# Date 2008-01-16 Time 03:07:00 PST -0800 (1200481620.24 s)
#phil __OFF__

Command line arguments: "../1104.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5313
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1104

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 45.9914, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.96392
Completeness in resolution range: 0.938395
Completeness with d_max=infinity: 0.935706

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9639

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.96392
Completeness in resolution range: 0.938395
Completeness with d_max=infinity: 0.935706

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2040 [2193/2220]  1976   217   9.9%
  bin  2:  4.2040 -  3.3486 [2104/2124]  1892   212  10.1%
  bin  3:  3.3486 -  2.9288 [2075/2094]  1866   209  10.1%
  bin  4:  2.9288 -  2.6626 [2051/2081]  1843   208  10.1%
  bin  5:  2.6626 -  2.4726 [2054/2073]  1859   195   9.5%
  bin  6:  2.4726 -  2.3274 [2036/2061]  1822   214  10.5%
  bin  7:  2.3274 -  2.2112 [2033/2061]  1827   206  10.1%
  bin  8:  2.2112 -  2.1152 [2010/2046]  1815   195   9.7%
  bin  9:  2.1152 -  2.0340 [2004/2054]  1805   199   9.9%
  bin 10:  2.0340 -  1.9639 [1029/2061]   925   104  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1104/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: 0.12 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:
        1.74 -     2.37: 31
        2.37 -     3.00: 1955
        3.00 -     3.64: 4643
        3.64 -     4.27: 9174
        4.27 -     4.90: 12584
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.738 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.811 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28382 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_1104/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1104/model_refine_001.geo

CPU time processing inputs: 8.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 45.9914 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4962   r_free= 0.4892   ksol= 0.00   Bsol= 0.00   scale= 0.781    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.297357                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.6898 0.99   1420  161 0.4212 0.4294      6.6232      6.6623|
|  2:  4.6898 -  3.7407 0.99   1365  149 0.4247 0.4120      6.8417      6.8043|
|  3:  3.7407 -  3.2733 0.99   1339  146 0.4541 0.4268      6.6884      6.7012|
|  4:  3.2733 -  2.9765 0.99   1348  155 0.4938 0.4920      6.5502      6.5213|
|  5:  2.9765 -  2.7645 0.99   1327  146 0.5196 0.5254      6.3832       6.406|
|  6:  2.7645 -  2.6023 0.99   1329  143 0.5288 0.5201      6.2888      6.2173|
|  7:  2.6023 -  2.4726 0.99   1308  141 0.5444 0.4831      6.2537      6.1936|
|  8:  2.4726 -  2.3654 0.98   1297  153 0.5291 0.4890      6.1832      6.2004|
|  9:  2.3654 -  2.2746 0.98   1308  148 0.5377 0.4965      6.1354      6.1272|
| 10:  2.2746 -  2.1964 1.00   1293  155 0.5330 0.5422      6.0933      6.0685|
| 11:  2.1964 -  2.1279 0.98   1312  128 0.5189 0.5395      6.0374      6.0611|
| 12:  2.1279 -  2.0672 0.98   1281  154 0.5332 0.6120      5.9552      6.0018|
| 13:  2.0672 -  2.0129 0.93   1228  125 0.5558 0.5107      5.8784       5.819|
| 14:  2.0129 -  1.9639 0.36    475   55 0.5685 0.5080      5.8808      5.8149|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.6898  1420   161  0.63  40.40   0.78     0.69      95537.20|
|  2:  4.6898 -  3.7407  1365   149  0.67  38.23   0.86     0.75     124788.89|
|  3:  3.7407 -  3.2733  1339   146  0.55  48.00   0.83     0.68     130911.08|
|  4:  3.2733 -  2.9765  1348   155  0.45  56.11   0.78     0.56     117511.43|
|  5:  2.9765 -  2.7645  1327   146  0.34  64.52   0.73     0.42      95246.59|
|  6:  2.7645 -  2.6023  1329   143  0.32  65.93   0.71     0.38      80678.14|
|  7:  2.6023 -  2.4726  1308   141  0.31  66.78   0.72     0.37      69723.31|
|  8:  2.4726 -  2.3654  1297   153  0.33  65.65   0.72     0.39      61845.27|
|  9:  2.3654 -  2.2746  1308   148  0.33  65.03   0.72     0.39      54523.01|
| 10:  2.2746 -  2.1964  1293   155  0.32  65.83   0.74     0.39      50714.85|
| 11:  2.1964 -  2.1279  1312   128  0.27  70.09   0.76     0.33      51412.79|
| 12:  2.1279 -  2.0672  1281   154  0.21  74.42   0.75     0.28      48965.80|
| 13:  2.0672 -  2.0129  1228   125  0.20  74.87   0.71     0.27      41760.16|
| 14:  2.0129 -  1.9639   475    55  0.33  65.79   0.70     0.36      30430.13|
|alpha:            min =        0.27 max =            0.75 mean =         0.46|
|beta:             min =    30430.13 max =       130911.08 mean =     78135.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.98 mean =        61.03|
|phase err.(test): min =        0.00 max =           90.00 mean =        61.20|
|-----------------------------------------------------------------------------|

