# Date 2008-01-16 Time 03:03:51 PST -0800 (1200481431.47 s)
#phil __OFF__

Command line arguments: "../1094.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9099
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1094

-------------------------------------------------------------------------------
  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, 45.7567, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 1.95433
Completeness in resolution range: 0.925275
Completeness with d_max=infinity: 0.92266

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2108
                             d_min =   1.9543

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, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 1.95433
Completeness in resolution range: 0.925275
Completeness with d_max=infinity: 0.92266

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2112 -  4.1840 [2223/2250]  2001   222  10.0%
  bin  2:  4.1840 -  3.3325 [2142/2162]  1929   213   9.9%
  bin  3:  3.3325 -  2.9146 [2114/2133]  1901   213  10.1%
  bin  4:  2.9146 -  2.6496 [2068/2098]  1859   209  10.1%
  bin  5:  2.6496 -  2.4606 [2086/2105]  1885   201   9.6%
  bin  6:  2.4606 -  2.3160 [2069/2094]  1856   213  10.3%
  bin  7:  2.3160 -  2.2004 [2055/2083]  1839   216  10.5%
  bin  8:  2.2004 -  2.1049 [2047/2083]  1849   198   9.7%
  bin  9:  2.1049 -  2.0240 [1995/2081]  1802   193   9.7%
  bin 10:  2.0240 -  1.9543 [ 790/2082]   709    81  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1094/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: 0.13 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:
        1.51 -     2.18: 21
        2.18 -     2.86: 1196
        2.86 -     3.54: 4497
        3.54 -     4.22: 9276
        4.22 -     4.90: 13424
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.506 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28409 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_1094/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1094/model_refine_001.geo

CPU time processing inputs: 9.29


============================ 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 45.75675 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5065   r_free= 0.5037   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.308699                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.6677 0.99   1440  163 0.4410 0.4434      6.6612      6.7051|
|  2:  4.6677 -  3.7228 0.99   1395  154 0.4434 0.4229      6.8712      6.8356|
|  3:  3.7228 -  3.2575 0.99   1355  144 0.4726 0.4760      6.7052      6.7023|
|  4:  3.2575 -  2.9620 0.99   1348  157 0.5023 0.5094      6.5519      6.5335|
|  5:  2.9620 -  2.7511 0.99   1359  145 0.5339 0.5326      6.3881      6.4032|
|  6:  2.7511 -  2.5897 0.99   1340  156 0.5395 0.5248      6.2967      6.2323|
|  7:  2.5897 -  2.4606 0.99   1338  139 0.5520 0.5020      6.2518      6.1687|
|  8:  2.4606 -  2.3539 0.98   1322  156 0.5365 0.5252      6.1711      6.2225|
|  9:  2.3539 -  2.2635 0.98   1320  144 0.5435 0.5149      6.1397      6.1424|
| 10:  2.2635 -  2.1857 1.00   1324  154 0.5355 0.5470      6.0824      6.0583|
| 11:  2.1857 -  2.1175 0.98   1313  137 0.5235 0.5462      6.0355      6.0692|
| 12:  2.1175 -  2.0571 0.98   1309  152 0.5352 0.5854      5.9383      5.9562|
| 13:  2.0571 -  2.0031 0.86   1140  124 0.5661 0.5264      5.8858      5.8091|
| 14:  2.0031 -  1.9543 0.24    327   34 0.5506 0.4970      5.8719      5.8856|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.6677  1440   163  0.62  41.02   0.77     0.69      98762.22|
|  2:  4.6677 -  3.7228  1395   154  0.64  40.41   0.84     0.72     137632.79|
|  3:  3.7228 -  3.2575  1355   144  0.49  52.33   0.83     0.64     146115.70|
|  4:  3.2575 -  2.9620  1348   157  0.38  61.44   0.76     0.48     131253.21|
|  5:  2.9620 -  2.7511  1359   145  0.27  69.59   0.72     0.35     103820.93|
|  6:  2.7511 -  2.5897  1340   156  0.26  70.69   0.70     0.32      86963.73|
|  7:  2.5897 -  2.4606  1338   139  0.25  71.40   0.73     0.30      74258.85|
|  8:  2.4606 -  2.3539  1322   156  0.25  71.31   0.71     0.31      66788.68|
|  9:  2.3539 -  2.2635  1320   144  0.25  71.47   0.73     0.30      60457.46|
| 10:  2.2635 -  2.1857  1324   154  0.26  70.87   0.73     0.32      54568.70|
| 11:  2.1857 -  2.1175  1313   137  0.23  72.52   0.76     0.30      53456.35|
| 12:  2.1175 -  2.0571  1309   152  0.21  74.18   0.75     0.29      48301.34|
| 13:  2.0571 -  2.0031  1140   124  0.22  73.56   0.69     0.30      41313.17|
| 14:  2.0031 -  1.9543   327    34  0.34  64.54   0.73     0.39      29792.24|
|alpha:            min =        0.29 max =            0.72 mean =         0.41|
|beta:             min =    29792.24 max =       146115.70 mean =     84895.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           89.98 mean =        64.31|
|phase err.(test): min =        0.00 max =           89.98 mean =        64.53|
|-----------------------------------------------------------------------------|

============================== 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 = 25.918176             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.035   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.073246              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.191   (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:        4 |
| 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:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      705 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1516 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2661 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3939 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5095 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6556 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7781 |
|-----------------------------------------------------------------------------|
|-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 |       53.545 |
| 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 |       2.289 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    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 = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5091   r_free= 0.5035   ksol= 0.00   Bsol= 0.00   scale= 0.744    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.309286                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4979   r_free= 0.4920   ksol= 0.35   Bsol= 4.93   scale= 0.961    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.46,9.11,6.99,0.00,0.00,0.00); trace/3= 8.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.304742                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.919254             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.260   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.092201              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.889   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4979      final r-factor (work) = 0.4420          |
| start r-factor (free) = 0.4920      final r-factor (free) = 0.4683          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 119.4677 = 20.92 * 0.50 * 6.3026 + 1.00 * 53.5446                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 65.6368 = 20.92 * 0.50 * 6.2607 + 1.00 * 0.1524                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4420      final r-factor (work) = 0.4062          |
| start r-factor (free) = 0.4683      final r-factor (free) = 0.4682          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1130 = 2.09 * 1.00 * 6.2607 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0357 = 2.09 * 1.00 * 6.2204 + 1.00 * 0.0214                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.05   16.02    None  None   None       |
|    all(noH): 2823   0      0.00    79.05   16.02    None  None   None       |
|    Sol.    : 438    0      0.00    79.05   22.31    None  None   None       |
|    Mac.    : 2385   0      0.00    78.13   14.86    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 -   7.905:  819   |   5:    39.526 -  47.431:   84        |
|      1:     7.905 -  15.810:  854   |   6:    47.431 -  55.336:   47        |
|      2:    15.810 -  23.715:  538   |   7:    55.336 -  63.241:   22        |
|      3:    23.715 -  31.621:  297   |   8:    63.241 -  71.146:   12        |
