# Date 2008-01-16 Time 02:52:17 PST -0800 (1200480737.66 s)
#phil __OFF__

Command line arguments: "../1010.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2954
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1010

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.4607, 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: (71.3037, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 1.98338
Completeness in resolution range: 0.938755
Completeness with d_max=infinity: 0.935974

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2391
                             d_min =   1.9834

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 1.98338
Completeness in resolution range: 0.938755
Completeness with d_max=infinity: 0.935974

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2395 -  4.2452 [2193/2218]  1972   221  10.1%
  bin  2:  4.2452 -  3.3816 [2106/2126]  1898   208   9.9%
  bin  3:  3.3816 -  2.9577 [2083/2102]  1875   208  10.0%
  bin  4:  2.9577 -  2.6889 [2056/2086]  1846   210  10.2%
  bin  5:  2.6889 -  2.4971 [2048/2067]  1852   196   9.6%
  bin  6:  2.4971 -  2.3504 [2039/2064]  1828   211  10.3%
  bin  7:  2.3504 -  2.2331 [2022/2050]  1818   204  10.1%
  bin  8:  2.2331 -  2.1361 [2031/2067]  1825   206  10.1%
  bin  9:  2.1361 -  2.0541 [2012/2054]  1819   193   9.6%
  bin 10:  2.0541 -  1.9834 [ 999/2033]   897   102  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1010/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 18
        2.42 -     3.04: 2172
        3.04 -     3.66: 4645
        3.66 -     4.28: 8908
        4.28 -     4.90: 12238
  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  42 " - " O   HOH Z 183 "  2.167 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.218 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.218 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27976 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_1010/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1010/model_refine_001.geo

CPU time processing inputs: 9.38


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.4607 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: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4849   r_free= 0.4718   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: 6.285295                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.7354 0.99   1420  157 0.4041 0.3747      6.6125      6.5503|
|  2:  4.7354 -  3.7775 0.99   1373  155 0.3982 0.4156      6.7914      6.8264|
|  3:  3.7775 -  3.3055 0.99   1344  145 0.4415 0.4102      6.6645      6.6291|
|  4:  3.3055 -  3.0058 0.99   1340  151 0.4820 0.4337        6.54      6.4649|
|  5:  3.0058 -  2.7918 0.99   1329  150 0.5210 0.4899      6.3706      6.3774|
|  6:  2.7918 -  2.6281 0.99   1313  145 0.5083 0.5271      6.2625      6.2066|
|  7:  2.6281 -  2.4971 0.99   1324  140 0.5360 0.5048      6.2517      6.2076|
|  8:  2.4971 -  2.3888 0.98   1297  152 0.5353 0.5155      6.1711      6.1854|
|  9:  2.3888 -  2.2972 0.98   1299  143 0.5257 0.5644      6.1253      6.1967|
| 10:  2.2972 -  2.2181 1.00   1305  148 0.5259 0.5129      6.0976      6.0647|
| 11:  2.2181 -  2.1490 0.98   1307  142 0.5204 0.5023      6.0401      6.0279|
| 12:  2.1490 -  2.0877 0.98   1293  143 0.5339 0.5160      5.9499      5.9848|
| 13:  2.0877 -  2.0329 0.98   1267  141 0.5309 0.5066      5.8809       5.787|
| 14:  2.0329 -  1.9834 0.31    419   47 0.5321 0.5021      5.8512      5.8311|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.7354  1420   157  0.70  34.31   0.78     0.74      71650.73|
|  2:  4.7354 -  3.7775  1373   155  0.72  33.43   0.86     0.79     101886.97|
|  3:  3.7775 -  3.3055  1344   145  0.62  42.50   0.83     0.74     107002.68|
|  4:  3.3055 -  3.0058  1340   151  0.54  48.86   0.77     0.63      94952.14|
|  5:  3.0058 -  2.7918  1329   150  0.45  56.04   0.72     0.54      77955.54|
|  6:  2.7918 -  2.6281  1313   145  0.40  59.94   0.71     0.46      70255.52|
|  7:  2.6281 -  2.4971  1324   140  0.35  64.06   0.72     0.40      67509.80|
|  8:  2.4971 -  2.3888  1297   152  0.31  66.92   0.70     0.36      61955.61|
|  9:  2.3888 -  2.2972  1299   143  0.31  66.76   0.71     0.37      57957.20|
| 10:  2.2972 -  2.2181  1305   148  0.32  65.98   0.74     0.37      50713.21|
| 11:  2.2181 -  2.1490  1307   142  0.32  66.36   0.77     0.39      48247.52|
| 12:  2.1490 -  2.0877  1293   143  0.32  65.89   0.72     0.41      43147.58|
| 13:  2.0877 -  2.0329  1267   141  0.32  66.28   0.71     0.41      37365.78|
| 14:  2.0329 -  1.9834   419    47  0.37  62.32   0.71     0.40      29641.89|
|alpha:            min =        0.36 max =            0.79 mean =         0.51|
|beta:             min =    29641.89 max =       107002.68 mean =     67972.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.54|
|phase err.(test): min =        0.00 max =           89.98 mean =        56.67|
|-----------------------------------------------------------------------------|

