distance to " CG BARG A 102 " =    1.918
peak=    3.473 closest distance to " ND2 ASN A 249 " =    1.874
peak=    3.472 closest distance to " O   HOH Z 193 " =    1.731
peak=    3.470 closest distance to " OE1 GLN A  55 " =    1.360
peak=    3.469 closest distance to " O   HOH Z  78 " =    2.112
peak=    3.466 closest distance to " CA  ILE A 234 " =    0.964
peak=    3.466 closest distance to " O   HOH Z 156 " =    2.936
peak=    3.458 closest distance to " O   HOH Z  21 " =    1.782
peak=    3.456 closest distance to " OG1 THR A 279 " =    1.480
peak=    3.455 closest distance to " CD2 TRP A 179 " =    1.307
peak=    3.454 closest distance to " CD1 ILE A  33 " =    1.959
peak=    3.451 closest distance to " CA  ASP A 124 " =    0.713
peak=    3.450 closest distance to " CB  GLN A  88 " =    1.244
peak=    3.450 closest distance to " O   HOH Z 124 " =    1.957
peak=    3.450 closest distance to " CB  ALA A  34 " =    0.964
peak=    3.450 closest distance to " CE3 TRP A  85 " =    1.205
peak=    3.443 closest distance to " CA  LEU A 282 " =    1.022
peak=    3.441 closest distance to " CA  THR A 264 " =    0.717
peak=    3.441 closest distance to " CA  GLY A 267 " =    0.936
peak=    3.438 closest distance to " O   HOH Z 258 " =    2.132
peak=    3.435 closest distance to " CB AVAL A  41 " =    1.317
peak=    3.431 closest distance to " O   MET A 105 " =    1.771
peak=    3.430 closest distance to " O   HOH Z 248 " =    1.758
peak=    3.429 closest distance to " O   THR A 251 " =    1.220
peak=    3.428 closest distance to " CB  ALA A 248 " =    1.158
peak=    3.425 closest distance to " NH1 ARG A  56 " =    1.077
peak=    3.424 closest distance to " CE1 TYR A 186 " =    1.231
peak=    3.420 closest distance to " O   ALA A 165 " =    1.562
peak=    3.416 closest distance to " ND2AASN A 224 " =    0.944
peak=    3.412 closest distance to " CA  ALA A 291 " =    0.907
peak=    3.409 closest distance to " CG2 ILE A  20 " =    1.491
peak=    3.403 closest distance to " O   HOH Z 128 " =    2.449
peak=    3.401 closest distance to " CB  SER A  62 " =    1.081
peak=    3.397 closest distance to " ND2 ASN A 249 " =    0.839
peak=    3.394 closest distance to " CB  TRP A 150 " =    1.378
peak=    3.393 closest distance to " O   HOH Z 291 " =    1.611
peak=    3.393 closest distance to " CB  ALA A   9 " =    1.611
peak=    3.391 closest distance to " CB  SER A 273 " =    1.006
peak=    3.386 closest distance to " O   HOH Z 148 " =    2.112
peak=    3.382 closest distance to " O   HOH Z 422 " =    2.713
peak=    3.379 closest distance to " O   THR A 220 " =    1.168
peak=    3.377 closest distance to " CA  VAL A 112 " =    1.117
peak=    3.375 closest distance to " O   HOH Z 215 " =    1.512
peak=    3.375 closest distance to " O   HOH Z 200 " =    3.217
peak=    3.375 closest distance to " CD1 ILE A 199 " =    1.003
peak=    3.371 closest distance to " CG1 ILE A  33 " =    1.339
peak=    3.370 closest distance to " CA  GLU A 152 " =    0.917
peak=    3.369 closest distance to " CB  ALA A 161 " =    0.969
peak=    3.367 closest distance to " CG  MET A 185 " =    0.950
peak=    3.363 closest distance to " OG  SER A 245 " =    1.710
peak=    3.361 closest distance to " OG  SER A  62 " =    3.042
peak=    3.360 closest distance to " N   SER A 271 " =    0.974
peak=    3.360 closest distance to " CG AARG A 275 " =    1.345
peak=    3.354 closest distance to " CA  GLY A 211 " =    1.397
peak=    3.353 closest distance to " O   HOH Z 410 " =    1.395
peak=    3.353 closest distance to " CA  ALA A  21 " =    1.225
peak=    3.348 closest distance to " O   HOH Z 132 " =    2.684
peak=    3.344 closest distance to " O   HOH Z 294 " =    1.590
peak=    3.342 closest distance to " O   HOH Z 109 " =    2.810
peak=    3.336 closest distance to " CB  MET A  47 " =    1.010
peak=    3.336 closest distance to " O   HOH Z 148 " =    3.562
peak=    3.335 closest distance to " O   HOH Z 145 " =    1.698
peak=    3.335 closest distance to " CG1 ILE A  49 " =    1.550
peak=    3.332 closest distance to " CB  ALA A 160 " =    1.293
peak=    3.331 closest distance to " CB  ALA A  10 " =    0.930
peak=    3.326 closest distance to " CB  MET A  40 " =    0.738
peak=    3.325 closest distance to " CA  GLN A  94 " =    0.813
peak=    3.322 closest distance to " O   HOH Z 273 " =    2.838
peak=    3.319 closest distance to " CA  ALA A 154 " =    1.020
peak=    3.314 closest distance to " CE2 TYR A 186 " =    0.897