============================== 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 = 21.167805             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.641   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.714141              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.207   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       33 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      698 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1534 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2646 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3943 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5083 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6563 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7755 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.586 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.991 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4995   r_free= 0.4915   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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.298443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4875   r_free= 0.4765   ksol= 0.37   Bsol= 20.00   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.53,9.19,6.76,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.292433                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.663440             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.702   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.577546              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.280   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4875      final r-factor (work) = 0.4187          |
| start r-factor (free) = 0.4765      final r-factor (free) = 0.4464          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 109.1622 = 17.66 * 0.50 * 6.2928 + 1.00 * 53.5856                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.1986 = 17.66 * 0.50 * 6.2328 + 1.00 * 0.1524                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4187      final r-factor (work) = 0.3801          |
| start r-factor (free) = 0.4464      final r-factor (free) = 0.4363          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8469 = 1.58 * 1.00 * 6.2328 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7615 = 1.58 * 1.00 * 6.1758 + 1.00 * 0.0188                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    59.45   12.77    None  None   None       |
|    all(noH): 2823   0      0.00    59.45   12.77    None  None   None       |
|    Sol.    : 438    0      0.00    52.48   19.62    None  None   None       |
|    Mac.    : 2385   0      0.00    59.45   11.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.945:  772   |   5:    29.724 -  35.669:   95        |
|      1:     5.945 -  11.890:  757   |   6:    35.669 -  41.614:   55        |
|      2:    11.890 -  17.834:  578   |   7:    41.614 -  47.558:   23        |
|      3:    17.834 -  23.779:  345   |   8:    47.558 -  53.503:    7        |
|      4:    23.779 -  29.724:  189   |   9:    53.503 -  59.448:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3801 r_free = 0.4363             target_work(ml) = 6.167         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3797 r_free = 0.4360             target_work(ml) = 6.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3797   r_free= 0.4360   ksol= 0.37   Bsol= 20.00   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.53,9.19,6.76,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.166490                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3784   r_free= 0.4345   ksol= 0.37   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.46,5.60,4.46,0.00,0.00,0.00); trace/3= 5.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.167960                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.738462             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.921  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.945525              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.400  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3784      final r-factor (work) = 0.3005          |
| start r-factor (free) = 0.4345      final r-factor (free) = 0.3596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.6482 = 14.74 * 0.50 * 6.1738 + 1.00 * 0.1524                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.9555 = 14.74 * 0.50 * 6.0850 + 1.00 * 0.1134                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3005      final r-factor (work) = 0.2724          |
| start r-factor (free) = 0.3596      final r-factor (free) = 0.3418          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7732 = 0.95 * 1.00 * 6.0850 + 1.00 * 0.0196                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6383 = 0.95 * 1.00 * 5.9468 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.21   13.80    None  None   None       |
|    all(noH): 2823   0      0.00    79.21   13.80    None  None   None       |
|    Sol.    : 438    0      0.00    79.21   30.77    None  None   None       |
|    Mac.    : 2385   0      0.00    64.31   10.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.921: 1163   |   5:    39.607 -  47.529:   85        |
|      1:     7.921 -  15.843:  766   |   6:    47.529 -  55.450:   39        |
|      2:    15.843 -  23.764:  389   |   7:    55.450 -  63.371:   22        |
|      3:    23.764 -  31.686:  204   |   8:    63.371 -  71.293:    9        |
|      4:    31.686 -  39.607:  144   |   9:    71.293 -  79.214:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2724 r_free = 0.3418             target_work(ml) = 5.922         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2722 r_free = 0.3415             target_work(ml) = 5.921         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2722   r_free= 0.3415   ksol= 0.37   Bsol= 50.00   scale= 1.058   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.46,5.60,4.46,0.00,0.00,0.00); trace/3= 5.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.921492                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2708   r_free= 0.3375   ksol= 0.34   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,3.20,3.49,0.00,0.00,0.00); trace/3= 3.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.917077                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.474959              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.559  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.306782              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.025  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2708      final r-factor (work) = 0.2022          |
| start r-factor (free) = 0.3375      final r-factor (free) = 0.2621          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3612 = 6.47 * 0.50 * 5.9453 + 1.00 * 0.1134                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8875 = 6.47 * 0.50 * 5.8094 + 1.00 * 0.0798                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2022      final r-factor (work) = 0.1827          |
| start r-factor (free) = 0.2621      final r-factor (free) = 0.2363          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7977 = 0.31 * 1.00 * 5.8094 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7311 = 0.31 * 1.00 * 5.6104 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.76   13.60    None  None   None       |
|    all(noH): 2823   0      0.00    80.76   13.60    None  None   None       |
|    Sol.    : 438    0      1.64    80.76   34.88    None  None   None       |
|    Mac.    : 2385   0      0.00    71.46   9.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.076: 1326   |   5:    40.379 -  48.455:  106        |
|      1:     8.076 -  16.152:  799   |   6:    48.455 -  56.531:   58        |
|      2:    16.152 -  24.228:  231   |   7:    56.531 -  64.607:   22        |
|      3:    24.228 -  32.303:  135   |   8:    64.607 -  72.683:    6        |
|      4:    32.303 -  40.379:  139   |   9:    72.683 -  80.758:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1827 r_free = 0.2363             target_work(ml) = 5.557         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1824 r_free = 0.2349             target_work(ml) = 5.554         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1824   r_free= 0.2349   ksol= 0.34   Bsol= 50.00   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,3.20,3.49,0.00,0.00,0.00); trace/3= 3.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.554488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1815   r_free= 0.2339   ksol= 0.34   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,1.44,2.56,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.553952                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.004386              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.306  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.257909              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.912  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1815      final r-factor (work) = 0.1522          |
| start r-factor (free) = 0.2339      final r-factor (free) = 0.2012          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7088 = 2.00 * 0.50 * 5.6166 + 1.00 * 0.0798                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5439 = 2.00 * 0.50 * 5.4782 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1522      final r-factor (work) = 0.1462          |
| start r-factor (free) = 0.2012      final r-factor (free) = 0.1951          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4227 = 0.26 * 1.00 * 5.4782 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3994 = 0.26 * 1.00 * 5.3887 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.84   13.52    None  None   None       |