|      4:    31.621 -  39.526:  146   |   9:    71.146 -  79.051:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4062 r_free = 0.4682             target_work(ml) = 6.219         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4060 r_free = 0.4671             target_work(ml) = 6.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4060   r_free= 0.4671   ksol= 0.35   Bsol= 4.93   scale= 1.104    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.46,9.11,6.99,0.00,0.00,0.00); trace/3= 8.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.218316                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4042   r_free= 0.4643   ksol= 0.35   Bsol= 33.82   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.03,5.03,3.76,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.218531                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.442838             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.256  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.903361              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.668  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4042      final r-factor (work) = 0.3565          |
| start r-factor (free) = 0.4643      final r-factor (free) = 0.4363          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.2668 = 16.44 * 0.50 * 6.2172 + 1.00 * 0.1524                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.8543 = 16.44 * 0.50 * 6.1718 + 1.00 * 0.1137                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3565      final r-factor (work) = 0.3415          |
| start r-factor (free) = 0.4363      final r-factor (free) = 0.4250          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5967 = 0.90 * 1.00 * 6.1718 + 1.00 * 0.0214                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5617 = 0.90 * 1.00 * 6.1131 + 1.00 * 0.0393                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.14   15.94    None  None   None       |
|    all(noH): 2823   0      0.00    78.14   15.94    None  None   None       |
|    Sol.    : 438    0      0.00    78.14   24.28    None  None   None       |
|    Mac.    : 2385   0      0.00    76.40   14.41    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 -   7.814:  774   |   5:    39.070 -  46.884:   76        |
|      1:     7.814 -  15.628:  847   |   6:    46.884 -  54.698:   39        |
|      2:    15.628 -  23.442:  607   |   7:    54.698 -  62.512:   15        |
|      3:    23.442 -  31.256:  312   |   8:    62.512 -  70.326:   10        |
|      4:    31.256 -  39.070:  140   |   9:    70.326 -  78.140:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3415 r_free = 0.4250             target_work(ml) = 6.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3411 r_free = 0.4246             target_work(ml) = 6.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3411   r_free= 0.4246   ksol= 0.35   Bsol= 33.82   scale= 1.060   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.03,5.03,3.76,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.100685                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3410   r_free= 0.4228   ksol= 0.32   Bsol= 41.34   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,2.73,3.05,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.101062                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.492835              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.492  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.655570              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.459   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3410      final r-factor (work) = 0.2919          |
| start r-factor (free) = 0.4228      final r-factor (free) = 0.3656          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1255 = 9.49 * 0.50 * 6.1124 + 1.00 * 0.1136                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.8058 = 9.49 * 0.50 * 6.0499 + 1.00 * 0.0904                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2919      final r-factor (work) = 0.2699          |
| start r-factor (free) = 0.3656      final r-factor (free) = 0.3478          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9821 = 0.66 * 1.00 * 6.0499 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9105 = 0.66 * 1.00 * 5.9460 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.72   15.95    None  None   None       |
|    all(noH): 2823   0      0.00    78.72   15.95    None  None   None       |
|    Sol.    : 438    0      0.00    78.72   31.00    None  None   None       |
|    Mac.    : 2385   0      0.00    70.33   13.19    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 -   7.872:  863   |   5:    39.361 -  47.233:  119        |
|      1:     7.872 -  15.744:  847   |   6:    47.233 -  55.105:   40        |
|      2:    15.744 -  23.616:  489   |   7:    55.105 -  62.977:   16        |
|      3:    23.616 -  31.489:  276   |   8:    62.977 -  70.849:    5        |
|      4:    31.489 -  39.361:  165   |   9:    70.849 -  78.721:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2699 r_free = 0.3478             target_work(ml) = 5.923         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2697 r_free = 0.3470             target_work(ml) = 5.922         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2697   r_free= 0.3470   ksol= 0.32   Bsol= 41.34   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,2.73,3.05,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.922056                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2687   r_free= 0.3471   ksol= 0.32   Bsol= 49.80   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.49,0.99,1.88,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.922604                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.816192              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.302   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.807620              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.252  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2687      final r-factor (work) = 0.2177          |
| start r-factor (free) = 0.3471      final r-factor (free) = 0.2869          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3546 = 6.82 * 0.50 * 5.9459 + 1.00 * 0.0904                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9887 = 6.82 * 0.50 * 5.8417 + 1.00 * 0.0795                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2177      final r-factor (work) = 0.1946          |
| start r-factor (free) = 0.2869      final r-factor (free) = 0.2622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7306 = 0.81 * 1.00 * 5.8417 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6090 = 0.81 * 1.00 * 5.6894 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.97   16.17    None  None   None       |
|    all(noH): 2823   0      0.00    83.97   16.17    None  None   None       |
|    Sol.    : 438    0      2.02    83.97   39.77    None  None   None       |
|    Mac.    : 2385   0      0.00    74.94   11.84    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 -   8.397: 1084   |   5:    41.983 -  50.379:  138        |
|      1:     8.397 -  16.793:  860   |   6:    50.379 -  58.776:   84        |
|      2:    16.793 -  25.190:  321   |   7:    58.776 -  67.173:   38        |
|      3:    25.190 -  33.586:  154   |   8:    67.173 -  75.569:   10        |
|      4:    33.586 -  41.983:  132   |   9:    75.569 -  83.966:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1946 r_free = 0.2622             target_work(ml) = 5.643         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1945 r_free = 0.2617             target_work(ml) = 5.641         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1945   r_free= 0.2617   ksol= 0.32   Bsol= 49.80   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.49,0.99,1.88,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.641252                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1943   r_free= 0.2619   ksol= 0.32   Bsol= 49.80   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.88,0.06,1.49,0.00,0.00,0.00); trace/3= 0.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.642069                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.073166              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.250  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.635033              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.786  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1943      final r-factor (work) = 0.1580          |