peak=    3.312 closest distance to " CA  MET A  40 " =    1.273
peak=    3.310 closest distance to " CA  ARG A 102 " =    1.226
peak=    3.308 closest distance to " OD1 ASN A  69 " =    2.594
peak=    3.304 closest distance to " CG2 ILE A 263 " =    1.071
peak=    3.300 closest distance to " CG BARG A 275 " =    1.489
peak=    3.298 closest distance to " CB  ASN A 173 " =    0.990
peak=    3.298 closest distance to " O   GLN A 278 " =    1.350
peak=    3.296 closest distance to " O   HOH Z 201 " =    2.723
peak=    3.296 closest distance to " O   HOH Z 350 " =    1.719
peak=    3.294 closest distance to " CB  LYS A 117 " =    1.188
peak=    3.294 closest distance to " CB  ASN A 110 " =    1.104
peak=    3.290 closest distance to " O   PHE A  61 " =    1.397
peak=    3.290 closest distance to " O   HOH Z   4 " =    1.759
peak=    3.283 closest distance to " O   TYR A 116 " =    1.238
peak=    3.283 closest distance to " O   HOH Z 153 " =    3.946
peak=    3.280 closest distance to " CB  TRP A 179 " =    1.342
peak=    3.272 closest distance to " O   HOH Z 280 " =    3.076
peak=    3.270 closest distance to " CH2 TRP A  70 " =    1.047
peak=    3.270 closest distance to " CA  VAL A 125 " =    1.213
peak=    3.268 closest distance to " O   HOH Z 332 " =    1.572
peak=    3.267 closest distance to " O   HOH Z 325 " =    2.275
peak=    3.265 closest distance to " CA  ALA A 100 " =    1.053
peak=    3.264 closest distance to " O   HOH Z  68 " =    1.924
peak=    3.264 closest distance to " CD  ARG A 138 " =    1.151
peak=    3.261 closest distance to " CB  VAL A 268 " =    0.845
peak=    3.246 closest distance to " O   HOH Z 167 " =    1.660
peak=    3.244 closest distance to " CA  ASN A 215 " =    1.179
peak=    3.243 closest distance to " N   TYR A  15 " =    0.804
peak=    3.239 closest distance to " O   HOH Z 134 " =    2.942
peak=    3.238 closest distance to " O   HOH Z 180 " =    2.092
peak=    3.237 closest distance to " CZ3 TRP A  85 " =    1.005
peak=    3.234 closest distance to " O   HOH Z  63 " =    1.841
peak=    3.232 closest distance to " OG  SER A  28 " =    1.623
peak=    3.230 closest distance to " CG2 ILE A 120 " =    0.928
peak=    3.226 closest distance to " CB  ARG A 145 " =    0.863
peak=    3.220 closest distance to " O   HOH Z 285 " =    2.380
peak=    3.220 closest distance to " CG1 ILE A 120 " =    1.041
peak=    3.218 closest distance to " N   CYS A 260 " =    0.712
peak=    3.215 closest distance to " O   HOH Z 238 " =    2.293
peak=    3.211 closest distance to " CB  ARG A 259 " =    1.942
peak=    3.210 closest distance to " CA  TYR A  30 " =    1.088
peak=    3.208 closest distance to " O   HOH Z  35 " =    4.803
peak=    3.207 closest distance to " O   THR A 294 " =    1.127
peak=    3.206 closest distance to " O   HOH Z 162 " =    4.164
peak=    3.205 closest distance to " ND1 HIS A  81 " =    1.826
peak=    3.204 closest distance to " CD  ARG A 219 " =    1.083
peak=    3.204 closest distance to " O   HOH Z 329 " =    2.963
peak=    3.203 closest distance to " C   ALA A 299 " =    0.956
peak=    3.203 closest distance to " O   HOH Z  49 " =    1.055
peak=    3.203 closest distance to " OG  SER A 135 " =    1.253
peak=    3.201 closest distance to " O   HOH Z  88 " =    3.566
peak=    3.200 closest distance to " O   HOH Z 117 " =    2.328
peak=    3.198 closest distance to " CA  ASN A 284 " =    0.906
peak=    3.196 closest distance to " CG2 ILE A 151 " =    0.759
peak=    3.195 closest distance to " O   HOH Z 172 " =    3.634
peak=    3.194 closest distance to " CB  ALA A   1 " =    4.857
peak=    3.194 closest distance to " CA  LYS A 290 " =    1.246
peak=    3.194 closest distance to " CE3 TRP A 274 " =    1.406
peak=    3.194 closest distance to " CB  ALA A 137 " =    1.045
peak=    3.192 closest distance to " O   HOH Z 359 " =    4.341
peak=    3.192 closest distance to " O   HOH Z 166 " =    3.581
peak=    3.191 closest distance to " CB  ALA A 248 " =    1.333
peak=    3.188 closest distance to " O   HOH Z 116 " =    1.900
peak=    3.187 closest distance to " O   HOH Z 238 " =    3.684
peak=    3.184 closest distance to " CA  MET A 105 " =    0.950
peak=    3.183 closest distance to " O   PRO A 213 " =    1.356
peak=    3.183 closest distance to " O   HOH Z 247 " =    1.458
peak=    3.183 closest distance to " O   HOH Z 263 " =    1.626
peak=    3.181 closest distance to " OG BSER A 134 " =    2.881
peak=    3.179 closest distance to " O   HOH Z 435 " =    1.962