|    all(noH): 2823   0      0.00    79.84   13.52    None  None   None       |
|    Sol.    : 438    0      2.74    79.84   36.11    None  None   None       |
|    Mac.    : 2385   0      0.00    73.53   9.37     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.985: 1375   |   5:    39.923 -  47.907:  124        |
|      1:     7.985 -  15.969:  777   |   6:    47.907 -  55.891:   62        |
|      2:    15.969 -  23.954:  215   |   7:    55.891 -  63.876:   36        |
|      3:    23.954 -  31.938:  111   |   8:    63.876 -  71.860:    6        |
|      4:    31.938 -  39.923:  115   |   9:    71.860 -  79.845:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1462 r_free = 0.1951             target_work(ml) = 5.373         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1461 r_free = 0.1948             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1461   r_free= 0.1948   ksol= 0.34   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,1.44,2.56,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.372141                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1463   r_free= 0.1949   ksol= 0.33   Bsol= 47.90   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.65,0.89,2.21,0.00,0.00,0.00); trace/3= 1.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.371400                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.797668              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.781  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.672800              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.347  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1463      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.1949      final r-factor (free) = 0.1779          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8978 = 1.80 * 0.50 * 5.3894 + 1.00 * 0.0536                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8442 = 1.80 * 0.50 * 5.3274 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1320      final r-factor (work) = 0.1281          |
| start r-factor (free) = 0.1779      final r-factor (free) = 0.1769          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5938 = 0.67 * 1.00 * 5.3274 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5529 = 0.67 * 1.00 * 5.2631 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.16   14.00    None  None   None       |
|    all(noH): 2823   0      0.00    84.16   14.00    None  None   None       |
|    Sol.    : 438    0      2.74    84.16   38.97    None  None   None       |
|    Mac.    : 2385   0      0.00    82.14   9.41     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 -   8.416: 1472   |   5:    42.079 -  50.495:  113        |
|      1:     8.416 -  16.832:  707   |   6:    50.495 -  58.911:   66        |
|      2:    16.832 -  25.248:  201   |   7:    58.911 -  67.327:   45        |
|      3:    25.248 -  33.664:  112   |   8:    67.327 -  75.743:   18        |
|      4:    33.664 -  42.079:   81   |   9:    75.743 -  84.159:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1281 r_free = 0.1769             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1280 r_free = 0.1767             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1767   ksol= 0.33   Bsol= 47.90   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.65,0.89,2.21,0.00,0.00,0.00); trace/3= 1.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.259427                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.6898 0.99   1420  161 0.1038 0.1366      5.4178      5.6102|
|  2:  4.6898 -  3.7407 0.99   1365  149 0.0934 0.1221      5.5134       5.716|
|  3:  3.7407 -  3.2733 0.99   1339  146 0.1221 0.1642      5.5757      5.8943|
|  4:  3.2733 -  2.9765 0.99   1348  155 0.1444 0.1852      5.5838      5.7043|
|  5:  2.9765 -  2.7645 0.99   1327  146 0.1573 0.2024      5.4552      5.6858|
|  6:  2.7645 -  2.6023 0.99   1329  143 0.1411 0.2032      5.3112      5.5442|
|  7:  2.6023 -  2.4726 0.99   1308  141 0.1495 0.1901      5.2917      5.4574|
|  8:  2.4726 -  2.3654 0.98   1297  153 0.1342 0.2030      5.1867      5.4716|
|  9:  2.3654 -  2.2746 0.98   1308  148 0.1403 0.2047       5.166      5.4192|
| 10:  2.2746 -  2.1964 1.00   1293  155 0.1287 0.1897      5.0684      5.2848|
| 11:  2.1964 -  2.1279 0.98   1312  128 0.1308 0.2045      5.0607      5.4062|
| 12:  2.1279 -  2.0672 0.98   1281  154 0.1272 0.2021       4.983      5.2487|
| 13:  2.0672 -  2.0129 0.93   1228  125 0.1303 0.1826       4.882       5.113|
| 14:  2.0129 -  1.9639 0.36    475   55 0.1034 0.1424      4.7092      4.8956|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.6898  1420   161  0.93   9.96   0.97     0.95       7965.63|
|  2:  4.6898 -  3.7407  1365   149  0.95   8.78   1.02     1.01      10408.24|
|  3:  3.7407 -  3.2733  1339   146  0.92  12.97   1.03     1.03      12416.16|
|  4:  3.2733 -  2.9765  1348   155  0.89  16.63   1.01     0.99      13113.72|
|  5:  2.9765 -  2.7645  1327   146  0.89  17.74   0.99     0.98      10267.99|
|  6:  2.7645 -  2.6023  1329   143  0.88  18.45   0.98     0.95       8636.09|
|  7:  2.6023 -  2.4726  1308   141  0.88  18.27   1.00     0.97       7981.93|
|  8:  2.4726 -  2.3654  1297   153  0.89  17.87   0.98     0.95       6722.33|
|  9:  2.3654 -  2.2746  1308   148  0.88  18.45   1.00     0.95       6481.73|
| 10:  2.2746 -  2.1964  1293   155  0.89  17.79   1.00     0.96       5601.35|
| 11:  2.1964 -  2.1279  1312   128  0.88  18.72   0.99     0.94       5580.11|
| 12:  2.1279 -  2.0672  1281   154  0.88  18.39   1.01     1.00       5109.31|
| 13:  2.0672 -  2.0129  1228   125  0.88  18.65   1.00     0.97       4109.13|
| 14:  2.0129 -  1.9639   475    55  0.90  15.98   0.98     0.95       3002.64|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3002.64 max =        13113.72 mean =      7949.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        16.27|
|phase err.(test): min =        0.00 max =           89.96 mean =        15.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1767   ksol= 0.32   Bsol= 49.50   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,-0.69,0.62,-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: 5.259263                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1767   ksol= 0.32   Bsol= 49.50   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,-0.69,0.62,-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: 5.259263                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.6898 0.99   1420  161 0.1036 0.1360      5.4153      5.6103|
|  2:  4.6898 -  3.7407 0.99   1365  149 0.0935 0.1222      5.5139      5.7174|
|  3:  3.7407 -  3.2733 0.99   1339  146 0.1221 0.1643      5.5762      5.8946|
|  4:  3.2733 -  2.9765 0.99   1348  155 0.1444 0.1851      5.5838      5.7042|
|  5:  2.9765 -  2.7645 0.99   1327  146 0.1573 0.2023      5.4551      5.6856|
|  6:  2.7645 -  2.6023 0.99   1329  143 0.1411 0.2032      5.3111      5.5442|
|  7:  2.6023 -  2.4726 0.99   1308  141 0.1495 0.1901      5.2916      5.4572|
|  8:  2.4726 -  2.3654 0.98   1297  153 0.1342 0.2030      5.1866      5.4715|
|  9:  2.3654 -  2.2746 0.98   1308  148 0.1403 0.2047      5.1659      5.4193|
| 10:  2.2746 -  2.1964 1.00   1293  155 0.1287 0.1897      5.0684      5.2847|
| 11:  2.1964 -  2.1279 0.98   1312  128 0.1308 0.2046      5.0607      5.4062|
| 12:  2.1279 -  2.0672 0.98   1281  154 0.1272 0.2021       4.983      5.2487|
| 13:  2.0672 -  2.0129 0.93   1228  125 0.1303 0.1825       4.882      5.1131|
| 14:  2.0129 -  1.9639 0.36    475   55 0.1034 0.1424      4.7094      4.8957|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.6898  1420   161  0.93   9.95   0.97     0.95       7933.96|
|  2:  4.6898 -  3.7407  1365   149  0.95   8.79   1.02     1.01      10411.03|
|  3:  3.7407 -  3.2733  1339   146  0.92  12.99   1.04     1.03      12441.10|
|  4:  3.2733 -  2.9765  1348   155  0.89  16.64   1.01     0.99      13118.75|
|  5:  2.9765 -  2.7645  1327   146  0.89  17.74   0.99     0.98      10266.78|
|  6:  2.7645 -  2.6023  1329   143  0.88  18.44   0.98     0.95       8633.29|
|  7:  2.6023 -  2.4726  1308   141  0.88  18.27   1.00     0.97       7979.63|
|  8:  2.4726 -  2.3654  1297   153  0.89  17.86   0.98     0.95       6720.84|
|  9:  2.3654 -  2.2746  1308   148  0.88  18.45   1.00     0.95       6480.58|
| 10:  2.2746 -  2.1964  1293   155  0.89  17.78   1.00     0.96       5600.36|
| 11:  2.1964 -  2.1279  1312   128  0.88  18.72   1.00     0.95       5579.17|
| 12:  2.1279 -  2.0672  1281   154  0.88  18.38   1.01     1.00       5108.61|
| 13:  2.0672 -  2.0129  1228   125  0.88  18.65   1.00     0.98       4109.09|
| 14:  2.0129 -  1.9639   475    55  0.90  15.98   0.98     0.95       3003.19|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     3003.19 max =        13118.75 mean =      7948.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.27|
|phase err.(test): min =        0.00 max =           89.38 mean =        15.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    85.76   15.60    None  None   None       |
|    all(noH): 2823   0      1.60    85.76   15.60    None  None   None       |
|    Sol.    : 438    0      4.34    85.76   40.57    None  None   None       |
|    Mac.    : 2385   0      1.60    83.74   11.01    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:     1.603 -  10.019: 1472   |   5:    43.683 -  52.099:  113        |
|      1:    10.019 -  18.435:  707   |   6:    52.099 -  60.515:   66        |
|      2:    18.435 -  26.851:  201   |   7:    60.515 -  68.930:   45        |
|      3:    26.851 -  35.267:  112   |   8:    68.930 -  77.346:   18        |
|      4:    35.267 -  43.683:   81   |   9:    77.346 -  85.762:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.392 - 5.636
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 330 from: 333
   mapped sites are within: 0.748 - 5.636