============================== 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 = 14.343485             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.024   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.249886              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.114   (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:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      683 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1483 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2595 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3876 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5023 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6497 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7598 |
|-----------------------------------------------------------------------------|
|-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 |       54.285 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.710 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    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 = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4907   r_free= 0.4779   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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.287028                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4770   r_free= 0.4626   ksol= 0.32   Bsol= 20.00   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.88,7.64,10.77,0.00,0.00,0.00); trace/3= 8.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.280771                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.500571             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.112   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.167274              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.908   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4770      final r-factor (work) = 0.3939          |
| start r-factor (free) = 0.4626      final r-factor (free) = 0.4136          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.5426 = 12.50 * 0.50 * 6.2810 + 1.00 * 54.2848                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.8671 = 12.50 * 0.50 * 6.1952 + 1.00 * 0.1455                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3939      final r-factor (work) = 0.3460          |
| start r-factor (free) = 0.4136      final r-factor (free) = 0.3991          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2459 = 1.17 * 1.00 * 6.1952 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1427 = 1.17 * 1.00 * 6.1042 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.78   13.87    None  None   None       |
|    all(noH): 2823   0      0.00    85.78   13.87    None  None   None       |
|    Sol.    : 438    0      0.00    85.78   27.76    None  None   None       |
|    Mac.    : 2385   0      0.00    69.26   11.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.579: 1208   |   5:    42.892 -  51.471:   76        |
|      1:     8.579 -  17.157:  779   |   6:    51.471 -  60.049:   34        |
|      2:    17.157 -  25.735:  431   |   7:    60.049 -  68.628:   10        |
|      3:    25.735 -  34.314:  176   |   8:    68.628 -  77.206:    7        |
|      4:    34.314 -  42.892:  101   |   9:    77.206 -  85.785:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3460 r_free = 0.3991             target_work(ml) = 6.086         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3456 r_free = 0.3993             target_work(ml) = 6.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3456   r_free= 0.3993   ksol= 0.32   Bsol= 20.00   scale= 1.103   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.88,7.64,10.77,0.00,0.00,0.00); trace/3= 8.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.085043                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3425   r_free= 0.3942   ksol= 0.33   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.78,4.23,7.31,0.00,0.00,0.00); trace/3= 5.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.084913                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.903662              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.860   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.511731              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.711  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3425      final r-factor (work) = 0.2556          |
| start r-factor (free) = 0.3942      final r-factor (free) = 0.3121          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1511 = 5.90 * 0.50 * 6.0998 + 1.00 * 0.1455                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6886 = 5.90 * 0.50 * 5.9659 + 1.00 * 0.0783                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2556      final r-factor (work) = 0.2325          |
| start r-factor (free) = 0.3121      final r-factor (free) = 0.2868          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0705 = 0.51 * 1.00 * 5.9659 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9844 = 0.51 * 1.00 * 5.8072 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.71   13.21    None  None   None       |
|    all(noH): 2823   0      0.00    87.71   13.21    None  None   None       |
|    Sol.    : 438    0      0.00    87.71   33.41    None  None   None       |
|    Mac.    : 2385   0      0.00    68.45   9.50     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 -   8.772: 1413   |   5:    43.858 -  52.629:   73        |
|      1:     8.772 -  17.543:  752   |   6:    52.629 -  61.400:   40        |
|      2:    17.543 -  26.315:  258   |   7:    61.400 -  70.172:   13        |
|      3:    26.315 -  35.086:  150   |   8:    70.172 -  78.943:    3        |
|      4:    35.086 -  43.858:  120   |   9:    78.943 -  87.715:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2325 r_free = 0.2868             target_work(ml) = 5.771         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2322 r_free = 0.2867             target_work(ml) = 5.771         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2322   r_free= 0.2867   ksol= 0.33   Bsol= 50.00   scale= 1.055   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.78,4.23,7.31,0.00,0.00,0.00); trace/3= 5.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.770615                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2307   r_free= 0.2857   ksol= 0.32   Bsol= 59.15   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,2.29,4.73,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.772503                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.583274              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.615  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.631636              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.207  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2307      final r-factor (work) = 0.1764          |
| start r-factor (free) = 0.2857      final r-factor (free) = 0.2289          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5872 = 2.58 * 0.50 * 5.8135 + 1.00 * 0.0783                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3758 = 2.58 * 0.50 * 5.6638 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1764      final r-factor (work) = 0.1629          |
| start r-factor (free) = 0.2289      final r-factor (free) = 0.2157          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5902 = 0.63 * 1.00 * 5.6638 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4870 = 0.63 * 1.00 * 5.4981 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.30   13.95    None  None   None       |
|    all(noH): 2823   0      0.00    86.30   13.95    None  None   None       |
|    Sol.    : 438    0      0.91    86.30   39.06    None  None   None       |
|    Mac.    : 2385   0      0.00    74.89   9.34     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 -   8.630: 1480   |   5:    43.150 -  51.780:   95        |
|      1:     8.630 -  17.260:  701   |   6:    51.780 -  60.411:   72        |
|      2:    17.260 -  25.890:  193   |   7:    60.411 -  69.041:   42        |
|      3:    25.890 -  34.520:  122   |   8:    69.041 -  77.671:   15        |
|      4:    34.520 -  43.150:   96   |   9:    77.671 -  86.301:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1629 r_free = 0.2157             target_work(ml) = 5.473         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1628 r_free = 0.2158             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1628   r_free= 0.2158   ksol= 0.32   Bsol= 59.15   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,2.29,4.73,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.472226                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1626   r_free= 0.2156   ksol= 0.33   Bsol= 67.85   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,1.67,3.84,0.00,0.00,0.00); trace/3= 2.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.472599                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.563414              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.274  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.333  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1626      final r-factor (work) = 0.1362          |
| start r-factor (free) = 0.2156      final r-factor (free) = 0.1888          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1094 = 2.56 * 0.50 * 5.4999 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9866 = 2.56 * 0.50 * 5.4010 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1327          |