| start r-factor (free) = 0.2619      final r-factor (free) = 0.2180          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6676 = 4.07 * 0.50 * 5.6900 + 1.00 * 0.0794                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3975 = 4.07 * 0.50 * 5.5640 + 1.00 * 0.0660                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1580      final r-factor (work) = 0.1463          |
| start r-factor (free) = 0.2180      final r-factor (free) = 0.2021          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5473 = 0.64 * 1.00 * 5.5640 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4615 = 0.64 * 1.00 * 5.4312 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.54   15.95    None  None   None       |
|    all(noH): 2823   0      0.00    87.54   15.95    None  None   None       |
|    Sol.    : 438    0      3.57    85.95   42.54    None  None   None       |
|    Mac.    : 2385   0      0.00    87.54   11.07    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 -   8.754: 1256   |   5:    43.771 -  52.526:  102        |
|      1:     8.754 -  17.509:  853   |   6:    52.526 -  61.280:   82        |
|      2:    17.509 -  26.263:  224   |   7:    61.280 -  70.034:   55        |
|      3:    26.263 -  35.017:  131   |   8:    70.034 -  78.788:   23        |
|      4:    35.017 -  43.771:   91   |   9:    78.788 -  87.543:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1463 r_free = 0.2021             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1461 r_free = 0.2018             target_work(ml) = 5.390         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1461   r_free= 0.2018   ksol= 0.32   Bsol= 49.80   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.88,0.06,1.49,0.00,0.00,0.00); trace/3= 0.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.389933                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.6677 0.99   1440  163 0.1060 0.1506      5.4612      5.7057|
|  2:  4.6677 -  3.7228 0.99   1395  154 0.0974 0.1300       5.582      5.8191|
|  3:  3.7228 -  3.2575 0.99   1355  144 0.1355 0.1987      5.6691      5.9872|
|  4:  3.2575 -  2.9620 0.99   1348  157 0.1671 0.2083      5.6996      5.8454|
|  5:  2.9620 -  2.7511 0.99   1359  145 0.1769 0.2384      5.5861      5.8451|
|  6:  2.7511 -  2.5897 0.99   1340  156 0.1642 0.2399      5.4574      5.6707|
|  7:  2.5897 -  2.4606 0.99   1338  139 0.1679 0.2091      5.4096      5.5614|
|  8:  2.4606 -  2.3539 0.98   1322  156 0.1700 0.2375      5.3539      5.6223|
|  9:  2.3539 -  2.2635 0.98   1320  144 0.1623 0.2412      5.3084      5.5465|
| 10:  2.2635 -  2.1857 1.00   1324  154 0.1509 0.2206      5.2158      5.4209|
| 11:  2.1857 -  2.1175 0.98   1313  137 0.1485 0.2274      5.1804      5.5478|
| 12:  2.1175 -  2.0571 0.98   1309  152 0.1553 0.2364      5.1331      5.3712|
| 13:  2.0571 -  2.0031 0.86   1140  124 0.1633 0.2229      5.0393      5.2345|
| 14:  2.0031 -  1.9543 0.24    327   34 0.1421 0.1709      4.9226      5.1437|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.6677  1440   163  0.93  11.06   0.97     0.96       9504.30|
|  2:  4.6677 -  3.7228  1395   154  0.94  10.31   1.03     1.02      12744.24|
|  3:  3.7228 -  3.2575  1355   144  0.90  15.38   1.06     1.04      15794.03|
|  4:  3.2575 -  2.9620  1348   157  0.86  19.91   1.03     1.00      17544.39|
|  5:  2.9620 -  2.7511  1359   145  0.85  21.70   1.01     0.99      14611.98|
|  6:  2.7511 -  2.5897  1340   156  0.84  22.62   1.00     0.93      12135.03|
|  7:  2.5897 -  2.4606  1338   139  0.85  21.84   1.01     0.97      10863.43|
|  8:  2.4606 -  2.3539  1322   156  0.84  22.71   1.00     0.94       9732.99|
|  9:  2.3539 -  2.2635  1320   144  0.84  22.59   1.01     0.95       9117.77|
| 10:  2.2635 -  2.1857  1324   154  0.84  22.32   1.01     0.96       7935.45|
| 11:  2.1857 -  2.1175  1313   137  0.84  22.36   1.02     0.97       7578.24|
| 12:  2.1175 -  2.0571  1309   152  0.84  22.75   1.03     1.02       7071.96|
| 13:  2.0571 -  2.0031  1140   124  0.84  22.95   1.01     0.96       5566.46|
| 14:  2.0031 -  1.9543   327    34  0.88  18.76   1.00     0.97       4130.45|
|alpha:            min =        0.93 max =            1.04 mean =         0.98|
|beta:             min =     4130.45 max =        17544.39 mean =     10747.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.90 mean =        19.73|
|phase err.(test): min =        0.00 max =           89.96 mean =        18.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1465   r_free= 0.2017   ksol= 0.32   Bsol= 53.10   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,-0.86,0.77,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.388984                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1465   r_free= 0.2017   ksol= 0.32   Bsol= 53.10   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,-0.86,0.77,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.388984                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.6677 0.99   1440  163 0.1065 0.1459      5.4449       5.685|
|  2:  4.6677 -  3.7228 0.99   1395  154 0.0992 0.1307      5.5854      5.8231|
|  3:  3.7228 -  3.2575 0.99   1355  144 0.1358 0.1988      5.6732      5.9872|
|  4:  3.2575 -  2.9620 0.99   1348  157 0.1667 0.2097      5.7004      5.8495|
|  5:  2.9620 -  2.7511 0.99   1359  145 0.1772 0.2381      5.5875      5.8463|
|  6:  2.7511 -  2.5897 0.99   1340  156 0.1639 0.2396      5.4559      5.6685|
|  7:  2.5897 -  2.4606 0.99   1338  139 0.1677 0.2096      5.4082      5.5617|
|  8:  2.4606 -  2.3539 0.98   1322  156 0.1698 0.2373      5.3527      5.6207|
|  9:  2.3539 -  2.2635 0.98   1320  144 0.1620 0.2410      5.3075      5.5449|
| 10:  2.2635 -  2.1857 1.00   1324  154 0.1507 0.2212      5.2159      5.4236|
| 11:  2.1857 -  2.1175 0.98   1313  137 0.1481 0.2277      5.1806      5.5487|
| 12:  2.1175 -  2.0571 0.98   1309  152 0.1552 0.2369      5.1339      5.3726|
| 13:  2.0571 -  2.0031 0.86   1140  124 0.1633 0.2222      5.0389      5.2324|
| 14:  2.0031 -  1.9543 0.24    327   34 0.1419 0.1702      4.9207      5.1407|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.6677  1440   163  0.93  10.58   0.96     0.95       8722.14|
|  2:  4.6677 -  3.7228  1395   154  0.94  10.08   1.03     1.02      12369.57|
|  3:  3.7228 -  3.2575  1355   144  0.90  15.41   1.05     1.04      15932.06|
|  4:  3.2575 -  2.9620  1348   157  0.86  19.93   1.02     0.99      17635.36|
|  5:  2.9620 -  2.7511  1359   145  0.85  21.69   1.00     0.98      14632.59|
|  6:  2.7511 -  2.5897  1340   156  0.84  22.59   0.99     0.92      12097.66|
|  7:  2.5897 -  2.4606  1338   139  0.85  21.78   1.00     0.96      10813.16|
|  8:  2.4606 -  2.3539  1322   156  0.84  22.68   0.98     0.93       9714.89|
|  9:  2.3539 -  2.2635  1320   144  0.84  22.57   1.00     0.93       9104.34|
| 10:  2.2635 -  2.1857  1324   154  0.84  22.34   1.00     0.94       7953.81|
| 11:  2.1857 -  2.1175  1313   137  0.84  22.39   1.01     0.95       7606.09|
| 12:  2.1175 -  2.0571  1309   152  0.84  22.78   1.01     1.00       7090.77|
| 13:  2.0571 -  2.0031  1140   124  0.84  22.93   0.99     0.95       5562.91|
| 14:  2.0031 -  1.9543   327    34  0.88  18.68   0.97     0.95       4104.86|
|alpha:            min =        0.92 max =            1.04 mean =         0.97|
|beta:             min =     4104.86 max =        17635.36 mean =     10668.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.80 mean =        19.67|
|phase err.(test): min =        0.00 max =           89.92 mean =        18.73|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    88.02   16.43    None  None   None       |
|    all(noH): 2823   0      0.48    88.02   16.43    None  None   None       |
|    Sol.    : 438    0      4.05    86.43   43.02    None  None   None       |
|    Mac.    : 2385   0      0.48    88.02   11.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.480 -   9.234: 1256   |   5:    44.251 -  53.005:  102        |
|      1:     9.234 -  17.988:  853   |   6:    53.005 -  61.760:   82        |
|      2:    17.988 -  26.743:  224   |   7:    61.760 -  70.514:   55        |