peak=    9.093 closest distance to " CB  VAL A 230 " =    1.466
peak=    7.335 closest distance to " CG2 VAL A 296 " =    1.172
peak=    6.927 closest distance to " CG  ARG A 138 " =    1.232
peak=    6.846 closest distance to " O   HOH Z 130 " =    1.316
peak=    6.436 closest distance to " CD2 LEU A   5 " =    1.337
peak=    6.028 closest distance to " O   HOH Z  65 " =    1.356
peak=    5.713 closest distance to " NH1 ARG A 138 " =    1.032
peak=    5.614 closest distance to " NE2 GLN A  11 " =    1.206
peak=    5.581 closest distance to " O   HOH Z 222 " =    1.445
peak=    5.484 closest distance to " CD1AILE A 234 " =    1.030
peak=    5.288 closest distance to " O   HOH Z   7 " =    1.791
peak=    5.253 closest distance to " CB  PRO A  54 " =    1.159
peak=    5.153 closest distance to " CD  ARG A 138 " =    1.001
peak=    5.114 closest distance to " O   HOH Z 410 " =    1.743
peak=    4.988 closest distance to " O   HOH Z 111 " =    1.897
peak=    4.946 closest distance to " O   HOH Z 147 " =    1.538
peak=    4.874 closest distance to " CB  VAL A 230 " =    1.198
peak=    4.865 closest distance to " O   HOH Z 425 " =    1.790
peak=    4.864 closest distance to " O   HOH Z 139 " =    1.833
peak=    4.857 closest distance to " CG  PRO A 198 " =    1.265
peak=    4.826 closest distance to " NH1 ARG A  56 " =    1.152
peak=    4.778 closest distance to " CG  LEU A   5 " =    1.185
peak=    4.775 closest distance to " O   HOH Z 374 " =    1.156
peak=    4.709 closest distance to " CB  ASN A 148 " =    1.380
peak=    4.707 closest distance to " O   HOH Z 369 " =    2.016
peak=    4.690 closest distance to " CD2 LEU A 228 " =    1.275
peak=    4.686 closest distance to " O   HOH Z 225 " =    1.574
peak=    4.668 closest distance to " O   HOH Z 268 " =    1.015
peak=    4.660 closest distance to " CB  SER A   3 " =    1.522
peak=    4.658 closest distance to " O   HOH Z  63 " =    1.518
peak=    4.635 closest distance to " O   HOH Z 232 " =    2.147
peak=    4.624 closest distance to " O   HOH Z  97 " =    1.400
peak=    4.604 closest distance to " O   HOH Z 236 " =    1.928
peak=    4.590 closest distance to " CB  ASP A 124 " =    0.882
peak=    4.577 closest distance to " O   HOH Z 183 " =    1.460
peak=    4.566 closest distance to " CB  SER A 216 " =    1.031
peak=    4.560 closest distance to " O   HOH Z 415 " =    1.132
peak=    4.530 closest distance to " CG  LEU A 228 " =    1.174
peak=    4.517 closest distance to " O   HOH Z   9 " =    1.348
peak=    4.513 closest distance to " O   HOH Z   2 " =    1.972
peak=    4.512 closest distance to " O   HOH Z 403 " =    1.357
peak=    4.499 closest distance to " O   HOH Z 186 " =    1.395
peak=    4.484 closest distance to " O   HOH Z 298 " =    2.079
peak=    4.466 closest distance to " CB  GLN A 183 " =    1.177
peak=    4.460 closest distance to " CB  SER A  63 " =    1.321
peak=    4.449 closest distance to " CG  PRO A  54 " =    1.445
peak=    4.445 closest distance to " O   HOH Z 193 " =    1.784
peak=    4.414 closest distance to " O   HOH Z 424 " =    1.248
peak=    4.398 closest distance to " O   HOH Z 414 " =    1.537
peak=    4.393 closest distance to " O   HOH Z 126 " =    1.923
peak=    4.309 closest distance to " O   HOH Z  69 " =    2.323
peak=    4.309 closest distance to " CG  PRO A 213 " =    1.258
peak=    4.288 closest distance to " O   HOH Z 316 " =    3.090
peak=    4.286 closest distance to " O   PRO A 198 " =    1.319
peak=    4.259 closest distance to " CG  LEU A 167 " =    1.258
peak=    4.245 closest distance to " O   HOH Z 427 " =    2.621
peak=    4.239 closest distance to " O   HOH Z 132 " =    1.217
peak=    4.230 closest distance to " CB  GLN A 223 " =    1.419
peak=    4.210 closest distance to " O   HOH Z  37 " =    1.220
peak=    4.196 closest distance to " CA  VAL A 296 " =    1.027
peak=    4.191 closest distance to " O   HOH Z 427 " =    1.240
peak=    4.181 closest distance to " O   HOH Z 361 " =    1.474
peak=    4.157 closest distance to " O   HOH Z  78 " =    1.635
peak=    4.157 closest distance to " CB  ARG A 275 " =    1.019
peak=    4.156 closest distance to " CD BLYS A 290 " =    1.053
peak=    4.156 closest distance to " O   HOH Z 417 " =    1.341
peak=    4.152 closest distance to " O   HOH Z 236 " =    1.723
peak=    4.143 closest distance to " CB  VAL A 202 " =    1.581
peak=    4.125 closest distance to " NZ ALYS A 290 " =    1.083
peak=    4.115 closest distance to " O   HOH Z 148 " =    1.620
peak=    4.057 closest distance to " O   HOH Z 133 " =    1.641
peak=    4.051 closest distance to " ND1 HIS A  86 " =    1.765
peak=    4.040 closest distance to " O   HOH Z 217 " =    2.469
peak=    4.039 closest distance to " O   HOH Z 144 " =    1.817
peak=    4.039 closest distance to " CB  LEU A 237 " =    0.910
peak=    4.005 closest distance to " O   HOH Z 214 " =    1.267
peak=    4.003 closest distance to " CA  ILE A 234 " =    1.023
peak=    3.999 closest distance to " CZ  PHE A 192 " =    0.936
peak=    3.977 closest distance to " CA  SER A  87 " =    0.935
peak=    3.976 closest distance to " CD2 TRP A 179 " =    2.162
peak=    3.970 closest distance to " O   HOH Z 411 " =    3.108
peak=    3.970 closest distance to " O   HOH Z 350 " =    1.519
peak=    3.954 closest distance to " O   HOH Z 127 " =    1.105
peak=    3.953 closest distance to " OD2 ASP A 286 " =    2.803
peak=    3.944 closest distance to " CB  TYR A 169 " =    0.779
peak=    3.943 closest distance to " O   HOH Z 133 " =    2.254
peak=    3.936 closest distance to " CB  MET A  40 " =    0.886
peak=    3.934 closest distance to " O   HOH Z  59 " =    2.239
peak=    3.930 closest distance to " O   HOH Z  61 " =    1.671
peak=    3.929 closest distance to " O   HOH Z 418 " =    1.114
peak=    3.923 closest distance to " CG1 ILE A  33 " =    1.231
peak=    3.920 closest distance to " NH1AARG A 145 " =    1.035
peak=    3.918 closest distance to " N   TYR A  15 " =    0.909
peak=    3.911 closest distance to " CG  GLN A  88 " =    1.065
peak=    3.908 closest distance to " CB  ASN A  39 " =    0.953
peak=    3.880 closest distance to " O   HOH Z  78 " =    2.525
peak=    3.876 closest distance to " O   HOH Z 255 " =    0.954
peak=    3.871 closest distance to " CB  TRP A 266 " =    1.021
peak=    3.863 closest distance to " O   HOH Z 371 " =    2.838
peak=    3.861 closest distance to " CB  VAL A 265 " =    1.297
peak=    3.852 closest distance to " O   HOH Z 380 " =    1.843
peak=    3.850 closest distance to " O   HOH Z 105 " =    1.192
peak=    3.842 closest distance to " O   HOH Z 233 " =    1.361
peak=    3.833 closest distance to " O   ASP A 132 " =    3.756
peak=    3.828 closest distance to " O   HOH Z 344 " =    1.167
peak=    3.827 closest distance to " CG2 VAL A 257 " =    0.998
peak=    3.827 closest distance to " O   HOH Z  57 " =    1.141
peak=    3.818 closest distance to " CB  GLU A 128 " =    1.155
peak=    3.816 closest distance to " O   HOH Z  58 " =    2.187
peak=    3.802 closest distance to " O   HOH Z 373 " =    2.195