| start r-factor (free) = 0.1888      final r-factor (free) = 0.1818          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6794 = 0.31 * 1.00 * 5.4010 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6508 = 0.31 * 1.00 * 5.3160 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.94   13.47    None  None   None       |
|    all(noH): 2823   0      0.00    85.94   13.47    None  None   None       |
|    Sol.    : 438    0      2.01    85.94   38.20    None  None   None       |
|    Mac.    : 2385   0      0.00    74.10   8.93     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 -   8.594: 1553   |   5:    42.969 -  51.563:  101        |
|      1:     8.594 -  17.188:  674   |   6:    51.563 -  60.157:   55        |
|      2:    17.188 -  25.782:  176   |   7:    60.157 -  68.751:   38        |
|      3:    25.782 -  34.375:  109   |   8:    68.751 -  77.345:   19        |
|      4:    34.375 -  42.969:   93   |   9:    77.345 -  85.938:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1327 r_free = 0.1818             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1326 r_free = 0.1817             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1817   ksol= 0.33   Bsol= 67.85   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,1.67,3.84,0.00,0.00,0.00); trace/3= 2.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.294373                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1817   ksol= 0.33   Bsol= 64.02   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.84,1.52,3.52,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.294721                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.914382              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.345  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.889722              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.516  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1328      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8107 = 2.91 * 0.50 * 5.3161 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7373 = 2.91 * 0.50 * 5.2581 + 1.00 * 0.0752                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6899 = 0.89 * 1.00 * 5.2581 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6519 = 0.89 * 1.00 * 5.2137 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.99   13.47    None  None   None       |
|    all(noH): 2823   0      0.00    90.99   13.47    None  None   None       |
|    Sol.    : 438    0      2.21    90.99   38.41    None  None   None       |
|    Mac.    : 2385   0      0.00    76.59   8.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.099: 1637   |   5:    45.497 -  54.596:   92        |
|      1:     9.099 -  18.199:  607   |   6:    54.596 -  63.696:   56        |
|      2:    18.199 -  27.298:  176   |   7:    63.696 -  72.795:   24        |
|      3:    27.298 -  36.398:  112   |   8:    72.795 -  81.895:   15        |
|      4:    36.398 -  45.497:  100   |   9:    81.895 -  90.994:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1196 r_free = 0.1684             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1195 r_free = 0.1683             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1683   ksol= 0.33   Bsol= 64.02   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.84,1.52,3.52,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.210671                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.7354 0.99   1420  157 0.0983 0.1350      5.3925      5.5771|
|  2:  4.7354 -  3.7775 0.99   1373  155 0.0866 0.1203      5.4577      5.6766|
|  3:  3.7775 -  3.3055 0.99   1344  145 0.1138 0.1570      5.5246      5.8466|
|  4:  3.3055 -  3.0058 0.99   1340  151 0.1305 0.1792       5.497      5.6755|
|  5:  3.0058 -  2.7918 0.99   1329  150 0.1463 0.1792      5.4052      5.6184|
|  6:  2.7918 -  2.6281 0.99   1313  145 0.1361 0.2191      5.2767      5.5721|
|  7:  2.6281 -  2.4971 0.99   1324  140 0.1375 0.1678      5.2511      5.3741|
|  8:  2.4971 -  2.3888 0.98   1297  152 0.1304 0.1782      5.1549      5.3943|
|  9:  2.3888 -  2.2972 0.98   1299  143 0.1307 0.2008      5.1212      5.4053|
| 10:  2.2972 -  2.2181 1.00   1305  148 0.1223 0.1678      5.0083      5.1983|
| 11:  2.2181 -  2.1490 0.98   1307  142 0.1183 0.1969       4.986      5.3889|
| 12:  2.1490 -  2.0877 0.98   1293  143 0.1211 0.1819      4.9126      5.1885|
| 13:  2.0877 -  2.0329 0.98   1267  141 0.1178 0.1714      4.8355      5.0547|
| 14:  2.0329 -  1.9834 0.31    419   47 0.1080 0.1599      4.7463      4.9102|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.7354  1420   157  0.94   9.39   0.97     0.94       7610.72|
|  2:  4.7354 -  3.7775  1373   155  0.95   8.35   1.00     0.99       9686.55|
|  3:  3.7775 -  3.3055  1344   145  0.93  12.17   1.02     1.02      11410.31|
|  4:  3.3055 -  3.0058  1340   151  0.91  14.87   1.01     0.99      11310.43|
|  5:  3.0058 -  2.7918  1329   150  0.89  17.29   1.00     0.98       9619.62|
|  6:  2.7918 -  2.6281  1313   145  0.89  17.60   0.98     0.95       8117.69|
|  7:  2.6281 -  2.4971  1324   140  0.89  17.20   0.98     0.95       7356.43|
|  8:  2.4971 -  2.3888  1297   152  0.89  17.51   0.98     0.96       6429.88|
|  9:  2.3888 -  2.2972  1299   143  0.89  17.45   0.99     0.94       5975.37|
| 10:  2.2972 -  2.2181  1305   148  0.90  16.49   0.99     0.96       4798.27|
| 11:  2.2181 -  2.1490  1307   142  0.89  16.89   0.98     0.93       4671.82|
| 12:  2.1490 -  2.0877  1293   143  0.90  16.38   0.99     1.00       4233.67|
| 13:  2.0877 -  2.0329  1267   141  0.88  18.38   0.99     0.96       3904.46|
| 14:  2.0329 -  1.9834   419    47  0.90  16.09   0.97     0.94       3178.75|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3178.75 max =        11410.31 mean =      7260.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.83 mean =        15.32|
|phase err.(test): min =        0.00 max =           89.95 mean =        14.66|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1683   ksol= 0.32   Bsol= 61.98   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.77,1.18,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.210668                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1683   ksol= 0.32   Bsol= 61.98   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.77,1.18,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.210668                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.7354 0.99   1420  157 0.0981 0.1348      5.3904      5.5762|
|  2:  4.7354 -  3.7775 0.99   1373  155 0.0865 0.1202      5.4563      5.6747|
|  3:  3.7775 -  3.3055 0.99   1344  145 0.1137 0.1569      5.5239      5.8464|
|  4:  3.3055 -  3.0058 0.99   1340  151 0.1306 0.1794      5.4978      5.6765|
|  5:  3.0058 -  2.7918 0.99   1329  150 0.1464 0.1793       5.406      5.6191|
|  6:  2.7918 -  2.6281 0.99   1313  145 0.1362 0.2196      5.2778      5.5739|
|  7:  2.6281 -  2.4971 0.99   1324  140 0.1376 0.1680      5.2521      5.3751|
|  8:  2.4971 -  2.3888 0.98   1297  152 0.1305 0.1783      5.1555      5.3947|
|  9:  2.3888 -  2.2972 0.98   1299  143 0.1307 0.2007      5.1214      5.4055|
| 10:  2.2972 -  2.2181 1.00   1305  148 0.1224 0.1678      5.0085       5.198|
| 11:  2.2181 -  2.1490 0.98   1307  142 0.1183 0.1966      4.9858      5.3882|
| 12:  2.1490 -  2.0877 0.98   1293  143 0.1211 0.1819      4.9121      5.1883|
| 13:  2.0877 -  2.0329 0.98   1267  141 0.1179 0.1715      4.8357      5.0548|
| 14:  2.0329 -  1.9834 0.31    419   47 0.1080 0.1600      4.7467      4.9105|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.7354  1420   157  0.94   9.37   0.97     0.94       7589.89|
|  2:  4.7354 -  3.7775  1373   155  0.95   8.34   1.01     0.99       9664.95|
|  3:  3.7775 -  3.3055  1344   145  0.93  12.15   1.02     1.02      11390.73|
|  4:  3.3055 -  3.0058  1340   151  0.91  14.88   1.01     0.99      11316.67|
|  5:  3.0058 -  2.7918  1329   150  0.89  17.30   1.00     0.99       9641.31|
|  6:  2.7918 -  2.6281  1313   145  0.89  17.63   0.98     0.95       8136.70|
|  7:  2.6281 -  2.4971  1324   140  0.89  17.24   0.99     0.95       7375.12|
|  8:  2.4971 -  2.3888  1297   152  0.89  17.53   0.99     0.96       6440.21|
|  9:  2.3888 -  2.2972  1299   143  0.89  17.46   0.99     0.95       5983.55|
| 10:  2.2972 -  2.2181  1305   148  0.90  16.48   1.00     0.96       4795.69|
| 11:  2.2181 -  2.1490  1307   142  0.90  16.87   0.99     0.93       4668.02|
| 12:  2.1490 -  2.0877  1293   143  0.90  16.37   1.00     1.00       4229.11|
| 13:  2.0877 -  2.0329  1267   141  0.88  18.38   0.99     0.96       3904.68|
| 14:  2.0329 -  1.9834   419    47  0.90  16.10   0.97     0.94       3181.31|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3181.31 max =        11390.73 mean =      7261.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.86 mean =        15.33|
|phase err.(test): min =        0.00 max =           89.78 mean =        14.66|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.38    93.37   15.85    None  None   None       |
|    all(noH): 2823   0      2.38    93.37   15.85    None  None   None       |
|    Sol.    : 438    0      4.59    93.37   40.78    None  None   None       |
|    Mac.    : 2385   0      2.38    78.97   11.27    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:     2.376 -  11.475: 1637   |   5:    47.873 -  56.972:   92        |
|      1:    11.475 -  20.575:  607   |   6:    56.972 -  66.072:   56        |
|      2:    20.575 -  29.674:  176   |   7:    66.072 -  75.171:   24        |
|      3:    29.674 -  38.773:  112   |   8:    75.171 -  84.270:   15        |
|      4:    38.773 -  47.873:  100   |   9:    84.270 -  93.370:    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)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.306 - 4.866
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 323
   mapped sites are within: 0.712 - 4.866