|      3:    26.743 -  35.497:  131   |   8:    70.514 -  79.268:   23        |
|      4:    35.497 -  44.251:   91   |   9:    79.268 -  88.023:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 348         
Filter by distance & map next to the model:
   mapped sites are within: 0.700 - 5.994
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 347 from: 348
   mapped sites are within: 0.700 - 5.994

peak=    8.173 closest distance to " CG1 VAL A 296 " =    1.412
peak=    7.537 closest distance to " O   HOH Z 390 " =    1.260
peak=    6.945 closest distance to " O   HOH Z 268 " =    1.262
peak=    6.940 closest distance to " O   HOH Z 130 " =    1.760
peak=    6.931 closest distance to " CB  VAL A 230 " =    1.534
peak=    6.420 closest distance to " O   HOH Z 375 " =    1.669
peak=    6.170 closest distance to " O   HOH Z 415 " =    1.521
peak=    6.166 closest distance to " O   HOH Z  41 " =    1.262
peak=    5.694 closest distance to " O   HOH Z 120 " =    1.247
peak=    5.689 closest distance to " CG  LEU A   5 " =    1.551
peak=    5.587 closest distance to " NH1 ARG A 138 " =    1.018
peak=    5.548 closest distance to " CG  ARG A 138 " =    1.292
peak=    5.484 closest distance to " O   HOH Z 374 " =    1.458
peak=    5.456 closest distance to " O   HOH Z 350 " =    1.629
peak=    5.433 closest distance to " O   HOH Z 255 " =    1.134
peak=    5.370 closest distance to " O   HOH Z  65 " =    1.799
peak=    5.268 closest distance to " O   HOH Z 410 " =    2.040
peak=    5.224 closest distance to " CD  ARG A 138 " =    0.977
peak=    5.202 closest distance to " O   HOH Z  27 " =    1.444
peak=    5.202 closest distance to " O   HOH Z 424 " =    2.132
peak=    5.184 closest distance to " O   HOH Z  46 " =    1.337
peak=    5.159 closest distance to " CB  PRO A  54 " =    1.190
peak=    5.115 closest distance to " O   HOH Z 403 " =    1.599
peak=    5.112 closest distance to " O   HOH Z 387 " =    1.436
peak=    5.107 closest distance to " O   HOH Z  63 " =    1.857
peak=    5.070 closest distance to " O   HOH Z 424 " =    1.653
peak=    5.049 closest distance to " O   HOH Z 214 " =    1.743
peak=    4.981 closest distance to " NE2 GLN A  11 " =    1.254
peak=    4.979 closest distance to " OG  SER A 276 " =    1.019
peak=    4.957 closest distance to " O   HOH Z  69 " =    2.139
peak=    4.954 closest distance to " CB  SER A 216 " =    1.094
peak=    4.951 closest distance to " NZ BLYS A 290 " =    1.245
peak=    4.906 closest distance to " CD1AILE A 234 " =    1.102
peak=    4.869 closest distance to " O   HOH Z 417 " =    1.600
peak=    4.860 closest distance to " O   PRO A 198 " =    1.331
peak=    4.839 closest distance to " O   HOH Z 117 " =    1.172
peak=    4.777 closest distance to " O   HOH Z 401 " =    1.382
peak=    4.739 closest distance to " O   HOH Z 226 " =    1.284
peak=    4.680 closest distance to " O   HOH Z  81 " =    1.065
peak=    4.647 closest distance to " OG ASER A 258 " =    3.105
peak=    4.644 closest distance to " CG2 THR A 279 " =    1.220
peak=    4.639 closest distance to " O   HOH Z 232 " =    2.092
peak=    4.604 closest distance to " O   HOH Z 133 " =    1.703
peak=    4.575 closest distance to " O   HOH Z 225 " =    1.796
peak=    4.526 closest distance to " O   HOH Z 105 " =    1.296
peak=    4.495 closest distance to " O   HOH Z 139 " =    2.003
peak=    4.467 closest distance to " CB  ASP A 124 " =    1.039
peak=    4.430 closest distance to " O   HOH Z   9 " =    1.735
peak=    4.422 closest distance to " CG  PRO A  54 " =    1.425
peak=    4.406 closest distance to " O   HOH Z 116 " =    1.716
peak=    4.398 closest distance to " O   HOH Z 416 " =    1.457
peak=    4.379 closest distance to " CD2 TRP A 179 " =    2.214
peak=    4.377 closest distance to " OG BSER A 258 " =    1.074
peak=    4.369 closest distance to " O   HOH Z 418 " =    1.230
peak=    4.363 closest distance to " O   HOH Z  97 " =    1.508
peak=    4.362 closest distance to " O   HOH Z 363 " =    1.252
peak=    4.361 closest distance to " CE  MET A  93 " =    1.507
peak=    4.357 closest distance to " O   HOH Z  57 " =    1.504
peak=    4.329 closest distance to " NH1 ARG A  56 " =    1.252
peak=    4.308 closest distance to " CB  VAL A 230 " =    1.272
peak=    4.291 closest distance to " O   HOH Z 426 " =    1.163
peak=    4.290 closest distance to " CD2 LEU A 228 " =    1.373
peak=    4.242 closest distance to " O   HOH Z 222 " =    1.479
peak=    4.209 closest distance to " O   HOH Z 411 " =    3.265
peak=    4.180 closest distance to " O   HOH Z 359 " =    1.500
peak=    4.147 closest distance to " CB  LYS A 290 " =    0.905
peak=    4.143 closest distance to " OE1 GLU A   2 " =    1.784
peak=    4.125 closest distance to " O   HOH Z  59 " =    1.657
peak=    4.114 closest distance to " O   HOH Z 427 " =    2.442
peak=    4.096 closest distance to " O   HOH Z 217 " =    2.788
peak=    4.092 closest distance to " O   HOH Z 233 " =    1.360
peak=    4.083 closest distance to " O   HOH Z 133 " =    2.545
peak=    4.077 closest distance to " CG  LEU A 228 " =    1.144
peak=    4.071 closest distance to " N   TYR A  15 " =    1.002
peak=    4.068 closest distance to " CG  LEU A   5 " =    1.190
peak=    4.063 closest distance to " CG  LEU A 167 " =    1.329
peak=    4.057 closest distance to " O   HOH Z  61 " =    1.320
peak=    4.048 closest distance to " O   HOH Z 238 " =    1.510
peak=    4.031 closest distance to " O   HOH Z  37 " =    1.235
peak=    4.026 closest distance to " CB  ARG A 275 " =    1.263
peak=    4.016 closest distance to " O   HOH Z 215 " =    1.741
peak=    4.015 closest distance to " CB  SER A   3 " =    1.588
peak=    3.990 closest distance to " O   HOH Z 126 " =    2.505
peak=    3.987 closest distance to " CD ALYS A 290 " =    1.163
peak=    3.979 closest distance to " CG2 THR A 221 " =    1.270
peak=    3.971 closest distance to " CA  ILE A 234 " =    1.171
peak=    3.961 closest distance to " O   HOH Z 147 " =    1.568
peak=    3.960 closest distance to " N   CYS A 260 " =    1.121
peak=    3.960 closest distance to " N   GLN A 278 " =    1.108
peak=    3.950 closest distance to " CB  ALA A  10 " =    1.286
peak=    3.933 closest distance to " O   HOH Z  30 " =    1.354
peak=    3.916 closest distance to " CB  ASN A 187 " =    1.052
peak=    3.898 closest distance to " O   HOH Z 116 " =    2.287
peak=    3.889 closest distance to " O   HOH Z 361 " =    1.659
peak=    3.887 closest distance to " O   HOH Z 400 " =    0.916
peak=    3.865 closest distance to " CB  SER A  63 " =    1.437
peak=    3.858 closest distance to " O   HOH Z 293 " =    1.307
peak=    3.857 closest distance to " O   HOH Z 239 " =    1.475
peak=    3.842 closest distance to " O   HOH Z 259 " =    2.346
peak=    3.826 closest distance to " CZ  PHE A 218 " =    1.167
peak=    3.805 closest distance to " NH1AARG A 145 " =    1.101
peak=    3.802 closest distance to " CG  GLN A  88 " =    1.034
peak=    3.801 closest distance to " ND2 ASN A 249 " =    0.861
peak=    3.799 closest distance to " O   HOH Z 158 " =    2.637
peak=    3.797 closest distance to " C   ASN A 209 " =    1.846
peak=    3.777 closest distance to " CD  ARG A  66 " =    2.182
peak=    3.773 closest distance to " O   HOH Z 183 " =    1.497
peak=    3.772 closest distance to " O   HOH Z 245 " =    1.047
peak=    3.772 closest distance to " O   HOH Z  24 " =    2.096
peak=    3.762 closest distance to " O   HOH Z 186 " =    1.483
peak=    3.757 closest distance to " O   HOH Z 193 " =    1.991
peak=    3.752 closest distance to " CZ3 TRP A 123 " =    1.469
peak=    3.745 closest distance to " CE3 TRP A 274 " =    1.437
peak=    3.743 closest distance to " O   HOH Z  57 " =    2.063
peak=    3.738 closest distance to " O   HOH Z 132 " =    1.209
peak=    3.737 closest distance to " CA  SER A  87 " =    0.933
peak=    3.736 closest distance to " CB  GLU A 128 " =    1.130
peak=    3.731 closest distance to " CB  ARG A 138 " =    1.232
peak=    3.729 closest distance to " O   HOH Z 287 " =    1.995
peak=    3.709 closest distance to " O   HOH Z 119 " =    1.428
peak=    3.707 closest distance to " O   HOH Z 144 " =    1.794
peak=    3.704 closest distance to " O   HOH Z  78 " =    1.858
peak=    3.695 closest distance to " N   GLY A 136 " =    1.118
peak=    3.693 closest distance to " O   HOH Z 112 " =    1.098
peak=    3.691 closest distance to " O   HOH Z 389 " =    1.686
peak=    3.688 closest distance to " CG2 THR A 251 " =    1.610