peak=    3.789 closest distance to " O   HOH Z 419 " =    1.878
peak=    3.788 closest distance to " O   HOH Z 126 " =    1.493
peak=    3.764 closest distance to " O   HOH Z  48 " =    1.584
peak=    3.760 closest distance to " O   HOH Z 181 " =    2.295
peak=    3.752 closest distance to " O   HOH Z 272 " =    1.897
peak=    3.751 closest distance to " O   HOH Z 193 " =    1.735
peak=    3.750 closest distance to " O   SER A  87 " =    2.402
peak=    3.745 closest distance to " O   HOH Z 184 " =    1.620
peak=    3.714 closest distance to " CG2 THR A 221 " =    1.297
peak=    3.710 closest distance to " O   HOH Z 425 " =    2.100
peak=    3.700 closest distance to " CA  GLY A 267 " =    1.236
peak=    3.695 closest distance to " O   HOH Z 384 " =    1.613
peak=    3.684 closest distance to " CE3 TRP A 274 " =    1.390
peak=    3.679 closest distance to " O   HOH Z 222 " =    1.929
peak=    3.675 closest distance to " O   HOH Z  44 " =    2.623
peak=    3.673 closest distance to " CB  ASN A 187 " =    1.046
peak=    3.659 closest distance to " O   HOH Z 132 " =    2.259
peak=    3.658 closest distance to " N   GLN A 278 " =    1.017
peak=    3.655 closest distance to " CA  ASN A 127 " =    1.058
peak=    3.651 closest distance to " O   HOH Z 217 " =    1.755
peak=    3.645 closest distance to " O   HOH Z  55 " =    1.804
peak=    3.643 closest distance to " NZ  LYS A 117 " =    1.287
peak=    3.637 closest distance to " CA  LEU A 282 " =    1.073
peak=    3.635 closest distance to " O   ASN A 209 " =    1.619
peak=    3.634 closest distance to " OG BSER A 212 " =    2.755
peak=    3.631 closest distance to " O   HOH Z 392 " =    1.300
peak=    3.628 closest distance to " CA  ALA A  51 " =    1.066
peak=    3.623 closest distance to " O   HOH Z 438 " =    2.222
peak=    3.621 closest distance to " CA  ASP A  50 " =    1.031
peak=    3.619 closest distance to " O   HOH Z 385 " =    0.951
peak=    3.618 closest distance to " O   HOH Z 368 " =    2.159
peak=    3.617 closest distance to " O   HOH Z 146 " =    1.746
peak=    3.617 closest distance to " O   HOH Z 119 " =    1.479
peak=    3.614 closest distance to " CG  PRO A 243 " =    1.117
peak=    3.609 closest distance to " CG1BVAL A  72 " =    0.798
peak=    3.608 closest distance to " CD  ARG A  66 " =    2.332
peak=    3.603 closest distance to " O   HOH Z   1 " =    2.054
peak=    3.599 closest distance to " O   HOH Z   9 " =    1.791
peak=    3.595 closest distance to " O   HOH Z  46 " =    1.025
peak=    3.588 closest distance to " CG  LYS A  76 " =    1.613
peak=    3.579 closest distance to " O   HOH Z 258 " =    2.151
peak=    3.570 closest distance to " CG1 ILE A 120 " =    1.384
peak=    3.565 closest distance to " O   HOH Z 334 " =    2.940
peak=    3.563 closest distance to " O   HOH Z 117 " =    1.077
peak=    3.558 closest distance to " OE2 GLU A   2 " =    1.911
peak=    3.556 closest distance to " O   ALA A 233 " =    1.902
peak=    3.554 closest distance to " CB  MET A  47 " =    1.064
peak=    3.553 closest distance to " NE AARG A 275 " =    1.488
peak=    3.546 closest distance to " CB  HIS A 108 " =    0.812
peak=    3.539 closest distance to " O   HOH Z 373 " =    1.529
peak=    3.538 closest distance to " CD  ARG A 159 " =    0.750
peak=    3.533 closest distance to " CB  ILE A 234 " =    1.065
peak=    3.524 closest distance to " CB  ASN A 142 " =    0.805
peak=    3.522 closest distance to " O   HOH Z 305 " =    3.393
peak=    3.518 closest distance to " O   HOH Z 389 " =    1.815
peak=    3.515 closest distance to " CD1 LEU A 300 " =    1.172
peak=    3.515 closest distance to " ND1 HIS A  81 " =    1.624
peak=    3.507 closest distance to " CB  ALA A 104 " =    0.770
peak=    3.500 closest distance to " CD1 ILE A  33 " =    1.801
peak=    3.496 closest distance to " CB  SER A 276 " =    1.200
peak=    3.491 closest distance to " ND2 ASN A  60 " =    3.070
peak=    3.489 closest distance to " OE1 GLN A 240 " =    1.729
peak=    3.486 closest distance to " OG  SER A  62 " =    2.748
peak=    3.483 closest distance to " O   HOH Z 357 " =    1.419
peak=    3.479 closest distance to " CG  GLN A  55 " =    1.863
peak=    3.478 closest distance to " O   HOH Z  59 " =    1.506
peak=    3.476 closest distance to " CB  ALA A  10 " =    1.001
peak=    3.475 closest distance to " OG BSER A  99 " =    2.210
peak=    3.475 closest distance to " O   HOH Z 109 " =    2.232
peak=    3.473 closest distance to " N   SER A 271 " =    1.043
peak=    3.472 closest distance to " CB  SER A 212 " =    1.215
peak=    3.462 closest distance to " CG1 ILE A 151 " =    1.062
peak=    3.461 closest distance to " CA  LEU A 101 " =    1.525
peak=    3.458 closest distance to " O   HOH Z 158 " =    2.685
peak=    3.457 closest distance to " CB  SER A 210 " =    0.897
peak=    3.455 closest distance to " N   SER A  97 " =    0.830
peak=    3.451 closest distance to " NH2BARG A 190 " =    1.554
peak=    3.448 closest distance to " CA  GLU A 152 " =    0.988
peak=    3.435 closest distance to " O   HOH Z  30 " =    1.876
peak=    3.435 closest distance to " CE  MET A  93 " =    1.471
peak=    3.432 closest distance to " CA  MET A  47 " =    1.216
peak=    3.425 closest distance to " NH1 ARG A  14 " =    0.920
peak=    3.424 closest distance to " O   HOH Z 359 " =    1.382
peak=    3.419 closest distance to " O   ALA A 165 " =    1.360
peak=    3.418 closest distance to " O   HOH Z 284 " =    1.513
peak=    3.418 closest distance to " N   PHE A 130 " =    1.288
peak=    3.417 closest distance to " O   HOH Z 263 " =    1.485
peak=    3.416 closest distance to " O   HOH Z 143 " =    1.247
peak=    3.413 closest distance to " O   HOH Z 282 " =    2.084
peak=    3.412 closest distance to " CA  ALA A 160 " =    0.991
peak=    3.408 closest distance to " ND2 ASN A 249 " =    0.748
peak=    3.405 closest distance to " O   HOH Z 207 " =    2.429
peak=    3.403 closest distance to " OH  TYR A 186 " =    1.091
peak=    3.398 closest distance to " NE1 TRP A 274 " =    0.967
peak=    3.398 closest distance to " OG BSER A 258 " =    0.837
peak=    3.392 closest distance to " CG  GLN A 278 " =    3.880
peak=    3.377 closest distance to " O   HOH Z 343 " =    3.430
peak=    3.376 closest distance to " CB  LEU A 143 " =    1.068
peak=    3.370 closest distance to " O   HOH Z 422 " =    2.699
peak=    3.370 closest distance to " O   HOH Z  20 " =    1.919
peak=    3.368 closest distance to " O   HOH Z  26 " =    1.590
peak=    3.367 closest distance to " O   HOH Z 153 " =    3.721
peak=    3.363 closest distance to " N   GLY A 136 " =    1.201
peak=    3.363 closest distance to " CB  TRP A 179 " =    1.587
peak=    3.362 closest distance to " O   HOH Z 193 " =    1.866
peak=    3.358 closest distance to " CG2 ILE A 234 " =    0.859
peak=    3.356 closest distance to " O   GLY A 302 " =    2.343
peak=    3.353 closest distance to " CB  VAL A 250 " =    1.129
peak=    3.347 closest distance to " O   HOH Z  32 " =    2.296
peak=    3.347 closest distance to " O   HOH Z 215 " =    1.363