peak=   10.541 closest distance to " CB  VAL A 230 " =    1.450
peak=    7.886 closest distance to " CG2 VAL A 296 " =    1.258
peak=    6.786 closest distance to " CG  ARG A 138 " =    1.160
peak=    6.519 closest distance to " CD2 LEU A   5 " =    1.233
peak=    5.550 closest distance to " NE2 GLN A  11 " =    1.156
peak=    5.538 closest distance to " CG  PRO A  54 " =    1.344
peak=    5.449 closest distance to " O   HOH Z 232 " =    2.265
peak=    5.441 closest distance to " O   HOH Z 142 " =    2.271
peak=    5.329 closest distance to " CD1AILE A 234 " =    1.079
peak=    5.281 closest distance to " CB  GLN A 223 " =    1.474
peak=    5.187 closest distance to " CG  LEU A   5 " =    1.172
peak=    5.133 closest distance to " NH1 ARG A 138 " =    1.058
peak=    5.072 closest distance to " CG  LEU A 228 " =    1.158
peak=    5.010 closest distance to " O   HOH Z 111 " =    1.999
peak=    4.945 closest distance to " CB  ASN A 148 " =    1.408
peak=    4.936 closest distance to " O   HOH Z 222 " =    1.299
peak=    4.821 closest distance to " CB  GLN A 183 " =    1.257
peak=    4.770 closest distance to " O   HOH Z   9 " =    1.942
peak=    4.764 closest distance to " O   HOH Z   7 " =    1.340
peak=    4.725 closest distance to " O   HOH Z 369 " =    2.072
peak=    4.605 closest distance to " CB  ASP A 124 " =    0.805
peak=    4.545 closest distance to " O   HOH Z 298 " =    1.996
peak=    4.538 closest distance to " O   HOH Z 427 " =    2.765
peak=    4.496 closest distance to " CZ  PHE A 218 " =    1.117
peak=    4.455 closest distance to " CG  LEU A 167 " =    1.239
peak=    4.453 closest distance to " CB  SER A  63 " =    1.232
peak=    4.305 closest distance to " O   HOH Z 287 " =    2.103
peak=    4.273 closest distance to " O   HOH Z 265 " =    1.997
peak=    4.263 closest distance to " CB  PRO A  54 " =    1.003
peak=    4.241 closest distance to " CG  PRO A 243 " =    1.144
peak=    4.220 closest distance to " CB  ASN A 142 " =    0.914
peak=    4.188 closest distance to " O   PRO A 198 " =    1.609
peak=    4.171 closest distance to " CG  PRO A 198 " =    1.259
peak=    4.144 closest distance to " CB  VAL A 265 " =    1.292
peak=    4.129 closest distance to " O   HOH Z 303 " =    2.218
peak=    4.124 closest distance to " NH1AARG A 145 " =    1.211
peak=    4.096 closest distance to " CG  PRO A 213 " =    1.242
peak=    4.094 closest distance to " O   SER A  87 " =    2.335
peak=    4.088 closest distance to " O   HOH Z 425 " =    1.514
peak=    4.085 closest distance to " CB  TRP A 266 " =    1.046
peak=    4.070 closest distance to " CD2 LEU A 228 " =    1.204
peak=    4.050 closest distance to " ND2 ASN A 187 " =    1.646
peak=    4.011 closest distance to " CD  ARG A 159 " =    0.748
peak=    4.009 closest distance to " CE  LYS A  76 " =    0.909
peak=    4.007 closest distance to " CA  ALA A  51 " =    1.026
peak=    3.984 closest distance to " O   HOH Z 353 " =    2.533
peak=    3.979 closest distance to " O   HOH Z 423 " =    1.609
peak=    3.976 closest distance to " CB  VAL A 230 " =    1.276
peak=    3.970 closest distance to " CB  ASN A  39 " =    0.994
peak=    3.968 closest distance to " NH2AARG A 190 " =    1.802
peak=    3.966 closest distance to " O   HOH Z 158 " =    3.070
peak=    3.958 closest distance to " O   HOH Z  88 " =    3.132
peak=    3.952 closest distance to " O   HOH Z  78 " =    1.592
peak=    3.917 closest distance to " O   HOH Z 272 " =    1.825
peak=    3.899 closest distance to " O   HOH Z 411 " =    3.321
peak=    3.880 closest distance to " CZ3 TRP A 266 " =    1.147
peak=    3.870 closest distance to " O   HOH Z 368 " =    2.115
peak=    3.855 closest distance to " O   HOH Z 126 " =    2.165
peak=    3.852 closest distance to " CD  ARG A 138 " =    1.295
peak=    3.830 closest distance to " CD  ARG A  66 " =    2.297
peak=    3.827 closest distance to " CD  ARG A 269 " =    0.937
peak=    3.821 closest distance to " CG1 ILE A 151 " =    1.255
peak=    3.812 closest distance to " CA  VAL A 125 " =    1.169
peak=    3.809 closest distance to " O   HOH Z 316 " =    3.092
peak=    3.808 closest distance to " O   HOH Z 214 " =    2.296
peak=    3.807 closest distance to " CB  ARG A 190 " =    1.469
peak=    3.801 closest distance to " O   HOH Z 346 " =    1.602
peak=    3.799 closest distance to " CG2 THR A 221 " =    1.115
peak=    3.796 closest distance to " O   HOH Z 180 " =    2.167
peak=    3.795 closest distance to " O   HOH Z 126 " =    1.604
peak=    3.794 closest distance to " O   HOH Z 156 " =    3.001
peak=    3.789 closest distance to " CB  ARG A 275 " =    0.970
peak=    3.783 closest distance to " CD1 LEU A 300 " =    1.121
peak=    3.780 closest distance to " CB  SER A 216 " =    0.974
peak=    3.774 closest distance to " CA  TYR A  30 " =    1.008
peak=    3.767 closest distance to " O   HOH Z 130 " =    0.894
peak=    3.766 closest distance to " CB  TYR A 169 " =    0.712
peak=    3.766 closest distance to " O   HOH Z 406 " =    1.539
peak=    3.758 closest distance to " CB  GLU A 152 " =    1.185
peak=    3.756 closest distance to " CB  GLU A 277 " =    3.669
peak=    3.740 closest distance to " CD  GLN A 240 " =    1.557
peak=    3.738 closest distance to " CD1 ILE A  33 " =    1.888
peak=    3.736 closest distance to " O   HOH Z 145 " =    1.982
peak=    3.730 closest distance to " CA  ASN A 127 " =    1.149
peak=    3.727 closest distance to " N   ALA A 256 " =    1.085
peak=    3.724 closest distance to " O   HOH Z 193 " =    1.919
peak=    3.724 closest distance to " CD2 TRP A 179 " =    1.247
peak=    3.723 closest distance to " CB  SER A 212 " =    1.287
peak=    3.708 closest distance to " O   HOH Z 188 " =    2.929
peak=    3.683 closest distance to " CA  ALA A 160 " =    1.047
peak=    3.678 closest distance to " CD  LYS A 166 " =    1.264
peak=    3.677 closest distance to " O   HOH Z 437 " =    1.629
peak=    3.675 closest distance to " CG2 ILE A 234 " =    0.860
peak=    3.666 closest distance to " CA  ARG A 195 " =    1.234
peak=    3.663 closest distance to " O   HOH Z 290 " =    1.112
peak=    3.657 closest distance to " O   HOH Z 380 " =    1.836
peak=    3.654 closest distance to " O   HOH Z   1 " =    1.817
peak=    3.651 closest distance to " CA  VAL A 296 " =    1.029
peak=    3.647 closest distance to " O   HOH Z 234 " =    3.769
peak=    3.647 closest distance to " CA  LYS A 117 " =    1.198
peak=    3.646 closest distance to " O   HOH Z 207 " =    1.127
peak=    3.645 closest distance to " O   HOH Z 183 " =    1.261
peak=    3.640 closest distance to " CB  VAL A 202 " =    1.591
peak=    3.639 closest distance to " CB  ARG A  79 " =    1.466
peak=    3.631 closest distance to " O   HOH Z 273 " =    2.816
peak=    3.625 closest distance to " CG2 ILE A  20 " =    1.546
peak=    3.625 closest distance to " CA  SER A  87 " =    0.936
peak=    3.622 closest distance to " O   HOH Z 167 " =    1.728
peak=    3.618 closest distance to " N   SER A 271 " =    0.976
peak=    3.614 closest distance to " CG1 VAL A 153 " =    0.954
peak=    3.611 closest distance to " O   HOH Z 359 " =    1.447
peak=    3.608 closest distance to " N   PHE A 130 " =    1.292
peak=    3.603 closest distance to " CB  LEU A 228 " =    1.240
peak=    3.601 closest distance to " O   HOH Z  10 " =    1.794
peak=    3.593 closest distance to " CB AVAL A  41 " =    1.274
peak=    3.589 closest distance to " O   ASP A 200 " =    1.602
peak=    3.584 closest distance to " O   HOH Z  53 " =    2.463
peak=    3.581 closest distance to " CB  ARG A 138 " =    1.260
peak=    3.580 closest distance to " CB  SER A 210 " =    0.830
peak=    3.578 closest distance to " O   HOH Z  90 " =    2.293
peak=    3.561 closest distance to " O   HOH Z 185 " =    1.901
peak=    3.557 closest distance to " CD BLYS A 290 " =    1.042
peak=    3.556 closest distance to " CA  ALA A 291 " =    0.907
peak=    3.553 closest distance to " CA  GLY A 267 " =    1.122
peak=    3.551 closest distance to " O   HOH Z 258 " =    1.897
peak=    3.550 closest distance to " O   HOH Z   2 " =    1.655
peak=    3.549 closest distance to " CB  GLU A  46 " =    0.954
peak=    3.542 closest distance to " OG  SER A 135 " =    1.269
peak=    3.526 closest distance to " O   HOH Z 422 " =    2.696
peak=    3.521 closest distance to " CA  ARG A 102 " =    1.146
peak=    3.518 closest distance to " O   HOH Z 128 " =    2.216
peak=    3.513 closest distance to " CB  LEU A 237 " =    0.895
peak=    3.499 closest distance to " O   HOH Z 329 " =    4.123
peak=    3.495 closest distance to " CZ  PHE A  38 " =    1.237
peak=    3.494 closest distance to " CG BARG A 102 " =    1.921
peak=    3.493 closest distance to " CA  ILE A 234 " =    0.976
peak=    3.490 closest distance to " CG  GLU A  37 " =    0.937
peak=    3.488 closest distance to " CB  GLN A  88 " =    1.284
peak=    3.484 closest distance to " O   HOH Z  44 " =    2.279
peak=    3.484 closest distance to " NE AARG A 275 " =    1.478
peak=    3.483 closest distance to " CE1 TYR A 186 " =    1.294
peak=    3.483 closest distance to " CB  TRP A 150 " =    1.284
peak=    3.482 closest distance to " O   HOH Z 211 " =    1.196
peak=    3.477 closest distance to " CB  SER A   3 " =    1.459
peak=    3.475 closest distance to " O   HOH Z 392 " =    1.259
peak=    3.473 closest distance to " CB  ASN A 110 " =    1.139
peak=    3.473 closest distance to " O   HOH Z 410 " =    1.457
peak=    3.471 closest distance to " CZ3 TRP A  92 " =    1.215
peak=    3.470 closest distance to " N   CYS A 260 " =    0.803
peak=    3.468 closest distance to " CA  ASP A 162 " =    1.004
peak=    3.462 closest distance to " CB  GLU A 128 " =    1.028
peak=    3.461 closest distance to " CB  GLN A  89 " =    1.233
peak=    3.457 closest distance to " CB  ASP A 140 " =    0.990
peak=    3.447 closest distance to " OD1 ASN A  69 " =    2.591
peak=    3.446 closest distance to " CA  MET A 105 " =    0.916
peak=    3.440 closest distance to " O   HOH Z 332 " =    1.603
peak=    3.439 closest distance to " O   HOH Z 184 " =    1.459
peak=    3.438 closest distance to " ND1 HIS A  81 " =    1.881
peak=    3.434 closest distance to " N   SER A 135 " =    1.332
peak=    3.430 closest distance to " CB  MET A  40 " =    0.814