peak=    3.686 closest distance to " CE2 TYR A 186 " =    0.881
peak=    3.664 closest distance to " CA  VAL A 153 " =    1.117
peak=    3.653 closest distance to " O   HOH Z  56 " =    2.161
peak=    3.653 closest distance to " O   HOH Z 423 " =    1.920
peak=    3.652 closest distance to " O   HOH Z 258 " =    2.466
peak=    3.647 closest distance to " CB  PHE A 225 " =    1.677
peak=    3.647 closest distance to " CZ  PHE A 192 " =    0.929
peak=    3.646 closest distance to " CG2 ILE A 234 " =    1.165
peak=    3.629 closest distance to " O   HOH Z 414 " =    2.132
peak=    3.628 closest distance to " CG  PRO A 213 " =    1.329
peak=    3.627 closest distance to " O   HOH Z 368 " =    2.005
peak=    3.624 closest distance to " CB  ASP A  50 " =    1.252
peak=    3.619 closest distance to " CG2 THR A 178 " =    1.345
peak=    3.616 closest distance to " CB  TRP A 179 " =    1.445
peak=    3.611 closest distance to " O   THR A 220 " =    1.804
peak=    3.610 closest distance to " CD  GLN A  58 " =    5.624
peak=    3.607 closest distance to " OE1 GLN A  88 " =    0.947
peak=    3.596 closest distance to " CB  ALA A 137 " =    1.025
peak=    3.585 closest distance to " N   GLN A  73 " =    1.111
peak=    3.576 closest distance to " CB  GLN A 103 " =    1.296
peak=    3.571 closest distance to " CB  MET A  47 " =    1.212
peak=    3.567 closest distance to " O   HOH Z 217 " =    1.964
peak=    3.566 closest distance to " OE1 GLN A 278 " =    1.474
peak=    3.566 closest distance to " O   HOH Z 247 " =    1.495
peak=    3.566 closest distance to " OD2 ASP A 270 " =    1.004
peak=    3.554 closest distance to " O   HOH Z 178 " =    1.178
peak=    3.549 closest distance to " CB  TYR A 169 " =    0.805
peak=    3.544 closest distance to " CB  SER A 273 " =    0.962
peak=    3.544 closest distance to " CG1BVAL A 121 " =    2.350
peak=    3.540 closest distance to " O   HOH Z 104 " =    1.644
peak=    3.533 closest distance to " CG  PRO A 280 " =    0.955
peak=    3.522 closest distance to " O   HOH Z 207 " =    2.388
peak=    3.521 closest distance to " O   HOH Z 248 " =    2.077
peak=    3.515 closest distance to " O   HOH Z 360 " =    1.185
peak=    3.509 closest distance to " OE1 GLN A 240 " =    1.808
peak=    3.509 closest distance to " O   HOH Z  49 " =    1.197
peak=    3.507 closest distance to " CB  GLN A 223 " =    1.274
peak=    3.504 closest distance to " O   HOH Z 412 " =    2.072
peak=    3.503 closest distance to " CG  PRO A 243 " =    1.119
peak=    3.503 closest distance to " O   HOH Z 143 " =    1.494
peak=    3.500 closest distance to " N   ALA A 154 " =    0.700
peak=    3.489 closest distance to " N   SER A  97 " =    0.747
peak=    3.486 closest distance to " CB  GLN A 183 " =    1.181
peak=    3.485 closest distance to " O   HOH Z 392 " =    1.310
peak=    3.480 closest distance to " O   HOH Z 167 " =    1.719
peak=    3.476 closest distance to " O   HOH Z  48 " =    1.597
peak=    3.471 closest distance to " CB  ALA A 184 " =    1.057
peak=    3.469 closest distance to " O   HOH Z 381 " =    1.081
peak=    3.468 closest distance to " O   HOH Z 184 " =    1.942
peak=    3.465 closest distance to " O   HOH Z 353 " =    2.279
peak=    3.458 closest distance to " CA  MET A  47 " =    1.177
peak=    3.456 closest distance to " CG  ARG A 159 " =    0.912
peak=    3.455 closest distance to " O   HOH Z 159 " =    0.958
peak=    3.454 closest distance to " CB  ASN A 285 " =    1.063
peak=    3.451 closest distance to " CG  LYS A  76 " =    1.595
peak=    3.450 closest distance to " O   HOH Z 357 " =    1.467
peak=    3.444 closest distance to " NH2 ARG A 269 " =    0.884
peak=    3.440 closest distance to " CA  ASP A 124 " =    0.818
peak=    3.437 closest distance to " ND2 ASN A  60 " =    2.986
peak=    3.436 closest distance to " N   SER A 210 " =    0.944
peak=    3.436 closest distance to " O   HOH Z 287 " =    1.745
peak=    3.436 closest distance to " O   HOH Z 380 " =    1.914
peak=    3.435 closest distance to " O   HOH Z  24 " =    2.078
peak=    3.431 closest distance to " O   HOH Z 332 " =    1.625
peak=    3.426 closest distance to " O   HOH Z 239 " =    1.674
peak=    3.422 closest distance to " CG2 THR A 235 " =    0.952
peak=    3.420 closest distance to " O   HOH Z 127 " =    1.156
peak=    3.419 closest distance to " O   THR A 251 " =    1.274
peak=    3.411 closest distance to " OD2 ASP A 286 " =    2.649
peak=    3.411 closest distance to " NH2BARG A 190 " =    1.502
peak=    3.405 closest distance to " O   HOH Z 358 " =    1.641
peak=    3.400 closest distance to " O   HOH Z 384 " =    1.759
peak=    3.399 closest distance to " CA  ASN A 284 " =    1.060
peak=    3.396 closest distance to " O   ARG A  14 " =    0.969
peak=    3.394 closest distance to " ND2 ASN A 285 " =    1.002
peak=    3.387 closest distance to " O   HOH Z 328 " =    1.655
peak=    3.387 closest distance to " O   HOH Z  26 " =    1.686
peak=    3.387 closest distance to " O   HOH Z 232 " =    2.147
peak=    3.384 closest distance to " O   HOH Z 148 " =    1.864
peak=    3.381 closest distance to " O   HOH Z  51 " =    1.996
peak=    3.378 closest distance to " C   ILE A 109 " =    1.359
peak=    3.374 closest distance to " NE AARG A 145 " =    1.200
peak=    3.374 closest distance to " N   LYS A 290 " =    1.248
peak=    3.372 closest distance to " CA  TRP A  92 " =    1.396
peak=    3.372 closest distance to " N   GLU A   2 " =    1.445
peak=    3.369 closest distance to " O   HOH Z 373 " =    2.188
peak=    3.368 closest distance to " O   HOH Z 411 " =    1.425
peak=    3.365 closest distance to " CB  ASN A 148 " =    1.281
peak=    3.364 closest distance to " CE1 HIS A  81 " =    1.769
peak=    3.362 closest distance to " CG  PRO A 198 " =    1.404
peak=    3.361 closest distance to " O   HOH Z  68 " =    1.833
peak=    3.360 closest distance to " CD1 LEU A   5 " =    1.103
peak=    3.359 closest distance to " O   HOH Z   6 " =    1.984
peak=    3.358 closest distance to " OD1 ASN A 217 " =    1.672
peak=    3.356 closest distance to " O   HOH Z 135 " =    1.528
peak=    3.355 closest distance to " CB  ASN A  39 " =    0.828
peak=    3.355 closest distance to " CG2 ILE A 109 " =    1.002
peak=    3.355 closest distance to " CB  ALA A  43 " =    1.113
peak=    3.352 closest distance to " CA  GLU A 152 " =    1.026
peak=    3.346 closest distance to " O   HOH Z 369 " =    2.325
peak=    3.343 closest distance to " O   HOH Z 434 " =    1.458
peak=    3.343 closest distance to " O   HOH Z  15 " =    1.431
peak=    3.341 closest distance to " CB  GLU A   2 " =    1.089
peak=    3.340 closest distance to " O   HOH Z  94 " =    2.295
peak=    3.339 closest distance to " NH2 ARG A 219 " =    1.827
peak=    3.336 closest distance to " CE1 TYR A  15 " =    1.338
peak=    3.333 closest distance to " O   HOH Z 286 " =    1.495
peak=    3.332 closest distance to " CG2 THR A   4 " =    1.026
peak=    3.332 closest distance to " N   VAL A 296 " =    1.825
peak=    3.330 closest distance to " O   HOH Z   7 " =    2.930
peak=    3.325 closest distance to " O   HOH Z 111 " =    1.334
peak=    3.324 closest distance to " CA  ASN A 127 " =    1.287
peak=    3.323 closest distance to " CE2 PHE A  16 " =    0.905
peak=    3.320 closest distance to " O   HOH Z 271 " =    1.469
peak=    3.319 closest distance to " CB  SER A 210 " =    1.004
peak=    3.317 closest distance to " O   HOH Z 298 " =    2.138
peak=    3.316 closest distance to " N   PHE A 130 " =    1.284
peak=    3.316 closest distance to " O   ASN A 285 " =    0.826
peak=    3.315 closest distance to " OD1 ASN A  45 " =    1.381
peak=    3.310 closest distance to " O   HOH Z  53 " =    2.211
peak=    3.304 closest distance to " O   HOH Z 153 " =    3.698
peak=    3.304 closest distance to " CB  LEU A 300 " =    0.963
peak=    3.302 closest distance to " CA  THR A 264 " =    0.796
peak=    3.293 closest distance to " CG1 ILE A 120 " =    1.532
peak=    3.285 closest distance to " CA  ALA A 295 " =    0.989
peak=    3.280 closest distance to " CB  ASN A 127 " =    0.813
peak=    3.279 closest distance to " O   HOH Z 168 " =    1.865
peak=    3.279 closest distance to " CA  SER A  12 " =    1.695
peak=    3.277 closest distance to " NE2 GLN A  89 " =    1.603
peak=    3.277 closest distance to " CA  ALA A 299 " =    0.957
peak=    3.274 closest distance to " CG2 THR A 294 " =    1.177
peak=    3.272 closest distance to " CD1 ILE A  33 " =    1.887