peak=    3.347 closest distance to " CA  ALA A  21 " =    1.094
peak=    3.347 closest distance to " CB  GLU A 236 " =    1.362
peak=    3.346 closest distance to " O   HOH Z 384 " =    1.569
peak=    3.337 closest distance to " CB  GLU A 277 " =    3.671
peak=    3.337 closest distance to " NH2BARG A 145 " =    2.039
peak=    3.335 closest distance to " O   HOH Z  50 " =    1.262
peak=    3.335 closest distance to " NE2 GLN A  58 " =    3.508
peak=    3.334 closest distance to " O   HOH Z  49 " =    1.567
peak=    3.334 closest distance to " O   HOH Z 302 " =    1.608
peak=    3.332 closest distance to " O   HOH Z 171 " =    2.813
peak=    3.330 closest distance to " O   HOH Z 134 " =    1.429
peak=    3.328 closest distance to " CG  ARG A 159 " =    1.003
peak=    3.325 closest distance to " CB  THR A 157 " =    1.127
peak=    3.322 closest distance to " O   HOH Z 166 " =    1.553
peak=    3.322 closest distance to " CA  ASN A 215 " =    1.204
peak=    3.320 closest distance to " O   HOH Z  55 " =    1.811
peak=    3.320 closest distance to " O   HOH Z 108 " =    2.124
peak=    3.320 closest distance to " CA  ALA A 299 " =    0.980
peak=    3.311 closest distance to " OG BSER A 134 " =    2.714
peak=    3.304 closest distance to " O   HOH Z 423 " =    1.550
peak=    3.301 closest distance to " O   HOH Z 110 " =    1.716
peak=    3.301 closest distance to " CB  LEU A 300 " =    0.916
peak=    3.297 closest distance to " O   HOH Z 406 " =    1.589
peak=    3.294 closest distance to " O   HOH Z  88 " =    3.454
peak=    3.288 closest distance to " CB  ALA A 248 " =    1.333
peak=    3.287 closest distance to " CD  PRO A 280 " =    0.858
peak=    3.287 closest distance to " CB  LYS A 117 " =    1.237
peak=    3.281 closest distance to " O   HOH Z 425 " =    2.098
peak=    3.281 closest distance to " NE2 GLN A  58 " =    5.636
peak=    3.280 closest distance to " CB  GLU A 152 " =    1.484
peak=    3.278 closest distance to " C   ASP A 298 " =    1.547
peak=    3.278 closest distance to " O   HOH Z 281 " =    2.005
peak=    3.277 closest distance to " O   HOH Z 145 " =    2.416
peak=    3.272 closest distance to " CG2 VAL A 202 " =    1.376
peak=    3.270 closest distance to " OD1 ASN A 217 " =    1.616
peak=    3.270 closest distance to " CB  THR A  82 " =    1.130
peak=    3.268 closest distance to " O   HOH Z  61 " =    1.529
peak=    3.266 closest distance to " O   ALA A 291 " =    1.431
peak=    3.263 closest distance to " NH2BARG A 102 " =    0.990
peak=    3.262 closest distance to " CD1 LEU A 281 " =    0.992
peak=    3.261 closest distance to " CG1 VAL A 197 " =    0.967
peak=    3.261 closest distance to " CB  GLU A 236 " =    1.141
peak=    3.256 closest distance to " O   HOH Z 409 " =    2.290
peak=    3.249 closest distance to " NH2 ARG A 219 " =    1.812
peak=    3.247 closest distance to " CA  TYR A  30 " =    1.037
peak=    3.245 closest distance to " O   HOH Z 367 " =    2.141
peak=    3.245 closest distance to " O   HOH Z 281 " =    4.541
peak=    3.242 closest distance to " CB  ARG A 138 " =    1.545
peak=    3.242 closest distance to " CA  THR A 221 " =    0.892
peak=    3.239 closest distance to " O   HOH Z 282 " =    2.560
peak=    3.233 closest distance to " CB  ALA A  43 " =    0.991
peak=    3.233 closest distance to " O   HOH Z 153 " =    3.983
peak=    3.232 closest distance to " O   HOH Z 115 " =    1.738
peak=    3.231 closest distance to " O   HOH Z 356 " =    1.377
peak=    3.230 closest distance to " CB  ALA A  34 " =    1.099
peak=    3.224 closest distance to " CB  ARG A  79 " =    1.368
peak=    3.223 closest distance to " O   PRO A 198 " =    1.497
peak=    3.221 closest distance to " CA  TYR A 116 " =    1.543
peak=    3.219 closest distance to " OE2 GLU A  53 " =    1.907
peak=    3.219 closest distance to " CH2 TRP A 150 " =    1.000
peak=    3.218 closest distance to " CB  SER A  62 " =    1.176
peak=    3.217 closest distance to " N   SER A  12 " =    1.573
peak=    3.215 closest distance to " O   HOH Z 412 " =    5.084
peak=    3.211 closest distance to " CD  ARG A 269 " =    1.018
peak=    3.209 closest distance to " O  BHOH Z  74 " =    1.397
peak=    3.209 closest distance to " O   HOH Z 145 " =    1.793
peak=    3.208 closest distance to " CE2 PHE A  16 " =    1.042
peak=    3.206 closest distance to " O   HOH Z 405 " =    1.653
peak=    3.199 closest distance to " CB  GLN A  89 " =    1.144
peak=    3.198 closest distance to " N   ARG A 156 " =    1.283
peak=    3.197 closest distance to " O   HOH Z 407 " =    1.573
peak=    3.189 closest distance to " CG2 THR A  18 " =    1.892
peak=    3.183 closest distance to " O   HOH Z  64 " =    2.183
peak=    3.182 closest distance to " O   HOH Z 371 " =    1.809
peak=    3.179 closest distance to " CB  ALA A 114 " =    1.000
peak=    3.174 closest distance to " N   ASP A 162 " =    1.439
peak=    3.162 closest distance to " OD1 ASN A  45 " =    1.370
peak=    3.158 closest distance to " O   HOH Z 368 " =    3.528
peak=    3.156 closest distance to " O   MET A 105 " =    1.673
peak=    3.155 closest distance to " CD  ARG A 195 " =    3.447
peak=    3.151 closest distance to " N   ASN A 127 " =    1.474
peak=    3.149 closest distance to " CG1 ILE A 263 " =    1.342
peak=    3.139 closest distance to " CA  ALA A 154 " =    0.983
peak=    3.138 closest distance to " O   HOH Z 383 " =    2.503
peak=    3.137 closest distance to " CB  PHE A 225 " =    1.476
peak=    3.136 closest distance to " CD2 LEU A 143 " =    1.703
peak=    3.132 closest distance to " CB  ALA A 161 " =    0.941
peak=    3.132 closest distance to " O   HOH Z 189 " =    2.796
peak=    3.131 closest distance to " O   HOH Z  10 " =    1.835
peak=    3.129 closest distance to " O   HOH Z 345 " =    1.750
peak=    3.125 closest distance to " CG  LYS A 119 " =    1.281
peak=    3.124 closest distance to " CE2 TYR A 186 " =    0.911
peak=    3.122 closest distance to " CD1 LEU A 167 " =    1.298
peak=    3.122 closest distance to " CG BARG A 102 " =    1.931
peak=    3.122 closest distance to " O   HOH Z  57 " =    1.574
peak=    3.112 closest distance to " CB  LYS A 290 " =    0.868
peak=    3.104 closest distance to " O   HOH Z 411 " =    1.512
peak=    3.097 closest distance to " O   HOH Z  64 " =    2.131
peak=    3.087 closest distance to " CA  ARG A 195 " =    1.356
peak=    3.081 closest distance to " O   HOH Z   1 " =    1.579
peak=    3.080 closest distance to " OG  SER A  22 " =    3.005
peak=    3.072 closest distance to " N   ALA A 256 " =    1.021
peak=    3.072 closest distance to " CA  TYR A 186 " =    1.513
peak=    3.068 closest distance to " O   HOH Z 172 " =    2.440
peak=    3.060 closest distance to " O   HOH Z 116 " =    1.418
peak=    3.059 closest distance to " CZ  PHE A 208 " =    1.131
peak=    3.056 closest distance to " CA  ILE A 106 " =    0.762
peak=    3.042 closest distance to " O   HOH Z   6 " =    2.021
peak=    3.029 closest distance to " ND2 ASN A 187 " =    1.543
peak=    3.007 closest distance to " O   HOH Z 143 " =    1.037