peak=    3.429 closest distance to " CB  THR A  82 " =    1.224
peak=    3.429 closest distance to " O   ASP A 124 " =    1.189
peak=    3.427 closest distance to " CB  TRP A 179 " =    1.415
peak=    3.426 closest distance to " O   HOH Z   3 " =    2.056
peak=    3.425 closest distance to " OE2 GLU A   2 " =    1.993
peak=    3.423 closest distance to " CD1 LEU A   5 " =    1.387
peak=    3.421 closest distance to " O   HOH Z  30 " =    1.683
peak=    3.419 closest distance to " O   HOH Z  20 " =    1.746
peak=    3.418 closest distance to " CG  GLN A  89 " =    1.505
peak=    3.417 closest distance to " CG BARG A 275 " =    1.309
peak=    3.413 closest distance to " O   MET A 105 " =    1.859
peak=    3.413 closest distance to " O   HOH Z  61 " =    1.665
peak=    3.413 closest distance to " CB  SER A 273 " =    0.946
peak=    3.412 closest distance to " O   HOH Z 302 " =    1.812
peak=    3.410 closest distance to " CB  PRO A 243 " =    1.484
peak=    3.410 closest distance to " O   HOH Z 193 " =    1.678
peak=    3.398 closest distance to " O   HOH Z 132 " =    2.544
peak=    3.392 closest distance to " CA  ARG A  36 " =    1.144
peak=    3.392 closest distance to " OG  SER A  62 " =    3.083
peak=    3.389 closest distance to " CG2 VAL A 257 " =    0.912
peak=    3.388 closest distance to " CA  TYR A 116 " =    1.419
peak=    3.387 closest distance to " O   THR A 182 " =    1.413
peak=    3.383 closest distance to " O   HOH Z 148 " =    2.271
peak=    3.377 closest distance to " CG  GLN A  88 " =    1.091
peak=    3.375 closest distance to " O   HOH Z 109 " =    2.714
peak=    3.374 closest distance to " O   HOH Z 133 " =    2.798
peak=    3.373 closest distance to " O   HOH Z 343 " =    3.400
peak=    3.370 closest distance to " NZ  LYS A 117 " =    3.139
peak=    3.370 closest distance to " CD  LYS A  76 " =    1.895
peak=    3.369 closest distance to " CB  LEU A 143 " =    1.210
peak=    3.367 closest distance to " O   HOH Z 409 " =    2.622
peak=    3.367 closest distance to " CA  LEU A 282 " =    1.055
peak=    3.366 closest distance to " O   HOH Z 218 " =    1.433
peak=    3.365 closest distance to " O   TYR A 116 " =    1.224
peak=    3.364 closest distance to " CA  TYR A 186 " =    1.563
peak=    3.362 closest distance to " O   HOH Z 248 " =    1.701
peak=    3.360 closest distance to " O   HOH Z   1 " =    1.868
peak=    3.359 closest distance to " CB  ALA A   1 " =    4.866
peak=    3.358 closest distance to " CA  ALA A 158 " =    1.253
peak=    3.355 closest distance to " CB  LYS A 117 " =    1.229
peak=    3.349 closest distance to " N   ASN A 127 " =    1.293
peak=    3.346 closest distance to " CE  LYS A  48 " =    1.182
peak=    3.345 closest distance to " CA  ASN A  74 " =    1.351
peak=    3.345 closest distance to " CE3 TRP A  85 " =    1.111
peak=    3.344 closest distance to " CE3 TRP A 150 " =    1.091
peak=    3.343 closest distance to " O   HOH Z  59 " =    1.949
peak=    3.341 closest distance to " CA  ALA A 295 " =    1.153
peak=    3.339 closest distance to " O   PHE A 192 " =    1.405
peak=    3.337 closest distance to " O   HOH Z  80 " =    1.558
peak=    3.331 closest distance to " O   HOH Z 421 " =    2.213
peak=    3.326 closest distance to " OG  SER A  62 " =    2.832
peak=    3.324 closest distance to " CG  ARG A 159 " =    0.983
peak=    3.323 closest distance to " O   HOH Z 285 " =    2.229
peak=    3.321 closest distance to " O   HOH Z 147 " =    1.678
peak=    3.320 closest distance to " CD  ARG A 195 " =    3.536
peak=    3.320 closest distance to " CA  ASN A 215 " =    1.172
peak=    3.309 closest distance to " CA  ARG A 159 " =    1.219
peak=    3.308 closest distance to " O   HOH Z 371 " =    2.935
peak=    3.306 closest distance to " NE2 HIS A 207 " =    1.130
peak=    3.305 closest distance to " CG  MET A 185 " =    1.233
peak=    3.304 closest distance to " CB  ALA A   9 " =    1.627
peak=    3.303 closest distance to " O   ASP A 191 " =    1.503
peak=    3.300 closest distance to " O   HOH Z 148 " =    3.581
peak=    3.294 closest distance to " CA  ILE A 263 " =    1.002
peak=    3.287 closest distance to " CB  HIS A 108 " =    0.853
peak=    3.287 closest distance to " O   HOH Z 368 " =    4.067
peak=    3.285 closest distance to " CA  ARG A 139 " =    1.025
peak=    3.284 closest distance to " O   HOH Z 403 " =    1.571
peak=    3.282 closest distance to " O   HOH Z 280 " =    3.090
peak=    3.282 closest distance to " O   HOH Z 281 " =    2.553
peak=    3.277 closest distance to " O   HOH Z  61 " =    1.553
peak=    3.277 closest distance to " O   HOH Z 325 " =    2.252
peak=    3.277 closest distance to " CE3 TRP A 274 " =    1.300
peak=    3.275 closest distance to " OG1 THR A 279 " =    1.464
peak=    3.273 closest distance to " CD1 LEU A 101 " =    1.179
peak=    3.271 closest distance to " CB  TYR A 116 " =    0.888
peak=    3.270 closest distance to " O   HOH Z 261 " =    1.543
peak=    3.263 closest distance to " O   HOH Z 368 " =    3.530
peak=    3.258 closest distance to " CB  ALA A 242 " =    1.036
peak=    3.258 closest distance to " O   HOH Z 389 " =    1.839
peak=    3.253 closest distance to " O   HOH Z   4 " =    1.517
peak=    3.251 closest distance to " CD2 TYR A 186 " =    1.158
peak=    3.251 closest distance to " CG1 ILE A  49 " =    1.590
peak=    3.250 closest distance to " CA  ALA A 184 " =    1.157
peak=    3.250 closest distance to " O   HOH Z 394 " =    3.942
peak=    3.249 closest distance to " OG1 THR A 264 " =    0.786
peak=    3.244 closest distance to " CB  ALA A 248 " =    1.046
peak=    3.241 closest distance to " CA  GLN A  94 " =    0.739
peak=    3.240 closest distance to " O   HOH Z  88 " =    3.375
peak=    3.239 closest distance to " CB  VAL A 268 " =    0.862
peak=    3.236 closest distance to " O   HOH Z 175 " =    3.733
peak=    3.234 closest distance to " O   ALA A 291 " =    1.636
peak=    3.233 closest distance to " CG  LYS A 119 " =    1.126
peak=    3.231 closest distance to " O   HOH Z 145 " =    1.660
peak=    3.229 closest distance to " O   HOH Z 124 " =    1.945
peak=    3.223 closest distance to " O   HOH Z 166 " =    3.821
peak=    3.222 closest distance to " O   HOH Z 130 " =    1.989
peak=    3.219 closest distance to " CB  ALA A 104 " =    0.788
peak=    3.219 closest distance to " CD2 LEU A 255 " =    1.626
peak=    3.218 closest distance to " CE  MET A  93 " =    1.555
peak=    3.216 closest distance to " CB  THR A  52 " =    0.829
peak=    3.213 closest distance to " O   HOH Z 196 " =    1.144
peak=    3.210 closest distance to " OG BSER A 134 " =    2.912
peak=    3.208 closest distance to " C   ALA A 299 " =    0.949
peak=    3.206 closest distance to " O  BHOH Z 338 " =    2.456
peak=    3.202 closest distance to " O   HOH Z 305 " =    3.342
peak=    3.200 closest distance to " O   HOH Z 238 " =    3.091
peak=    3.193 closest distance to " CA  ALA A  21 " =    1.244
peak=    3.193 closest distance to " CA  THR A 221 " =    0.949
peak=    3.191 closest distance to " O   HOH Z 197 " =    3.271
peak=    3.189 closest distance to " O   HOH Z  68 " =    2.141
peak=    3.188 closest distance to " CB  LEU A 300 " =    0.866
peak=    3.187 closest distance to " CD2 LEU A 297 " =    0.920
peak=    3.186 closest distance to " O   HOH Z 222 " =    2.076
peak=    3.180 closest distance to " O   HOH Z 171 " =    4.270
peak=    3.178 closest distance to " CA  ASN A 217 " =    1.277
peak=    3.176 closest distance to " CA  THR A 264 " =    0.800
peak=    3.176 closest distance to " O   ASN A  74 " =    1.447
peak=    3.174 closest distance to " CA  ILE A 106 " =    0.804
peak=    3.171 closest distance to " O   HOH Z 222 " =    2.326
peak=    3.170 closest distance to " O   HOH Z 294 " =    1.506
peak=    3.167 closest distance to " CG2 ILE A 151 " =    0.891
peak=    3.166 closest distance to " O   HOH Z 172 " =    3.047
peak=    3.162 closest distance to " CD1 ILE A 199 " =    0.952
peak=    3.150 closest distance to " CB  ILE A 120 " =    1.390
peak=    3.148 closest distance to " NZ  LYS A  48 " =    1.357
peak=    3.147 closest distance to " O   HOH Z  57 " =    1.210
peak=    3.142 closest distance to " O   HOH Z 352 " =    1.805
peak=    3.140 closest distance to " CB  SER A  62 " =    1.017
peak=    3.139 closest distance to " O   HOH Z 218 " =    1.943
peak=    3.139 closest distance to " CB  ASN A 187 " =    1.100
peak=    3.133 closest distance to " O   HOH Z 110 " =    1.642
peak=    3.133 closest distance to " CB  SER A  26 " =    1.806
peak=    3.129 closest distance to " CA  LYS A 290 " =    1.327
peak=    3.127 closest distance to " O   HOH Z 176 " =    1.699
peak=    3.125 closest distance to " CB  ALA A 160 " =    1.501
peak=    3.124 closest distance to " CD  ARG A 195 " =    1.015
peak=    3.123 closest distance to " O   HOH Z 153 " =    3.782
peak=    3.123 closest distance to " O   ASN A 284 " =    1.819
peak=    3.118 closest distance to " NH2AARG A 145 " =    1.185
peak=    3.114 closest distance to " CA  ALA A 154 " =    1.096
peak=    3.104 closest distance to " CB  LEU A 261 " =    0.787
peak=    3.103 closest distance to " CB  ALA A  43 " =    0.824
peak=    3.101 closest distance to " O   HOH Z  85 " =    2.106
peak=    3.095 closest distance to " N   SER A  12 " =    1.569
peak=    3.087 closest distance to " O   PHE A  61 " =    1.417
peak=    3.084 closest distance to " CG1 ILE A  33 " =    1.263
peak=    3.076 closest distance to " CA  TYR A  30 " =    1.085
peak=    3.074 closest distance to " CB  THR A  31 " =    1.525
peak=    3.070 closest distance to " CB  LEU A  83 " =    0.720
peak=    3.066 closest distance to " CA  ALA A 129 " =    1.381
peak=    3.066 closest distance to " CB  TRP A 150 " =    1.178
peak=    3.057 closest distance to " O   HOH Z 173 " =    1.740
peak=    3.052 closest distance to " O   THR A 294 " =    1.048
peak=    3.052 closest distance to " O   PRO A  90 " =    1.656
peak=    3.052 closest distance to " CB  LEU A  96 " =    1.454
peak=    3.050 closest distance to " O   HOH Z 213 " =    3.250
peak=    3.042 closest distance to " O   HOH Z 216 " =    3.610
peak=    3.012 closest distance to " OG ASER A 212 " =    1.849