peak=    3.272 closest distance to " O   HOH Z 406 " =    1.890
peak=    3.270 closest distance to " CH2 TRP A 150 " =    0.918
peak=    3.270 closest distance to " NH1AARG A 275 " =    1.107
peak=    3.268 closest distance to " O   HOH Z 172 " =    5.994
peak=    3.266 closest distance to " CB  MET A  40 " =    0.800
peak=    3.265 closest distance to " CG1 ILE A 263 " =    1.491
peak=    3.264 closest distance to " O   HOH Z 189 " =    3.034
peak=    3.264 closest distance to " CB  THR A  82 " =    1.076
peak=    3.264 closest distance to " O   HOH Z  55 " =    2.220
peak=    3.262 closest distance to " CE AMET A  47 " =    1.534
peak=    3.259 closest distance to " CB  ASN A  60 " =    0.981
peak=    3.258 closest distance to " CB  ARG A 156 " =    1.273
peak=    3.256 closest distance to " O   HOH Z 197 " =    2.202
peak=    3.256 closest distance to " NE2 GLN A  58 " =    3.934
peak=    3.254 closest distance to " CA  GLY A 267 " =    1.393
peak=    3.252 closest distance to " O   HOH Z 371 " =    2.060
peak=    3.250 closest distance to " CG2 ILE A 151 " =    0.966
peak=    3.247 closest distance to " NZ  LYS A 117 " =    1.337
peak=    3.247 closest distance to " O   HOH Z 261 " =    2.072
peak=    3.242 closest distance to " O   HOH Z 158 " =    2.731
peak=    3.235 closest distance to " CG  GLU A   2 " =    1.141
peak=    3.235 closest distance to " O   HOH Z 433 " =    2.817
peak=    3.233 closest distance to " O   HOH Z 124 " =    2.576
peak=    3.232 closest distance to " O   HOH Z 110 " =    1.469
peak=    3.231 closest distance to " O   HOH Z   9 " =    1.995
peak=    3.230 closest distance to " CG  LYS A 193 " =    1.658
peak=    3.226 closest distance to " CA  ALA A 160 " =    0.999
peak=    3.219 closest distance to " CD2 LEU A 237 " =    0.831
peak=    3.219 closest distance to " O   HOH Z  88 " =    2.592
peak=    3.216 closest distance to " OG ASER A 134 " =    1.216
peak=    3.214 closest distance to " O   HOH Z 325 " =    1.802
peak=    3.207 closest distance to " O   HOH Z 343 " =    1.696
peak=    3.195 closest distance to " CG2 VAL A 296 " =    0.998
peak=    3.194 closest distance to " NH1BARG A 190 " =    1.660
peak=    3.194 closest distance to " CG1AVAL A  72 " =    1.338
peak=    3.193 closest distance to " O   HOH Z  50 " =    1.507
peak=    3.190 closest distance to " CB  TRP A 266 " =    0.902
peak=    3.190 closest distance to " O   SER A  26 " =    1.457
peak=    3.188 closest distance to " O   HOH Z   1 " =    1.871
peak=    3.186 closest distance to " OD1 ASP A  50 " =    1.014
peak=    3.185 closest distance to " CB  PHE A  16 " =    1.143
peak=    3.184 closest distance to " O   HOH Z 284 " =    2.872
peak=    3.183 closest distance to " CB  ALA A 114 " =    1.072
peak=    3.182 closest distance to " N   ASN A 285 " =    0.702
peak=    3.182 closest distance to " O   HOH Z 118 " =    1.843
peak=    3.179 closest distance to " ND2 ASN A 284 " =    0.858
peak=    3.176 closest distance to " O   ALA A 165 " =    1.373
peak=    3.175 closest distance to " OD2 ASP A  50 " =    1.060
peak=    3.174 closest distance to " ND2BASN A 224 " =    0.937
peak=    3.174 closest distance to " O   HOH Z 427 " =    1.326
peak=    3.173 closest distance to " CG2 VAL A 202 " =    1.483
peak=    3.169 closest distance to " CA  PHE A 283 " =    1.521
peak=    3.162 closest distance to " CG2 VAL A 202 " =    1.439
peak=    3.160 closest distance to " CA  LEU A 222 " =    1.127
peak=    3.156 closest distance to " O   HOH Z 407 " =    2.528
peak=    3.152 closest distance to " CB  GLU A 236 " =    1.347
peak=    3.150 closest distance to " CG2 ILE A 239 " =    1.793
peak=    3.149 closest distance to " CB  VAL A 202 " =    1.518
peak=    3.148 closest distance to " O   HOH Z 129 " =    1.122
peak=    3.147 closest distance to " CA  TYR A  30 " =    1.070
peak=    3.139 closest distance to " CD2 LEU A 281 " =    1.083
peak=    3.135 closest distance to " CB  ALA A 104 " =    0.893
peak=    3.131 closest distance to " CB  GLU A 277 " =    3.627
peak=    3.129 closest distance to " N   SER A  63 " =    0.877
peak=    3.127 closest distance to " O   HOH Z 272 " =    1.883
peak=    3.116 closest distance to " O   HOH Z 378 " =    1.189
peak=    3.115 closest distance to " O   HOH Z 171 " =    2.101
peak=    3.114 closest distance to " O   HOH Z 371 " =    2.506
peak=    3.110 closest distance to " CA  ALA A  51 " =    1.069
peak=    3.106 closest distance to " O   HOH Z 151 " =    1.295
peak=    3.097 closest distance to " O   ALA A 158 " =    1.342
peak=    3.090 closest distance to " O   HOH Z 115 " =    1.762
peak=    3.089 closest distance to " N   GLY A 287 " =    0.986
peak=    3.088 closest distance to " CZ  PHE A  16 " =    0.986
peak=    3.079 closest distance to " CB  SER A  62 " =    1.281
peak=    3.076 closest distance to " ND2 ASN A  60 " =    1.243
peak=    3.073 closest distance to " O   HOH Z  11 " =    1.096
peak=    3.072 closest distance to " O   HOH Z 353 " =    1.976
peak=    3.065 closest distance to " CB  ARG A  79 " =    1.289
peak=    3.063 closest distance to " O   HOH Z 375 " =    1.991
peak=    3.058 closest distance to " O   HOH Z 368 " =    1.110
peak=    3.055 closest distance to " CE3 TRP A  85 " =    0.879
peak=    3.053 closest distance to " CD1 LEU A 228 " =    1.660
peak=    3.052 closest distance to " O   HOH Z 279 " =    2.539
peak=    3.045 closest distance to " CA  ARG A 195 " =    1.344
peak=    3.039 closest distance to " CB  SER A 276 " =    1.245
peak=    3.030 closest distance to " O   HOH Z  91 " =    2.211
peak=    3.029 closest distance to " O   HOH Z  48 " =    1.581
peak=    3.025 closest distance to " OD1 ASP A 298 " =    2.440

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.200 - 5.738
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 202
   mapped sites are within: 0.713 - 5.738

peak=   -5.091 closest distance to " CD  ARG A 138 " =    1.077
peak=   -4.820 closest distance to " O   HOH Z 163 " =    1.259
peak=   -4.776 closest distance to " CG1 VAL A 296 " =    0.822
peak=   -4.523 closest distance to " CG2 VAL A 230 " =    0.902
peak=   -4.457 closest distance to " CB  ASP A  27 " =    2.588
peak=   -4.456 closest distance to " CG  MET A 105 " =    0.920
peak=   -4.297 closest distance to " OE1 GLU A 277 " =    2.556
peak=   -4.198 closest distance to " O   PRO A 198 " =    1.266
peak=   -4.151 closest distance to " CD  ARG A  14 " =    3.103
peak=   -4.145 closest distance to " OG  SER A  97 " =    2.036
peak=   -4.144 closest distance to " OE1 GLN A  88 " =    0.980
peak=   -4.107 closest distance to " CB  PHE A 130 " =    1.122
peak=   -4.048 closest distance to " OG BSER A 134 " =    1.797
peak=   -4.024 closest distance to " O   THR A 178 " =    0.905
peak=   -3.994 closest distance to " C   ASP A  50 " =    1.343
peak=   -3.936 closest distance to " CD2 TYR A 116 " =    2.169
peak=   -3.908 closest distance to " OG1 THR A 157 " =    1.492
peak=   -3.895 closest distance to " CA  GLY A 133 " =    2.015
peak=   -3.874 closest distance to " O   ALA A  51 " =    1.480
peak=   -3.854 closest distance to " CG BLYS A 290 " =    0.798
peak=   -3.837 closest distance to " O   HOH Z  28 " =    1.167
peak=   -3.826 closest distance to " OG  SER A  26 " =    1.058
peak=   -3.825 closest distance to " O   HOH Z  52 " =    0.925
peak=   -3.820 closest distance to " OG ASER A 134 " =    0.995
peak=   -3.817 closest distance to " O   HOH Z 371 " =    1.984
peak=   -3.807 closest distance to " CG  GLN A  88 " =    0.880
peak=   -3.797 closest distance to " O   HOH Z 255 " =    0.919
peak=   -3.794 closest distance to " O   HOH Z 313 " =    1.485
peak=   -3.793 closest distance to " CD  LYS A 289 " =    2.214
peak=   -3.759 closest distance to " N   SER A  12 " =    1.097
peak=   -3.739 closest distance to " O   HOH Z 389 " =    2.190
peak=   -3.738 closest distance to " N   GLN A  58 " =    1.244
peak=   -3.732 closest distance to " O   HOH Z 431 " =    1.260
peak=   -3.697 closest distance to " O   HOH Z 111 " =    1.891
peak=   -3.697 closest distance to " O   HOH Z 207 " =    2.180
peak=   -3.696 closest distance to " O   HOH Z 404 " =    1.053
peak=   -3.683 closest distance to " CA  GLY A  35 " =    1.839
peak=   -3.659 closest distance to " O   HOH Z  52 " =    1.670
peak=   -3.641 closest distance to " N   VAL A 125 " =    1.017
peak=   -3.639 closest distance to " O   HOH Z 231 " =    0.787