peak=    3.174 closest distance to " O   ASN A 209 " =    1.374
peak=    3.173 closest distance to " CA  ALA A 180 " =    1.334
peak=    3.172 closest distance to " O   HOH Z 215 " =    2.775
peak=    3.171 closest distance to " O   HOH Z 185 " =    2.360
peak=    3.168 closest distance to " CA  ASN A 217 " =    1.478
peak=    3.168 closest distance to " CB  ALA A 227 " =    0.945
peak=    3.164 closest distance to " O   HOH Z 437 " =    1.375
peak=    3.161 closest distance to " O   HOH Z 302 " =    1.913
peak=    3.160 closest distance to " O   HOH Z 403 " =    1.668
peak=    3.156 closest distance to " O  BHOH Z 338 " =    2.391
peak=    3.154 closest distance to " CA  PRO A  54 " =    1.396
peak=    3.152 closest distance to " CZ  PHE A 208 " =    1.103
peak=    3.149 closest distance to " O   HOH Z 163 " =    1.536
peak=    3.149 closest distance to " N   ARG A 156 " =    1.416
peak=    3.148 closest distance to " CA  ILE A  33 " =    1.679
peak=    3.145 closest distance to " OE2 GLU A   2 " =    1.939
peak=    3.144 closest distance to " O   HOH Z 295 " =    1.564
peak=    3.144 closest distance to " CD1 ILE A 106 " =    0.857
peak=    3.142 closest distance to " CD  GLU A 236 " =    1.055
peak=    3.138 closest distance to " O   HOH Z 293 " =    1.966
peak=    3.136 closest distance to " OD1 ASN A 217 " =    1.536
peak=    3.134 closest distance to " CB  GLN A 103 " =    1.093
peak=    3.133 closest distance to " O   HOH Z 281 " =    2.513
peak=    3.130 closest distance to " CB  ALA A  43 " =    0.908
peak=    3.120 closest distance to " O   ILE A  49 " =    1.221
peak=    3.117 closest distance to " O   HOH Z 171 " =    3.697
peak=    3.116 closest distance to " O   PHE A 192 " =    1.389
peak=    3.113 closest distance to " CG1 ILE A  20 " =    1.308
peak=    3.112 closest distance to " CA  GLN A 223 " =    0.948
peak=    3.109 closest distance to " CB  THR A  31 " =    1.451
peak=    3.107 closest distance to " CG  MET A 113 " =    1.641
peak=    3.107 closest distance to " O   PRO A 198 " =    1.322
peak=    3.106 closest distance to " O   HOH Z 368 " =    3.528
peak=    3.105 closest distance to " CB  ALA A 114 " =    0.762
peak=    3.103 closest distance to " CG  GLN A  89 " =    1.513
peak=    3.103 closest distance to " O   ASN A  74 " =    1.422
peak=    3.103 closest distance to " O   HOH Z  49 " =    3.382
peak=    3.088 closest distance to " CG  ARG A 159 " =    1.068
peak=    3.076 closest distance to " CB  GLU A  37 " =    0.886
peak=    3.073 closest distance to " O   PRO A  90 " =    1.678
peak=    3.072 closest distance to " CB  LEU A 300 " =    0.846
peak=    3.072 closest distance to " O   GLY A 203 " =    1.435
peak=    3.067 closest distance to " O   HOH Z 329 " =    4.137
peak=    3.064 closest distance to " CA  VAL A 153 " =    0.892
peak=    3.046 closest distance to " O   HOH Z  59 " =    2.064
peak=    3.046 closest distance to " CB  SER A 146 " =    1.002
peak=    3.036 closest distance to " CA  GLY A  98 " =    1.162
peak=    3.022 closest distance to " CB  TYR A 169 " =    1.245

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.445 - 5.554
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 204
   mapped sites are within: 0.776 - 5.554

peak=   -5.391 closest distance to " CG2 VAL A 230 " =    0.801
peak=   -4.388 closest distance to " CG1 VAL A 112 " =    2.691
peak=   -4.339 closest distance to " OE1 GLN A  88 " =    0.970
peak=   -4.274 closest distance to " O   HOH Z 196 " =    2.394
peak=   -4.246 closest distance to " O   PRO A 198 " =    1.262
peak=   -4.219 closest distance to " CD  GLN A  58 " =    0.842
peak=   -4.157 closest distance to " CD  ARG A  14 " =    3.233
peak=   -4.106 closest distance to " CD  ARG A 156 " =    2.208
peak=   -4.092 closest distance to " CA  GLY A 241 " =    2.361
peak=   -4.086 closest distance to " O   HOH Z 231 " =    1.890
peak=   -4.059 closest distance to " O   HOH Z 162 " =    2.660
peak=   -3.994 closest distance to " O   HOH Z 394 " =    1.515
peak=   -3.943 closest distance to " O   HOH Z 216 " =    1.051
peak=   -3.943 closest distance to " CZ2 TRP A  92 " =    2.896
peak=   -3.940 closest distance to " CG1 VAL A 250 " =    2.733
peak=   -3.911 closest distance to " O   HOH Z 231 " =    0.932
peak=   -3.910 closest distance to " OE1 GLN A 223 " =    2.365
peak=   -3.901 closest distance to " CD  GLN A  55 " =    1.014
peak=   -3.889 closest distance to " OG  SER A  97 " =    2.324