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.482 - 5.547
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 215
   mapped sites are within: 0.826 - 5.547

peak=   -4.813 closest distance to " CG2 VAL A 230 " =    0.826
peak=   -4.271 closest distance to " CZ2 TRP A  92 " =    2.859
peak=   -4.254 closest distance to " OG BSER A 134 " =    1.490
peak=   -4.215 closest distance to " CD  ARG A 156 " =    2.096
peak=   -4.207 closest distance to " CD  ARG A  14 " =    3.282
peak=   -4.169 closest distance to " O   HOH Z 231 " =    1.904
peak=   -4.143 closest distance to " O   HOH Z 162 " =    2.621
peak=   -4.136 closest distance to " CG1 VAL A 112 " =    2.663
peak=   -4.082 closest distance to " CD  ARG A 138 " =    1.202
peak=   -4.074 closest distance to " CD1 LEU A 101 " =    2.361
peak=   -4.009 closest distance to " O   HOH Z 231 " =    0.840
peak=   -3.991 closest distance to " CB  VAL A 230 " =    1.188
peak=   -3.970 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.969 closest distance to " CG2 THR A 178 " =    2.385
peak=   -3.963 closest distance to " O   HOH Z 103 " =    1.372
peak=   -3.957 closest distance to " O   HOH Z  52 " =    1.490
peak=   -3.948 closest distance to " CB  ASP A  27 " =    2.453
peak=   -3.888 closest distance to " CG1 VAL A 250 " =    2.669
peak=   -3.886 closest distance to " CG  GLN A 223 " =    2.398
peak=   -3.882 closest distance to " CG2 VAL A 202 " =    2.720
peak=   -3.872 closest distance to " OG  SER A  97 " =    2.349
peak=   -3.868 closest distance to " CB  ALA A  43 " =    2.653
peak=   -3.863 closest distance to " CG2 VAL A 296 " =    1.139
peak=   -3.839 closest distance to " CB  PRO A 163 " =    2.405
peak=   -3.819 closest distance to " CG  ARG A 138 " =    0.866
peak=   -3.788 closest distance to " O   HOH Z 359 " =    3.066
peak=   -3.781 closest distance to " O   HOH Z 166 " =    2.296
peak=   -3.778 closest distance to " O   GLY A 203 " =    2.469
peak=   -3.768 closest distance to " O   HOH Z 131 " =    4.084
peak=   -3.766 closest distance to " CG2AVAL A  41 " =    2.891
peak=   -3.754 closest distance to " CA  GLY A 241 " =    2.348
peak=   -3.737 closest distance to " OE1 GLN A  88 " =    0.991
peak=   -3.734 closest distance to " O   HOH Z 411 " =    5.282
peak=   -3.728 closest distance to " O   PRO A 163 " =    1.991
peak=   -3.723 closest distance to " O   HOH Z 275 " =    1.889
peak=   -3.707 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -3.705 closest distance to " CG2BVAL A  41 " =    2.374
peak=   -3.700 closest distance to " CG1 VAL A 112 " =    3.095
peak=   -3.696 closest distance to " O   HOH Z 216 " =    1.144
peak=   -3.686 closest distance to " O   HOH Z 394 " =    1.551
peak=   -3.677 closest distance to " O   GLY A  17 " =    1.213
peak=   -3.671 closest distance to " O   HOH Z  73 " =    2.114
peak=   -3.660 closest distance to " O   HOH Z 377 " =    1.924
peak=   -3.645 closest distance to " O   HOH Z 389 " =    2.105
peak=   -3.633 closest distance to " CB  TRP A  85 " =    2.535
peak=   -3.623 closest distance to " O   HOH Z 108 " =    1.330
peak=   -3.623 closest distance to " O   HOH Z 183 " =    1.368
peak=   -3.623 closest distance to " CE3 TRP A 150 " =    2.418
peak=   -3.619 closest distance to " CD2 LEU A   5 " =    1.022
peak=   -3.618 closest distance to " OG  SER A  87 " =    1.337
peak=   -3.607 closest distance to " O   HOH Z 290 " =    1.289
peak=   -3.601 closest distance to " CA  ALA A 158 " =    1.325
peak=   -3.598 closest distance to " N   THR A 157 " =    1.531
peak=   -3.592 closest distance to " CG  TRP A 266 " =    1.770
peak=   -3.584 closest distance to " CD  GLN A  58 " =    0.949
peak=   -3.583 closest distance to " CA  GLY A 241 " =    3.147
peak=   -3.582 closest distance to " O   HOH Z 295 " =    1.573
peak=   -3.582 closest distance to " C   LEU A 222 " =    0.996
peak=   -3.579 closest distance to " O   HOH Z 351 " =    1.601
peak=   -3.568 closest distance to " O   HOH Z  43 " =    1.704
peak=   -3.566 closest distance to " OD1 ASP A 171 " =    1.677
peak=   -3.566 closest distance to " O   HOH Z  38 " =    1.638
peak=   -3.563 closest distance to " O   HOH Z 147 " =    2.018
peak=   -3.550 closest distance to " O   HOH Z 429 " =    1.955
peak=   -3.546 closest distance to " CA  GLY A  98 " =    1.966
peak=   -3.546 closest distance to " ND2 ASN A  60 " =    1.590
peak=   -3.541 closest distance to " CD1 LEU A 255 " =    2.943
peak=   -3.535 closest distance to " CB  PHE A 130 " =    1.286
peak=   -3.534 closest distance to " O   HOH Z  65 " =    1.338
peak=   -3.518 closest distance to " CD1 LEU A 228 " =    2.426
peak=   -3.517 closest distance to " N   ALA A  43 " =    2.766
peak=   -3.513 closest distance to " O   HOH Z 185 " =    2.277
peak=   -3.512 closest distance to " O   HOH Z 111 " =    1.741
peak=   -3.510 closest distance to " ND2 ASN A 187 " =    1.455
peak=   -3.506 closest distance to " O   ASP A  27 " =    1.805
peak=   -3.499 closest distance to " CB  ALA A 161 " =    2.578
peak=   -3.495 closest distance to " CD2 LEU A 237 " =    2.869
peak=   -3.488 closest distance to " O   HOH Z 412 " =    4.476
peak=   -3.477 closest distance to " O   VAL A 189 " =    2.628
peak=   -3.475 closest distance to " N   ALA A 226 " =    2.023
peak=   -3.474 closest distance to " C   ASN A 285 " =    2.445
peak=   -3.450 closest distance to " O   HOH Z 144 " =    1.313
peak=   -3.450 closest distance to " CG2 ILE A 263 " =    2.496
peak=   -3.440 closest distance to " CZ3 TRP A 179 " =    1.179
peak=   -3.437 closest distance to " O   HOH Z 350 " =    1.674
peak=   -3.434 closest distance to " NH2AARG A 275 " =    5.480
peak=   -3.434 closest distance to " O   HOH Z  63 " =    1.809
peak=   -3.433 closest distance to " O   HOH Z 368 " =    1.696
peak=   -3.425 closest distance to " CB  PHE A 192 " =    1.852
peak=   -3.424 closest distance to " O   ILE A  49 " =    1.717
peak=   -3.424 closest distance to " CD  GLN A  88 " =    0.860
peak=   -3.422 closest distance to " C   HIS A 108 " =    1.185
peak=   -3.416 closest distance to " O   PHE A 218 " =    1.522
peak=   -3.409 closest distance to " CE BMET A  47 " =    1.351
peak=   -3.409 closest distance to " OG  SER A  62 " =    4.489
peak=   -3.406 closest distance to " O   HOH Z  11 " =    1.841
peak=   -3.404 closest distance to " CA  GLY A 133 " =    2.232
peak=   -3.401 closest distance to " O   HOH Z   9 " =    1.743
peak=   -3.375 closest distance to " CD2 HIS A 207 " =    2.310
peak=   -3.373 closest distance to " CG  MET A 105 " =    1.001
peak=   -3.372 closest distance to " O   HOH Z 145 " =    1.451
peak=   -3.371 closest distance to " CG2 ILE A 151 " =    2.623
peak=   -3.367 closest distance to " O   HOH Z 389 " =    1.566
peak=   -3.365 closest distance to " O   SER A  22 " =    2.521
peak=   -3.360 closest distance to " CD  LYS A 289 " =    2.360