peak=   -3.630 closest distance to " O   HOH Z  54 " =    0.864
peak=   -3.624 closest distance to " O   HOH Z  39 " =    0.929
peak=   -3.617 closest distance to " NE2 GLN A 223 " =    1.413
peak=   -3.617 closest distance to " CD2 LEU A 228 " =    1.165
peak=   -3.611 closest distance to " CD1 TRP A 179 " =    1.054
peak=   -3.601 closest distance to " C   PHE A 155 " =    0.856
peak=   -3.599 closest distance to " CG  PRO A 163 " =    2.458
peak=   -3.597 closest distance to " O   HOH Z 300 " =    1.042
peak=   -3.594 closest distance to " C   ILE A 239 " =    1.869
peak=   -3.591 closest distance to " O   HOH Z 102 " =    1.968
peak=   -3.588 closest distance to " CD2 LEU A 237 " =    2.555
peak=   -3.580 closest distance to " OD1 ASN A 249 " =    1.293
peak=   -3.578 closest distance to " O   ASN A 187 " =    1.764
peak=   -3.577 closest distance to " O   HOH Z  24 " =    1.343
peak=   -3.567 closest distance to " O   HOH Z 198 " =    2.467
peak=   -3.564 closest distance to " CB  ALA A 291 " =    1.646
peak=   -3.564 closest distance to " O   SER A 245 " =    1.461
peak=   -3.563 closest distance to " O   GLY A  80 " =    2.444
peak=   -3.557 closest distance to " C   ASN A 285 " =    2.330
peak=   -3.544 closest distance to " O   HOH Z 385 " =    1.021
peak=   -3.538 closest distance to " CG  MET A 185 " =    2.418
peak=   -3.536 closest distance to " OD1 ASP A 107 " =    1.140
peak=   -3.534 closest distance to " O   HOH Z  51 " =    0.972
peak=   -3.530 closest distance to " O   HOH Z 286 " =    1.600
peak=   -3.527 closest distance to " O  BHOH Z  74 " =    2.865
peak=   -3.518 closest distance to " O   MET A  47 " =    2.627
peak=   -3.507 closest distance to " O   ALA A 226 " =    1.446
peak=   -3.501 closest distance to " CG  GLN A 223 " =    2.406
peak=   -3.493 closest distance to " ND2BASN A 224 " =    1.401
peak=   -3.489 closest distance to " O   HOH Z 435 " =    2.380
peak=   -3.487 closest distance to " CA  GLY A  98 " =    2.119
peak=   -3.466 closest distance to " O   HOH Z 369 " =    1.598
peak=   -3.453 closest distance to " O   HOH Z 177 " =    2.590
peak=   -3.451 closest distance to " O   GLY A 136 " =    1.989
peak=   -3.438 closest distance to " O   HOH Z 426 " =    1.740
peak=   -3.433 closest distance to " O   HOH Z 290 " =    1.365
peak=   -3.432 closest distance to " O   THR A  82 " =    1.320
peak=   -3.432 closest distance to " O   GLN A  11 " =    1.458
peak=   -3.423 closest distance to " CG  ARG A 139 " =    1.699
peak=   -3.413 closest distance to " O   HOH Z 381 " =    1.076
peak=   -3.413 closest distance to " CZ  PHE A  38 " =    2.570
peak=   -3.412 closest distance to " CD1 PHE A  59 " =    1.908
peak=   -3.408 closest distance to " O   HOH Z 300 " =    2.243
peak=   -3.405 closest distance to " O   HOH Z  14 " =    1.465
peak=   -3.403 closest distance to " O   HOH Z 117 " =    1.056
peak=   -3.402 closest distance to " OG  SER A  63 " =    1.404
peak=   -3.401 closest distance to " NE2 GLN A  55 " =    0.713
peak=   -3.394 closest distance to " CG  LEU A 228 " =    0.896
peak=   -3.381 closest distance to " OG  SER A 206 " =    1.686
peak=   -3.377 closest distance to " CD  GLU A 277 " =    1.260
peak=   -3.375 closest distance to " OD1 ASP A 171 " =    1.520
peak=   -3.375 closest distance to " CB  ASN A  45 " =    2.331
peak=   -3.373 closest distance to " O   TRP A  70 " =    1.473
peak=   -3.372 closest distance to " OE1 GLN A  58 " =    5.319
peak=   -3.368 closest distance to " O   HOH Z  61 " =    0.768
peak=   -3.367 closest distance to " N   PHE A 283 " =    1.519
peak=   -3.367 closest distance to " OD1 ASN A  60 " =    1.071
peak=   -3.362 closest distance to " CG2 THR A  31 " =    2.207
peak=   -3.356 closest distance to " OE1 GLN A 278 " =    1.218
peak=   -3.354 closest distance to " OG  SER A  87 " =    1.440
peak=   -3.349 closest distance to " ND2 ASN A 284 " =    1.244
peak=   -3.346 closest distance to " CG  ASN A 127 " =    1.165
peak=   -3.346 closest distance to " CB  ASN A 301 " =    1.935
peak=   -3.345 closest distance to " CG2 ILE A 120 " =    1.384
peak=   -3.344 closest distance to " O   HOH Z 177 " =    1.495
peak=   -3.340 closest distance to " O   HOH Z  84 " =    1.050
peak=   -3.337 closest distance to " NH1 ARG A 138 " =    1.017
peak=   -3.337 closest distance to " CB  ASN A  39 " =    2.282
peak=   -3.336 closest distance to " O   ALA A   1 " =    1.283
peak=   -3.330 closest distance to " N   ARG A 138 " =    1.696
peak=   -3.323 closest distance to " CB  SER A  62 " =    5.400
peak=   -3.323 closest distance to " O   GLY A 118 " =    1.918
peak=   -3.322 closest distance to " CB  ALA A 114 " =    2.502
peak=   -3.316 closest distance to " O   ASP A 298 " =    1.904
peak=   -3.315 closest distance to " NH2 ARG A  79 " =    2.040
peak=   -3.313 closest distance to " O   HOH Z  95 " =    1.570
peak=   -3.313 closest distance to " O   HOH Z 359 " =    1.813
peak=   -3.309 closest distance to " OD2 ASP A 140 " =    0.968
peak=   -3.304 closest distance to " O   HOH Z 368 " =    1.841
peak=   -3.303 closest distance to " O   HOH Z 121 " =    3.743
peak=   -3.298 closest distance to " O   SER A   3 " =    2.326
peak=   -3.295 closest distance to " O   HOH Z 378 " =    2.098
peak=   -3.292 closest distance to " CA  GLY A 203 " =    2.428
peak=   -3.292 closest distance to " O   HOH Z 257 " =    1.188
peak=   -3.292 closest distance to " CA  SER A  32 " =    1.555
peak=   -3.290 closest distance to " O   HOH Z 337 " =    1.494
peak=   -3.290 closest distance to " O   HOH Z 245 " =    0.825
peak=   -3.284 closest distance to " CG  MET A  40 " =    2.232
peak=   -3.283 closest distance to " O   HOH Z 390 " =    2.373
peak=   -3.278 closest distance to " O   HOH Z 275 " =    1.877
peak=   -3.275 closest distance to " O   ILE A 106 " =    2.146
peak=   -3.272 closest distance to " O   HOH Z 416 " =    1.070
peak=   -3.270 closest distance to " CB  ALA A 161 " =    1.443
peak=   -3.270 closest distance to " O   ASP A 253 " =    1.684
peak=   -3.269 closest distance to " CD  GLN A  77 " =    1.276
peak=   -3.267 closest distance to " CZ  ARG A  24 " =    2.005
peak=   -3.265 closest distance to " O   HOH Z 432 " =    3.786
peak=   -3.264 closest distance to " O   SER A 135 " =    1.518
peak=   -3.262 closest distance to " O   HOH Z  88 " =    2.036
peak=   -3.259 closest distance to " OG  SER A 245 " =    1.502
peak=   -3.249 closest distance to " O   ARG A 145 " =    1.438
peak=   -3.247 closest distance to " O   ASN A 301 " =    1.433
peak=   -3.244 closest distance to " CB  ILE A 199 " =    2.612
peak=   -3.242 closest distance to " CA  TYR A  68 " =    1.099
peak=   -3.241 closest distance to " O   HOH Z 246 " =    0.823
peak=   -3.241 closest distance to " O   HOH Z  97 " =    1.079
peak=   -3.240 closest distance to " O   HOH Z  56 " =    0.855
peak=   -3.232 closest distance to " OG  SER A 273 " =    2.379
peak=   -3.231 closest distance to " C   GLU A 236 " =    1.030
peak=   -3.231 closest distance to " O   HOH Z 166 " =    1.493
peak=   -3.230 closest distance to " O   LEU A 297 " =    0.944
peak=   -3.220 closest distance to " CA  GLY A 241 " =    2.109
peak=   -3.218 closest distance to " O   HOH Z 189 " =    3.298
peak=   -3.212 closest distance to " O   GLY A 203 " =    2.537
peak=   -3.205 closest distance to " O   HOH Z  69 " =    1.045
peak=   -3.205 closest distance to " OE1 GLU A  44 " =    1.659
peak=   -3.203 closest distance to " NH2AARG A 275 " =    5.738
peak=   -3.197 closest distance to " O   HOH Z 139 " =    2.194
peak=   -3.196 closest distance to " O   HOH Z 354 " =    2.686
peak=   -3.195 closest distance to " O   HOH Z 211 " =    1.156
peak=   -3.191 closest distance to " O   LEU A 101 " =    1.333
peak=   -3.190 closest distance to " C   ALA A 299 " =    1.232
peak=   -3.189 closest distance to " O   HOH Z  43 " =    1.726
peak=   -3.186 closest distance to " CG1 VAL A  78 " =    2.183
peak=   -3.185 closest distance to " O   HOH Z 166 " =    1.746
peak=   -3.183 closest distance to " OD2 ASP A 270 " =    1.049
peak=   -3.171 closest distance to " CB  ALA A 248 " =    1.969
peak=   -3.170 closest distance to " CB  PHE A  61 " =    1.405
peak=   -3.169 closest distance to " CA  GLY A  57 " =    2.142
peak=   -3.169 closest distance to " ND2 ASN A 285 " =    2.123
peak=   -3.165 closest distance to " O   HOH Z 352 " =    1.641
peak=   -3.158 closest distance to " CB  ALA A   9 " =    2.641