peak=   -3.876 closest distance to " O   HOH Z 102 " =    1.204
peak=   -3.876 closest distance to " O   HOH Z 133 " =    1.180
peak=   -3.868 closest distance to " O   GLY A  17 " =    1.329
peak=   -3.818 closest distance to " CB  HIS A  86 " =    1.152
peak=   -3.818 closest distance to " O   HOH Z 351 " =    1.487
peak=   -3.810 closest distance to " O   GLY A 203 " =    2.458
peak=   -3.795 closest distance to " O   HOH Z 118 " =    1.208
peak=   -3.793 closest distance to " CG1 VAL A 296 " =    1.361
peak=   -3.783 closest distance to " C   ALA A 158 " =    1.331
peak=   -3.760 closest distance to " CB  VAL A 230 " =    1.119
peak=   -3.752 closest distance to " CD1 LEU A 101 " =    2.421
peak=   -3.734 closest distance to " O   HOH Z 166 " =    1.866
peak=   -3.717 closest distance to " CD2 TYR A 293 " =    1.773
peak=   -3.698 closest distance to " CG2 VAL A 296 " =    1.668
peak=   -3.693 closest distance to " O   ILE A 109 " =    2.659
peak=   -3.691 closest distance to " O   HOH Z 179 " =    2.305
peak=   -3.684 closest distance to " CE2 TYR A  30 " =    2.710
peak=   -3.679 closest distance to " O   PRO A 163 " =    2.164
peak=   -3.676 closest distance to " CA  GLY A 241 " =    3.143
peak=   -3.671 closest distance to " CG  TRP A 266 " =    1.886
peak=   -3.656 closest distance to " O   HOH Z 411 " =    5.351
peak=   -3.649 closest distance to " O   HOH Z  73 " =    2.265
peak=   -3.648 closest distance to " O   VAL A 189 " =    2.569
peak=   -3.613 closest distance to " CE3 TRP A  70 " =    1.784
peak=   -3.606 closest distance to " CG1 VAL A 112 " =    2.801
peak=   -3.589 closest distance to " CG  MET A 105 " =    1.014
peak=   -3.579 closest distance to " CG2BVAL A  41 " =    2.556
peak=   -3.574 closest distance to " O   GLY A 211 " =    1.362
peak=   -3.572 closest distance to " CA  ASP A  27 " =    2.512
peak=   -3.568 closest distance to " CE3 TRP A 150 " =    2.313
peak=   -3.564 closest distance to " CD1 ILE A  33 " =    2.600
peak=   -3.563 closest distance to " CA  ASP A 298 " =    1.061
peak=   -3.555 closest distance to " CD2 LEU A 167 " =    1.838
peak=   -3.553 closest distance to " O   HOH Z 251 " =    4.850
peak=   -3.549 closest distance to " OG BSER A 134 " =    1.431
peak=   -3.537 closest distance to " O   HOH Z  10 " =    1.600
peak=   -3.533 closest distance to " C   ALA A 165 " =    2.003
peak=   -3.531 closest distance to " CG  GLU A  53 " =    1.352
peak=   -3.527 closest distance to " CD2 LEU A 237 " =    2.943
peak=   -3.522 closest distance to " N   ALA A  43 " =    2.543
peak=   -3.519 closest distance to " CD1 LEU A 228 " =    2.451
peak=   -3.518 closest distance to " CD1 LEU A 101 " =    2.739
peak=   -3.510 closest distance to " O   HOH Z 177 " =    1.895
peak=   -3.505 closest distance to " CG1 VAL A 265 " =    2.453
peak=   -3.505 closest distance to " CG  ASP A 231 " =    0.776
peak=   -3.496 closest distance to " CB  ALA A  43 " =    2.687
peak=   -3.494 closest distance to " CD1 LEU A   5 " =    2.651
peak=   -3.491 closest distance to " NE2 GLN A  55 " =    2.461
peak=   -3.487 closest distance to " O   HOH Z 359 " =    2.977
peak=   -3.483 closest distance to " O   HOH Z  44 " =    0.998
peak=   -3.480 closest distance to " O   ASP A  27 " =    1.929
peak=   -3.480 closest distance to " CB  HIS A  81 " =    1.029
peak=   -3.471 closest distance to " C   LEU A 222 " =    0.993
peak=   -3.466 closest distance to " CE BMET A  47 " =    1.527
peak=   -3.463 closest distance to " CG2 THR A 178 " =    2.374
peak=   -3.462 closest distance to " N   THR A 157 " =    1.540
peak=   -3.453 closest distance to " O   HOH Z  38 " =    1.543
peak=   -3.451 closest distance to " O   HOH Z 128 " =    2.704
peak=   -3.449 closest distance to " CG2 VAL A 202 " =    2.804
peak=   -3.444 closest distance to " CZ3 TRP A 179 " =    1.151
peak=   -3.435 closest distance to " N   ALA A 226 " =    2.187
peak=   -3.428 closest distance to " CB  PRO A 163 " =    2.476
peak=   -3.426 closest distance to " CA  GLY A 203 " =    2.568
peak=   -3.425 closest distance to " CG2AVAL A  41 " =    2.770
peak=   -3.424 closest distance to " O   HOH Z 183 " =    1.126
peak=   -3.421 closest distance to " NH2AARG A 275 " =    5.554
peak=   -3.419 closest distance to " CG  LEU A 101 " =    2.469
peak=   -3.418 closest distance to " C   HIS A 108 " =    1.101
peak=   -3.418 closest distance to " CA  GLY A  98 " =    2.116
peak=   -3.415 closest distance to " C   MET A 188 " =    1.428