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.176 - 5.931
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 197
   mapped sites are within: 0.741 - 5.931

peak=   -5.189 closest distance to " CD  ARG A 138 " =    1.105
peak=   -4.957 closest distance to " CG2 VAL A 230 " =    0.896
peak=   -4.843 closest distance to " OE1 GLN A  88 " =    0.904
peak=   -4.316 closest distance to " O   PRO A 198 " =    1.226
peak=   -4.260 closest distance to " CD  ARG A  14 " =    3.118
peak=   -4.079 closest distance to " O   HOH Z 266 " =    4.880
peak=   -4.071 closest distance to " CG  MET A 105 " =    0.952
peak=   -4.062 closest distance to " O   HOH Z 385 " =    0.875
peak=   -4.045 closest distance to " OG  SER A  87 " =    1.364
peak=   -4.031 closest distance to " OG ASER A 134 " =    1.100
peak=   -4.025 closest distance to " CD2 LEU A 143 " =    2.513
peak=   -4.022 closest distance to " O   HOH Z 298 " =    0.940
peak=   -3.998 closest distance to " O   HOH Z 415 " =    0.984
peak=   -3.976 closest distance to " OG BSER A 134 " =    1.644
peak=   -3.975 closest distance to " O   HOH Z 290 " =    1.166
peak=   -3.964 closest distance to " CA  GLY A 133 " =    2.002
peak=   -3.949 closest distance to " CG  GLN A  88 " =    0.854
peak=   -3.943 closest distance to " O   HOH Z 377 " =    1.756
peak=   -3.885 closest distance to " NH2AARG A 275 " =    5.734
peak=   -3.861 closest distance to " O   HOH Z 359 " =    1.746
peak=   -3.849 closest distance to " OE1 GLU A 277 " =    2.456
peak=   -3.841 closest distance to " O   HOH Z  43 " =    1.637
peak=   -3.819 closest distance to " O   HOH Z 111 " =    2.249
peak=   -3.799 closest distance to " O   HOH Z 185 " =    2.328
peak=   -3.784 closest distance to " CD  ARG A 156 " =    1.941
peak=   -3.783 closest distance to " NH2 ARG A  79 " =    1.981
peak=   -3.761 closest distance to " N   THR A 157 " =    1.586
peak=   -3.760 closest distance to " CB  ALA A 227 " =    2.370
peak=   -3.759 closest distance to " CB  ASP A  27 " =    2.364
peak=   -3.757 closest distance to " O   HOH Z  13 " =    1.707
peak=   -3.741 closest distance to " CG  ARG A 138 " =    0.935
peak=   -3.736 closest distance to " O   ALA A   1 " =    1.119
peak=   -3.729 closest distance to " O   HOH Z  39 " =    1.163
peak=   -3.725 closest distance to " CG1 VAL A 268 " =    2.670
peak=   -3.699 closest distance to " CB  VAL A 230 " =    1.001
peak=   -3.692 closest distance to " CB  PHE A 130 " =    1.249
peak=   -3.687 closest distance to " CG  PRO A 163 " =    2.416
peak=   -3.687 closest distance to " CD  LYS A 289 " =    2.411
peak=   -3.683 closest distance to " CB  ALA A  43 " =    2.392
peak=   -3.682 closest distance to " O   HOH Z 134 " =    2.632
peak=   -3.679 closest distance to " C   ASN A 285 " =    2.357
peak=   -3.675 closest distance to " CG1 VAL A 296 " =    1.304
peak=   -3.673 closest distance to " N   ALA A  43 " =    2.647
peak=   -3.670 closest distance to " CE2 TYR A  30 " =    2.731
peak=   -3.663 closest distance to " CB  ALA A   9 " =    2.521
peak=   -3.648 closest distance to " CG  TRP A 266 " =    1.687
peak=   -3.640 closest distance to " O   HOH Z 409 " =    5.931
peak=   -3.604 closest distance to " O   ASN A 301 " =    1.294
peak=   -3.589 closest distance to " O   HOH Z 207 " =    2.008
peak=   -3.583 closest distance to " O   HOH Z 385 " =    1.129
peak=   -3.574 closest distance to " CB  ALA A 248 " =    1.936
peak=   -3.572 closest distance to " O   HOH Z 388 " =    2.047
peak=   -3.562 closest distance to " O   HOH Z 231 " =    1.812
peak=   -3.561 closest distance to " CB  PRO A 243 " =    2.561
peak=   -3.542 closest distance to " CB  SER A 271 " =    1.107
peak=   -3.534 closest distance to " CD  GLN A 223 " =    2.452
peak=   -3.524 closest distance to " O   HOH Z 211 " =    1.366
peak=   -3.523 closest distance to " OH  TYR A 214 " =    1.047
peak=   -3.509 closest distance to " O   HOH Z 184 " =    1.747
peak=   -3.508 closest distance to " O   HOH Z 166 " =    1.459
peak=   -3.504 closest distance to " CD1 LEU A 101 " =    2.329
peak=   -3.504 closest distance to " C   ALA A 158 " =    1.327
peak=   -3.502 closest distance to " O   HOH Z  52 " =    1.686
peak=   -3.491 closest distance to " CD2 LEU A   5 " =    0.881
peak=   -3.484 closest distance to " O   HOH Z 111 " =    1.050
peak=   -3.484 closest distance to " O   HOH Z 131 " =    3.906
peak=   -3.480 closest distance to " CG  TYR A 172 " =    2.159
peak=   -3.475 closest distance to " O   HOH Z 189 " =    2.950
peak=   -3.471 closest distance to " CG2 VAL A 296 " =    1.848
peak=   -3.470 closest distance to " O   HOH Z  71 " =    1.348
peak=   -3.469 closest distance to " O   SER A 135 " =    1.542
peak=   -3.454 closest distance to " O   HOH Z 102 " =    1.410
peak=   -3.437 closest distance to " O   HOH Z 143 " =    0.922
peak=   -3.429 closest distance to " O   ALA A  51 " =    1.439
peak=   -3.426 closest distance to " OG  SER A 245 " =    1.353
peak=   -3.420 closest distance to " OD2 ASP A  50 " =    1.699
peak=   -3.420 closest distance to " O   VAL A 197 " =    1.775
peak=   -3.417 closest distance to " CB  ALA A 248 " =    2.456
peak=   -3.413 closest distance to " O   GLY A  80 " =    2.444
peak=   -3.412 closest distance to " CG2 ILE A 151 " =    2.524
peak=   -3.409 closest distance to " O   HOH Z 292 " =    1.605
peak=   -3.407 closest distance to " CD  GLU A 277 " =    1.148
peak=   -3.400 closest distance to " C   PHE A 155 " =    0.741
peak=   -3.396 closest distance to " O   GLY A 203 " =    2.566
peak=   -3.390 closest distance to " CB  ALA A 114 " =    2.369
peak=   -3.385 closest distance to " C   ARG A 269 " =    1.389
peak=   -3.384 closest distance to " OG  SER A  97 " =    2.109
peak=   -3.376 closest distance to " O   HOH Z 389 " =    2.047
peak=   -3.373 closest distance to " CD  GLN A  58 " =    0.930
peak=   -3.373 closest distance to " CD  LYS A 166 " =    2.434
peak=   -3.362 closest distance to " CB  PRO A 163 " =    2.345
peak=   -3.358 closest distance to " CD1 ILE A 239 " =    2.553
peak=   -3.357 closest distance to " CB  ASN A  39 " =    2.176
peak=   -3.357 closest distance to " CG  ASP A 231 " =    0.812
peak=   -3.357 closest distance to " O   PRO A 163 " =    1.917
peak=   -3.355 closest distance to " O   HOH Z 177 " =    2.596
peak=   -3.352 closest distance to " O   SER A  22 " =    2.759
peak=   -3.349 closest distance to " OE1 GLN A 278 " =    1.181
peak=   -3.348 closest distance to " O   HOH Z 389 " =    4.624
peak=   -3.347 closest distance to " OG  SER A  63 " =    1.287
peak=   -3.346 closest distance to " O   HOH Z  52 " =    1.622
peak=   -3.343 closest distance to " O   ARG A 159 " =    1.632
peak=   -3.342 closest distance to " O   HOH Z  60 " =    1.768
peak=   -3.341 closest distance to " CA  GLY A  98 " =    1.836
peak=   -3.337 closest distance to " O   HOH Z 350 " =    1.693
peak=   -3.336 closest distance to " N   ALA A 226 " =    2.191
peak=   -3.335 closest distance to " C   ASP A 124 " =    1.206
peak=   -3.335 closest distance to " O   HOH Z 426 " =    1.708
peak=   -3.329 closest distance to " O   TYR A 247 " =    2.842
peak=   -3.327 closest distance to " O   HOH Z 407 " =    3.252
peak=   -3.324 closest distance to " OD1 ASN A  60 " =    0.974
peak=   -3.324 closest distance to " CB  PRO A  54 " =    2.506
peak=   -3.322 closest distance to " CE2 TYR A 116 " =    3.116
peak=   -3.321 closest distance to " O   GLY A 211 " =    1.268
peak=   -3.317 closest distance to " O   HOH Z  53 " =    1.713
peak=   -3.315 closest distance to " O   HOH Z 275 " =    1.641
peak=   -3.315 closest distance to " CB  ALA A 291 " =    1.931
peak=   -3.312 closest distance to " CD1 TRP A 179 " =    0.977
peak=   -3.311 closest distance to " O   TRP A  70 " =    1.478
peak=   -3.308 closest distance to " O   GLN A 194 " =    1.436
peak=   -3.306 closest distance to " CG BLYS A 290 " =    1.000
peak=   -3.306 closest distance to " N   THR A 235 " =    1.122
peak=   -3.305 closest distance to " NH1 ARG A 138 " =    1.157
peak=   -3.301 closest distance to " CZ  PHE A  38 " =    2.576
peak=   -3.295 closest distance to " CD1 ILE A 199 " =    2.694
peak=   -3.291 closest distance to " O   ILE A  49 " =    1.683
peak=   -3.286 closest distance to " CD2 TYR A 116 " =    2.208
peak=   -3.284 closest distance to " CA  GLY A 241 " =    2.073
peak=   -3.283 closest distance to " O   HOH Z 281 " =    4.606
peak=   -3.280 closest distance to " CB  ASP A 132 " =    2.287
peak=   -3.274 closest distance to " OG  SER A 206 " =    1.876
peak=   -3.274 closest distance to " O   HOH Z  56 " =    0.894
peak=   -3.267 closest distance to " CB  TYR A  15 " =    2.046
peak=   -3.265 closest distance to " CD1 PHE A  59 " =    2.015
peak=   -3.265 closest distance to " O   HOH Z  51 " =    0.971
peak=   -3.258 closest distance to " O   HOH Z 125 " =    3.038
peak=   -3.253 closest distance to " CB  PHE A 192 " =    1.526
peak=   -3.251 closest distance to " O   HOH Z 174 " =    1.538
peak=   -3.246 closest distance to " O   HOH Z  49 " =    1.844
peak=   -3.246 closest distance to " O   THR A  42 " =    2.460
peak=   -3.241 closest distance to " NH1 ARG A 195 " =    2.289
peak=   -3.241 closest distance to " CD2 TYR A 293 " =    1.949
peak=   -3.239 closest distance to " CB  ALA A 291 " =    2.039
peak=   -3.235 closest distance to " CB  SER A  63 " =    3.263
peak=   -3.232 closest distance to " O   GLN A  11 " =    1.453
peak=   -3.230 closest distance to " CD1 LEU A 255 " =    3.053
peak=   -3.222 closest distance to " O   HOH Z 139 " =    2.477
peak=   -3.218 closest distance to " O   HOH Z 348 " =    1.811
peak=   -3.214 closest distance to " O   HOH Z 297 " =    3.715
peak=   -3.214 closest distance to " CB  CYS A 254 " =    1.700
peak=   -3.214 closest distance to " O   ARG A 145 " =    1.501
peak=   -3.206 closest distance to " CA  GLY A  35 " =    2.024
peak=   -3.201 closest distance to " O   HOH Z 148 " =    2.515
peak=   -3.193 closest distance to " OG1 THR A 178 " =    1.267
peak=   -3.190 closest distance to " CD2 LEU A 237 " =    2.626
peak=   -3.183 closest distance to " CG2 THR A 178 " =    2.103
peak=   -3.183 closest distance to " O   HOH Z  97 " =    1.145
peak=   -3.181 closest distance to " OE1 GLN A  58 " =    2.935
peak=   -3.178 closest distance to " O   HOH Z 351 " =    1.379
peak=   -3.174 closest distance to " O   HOH Z 112 " =    1.360
peak=   -3.163 closest distance to " C   LEU A 222 " =    0.861
peak=   -3.163 closest distance to " OG  SER A  87 " =    1.573
peak=   -3.161 closest distance to " O   HOH Z 417 " =    2.807
peak=   -3.156 closest distance to " OD1 ASP A 191 " =    1.922
peak=   -3.148 closest distance to " N   PHE A  59 " =    1.989
peak=   -3.147 closest distance to " CG  GLN A 278 " =    2.262
peak=   -3.137 closest distance to " OD1 ASN A 301 " =    1.897
peak=   -3.136 closest distance to " C   ASN A 187 " =    1.789
peak=   -3.131 closest distance to " O   HOH Z 298 " =    2.620
peak=   -3.130 closest distance to " O   HOH Z 414 " =    1.824
peak=   -3.124 closest distance to " O   HOH Z 163 " =    1.731
peak=   -3.120 closest distance to " NH2 ARG A 219 " =    1.704
peak=   -3.120 closest distance to " OG  SER A  28 " =    1.911
peak=   -3.117 closest distance to " O   HOH Z 420 " =    3.161
peak=   -3.117 closest distance to " O   HOH Z 285 " =    2.966
peak=   -3.115 closest distance to " CZ  PHE A  59 " =    1.506
peak=   -3.114 closest distance to " C   MET A 188 " =    1.599
peak=   -3.108 closest distance to " CZ BARG A 275 " =    1.534
peak=   -3.107 closest distance to " O   HOH Z 200 " =    3.593
peak=   -3.102 closest distance to " CG2 THR A   4 " =    1.962
peak=   -3.099 closest distance to " O   HOH Z  20 " =    2.530
peak=   -3.087 closest distance to " O   HOH Z 372 " =    1.552
peak=   -3.086 closest distance to " CG1 VAL A  78 " =    2.235
peak=   -3.086 closest distance to " O   HOH Z 131 " =    3.807
peak=   -3.083 closest distance to " O   HOH Z 103 " =    1.703
peak=   -3.071 closest distance to " N   LYS A 166 " =    1.861
peak=   -3.063 closest distance to " O   SER A 271 " =    2.282
peak=   -3.059 closest distance to " O   HOH Z 124 " =    1.295
peak=   -3.053 closest distance to " CG  MET A  40 " =    2.111
peak=   -3.053 closest distance to " O   HOH Z 166 " =    1.705
peak=   -3.050 closest distance to " CD  ARG A 139 " =    1.772
peak=   -3.033 closest distance to " CG2 THR A  31 " =    2.371
peak=   -3.016 closest distance to " CB  SER A 273 " =    2.383