peak=   -3.359 closest distance to " O   HOH Z 281 " =    2.736
peak=   -3.359 closest distance to " C   LYS A  76 " =    1.485
peak=   -3.353 closest distance to " O   HOH Z 426 " =    1.707
peak=   -3.345 closest distance to " CG1 VAL A 296 " =    1.479
peak=   -3.345 closest distance to " CD2 TYR A 293 " =    1.984
peak=   -3.345 closest distance to " C   GLU A 236 " =    0.899
peak=   -3.344 closest distance to " CD2 TYR A 247 " =    2.458
peak=   -3.340 closest distance to " CG  GLU A 277 " =    1.266
peak=   -3.337 closest distance to " CA  ASP A 298 " =    1.112
peak=   -3.337 closest distance to " CE2 TRP A  70 " =    2.388
peak=   -3.331 closest distance to " O   GLN A 240 " =    2.555
peak=   -3.316 closest distance to " CZ2 TRP A 274 " =    0.917
peak=   -3.315 closest distance to " O   HOH Z 102 " =    1.511
peak=   -3.313 closest distance to " CD1 ILE A  33 " =    2.568
peak=   -3.311 closest distance to " SD  MET A 188 " =    2.369
peak=   -3.308 closest distance to " OG  SER A  28 " =    2.182
peak=   -3.307 closest distance to " CB  TYR A  15 " =    2.261
peak=   -3.307 closest distance to " O   HOH Z 251 " =    4.899
peak=   -3.306 closest distance to " CA  SER A  62 " =    2.652
peak=   -3.303 closest distance to " O   HOH Z  60 " =    2.401
peak=   -3.288 closest distance to " O   HOH Z 198 " =    2.098
peak=   -3.287 closest distance to " OH  TYR A 214 " =    1.122
peak=   -3.284 closest distance to " CG  PRO A 163 " =    2.392
peak=   -3.283 closest distance to " CB  ALA A 227 " =    2.448
peak=   -3.283 closest distance to " O   SER A 271 " =    2.190
peak=   -3.282 closest distance to " O   HOH Z 140 " =    1.415
peak=   -3.280 closest distance to " CD  PRO A 243 " =    1.929
peak=   -3.279 closest distance to " CZ  PHE A 130 " =    1.094
peak=   -3.276 closest distance to " O   HOH Z 166 " =    1.354
peak=   -3.276 closest distance to " O   HOH Z 357 " =    2.020
peak=   -3.266 closest distance to " CB  ASP A 132 " =    2.374
peak=   -3.265 closest distance to " CA  VAL A  67 " =    2.856
peak=   -3.263 closest distance to " O   HOH Z 364 " =    2.768
peak=   -3.260 closest distance to " ND2 ASN A 249 " =    2.437
peak=   -3.260 closest distance to " O   HOH Z 112 " =    1.297
peak=   -3.259 closest distance to " CE2 PHE A 218 " =    2.524
peak=   -3.256 closest distance to " O   HOH Z 313 " =    1.445
peak=   -3.256 closest distance to " C   LEU A 143 " =    1.156
peak=   -3.254 closest distance to " OH  TYR A 172 " =    1.748
peak=   -3.251 closest distance to " O   HOH Z 359 " =    1.586
peak=   -3.251 closest distance to " O   GLY A  80 " =    2.550
peak=   -3.248 closest distance to " CA  GLY A 203 " =    2.561
peak=   -3.238 closest distance to " NH2 ARG A 219 " =    1.719
peak=   -3.237 closest distance to " C   MET A 188 " =    1.470
peak=   -3.234 closest distance to " O   HOH Z 118 " =    1.240
peak=   -3.232 closest distance to " O   HOH Z 166 " =    2.052
peak=   -3.231 closest distance to " CG1 VAL A 257 " =    2.410
peak=   -3.227 closest distance to " CD2 PHE A 225 " =    1.128
peak=   -3.227 closest distance to " OG  SER A 141 " =    1.770
peak=   -3.227 closest distance to " O   HOH Z 292 " =    1.654
peak=   -3.227 closest distance to " CD1 ILE A 199 " =    2.579
peak=   -3.224 closest distance to " O   HOH Z  60 " =    1.750
peak=   -3.219 closest distance to " N   ASP A 270 " =    1.549
peak=   -3.211 closest distance to " CB  HIS A  81 " =    1.002
peak=   -3.206 closest distance to " C   ASN A 148 " =    1.663
peak=   -3.204 closest distance to " O   HOH Z 201 " =    1.678
peak=   -3.200 closest distance to " CD  LYS A 166 " =    2.665
peak=   -3.197 closest distance to " OG BSER A 134 " =    1.866
peak=   -3.196 closest distance to " O   ALA A  10 " =    1.696
peak=   -3.190 closest distance to " O   HOH Z 353 " =    1.991
peak=   -3.190 closest distance to " OG ASER A 134 " =    1.249
peak=   -3.190 closest distance to " CB  HIS A  86 " =    1.118
peak=   -3.188 closest distance to " CG2 THR A 178 " =    2.259
peak=   -3.188 closest distance to " CE3 TRP A  70 " =    1.702
peak=   -3.188 closest distance to " CB  ALA A   9 " =    2.508
peak=   -3.184 closest distance to " OH  TYR A 247 " =    1.842
peak=   -3.182 closest distance to " ND2 ASN A  45 " =    2.374
peak=   -3.176 closest distance to " NE2 GLN A 194 " =    1.917
peak=   -3.168 closest distance to " CG  LEU A 282 " =    2.349
peak=   -3.166 closest distance to " CD  PRO A 213 " =    2.079
peak=   -3.164 closest distance to " O   HOH Z 191 " =    5.547
peak=   -3.160 closest distance to " O   ARG A 145 " =    1.421
peak=   -3.160 closest distance to " CG  PHE A 283 " =    2.731
peak=   -3.159 closest distance to " O   HOH Z 106 " =    1.895
peak=   -3.159 closest distance to " CE1 PHE A  59 " =    2.032
peak=   -3.158 closest distance to " OG  SER A 206 " =    1.841
peak=   -3.156 closest distance to " O   HOH Z 250 " =    1.704
peak=   -3.151 closest distance to " CG  GLN A 278 " =    2.208
peak=   -3.144 closest distance to " O   HOH Z 252 " =    3.699
peak=   -3.140 closest distance to " O   SER A 276 " =    1.631
peak=   -3.139 closest distance to " N   LYS A 166 " =    1.837
peak=   -3.130 closest distance to " O   HOH Z  10 " =    1.589
peak=   -3.122 closest distance to " O   SER A 210 " =    1.859
peak=   -3.120 closest distance to " O   HOH Z 118 " =    1.545
peak=   -3.120 closest distance to " NE2 GLN A 240 " =    1.616
peak=   -3.117 closest distance to " O   HOH Z 407 " =    3.079
peak=   -3.114 closest distance to " CB  PRO A  54 " =    2.557
peak=   -3.113 closest distance to " O   HOH Z   9 " =    3.220
peak=   -3.112 closest distance to " O   HOH Z 189 " =    2.591
peak=   -3.110 closest distance to " OG  SER A 245 " =    1.292
peak=   -3.109 closest distance to " CB  ALA A 248 " =    2.345
peak=   -3.103 closest distance to " O   HOH Z 111 " =    4.743
peak=   -3.099 closest distance to " O   ALA A  51 " =    1.410
peak=   -3.092 closest distance to " CB  ALA A 291 " =    1.982
peak=   -3.092 closest distance to " N   ASP A 191 " =    1.097
peak=   -3.091 closest distance to " CD1 PHE A  61 " =    2.984
peak=   -3.090 closest distance to " CB  ALA A 129 " =    2.548
peak=   -3.086 closest distance to " CG  PRO A 163 " =    2.168
peak=   -3.081 closest distance to " O   HOH Z  51 " =    1.106
peak=   -3.074 closest distance to " O   HOH Z  32 " =    1.901
peak=   -3.073 closest distance to " N   ALA A 248 " =    1.615
peak=   -3.067 closest distance to " CB  GLU A 277 " =    2.920
peak=   -3.058 closest distance to " SD BMET A  47 " =    1.095
peak=   -3.053 closest distance to " OE1 GLN A  89 " =    1.936
peak=   -3.049 closest distance to " O   HOH Z  44 " =    1.073
peak=   -3.047 closest distance to " N   VAL A 125 " =    0.971
peak=   -3.036 closest distance to " N   SER A 276 " =    1.425
peak=   -3.029 closest distance to " O   TRP A  70 " =    1.491