peak=   -3.411 closest distance to " OG  SER A  87 " =    1.606
peak=   -3.402 closest distance to " O   HOH Z 290 " =    1.376
peak=   -3.402 closest distance to " O   HOH Z 185 " =    2.413
peak=   -3.401 closest distance to " CG  ARG A 269 " =    2.317
peak=   -3.395 closest distance to " CG  LEU A   5 " =    1.605
peak=   -3.387 closest distance to " O   HOH Z  11 " =    1.881
peak=   -3.386 closest distance to " O   HOH Z 407 " =    3.118
peak=   -3.381 closest distance to " CG  GLN A 103 " =    2.404
peak=   -3.373 closest distance to " OD2 ASP A  50 " =    2.280
peak=   -3.372 closest distance to " CG2 VAL A 189 " =    2.041
peak=   -3.369 closest distance to " CB  PHE A 192 " =    1.953
peak=   -3.367 closest distance to " OD1 ASN A 148 " =    1.376
peak=   -3.361 closest distance to " O   HOH Z 201 " =    1.939
peak=   -3.359 closest distance to " CG1 VAL A 125 " =    1.840
peak=   -3.358 closest distance to " ND2 ASN A 249 " =    2.535
peak=   -3.357 closest distance to " OG1 THR A  82 " =    1.441
peak=   -3.356 closest distance to " O   HOH Z 357 " =    2.079
peak=   -3.355 closest distance to " CG  GLU A 277 " =    1.222
peak=   -3.355 closest distance to " C   ASP A 270 " =    1.179
peak=   -3.353 closest distance to " O   HOH Z  70 " =    2.172
peak=   -3.352 closest distance to " O   HOH Z 377 " =    1.813
peak=   -3.350 closest distance to " N   ASP A 191 " =    1.111
peak=   -3.349 closest distance to " O   HOH Z 103 " =    1.777
peak=   -3.349 closest distance to " O   HOH Z  52 " =    1.627
peak=   -3.348 closest distance to " O   HOH Z 435 " =    2.895
peak=   -3.348 closest distance to " CB  ALA A 248 " =    2.132
peak=   -3.346 closest distance to " CB  ALA A   9 " =    2.630
peak=   -3.336 closest distance to " CD1 PHE A  59 " =    2.014
peak=   -3.334 closest distance to " CB  TRP A  85 " =    2.616
peak=   -3.332 closest distance to " CB  ARG A  79 " =    2.502
peak=   -3.331 closest distance to " SD BMET A  47 " =    1.109
peak=   -3.330 closest distance to " O   HOH Z 232 " =    1.895
peak=   -3.329 closest distance to " O   GLY A 196 " =    1.336
peak=   -3.324 closest distance to " CG2 VAL A 296 " =    1.045
peak=   -3.319 closest distance to " N   SER A 212 " =    1.781
peak=   -3.316 closest distance to " O   HOH Z 390 " =    2.021
peak=   -3.315 closest distance to " O   HOH Z 106 " =    1.934
peak=   -3.307 closest distance to " CA  GLY A 133 " =    2.281
peak=   -3.307 closest distance to " ND2 ASN A  45 " =    2.334
peak=   -3.306 closest distance to " O   ASP A 270 " =    1.650
peak=   -3.302 closest distance to " NH2 ARG A  79 " =    1.516
peak=   -3.300 closest distance to " CZ2 TRP A 274 " =    0.937
peak=   -3.298 closest distance to " C   PHE A  59 " =    1.190
peak=   -3.297 closest distance to " O   HOH Z 275 " =    1.600
peak=   -3.295 closest distance to " O   HOH Z   9 " =    1.563
peak=   -3.294 closest distance to " N   THR A  52 " =    1.688
peak=   -3.293 closest distance to " CG  GLN A  88 " =    0.859
peak=   -3.293 closest distance to " CD2 PHE A  61 " =    2.009
peak=   -3.288 closest distance to " OH  TYR A 247 " =    1.835
peak=   -3.266 closest distance to " CD  LYS A 289 " =    2.440
peak=   -3.261 closest distance to " NH2 ARG A  66 " =    2.354
peak=   -3.260 closest distance to " CB  TYR A  15 " =    2.222
peak=   -3.258 closest distance to " OG  SER A  28 " =    2.124
peak=   -3.256 closest distance to " ND2 ASN A  60 " =    1.657
peak=   -3.252 closest distance to " NE2 GLN A  88 " =    1.000
peak=   -3.251 closest distance to " CA  SER A 135 " =    1.271
peak=   -3.250 closest distance to " O   HOH Z 350 " =    2.000
peak=   -3.246 closest distance to " CG1 VAL A  67 " =    2.878
peak=   -3.236 closest distance to " O   HOH Z 140 " =    1.760
peak=   -3.235 closest distance to " CB  ASN A  69 " =    1.430
peak=   -3.235 closest distance to " CG  PRO A 163 " =    2.367
peak=   -3.226 closest distance to " CG2 ILE A 151 " =    2.680
peak=   -3.219 closest distance to " CE1 PHE A 225 " =    2.267
peak=   -3.216 closest distance to " O   HOH Z  43 " =    1.732
peak=   -3.213 closest distance to " OG BSER A 134 " =    1.928
peak=   -3.211 closest distance to " N   TRP A 274 " =    1.157
peak=   -3.211 closest distance to " O   VAL A 121 " =    1.227
peak=   -3.209 closest distance to " NE2 GLN A 240 " =    1.635
peak=   -3.207 closest distance to " OH  TYR A 247 " =    2.094