================= 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    :  0.4962 0.4892   6.297357e+00   6.287235e+00
   1_bss:  0.4875 0.4765   6.292433e+00   6.279853e+00
   1_xyz:  0.4187 0.4464   6.213299e+00   6.241336e+00
   1_adp:  0.3801 0.4363   6.167294e+00   6.236060e+00
   1_occ:  0.3797 0.4360   6.166490e+00   6.236077e+00
   2_bss:  0.3784 0.4345   6.167960e+00   6.235878e+00
   2_xyz:  0.3005 0.3596   5.985433e+00   6.111719e+00
   2_adp:  0.2724 0.3418   5.922031e+00   6.072613e+00
   2_occ:  0.2722 0.3415   5.921492e+00   6.072194e+00
   3_bss:  0.2708 0.3375   5.917077e+00   6.066456e+00
   3_xyz:  0.2022 0.2621   5.656729e+00   5.850258e+00
   3_adp:  0.1827 0.2363   5.557089e+00   5.756849e+00
   3_occ:  0.1824 0.2349   5.554488e+00   5.753537e+00
   4_bss:  0.1815 0.2339   5.553952e+00   5.751567e+00
   4_xyz:  0.1522 0.2012   5.407452e+00   5.619922e+00
   4_adp:  0.1462 0.1951   5.372654e+00   5.588881e+00
   4_occ:  0.1461 0.1948   5.372141e+00   5.588098e+00
   5_bss:  0.1463 0.1949   5.371400e+00   5.587499e+00
   5_xyz:  0.1320 0.1779   5.277203e+00   5.500759e+00
   5_adp:  0.1281 0.1769   5.260054e+00   5.493102e+00
   5_occ:  0.1280 0.1767   5.259427e+00   5.492153e+00
   5_bss:  0.1280 0.1767   5.259263e+00   5.492236e+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:  0.372  20.000   8.533   9.194   6.759   0.000   0.000   0.000
   1_xyz:  0.372  20.000   8.533   9.194   6.759   0.000   0.000   0.000
   1_adp:  0.372  20.000   8.533   9.194   6.759   0.000   0.000   0.000
   1_occ:  0.372  20.000   8.533   9.194   6.759   0.000   0.000   0.000
   2_bss:  0.372  50.001   5.457   5.599   4.458   0.000   0.000   0.000
   2_xyz:  0.372  50.001   5.457   5.599   4.458   0.000   0.000   0.000
   2_adp:  0.372  50.001   5.457   5.599   4.458   0.000   0.000   0.000
   2_occ:  0.372  50.001   5.457   5.599   4.458   0.000   0.000   0.000
   3_bss:  0.345  50.001   3.556   3.202   3.486   0.000   0.000   0.000
   3_xyz:  0.345  50.001   3.556   3.202   3.486   0.000   0.000   0.000
   3_adp:  0.345  50.001   3.556   3.202   3.486   0.000   0.000   0.000
   3_occ:  0.345  50.001   3.556   3.202   3.486   0.000   0.000   0.000
   4_bss:  0.345  50.001   2.131   1.445   2.555   0.000   0.000   0.000
   4_xyz:  0.345  50.001   2.131   1.445   2.555   0.000   0.000   0.000
   4_adp:  0.345  50.001   2.131   1.445   2.555   0.000   0.000   0.000
   4_occ:  0.345  50.001   2.131   1.445   2.555   0.000   0.000   0.000
   5_bss:  0.325  47.897   1.651   0.888   2.207   0.000   0.000   0.000
   5_xyz:  0.325  47.897   1.651   0.888   2.207   0.000   0.000   0.000
   5_adp:  0.325  47.897   1.651   0.888   2.207   0.000   0.000   0.000
   5_occ:  0.325  47.897   1.651   0.888   2.207   0.000   0.000   0.000
   5_bss:  0.319  49.501   0.068  -0.688   0.621  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.042 0.3806  0.4559    78131.038
   1_bss:  60.712 0.3840  0.5818    76360.602
   1_xyz:  54.428 0.4635  0.6879    62768.047
   1_adp:  52.572 0.4871  0.7632    60649.696
   1_occ:  52.602 0.4867  0.7619    60662.071
   2_bss:  52.420 0.4888  0.6926    60366.904
   2_xyz:  40.196 0.6392  0.8858    38122.034
   2_adp:  36.974 0.6781  0.9322    33563.796
   2_occ:  36.969 0.6781  0.9316    33536.527
   3_bss:  36.542 0.6827  0.8797    32746.261
   3_xyz:  26.321 0.7964  0.9866    17707.647
   3_adp:  22.949 0.8324  1.0122    14301.350
   3_occ:  22.848 0.8333  1.0121    14145.545
   4_bss:  22.778 0.8339  0.9640    14060.265
   4_xyz:  19.310 0.8682  0.9800    10548.890
   4_adp:  18.462 0.8766  0.9813     9939.270
   4_occ:  18.450 0.8767  0.9810     9908.617
   5_bss:  18.430 0.8768  0.9645     9875.433
   5_xyz:  16.454 0.8943  0.9748     8139.618
   5_adp:  16.225 0.8965  0.9720     7970.041
   5_occ:  16.203 0.8967  0.9720     7949.171
   5_bss:  16.203 0.8967  0.9727     7948.261
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3586e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3586e+01
   1_xyz:   1.749  0.014  0.109 18.467  0.007  4.108   1.5240e-01
   1_adp:   1.749  0.014  0.109 18.467  0.007  4.108   1.5240e-01
   1_occ:   1.749  0.014  0.109 18.467  0.007  4.108   1.5240e-01
   2_bss:   1.749  0.014  0.109 18.467  0.007  4.108   1.5240e-01
   2_xyz:   1.321  0.010  0.097 17.189  0.006  4.103   1.1341e-01
   2_adp:   1.321  0.010  0.097 17.189  0.006  4.103   1.1341e-01
   2_occ:   1.321  0.010  0.097 17.189  0.006  4.103   1.1341e-01
   3_bss:   1.321  0.010  0.097 17.189  0.006  4.103   1.1341e-01
   3_xyz:   1.158  0.009  0.083 15.859  0.004  4.123   7.9836e-02
   3_adp:   1.158  0.009  0.083 15.859  0.004  4.123   7.9836e-02
   3_occ:   1.158  0.009  0.083 15.859  0.004  4.123   7.9836e-02
   4_bss:   1.158  0.009  0.083 15.859  0.004  4.123   7.9836e-02
   4_xyz:   0.901  0.005  0.067 15.310  0.003  4.115   5.3623e-02
   4_adp:   0.901  0.005  0.067 15.310  0.003  4.115   5.3623e-02
   4_occ:   0.901  0.005  0.067 15.310  0.003  4.115   5.3623e-02
   5_bss:   0.901  0.005  0.067 15.310  0.003  4.115   5.3623e-02
   5_xyz:   0.944  0.006  0.073 15.205  0.003  4.121   5.5748e-02
   5_adp:   0.944  0.006  0.073 15.205  0.003  4.121   5.5748e-02
   5_occ:   0.944  0.006  0.073 15.205  0.003  4.121   5.5748e-02
   5_bss:   0.944  0.006  0.073 15.205  0.003  4.121   5.5748e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9456e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9456e+00
   1_xyz:  13.931  0.179  0.467 87.133  0.046  2.189   1.0666e-01
   1_adp:  13.931  0.179  0.467 87.133  0.046  2.189   1.0666e-01
   1_occ:  13.931  0.179  0.467 87.133  0.046  2.189   1.0666e-01
   2_bss:  13.931  0.179  0.467 87.133  0.046  2.189   1.0666e-01
   2_xyz:   8.328  0.091  0.394 76.884  0.060  2.057   7.0647e-02
   2_adp:   8.328  0.091  0.394 76.884  0.060  2.057   7.0647e-02
   2_occ:   8.328  0.091  0.394 76.884  0.060  2.057   7.0647e-02
   3_bss:   8.328  0.091  0.394 76.884  0.060  2.057   7.0647e-02
   3_xyz:   8.268  0.049  0.355 79.928  0.032  2.206   7.8335e-02
   3_adp:   8.268  0.049  0.355 79.928  0.032  2.206   7.8335e-02
   3_occ:   8.268  0.049  0.355 79.928  0.032  2.206   7.8335e-02
   4_bss:   8.268  0.049  0.355 79.928  0.032  2.206   7.8335e-02
   4_xyz:   7.493  0.041  0.328 82.499  0.034  2.343   3.4322e-02
   4_adp:   7.493  0.041  0.328 82.499  0.034  2.343   3.4322e-02
   4_occ:   7.493  0.041  0.328 82.499  0.034  2.343   3.4322e-02
   5_bss:   7.493  0.041  0.328 82.499  0.034  2.343   3.4322e-02
   5_xyz:   7.976  0.053  0.391 82.486  0.033  2.361   4.7115e-02
   5_adp:   7.976  0.053  0.391 82.486  0.033  2.361   4.7115e-02
   5_occ:   7.976  0.053  0.391 82.486  0.033  2.361   4.7115e-02
   5_bss:   7.976  0.053  0.391 82.486  0.033  2.361   4.7115e-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:  59.45   0.00  12.77  59.45   0.00  11.52  52.48   0.00  19.62
   1_occ:  59.45   0.00  12.77  59.45   0.00  11.52  52.48   0.00  19.62
   2_bss:  59.45   0.00  12.77  59.45   0.00  11.52  52.48   0.00  19.62
   2_xyz:  59.45   0.00  12.77  59.45   0.00  11.52  52.48   0.00  19.62
   2_adp:  79.21   0.00  13.80  64.31   0.00  10.68  79.21   0.00  30.77
   2_occ:  79.21   0.00  13.80  64.31   0.00  10.68  79.21   0.00  30.77
   3_bss:  79.21   0.00  13.80  64.31   0.00  10.68  79.21   0.00  30.77
   3_xyz:  79.21   0.00  13.80  64.31   0.00  10.68  79.21   0.00  30.77
   3_adp:  80.76   0.00  13.60  71.46   0.00   9.70  80.76   1.64  34.88
   3_occ:  80.76   0.00  13.60  71.46   0.00   9.70  80.76   1.64  34.88
   4_bss:  80.76   0.00  13.60  71.46   0.00   9.70  80.76   1.64  34.88
   4_xyz:  80.76   0.00  13.60  71.46   0.00   9.70  80.76   1.64  34.88
   4_adp:  79.84   0.00  13.52  73.53   0.00   9.37  79.84   2.74  36.11
   4_occ:  79.84   0.00  13.52  73.53   0.00   9.37  79.84   2.74  36.11
   5_bss:  79.84   0.00  13.52  73.53   0.00   9.37  79.84   2.74  36.11
   5_xyz:  79.84   0.00  13.52  73.53   0.00   9.37  79.84   2.74  36.11
   5_adp:  84.16   0.00  14.00  82.14   0.00   9.41  84.16   2.74  38.97
   5_occ:  84.16   0.00  14.00  82.14   0.00   9.41  84.16   2.74  38.97
   5_bss:  85.76   1.60  15.60  83.74   1.60  11.01  85.76   4.34  40.57
------------------------------------------------------------------------
 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:    1.248    0.027    0.416
   1_adp:    1.248    0.027    0.416
   1_occ:    1.248    0.027    0.416
   2_bss:    1.248    0.027    0.416
   2_xyz:    1.589    0.042    0.633
   2_adp:    1.589    0.042    0.633
   2_occ:    1.589    0.042    0.633
   3_bss:    1.589    0.042    0.633
   3_xyz:    1.908    0.043    0.743
   3_adp:    1.908    0.043    0.743
   3_occ:    1.908    0.043    0.743
   4_bss:    1.908    0.043    0.743
   4_xyz:    2.137    0.074    0.798
   4_adp:    2.137    0.074    0.798
   4_occ:    2.137    0.074    0.798
   5_bss:    2.137    0.074    0.798
   5_xyz:    2.222    0.037    0.822
   5_adp:    2.222    0.037    0.822
   5_occ:    2.222    0.037    0.822
   5_bss:    2.222    0.037    0.822
------------------------------------------------------------------------

CPU time actual refinement: 290.46


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1104/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_1104/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1104/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1104/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1104/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 290.32 
  Macro-tasks:
    bulk solvent and scale       = 34.53  
    individual site refinement   = 122.01 
    weights calculation          = 27.74  
    collect and process          = 5.43   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 189.85 
  Micro-tasks:
    mask                            = 2.07   
    f_calc                          = 91.92  
    alpha_beta                      = 7.01   
    target                          = 0.93   
    gradients_wrt_atomic_parameters = 99.76  
    fmodel                         = 6.07   
    r_factors                      = 0.30   
    phase_errors                   = 8.44   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 216.77 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.123 micro seconds
Total CPU time: 5.04 minutes
from_scatterers_fft:    622 calls, 91.57 s
gradients_fft:          566 calls, 88.55 s

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

# Date 2008-01-16 Time 03:12:01 PST -0800 (1200481921.04 s)
Start R-work = 0.4962, R-free = 0.4892 (no bulk solvent and anisotropic scale)
Final R-work = 0.1438, R-free = 0.1917 (no bulk solvent and anisotropic scale)

Start R-work = 0.4875, R-free = 0.4765
Final R-work = 0.1280, R-free = 0.1767