================= 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    :  0.4849 0.4718   6.285295e+00   6.266086e+00
   1_bss:  0.4770 0.4626   6.280771e+00   6.260874e+00
   1_xyz:  0.3939 0.4136   6.168032e+00   6.192495e+00
   1_adp:  0.3460 0.3991   6.085657e+00   6.169065e+00
   1_occ:  0.3456 0.3993   6.085043e+00   6.169802e+00
   2_bss:  0.3425 0.3942   6.084913e+00   6.166985e+00
   2_xyz:  0.2556 0.3121   5.850305e+00   5.998936e+00
   2_adp:  0.2325 0.2868   5.771063e+00   5.930405e+00
   2_occ:  0.2322 0.2867   5.770615e+00   5.930109e+00
   3_bss:  0.2307 0.2857   5.772503e+00   5.931682e+00
   3_xyz:  0.1764 0.2289   5.535605e+00   5.732686e+00
   3_adp:  0.1629 0.2157   5.472523e+00   5.681618e+00
   3_occ:  0.1628 0.2158   5.472226e+00   5.681518e+00
   4_bss:  0.1626 0.2156   5.472599e+00   5.681612e+00
   4_xyz:  0.1362 0.1888   5.326241e+00   5.552185e+00
   4_adp:  0.1327 0.1818   5.294901e+00   5.513754e+00
   4_occ:  0.1326 0.1817   5.294373e+00   5.513042e+00
   5_bss:  0.1328 0.1817   5.294721e+00   5.512597e+00
   5_xyz:  0.1218 0.1697   5.223038e+00   5.454679e+00
   5_adp:  0.1196 0.1684   5.210894e+00   5.450036e+00
   5_occ:  0.1195 0.1683   5.210671e+00   5.449839e+00
   5_bss:  0.1195 0.1683   5.210668e+00   5.449906e+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:  0.325  20.001   7.884   7.637  10.770   0.000   0.000   0.000
   1_xyz:  0.325  20.001   7.884   7.637  10.770   0.000   0.000   0.000
   1_adp:  0.325  20.001   7.884   7.637  10.770   0.000   0.000   0.000
   1_occ:  0.325  20.001   7.884   7.637  10.770   0.000   0.000   0.000
   2_bss:  0.332  50.001   4.780   4.229   7.311   0.000   0.000   0.000
   2_xyz:  0.332  50.001   4.780   4.229   7.311   0.000   0.000   0.000
   2_adp:  0.332  50.001   4.780   4.229   7.311   0.000   0.000   0.000
   2_occ:  0.332  50.001   4.780   4.229   7.311   0.000   0.000   0.000
   3_bss:  0.320  59.152   2.715   2.287   4.731   0.000   0.000   0.000
   3_xyz:  0.320  59.152   2.715   2.287   4.731   0.000   0.000   0.000
   3_adp:  0.320  59.152   2.715   2.287   4.731   0.000   0.000   0.000
   3_occ:  0.320  59.152   2.715   2.287   4.731   0.000   0.000   0.000
   4_bss:  0.330  67.849   1.995   1.673   3.844   0.000   0.000   0.000
   4_xyz:  0.330  67.849   1.995   1.673   3.844   0.000   0.000   0.000
   4_adp:  0.330  67.849   1.995   1.673   3.844   0.000   0.000   0.000
   4_occ:  0.330  67.849   1.995   1.673   3.844   0.000   0.000   0.000
   5_bss:  0.327  64.023   1.836   1.517   3.516   0.000   0.000   0.000
   5_xyz:  0.327  64.023   1.836   1.517   3.516   0.000   0.000   0.000
   5_adp:  0.327  64.023   1.836   1.517   3.516   0.000   0.000   0.000
   5_occ:  0.327  64.023   1.836   1.517   3.516   0.000   0.000   0.000
   5_bss:  0.320  61.978  -0.409  -0.767   1.176  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.554 0.4378  0.5085    67970.251
   1_bss:  56.557 0.4369  0.6574    66939.564
   1_xyz:  47.639 0.5485  0.7995    49500.636
   1_adp:  44.105 0.5927  0.9096    45190.519
   1_occ:  44.161 0.5919  0.9076    45282.292
   2_bss:  43.838 0.5957  0.8142    44669.632
   2_xyz:  33.000 0.7231  0.9541    26567.717
   2_adp:  29.522 0.7630  0.9804    22099.862
   2_occ:  29.527 0.7628  0.9791    22053.531
   3_bss:  29.539 0.7629  0.9068    22172.787
   3_xyz:  22.286 0.8390  0.9739    13366.720
   3_adp:  20.771 0.8543  0.9814    11954.252
   3_occ:  20.774 0.8542  0.9812    11940.015
   4_bss:  20.779 0.8542  0.9560    11963.356
   4_xyz:  17.777 0.8823  0.9695     9088.201
   4_adp:  16.816 0.8914  0.9687     8460.218
   4_occ:  16.805 0.8915  0.9686     8443.493
   5_bss:  16.797 0.8915  0.9613     8436.712
   5_xyz:  15.430 0.9034  0.9692     7381.554
   5_adp:  15.258 0.9049  0.9658     7264.705
   5_occ:  15.256 0.9050  0.9658     7260.342
   5_bss:  15.259 0.9049  0.9686     7261.053
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4285e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4285e+01
   1_xyz:   1.726  0.014  0.110 18.284  0.006  4.110   1.4553e-01
   1_adp:   1.726  0.014  0.110 18.284  0.006  4.110   1.4553e-01
   1_occ:   1.726  0.014  0.110 18.284  0.006  4.110   1.4553e-01
   2_bss:   1.726  0.014  0.110 18.284  0.006  4.110   1.4553e-01
   2_xyz:   1.129  0.008  0.080 16.427  0.005  4.110   7.8289e-02
   2_adp:   1.129  0.008  0.080 16.427  0.005  4.110   7.8289e-02
   2_occ:   1.129  0.008  0.080 16.427  0.005  4.110   7.8289e-02
   3_bss:   1.129  0.008  0.080 16.427  0.005  4.110   7.8289e-02
   3_xyz:   1.003  0.007  0.076 15.722  0.003  4.127   6.0164e-02
   3_adp:   1.003  0.007  0.076 15.722  0.003  4.127   6.0164e-02
   3_occ:   1.003  0.007  0.076 15.722  0.003  4.127   6.0164e-02
   4_bss:   1.003  0.007  0.076 15.722  0.003  4.127   6.0164e-02
   4_xyz:   1.022  0.008  0.078 15.559  0.003  4.138   6.4112e-02
   4_adp:   1.022  0.008  0.078 15.559  0.003  4.138   6.4112e-02
   4_occ:   1.022  0.008  0.078 15.559  0.003  4.138   6.4112e-02
   5_bss:   1.022  0.008  0.078 15.559  0.003  4.138   6.4112e-02
   5_xyz:   1.112  0.010  0.086 15.604  0.004  4.115   7.5216e-02
   5_adp:   1.112  0.010  0.086 15.604  0.004  4.115   7.5216e-02
   5_occ:   1.112  0.010  0.086 15.604  0.004  4.115   7.5216e-02
   5_bss:   1.112  0.010  0.086 15.604  0.004  4.115   7.5216e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0383e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0383e+00
   1_xyz:  14.397  0.176  0.437 85.418  0.038  2.248   1.0615e-01
   1_adp:  14.397  0.176  0.437 85.418  0.038  2.248   1.0615e-01
   1_occ:  14.397  0.176  0.437 85.418  0.038  2.248   1.0615e-01
   2_bss:  14.397  0.176  0.437 85.418  0.038  2.248   1.0615e-01
   2_xyz:   6.492  0.065  0.272 86.853  0.045  2.200   6.9515e-02
   2_adp:   6.492  0.065  0.272 86.853  0.045  2.200   6.9515e-02
   2_occ:   6.492  0.065  0.272 86.853  0.045  2.200   6.9515e-02
   3_bss:   6.492  0.065  0.272 86.853  0.045  2.200   6.9515e-02
   3_xyz:   8.064  0.045  0.333 85.424  0.029  2.365   4.1634e-02
   3_adp:   8.064  0.045  0.333 85.424  0.029  2.365   4.1634e-02
   3_occ:   8.064  0.045  0.333 85.424  0.029  2.365   4.1634e-02
   4_bss:   8.064  0.045  0.333 85.424  0.029  2.365   4.1634e-02
   4_xyz:   8.092  0.057  0.349 82.744  0.035  2.380   5.1009e-02
   4_adp:   8.092  0.057  0.349 82.744  0.035  2.380   5.1009e-02
   4_occ:   8.092  0.057  0.349 82.744  0.035  2.380   5.1009e-02
   5_bss:   8.092  0.057  0.349 82.744  0.035  2.380   5.1009e-02
   5_xyz:   9.275  0.073  0.488 83.269  0.038  2.331   4.8080e-02
   5_adp:   9.275  0.073  0.488 83.269  0.038  2.331   4.8080e-02
   5_occ:   9.275  0.073  0.488 83.269  0.038  2.331   4.8080e-02
   5_bss:   9.275  0.073  0.488 83.269  0.038  2.331   4.8080e-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:  85.78   0.00  13.87  69.26   0.00  11.32  85.78   0.00  27.76
   1_occ:  85.78   0.00  13.87  69.26   0.00  11.32  85.78   0.00  27.76
   2_bss:  85.78   0.00  13.87  69.26   0.00  11.32  85.78   0.00  27.76
   2_xyz:  85.78   0.00  13.87  69.26   0.00  11.32  85.78   0.00  27.76
   2_adp:  87.71   0.00  13.21  68.45   0.00   9.50  87.71   0.00  33.41
   2_occ:  87.71   0.00  13.21  68.45   0.00   9.50  87.71   0.00  33.41
   3_bss:  87.71   0.00  13.21  68.45   0.00   9.50  87.71   0.00  33.41
   3_xyz:  87.71   0.00  13.21  68.45   0.00   9.50  87.71   0.00  33.41
   3_adp:  86.30   0.00  13.95  74.89   0.00   9.34  86.30   0.91  39.06
   3_occ:  86.30   0.00  13.95  74.89   0.00   9.34  86.30   0.91  39.06
   4_bss:  86.30   0.00  13.95  74.89   0.00   9.34  86.30   0.91  39.06
   4_xyz:  86.30   0.00  13.95  74.89   0.00   9.34  86.30   0.91  39.06
   4_adp:  85.94   0.00  13.47  74.10   0.00   8.93  85.94   2.01  38.20
   4_occ:  85.94   0.00  13.47  74.10   0.00   8.93  85.94   2.01  38.20
   5_bss:  85.94   0.00  13.47  74.10   0.00   8.93  85.94   2.01  38.20
   5_xyz:  85.94   0.00  13.47  74.10   0.00   8.93  85.94   2.01  38.20
   5_adp:  90.99   0.00  13.47  76.59   0.00   8.89  90.99   2.21  38.41
   5_occ:  90.99   0.00  13.47  76.59   0.00   8.89  90.99   2.21  38.41
   5_bss:  93.37   2.38  15.85  78.97   2.38  11.27  93.37   4.59  40.78
------------------------------------------------------------------------
 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:    1.255    0.003    0.412
   1_adp:    1.255    0.003    0.412
   1_occ:    1.255    0.003    0.412
   2_bss:    1.255    0.003    0.412
   2_xyz:    1.660    0.025    0.571
   2_adp:    1.660    0.025    0.571
   2_occ:    1.660    0.025    0.571
   3_bss:    1.660    0.025    0.571
   3_xyz:    1.572    0.045    0.644
   3_adp:    1.572    0.045    0.644
   3_occ:    1.572    0.045    0.644
   4_bss:    1.572    0.045    0.644
   4_xyz:    1.761    0.028    0.697
   4_adp:    1.761    0.028    0.697
   4_occ:    1.761    0.028    0.697
   5_bss:    1.761    0.028    0.697
   5_xyz:    1.776    0.036    0.719
   5_adp:    1.776    0.036    0.719
   5_occ:    1.776    0.036    0.719
   5_bss:    1.776    0.036    0.719
------------------------------------------------------------------------

CPU time actual refinement: 321.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1010/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_1010/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1010/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1010/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1010/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.65 
  Macro-tasks:
    bulk solvent and scale       = 41.95  
    individual site refinement   = 129.56 
    weights calculation          = 31.98  
    collect and process          = 6.42   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.03 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 96.47  
    alpha_beta                      = 8.07   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 106.55 
    fmodel                         = 7.07   
    r_factors                      = 0.28   
    phase_errors                   = 10.26  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 232.46 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.584 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    623 calls, 96.05 s
gradients_fft:          568 calls, 93.72 s

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

# Date 2008-01-16 Time 02:57:51 PST -0800 (1200481071.86 s)
Start R-work = 0.4849, R-free = 0.4718 (no bulk solvent and anisotropic scale)
Final R-work = 0.1365, R-free = 0.1849 (no bulk solvent and anisotropic scale)

Start R-work = 0.4770, R-free = 0.4626
Final R-work = 0.1195, R-free = 0.1683