peak=   -3.205 closest distance to " NE  ARG A 138 " =    1.531
peak=   -3.202 closest distance to " CE2 TRP A  70 " =    2.355
peak=   -3.202 closest distance to " O   GLY A  80 " =    2.619
peak=   -3.199 closest distance to " CD2 HIS A 207 " =    2.194
peak=   -3.188 closest distance to " CA  ARG A  36 " =    1.276
peak=   -3.186 closest distance to " OXT GLY A 302 " =    3.227
peak=   -3.184 closest distance to " C   LEU A 143 " =    1.150
peak=   -3.183 closest distance to " CD  GLN A 223 " =    1.199
peak=   -3.181 closest distance to " CB  ALA A 114 " =    2.573
peak=   -3.179 closest distance to " O   HOH Z  17 " =    1.563
peak=   -3.176 closest distance to " CZ  PHE A 218 " =    1.241
peak=   -3.166 closest distance to " CD1 TYR A 247 " =    2.453
peak=   -3.164 closest distance to " CD  PRO A 243 " =    2.015
peak=   -3.162 closest distance to " CB  PHE A 130 " =    1.360
peak=   -3.155 closest distance to " CA  VAL A  67 " =    2.804
peak=   -3.153 closest distance to " O   HOH Z 243 " =    1.643
peak=   -3.147 closest distance to " CZ  PHE A 130 " =    1.149
peak=   -3.147 closest distance to " O   TYR A  30 " =    2.421
peak=   -3.143 closest distance to " O   TRP A  70 " =    1.505
peak=   -3.140 closest distance to " CD  GLU A 236 " =    1.065
peak=   -3.139 closest distance to " OD2 ASP A 171 " =    1.880
peak=   -3.135 closest distance to " O   HOH Z 295 " =    1.474
peak=   -3.128 closest distance to " CE  MET A 105 " =    2.384
peak=   -3.128 closest distance to " O   HOH Z 108 " =    1.420
peak=   -3.125 closest distance to " O   HOH Z 377 " =    1.058
peak=   -3.124 closest distance to " O   HOH Z 285 " =    1.862
peak=   -3.124 closest distance to " O   HOH Z 372 " =    2.430
peak=   -3.120 closest distance to " CG  LEU A 281 " =    1.852
peak=   -3.116 closest distance to " O   HOH Z 259 " =    4.014
peak=   -3.115 closest distance to " O   HOH Z 389 " =    2.217
peak=   -3.111 closest distance to " O   HOH Z  13 " =    1.823
peak=   -3.108 closest distance to " OE1 GLU A  44 " =    0.834
peak=   -3.104 closest distance to " CE  LYS A  76 " =    2.572
peak=   -3.092 closest distance to " OE1 GLN A  77 " =    0.989
peak=   -3.089 closest distance to " OG  SER A 206 " =    1.842
peak=   -3.077 closest distance to " O   HOH Z  60 " =    2.304
peak=   -3.074 closest distance to " CD2 TYR A 169 " =    2.250
peak=   -3.061 closest distance to " O   HOH Z 290 " =    0.834
peak=   -3.050 closest distance to " O   HOH Z  65 " =    0.816
peak=   -3.048 closest distance to " O   HOH Z 365 " =    1.515
peak=   -3.037 closest distance to " O   ARG A  56 " =    1.780
peak=   -3.034 closest distance to " O   HOH Z  60 " =    2.272
peak=   -3.019 closest distance to " O   HOH Z 399 " =    2.104

================= 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    :  0.4757 0.4699   6.277692e+00   6.260634e+00
   1_bss:  0.4678 0.4617   6.271797e+00   6.253087e+00
   1_xyz:  0.3786 0.4039   6.144170e+00   6.179492e+00
   1_adp:  0.3307 0.3788   6.052359e+00   6.139262e+00
   1_occ:  0.3304 0.3800   6.051601e+00   6.140157e+00
   2_bss:  0.3289 0.3775   6.053401e+00   6.139810e+00
   2_xyz:  0.2371 0.2905   5.779425e+00   5.933964e+00
   2_adp:  0.2186 0.2729   5.709949e+00   5.882234e+00
   2_occ:  0.2183 0.2726   5.709081e+00   5.881463e+00
   3_bss:  0.2164 0.2711   5.710499e+00   5.881280e+00
   3_xyz:  0.1685 0.2182   5.488950e+00   5.689142e+00
   3_adp:  0.1460 0.1986   5.380262e+00   5.608111e+00
   3_occ:  0.1459 0.1986   5.380524e+00   5.609067e+00
   4_bss:  0.1459 0.1986   5.380354e+00   5.607866e+00
   4_xyz:  0.1260 0.1812   5.269828e+00   5.519703e+00
   4_adp:  0.1242 0.1734   5.241726e+00   5.476076e+00
   4_occ:  0.1241 0.1734   5.241354e+00   5.475996e+00
   5_bss:  0.1240 0.1734   5.241050e+00   5.475763e+00
   5_xyz:  0.1263 0.1723   5.251102e+00   5.473117e+00
   5_adp:  0.1252 0.1724   5.248390e+00   5.475565e+00
   5_occ:  0.1251 0.1725   5.248277e+00   5.475536e+00
   5_bss:  0.1252 0.1719   5.247370e+00   5.474084e+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:  0.330  50.000   8.475   6.278  10.563   0.000   0.000   0.000
   1_xyz:  0.330  50.000   8.475   6.278  10.563   0.000   0.000   0.000
   1_adp:  0.330  50.000   8.475   6.278  10.563   0.000   0.000   0.000
   1_occ:  0.330  50.000   8.475   6.278  10.563   0.000   0.000   0.000
   2_bss:  0.320  50.000   5.533   3.849   7.546   0.000   0.000   0.000
   2_xyz:  0.320  50.000   5.533   3.849   7.546   0.000   0.000   0.000
   2_adp:  0.320  50.000   5.533   3.849   7.546   0.000   0.000   0.000
   2_occ:  0.320  50.000   5.533   3.849   7.546   0.000   0.000   0.000
   3_bss:  0.323  61.782   3.064   2.637   4.720   0.000   0.000   0.000
   3_xyz:  0.323  61.782   3.064   2.637   4.720   0.000   0.000   0.000
   3_adp:  0.323  61.782   3.064   2.637   4.720   0.000   0.000   0.000
   3_occ:  0.323  61.782   3.064   2.637   4.720   0.000   0.000   0.000
   4_bss:  0.335  76.374   2.232   1.901   3.797   0.000   0.000   0.000
   4_xyz:  0.335  76.374   2.232   1.901   3.797   0.000   0.000   0.000
   4_adp:  0.335  76.374   2.232   1.901   3.797   0.000   0.000   0.000
   4_occ:  0.335  76.374   2.232   1.901   3.797   0.000   0.000   0.000
   5_bss:  0.324  65.627   2.152   1.921   3.639   0.000   0.000   0.000
   5_xyz:  0.324  65.627   2.152   1.921   3.639   0.000   0.000   0.000
   5_adp:  0.324  65.627   2.152   1.921   3.639   0.000   0.000   0.000
   5_occ:  0.324  65.627   2.152   1.921   3.639   0.000   0.000   0.000
   5_bss:  0.325  68.198  -0.419  -0.650   1.068   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.065 0.4570  0.5186    65240.353
   1_bss:  54.564 0.4627  0.6762    63789.440
   1_xyz:  46.508 0.5624  0.7938    46924.520
   1_adp:  42.249 0.6152  0.8891    41088.708
   1_occ:  42.304 0.6144  0.8876    41160.395
   2_bss:  42.222 0.6154  0.8075    41045.537
   2_xyz:  29.841 0.7590  0.9691    22399.292
   2_adp:  27.300 0.7874  1.0100    19574.050
   2_occ:  27.285 0.7876  1.0095    19512.046
   3_bss:  27.253 0.7881  0.9352    19564.521
   3_xyz:  20.895 0.8532  0.9801    12159.199
   3_adp:  18.985 0.8713  0.9812    10114.307
   3_occ:  19.005 0.8711  0.9808    10123.276
   4_bss:  18.969 0.8714  0.9524    10091.298
   4_xyz:  16.912 0.8901  0.9638     8352.780
   4_adp:  15.855 0.8999  0.9649     7716.331
   4_occ:  15.862 0.8998  0.9649     7711.549
   5_bss:  15.862 0.8998  0.9624     7703.349
   5_xyz:  15.692 0.9016  0.9623     7612.757
   5_adp:  15.741 0.9012  0.9579     7648.394
   5_occ:  15.745 0.9012  0.9578     7651.064
   5_bss:  15.741 0.9011  0.9574     7618.437
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4588e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4588e+01
   1_xyz:   1.735  0.014  0.112 18.318  0.007  4.111   1.4863e-01
   1_adp:   1.735  0.014  0.112 18.318  0.007  4.111   1.4863e-01
   1_occ:   1.735  0.014  0.112 18.318  0.007  4.111   1.4863e-01
   2_bss:   1.735  0.014  0.112 18.318  0.007  4.111   1.4863e-01
   2_xyz:   1.147  0.009  0.080 16.701  0.005  4.113   8.1912e-02
   2_adp:   1.147  0.009  0.080 16.701  0.005  4.113   8.1912e-02
   2_occ:   1.147  0.009  0.080 16.701  0.005  4.113   8.1912e-02
   3_bss:   1.147  0.009  0.080 16.701  0.005  4.113   8.1912e-02
   3_xyz:   1.152  0.009  0.085 16.346  0.004  4.136   7.7608e-02
   3_adp:   1.152  0.009  0.085 16.346  0.004  4.136   7.7608e-02
   3_occ:   1.152  0.009  0.085 16.346  0.004  4.136   7.7608e-02
   4_bss:   1.152  0.009  0.085 16.346  0.004  4.136   7.7608e-02
   4_xyz:   1.221  0.012  0.093 16.191  0.004  4.116   9.2287e-02
   4_adp:   1.221  0.012  0.093 16.191  0.004  4.116   9.2287e-02
   4_occ:   1.221  0.012  0.093 16.191  0.004  4.116   9.2287e-02
   5_bss:   1.221  0.012  0.093 16.191  0.004  4.116   9.2287e-02
   5_xyz:   0.983  0.008  0.077 15.566  0.004  4.117   6.2114e-02
   5_adp:   0.983  0.008  0.077 15.566  0.004  4.117   6.2114e-02
   5_occ:   0.983  0.008  0.077 15.566  0.004  4.117   6.2114e-02
   5_bss:   0.983  0.008  0.077 15.566  0.004  4.117   6.2114e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0782e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0782e+00
   1_xyz:  14.810  0.167  0.457 85.555  0.039  2.264   1.1144e-01
   1_adp:  14.810  0.167  0.457 85.555  0.039  2.264   1.1144e-01
   1_occ:  14.810  0.167  0.457 85.555  0.039  2.264   1.1144e-01
   2_bss:  14.810  0.167  0.457 85.555  0.039  2.264   1.1144e-01
   2_xyz:   7.113  0.079  0.278 82.694  0.048  2.199   8.5294e-02
   2_adp:   7.113  0.079  0.278 82.694  0.048  2.199   8.5294e-02
   2_occ:   7.113  0.079  0.278 82.694  0.048  2.199   8.5294e-02
   3_bss:   7.113  0.079  0.278 82.694  0.048  2.199   8.5294e-02
   3_xyz:   8.686  0.068  0.400 84.571  0.037  2.313   7.4846e-02
   3_adp:   8.686  0.068  0.400 84.571  0.037  2.313   7.4846e-02
   3_occ:   8.686  0.068  0.400 84.571  0.037  2.313   7.4846e-02
   4_bss:   8.686  0.068  0.400 84.571  0.037  2.313   7.4846e-02
   4_xyz:  10.347  0.074  0.517 84.835  0.044  2.324   8.1881e-02
   4_adp:  10.347  0.074  0.517 84.835  0.044  2.324   8.1881e-02
   4_occ:  10.347  0.074  0.517 84.835  0.044  2.324   8.1881e-02
   5_bss:  10.347  0.074  0.517 84.835  0.044  2.324   8.1881e-02
   5_xyz:   8.171  0.050  0.399 82.902  0.038  2.429   3.5913e-02
   5_adp:   8.171  0.050  0.399 82.902  0.038  2.429   3.5913e-02
   5_occ:   8.171  0.050  0.399 82.902  0.038  2.429   3.5913e-02
   5_bss:   8.171  0.050  0.399 82.902  0.038  2.429   3.5913e-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:  71.79   0.00  12.50  63.25   0.00   9.81  71.79   0.00  27.13
   1_occ:  71.79   0.00  12.50  63.25   0.00   9.81  71.79   0.00  27.13
   2_bss:  71.79   0.00  12.50  63.25   0.00   9.81  71.79   0.00  27.13
   2_xyz:  71.79   0.00  12.50  63.25   0.00   9.81  71.79   0.00  27.13
   2_adp:  87.45   0.00  12.60  87.45   0.00   9.44  72.49   0.00  29.80
   2_occ:  87.45   0.00  12.60  87.45   0.00   9.44  72.49   0.00  29.80
   3_bss:  87.45   0.00  12.60  87.45   0.00   9.44  72.49   0.00  29.80
   3_xyz:  87.45   0.00  12.60  87.45   0.00   9.44  72.49   0.00  29.80
   3_adp:  97.77   0.00  13.89  85.99   0.00   9.16  97.77   0.00  39.69
   3_occ:  97.77   0.00  13.89  85.99   0.00   9.16  97.77   0.00  39.69
   4_bss:  97.77   0.00  13.89  85.99   0.00   9.16  97.77   0.00  39.69
   4_xyz:  97.77   0.00  13.89  85.99   0.00   9.16  97.77   0.00  39.69
   4_adp:  92.90   0.00  13.03  76.33   0.00   8.70  92.90   1.65  36.62
   4_occ:  92.90   0.00  13.03  76.33   0.00   8.70  92.90   1.65  36.62
   5_bss:  92.90   0.00  13.03  76.33   0.00   8.70  92.90   1.65  36.62
   5_xyz:  92.90   0.00  13.03  76.33   0.00   8.70  92.90   1.65  36.62
   5_adp:  93.61   0.00  12.93  78.13   0.00   8.63  93.61   1.96  36.33
   5_occ:  93.61   0.00  12.93  78.13   0.00   8.63  93.61   1.96  36.33
   5_bss:  96.18   2.57  15.50  80.70   2.57  11.20  96.18   4.54  38.90
------------------------------------------------------------------------
 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:    1.264    0.009    0.416
   1_adp:    1.264    0.009    0.416
   1_occ:    1.264    0.009    0.416
   2_bss:    1.264    0.009    0.416
   2_xyz:    1.670    0.026    0.587
   2_adp:    1.670    0.026    0.587
   2_occ:    1.670    0.026    0.587
   3_bss:    1.670    0.026    0.587
   3_xyz:    1.647    0.041    0.653
   3_adp:    1.647    0.041    0.653
   3_occ:    1.647    0.041    0.653
   4_bss:    1.647    0.041    0.653
   4_xyz:    1.662    0.050    0.689
   4_adp:    1.662    0.050    0.689
   4_occ:    1.662    0.050    0.689
   5_bss:    1.662    0.050    0.689
   5_xyz:    1.711    0.061    0.696
   5_adp:    1.711    0.061    0.696
   5_occ:    1.711    0.061    0.696
   5_bss:    1.711    0.061    0.696
------------------------------------------------------------------------

CPU time actual refinement: 334.63


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1153/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_1153/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1153/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1153/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1153/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.48 
  Macro-tasks:
    bulk solvent and scale       = 39.75  
    individual site refinement   = 144.72 
    weights calculation          = 30.59  
    collect and process          = 6.43   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 221.62 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 102.58 
    alpha_beta                      = 8.18   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 115.94 
    fmodel                         = 7.03   
    r_factors                      = 0.21   
    phase_errors                   = 10.66  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 248.35 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.583 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    679 calls, 102.37 s
gradients_fft:          624 calls, 101.43 s

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

# Date 2008-01-16 Time 03:19:50 PST -0800 (1200482390.13 s)
Start R-work = 0.4757, R-free = 0.4699 (no bulk solvent and anisotropic scale)
Final R-work = 0.1415, R-free = 0.1888 (no bulk solvent and anisotropic scale)

Start R-work = 0.4678, R-free = 0.4617
Final R-work = 0.1252, R-free = 0.1719