peak=   -3.156 closest distance to " O   HOH Z 174 " =    2.870
peak=   -3.152 closest distance to " O   HOH Z 135 " =    0.875
peak=   -3.151 closest distance to " CB  PHE A 208 " =    2.069
peak=   -3.131 closest distance to " OD1 ASN A  60 " =    1.376
peak=   -3.126 closest distance to " O   TYR A  30 " =    1.795
peak=   -3.122 closest distance to " CA  VAL A 296 " =    1.276
peak=   -3.120 closest distance to " CD2 LEU A   5 " =    0.896
peak=   -3.120 closest distance to " C   VAL A 265 " =    1.093
peak=   -3.119 closest distance to " CA  ASN A 110 " =    0.922
peak=   -3.118 closest distance to " O   SER A 216 " =    2.205
peak=   -3.116 closest distance to " CE3 TRP A 179 " =    1.281
peak=   -3.107 closest distance to " CG2 THR A 279 " =    2.530
peak=   -3.107 closest distance to " CD  LYS A 166 " =    2.583
peak=   -3.105 closest distance to " CG  PRO A 243 " =    1.586
peak=   -3.104 closest distance to " O   HOH Z 105 " =    2.141
peak=   -3.097 closest distance to " O   HOH Z  37 " =    1.334
peak=   -3.095 closest distance to " O   HOH Z 282 " =    4.240
peak=   -3.095 closest distance to " O   HOH Z 280 " =    1.608
peak=   -3.093 closest distance to " CG  TYR A 172 " =    1.982
peak=   -3.091 closest distance to " N   ASN A 127 " =    1.411
peak=   -3.081 closest distance to " O   HOH Z 298 " =    0.927
peak=   -3.079 closest distance to " O   HOH Z  83 " =    1.473
peak=   -3.064 closest distance to " O   HOH Z 433 " =    1.705
peak=   -3.057 closest distance to " C   PHE A  59 " =    1.089
peak=   -3.048 closest distance to " O   HOH Z  60 " =    1.559
peak=   -3.001 closest distance to " O   HOH Z  51 " =    1.407
peak=   -2.967 closest distance to " CG1 VAL A 296 " =    1.705

================= 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    :  0.5065 0.5037   6.308699e+00   6.299203e+00
   1_bss:  0.4979 0.4920   6.304742e+00   6.294186e+00
   1_xyz:  0.4420 0.4683   6.249245e+00   6.272333e+00
   1_adp:  0.4062 0.4682   6.218805e+00   6.275381e+00
   1_occ:  0.4060 0.4671   6.218316e+00   6.275426e+00
   2_bss:  0.4042 0.4643   6.218531e+00   6.274071e+00
   2_xyz:  0.3565 0.4363   6.121777e+00   6.227013e+00
   2_adp:  0.3415 0.4250   6.101198e+00   6.212575e+00
   2_occ:  0.3411 0.4246   6.100685e+00   6.212418e+00
   3_bss:  0.3410 0.4228   6.101062e+00   6.211414e+00
   3_xyz:  0.2919 0.3656   5.972383e+00   6.116006e+00
   3_adp:  0.2699 0.3478   5.923309e+00   6.085460e+00
   3_occ:  0.2697 0.3470   5.922056e+00   6.084664e+00
   4_bss:  0.2687 0.3471   5.922604e+00   6.083695e+00
   4_xyz:  0.2177 0.2869   5.735151e+00   5.928702e+00
   4_adp:  0.1946 0.2622   5.642610e+00   5.856531e+00
   4_occ:  0.1945 0.2617   5.641252e+00   5.855260e+00
   5_bss:  0.1943 0.2619   5.642069e+00   5.854375e+00
   5_xyz:  0.1580 0.2180   5.459019e+00   5.695415e+00
   5_adp:  0.1463 0.2021   5.391373e+00   5.628113e+00
   5_occ:  0.1461 0.2018   5.389933e+00   5.626493e+00
   5_bss:  0.1465 0.2017   5.388984e+00   5.625287e+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:  0.350   4.929   8.460   9.110   6.994   0.000   0.000   0.000
   1_xyz:  0.350   4.929   8.460   9.110   6.994   0.000   0.000   0.000
   1_adp:  0.350   4.929   8.460   9.110   6.994   0.000   0.000   0.000
   1_occ:  0.350   4.929   8.460   9.110   6.994   0.000   0.000   0.000
   2_bss:  0.346  33.816   5.028   5.030   3.762   0.000   0.000   0.000
   2_xyz:  0.346  33.816   5.028   5.030   3.762   0.000   0.000   0.000
   2_adp:  0.346  33.816   5.028   5.030   3.762   0.000   0.000   0.000
   2_occ:  0.346  33.816   5.028   5.030   3.762   0.000   0.000   0.000
   3_bss:  0.322  41.338   3.135   2.732   3.046   0.000   0.000   0.000
   3_xyz:  0.322  41.338   3.135   2.732   3.046   0.000   0.000   0.000
   3_adp:  0.322  41.338   3.135   2.732   3.046   0.000   0.000   0.000
   3_occ:  0.322  41.338   3.135   2.732   3.046   0.000   0.000   0.000
   4_bss:  0.315  49.800   1.493   0.988   1.877   0.000   0.000   0.000
   4_xyz:  0.315  49.800   1.493   0.988   1.877   0.000   0.000   0.000
   4_adp:  0.315  49.800   1.493   0.988   1.877   0.000   0.000   0.000
   4_occ:  0.315  49.800   1.493   0.988   1.877   0.000   0.000   0.000
   5_bss:  0.323  49.800   0.876   0.061   1.491   0.000   0.000   0.000
   5_xyz:  0.323  49.800   0.876   0.061   1.491   0.000   0.000   0.000
   5_adp:  0.323  49.800   0.876   0.061   1.491   0.000   0.000   0.000
   5_occ:  0.323  49.800   0.876   0.061   1.491   0.000   0.000   0.000
   5_bss:  0.318  53.096   0.084  -0.857   0.773  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.330 0.3378  0.4127    84890.910
   1_bss:  64.163 0.3392  0.5238    83824.108
   1_xyz:  59.528 0.3984  0.6026    73787.058
   1_adp:  59.970 0.3923  0.6519    74871.495
   1_occ:  59.958 0.3926  0.6518    74983.621
   2_bss:  59.523 0.3980  0.5907    74145.345
   2_xyz:  51.638 0.4981  0.7386    58386.655
   2_adp:  49.390 0.5268  0.7874    55202.118
   2_occ:  49.391 0.5268  0.7866    55146.628
   3_bss:  49.140 0.5298  0.7477    54690.751
   3_xyz:  40.070 0.6404  0.8876    38455.197
   3_adp:  37.400 0.6726  0.9250    34679.998
   3_occ:  37.364 0.6729  0.9246    34532.578
   4_bss:  37.301 0.6738  0.8777    34523.326
   4_xyz:  29.889 0.7574  0.9516    22150.842
   4_adp:  26.622 0.7936  0.9637    18316.686
   4_occ:  26.575 0.7940  0.9636    18230.267
   5_bss:  26.582 0.7941  0.9420    18258.188
   5_xyz:  21.604 0.8448  0.9758    12411.636
   5_adp:  19.673 0.8645  0.9780    10813.621
   5_occ:  19.634 0.8648  0.9777    10747.946
   5_bss:  19.574 0.8652  0.9661    10668.584
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3545e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3545e+01
   1_xyz:   1.728  0.014  0.109 18.544  0.007  4.106   1.5237e-01
   1_adp:   1.728  0.014  0.109 18.544  0.007  4.106   1.5237e-01
   1_occ:   1.728  0.014  0.109 18.544  0.007  4.106   1.5237e-01
   2_bss:   1.728  0.014  0.109 18.544  0.007  4.106   1.5237e-01
   2_xyz:   1.314  0.010  0.090 17.128  0.005  4.102   1.1366e-01
   2_adp:   1.314  0.010  0.090 17.128  0.005  4.102   1.1366e-01
   2_occ:   1.314  0.010  0.090 17.128  0.005  4.102   1.1366e-01
   3_bss:   1.314  0.010  0.090 17.128  0.005  4.102   1.1366e-01
   3_xyz:   1.187  0.009  0.082 16.151  0.005  4.104   9.0405e-02
   3_adp:   1.187  0.009  0.082 16.151  0.005  4.104   9.0405e-02
   3_occ:   1.187  0.009  0.082 16.151  0.005  4.104   9.0405e-02
   4_bss:   1.187  0.009  0.082 16.151  0.005  4.104   9.0405e-02
   4_xyz:   1.124  0.008  0.078 15.913  0.004  4.116   7.9502e-02
   4_adp:   1.124  0.008  0.078 15.913  0.004  4.116   7.9502e-02
   4_occ:   1.124  0.008  0.078 15.913  0.004  4.116   7.9502e-02
   5_bss:   1.124  0.008  0.078 15.913  0.004  4.116   7.9502e-02
   5_xyz:   1.040  0.007  0.075 15.356  0.004  4.118   6.6008e-02
   5_adp:   1.040  0.007  0.075 15.356  0.004  4.118   6.6008e-02
   5_occ:   1.040  0.007  0.075 15.356  0.004  4.118   6.6008e-02
   5_bss:   1.040  0.007  0.075 15.356  0.004  4.118   6.6008e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9380e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9380e+00
   1_xyz:  13.122  0.191  0.423 86.857  0.039  2.134   1.0291e-01
   1_adp:  13.122  0.191  0.423 86.857  0.039  2.134   1.0291e-01
   1_occ:  13.122  0.191  0.423 86.857  0.039  2.134   1.0291e-01
   2_bss:  13.122  0.191  0.423 86.857  0.039  2.134   1.0291e-01
   2_xyz:   8.244  0.096  0.322 80.860  0.048  1.855   7.8990e-02
   2_adp:   8.244  0.096  0.322 80.860  0.048  1.855   7.8990e-02
   2_occ:   8.244  0.096  0.322 80.860  0.048  1.855   7.8990e-02
   3_bss:   8.244  0.096  0.322 80.860  0.048  1.855   7.8990e-02
   3_xyz:   8.329  0.125  0.306 81.465  0.056  2.116   1.0258e-01
   3_adp:   8.329  0.125  0.306 81.465  0.056  2.116   1.0258e-01
   3_occ:   8.329  0.125  0.306 81.465  0.056  2.116   1.0258e-01
   4_bss:   8.329  0.125  0.306 81.465  0.056  2.116   1.0258e-01
   4_xyz:   8.223  0.051  0.328 76.710  0.023  2.201   5.5228e-02
   4_adp:   8.223  0.051  0.328 76.710  0.023  2.201   5.5228e-02
   4_occ:   8.223  0.051  0.328 76.710  0.023  2.201   5.5228e-02
   5_bss:   8.223  0.051  0.328 76.710  0.023  2.201   5.5228e-02
   5_xyz:   8.871  0.068  0.245 83.345  0.035  2.312   5.6790e-02
   5_adp:   8.871  0.068  0.245 83.345  0.035  2.312   5.6790e-02
   5_occ:   8.871  0.068  0.245 83.345  0.035  2.312   5.6790e-02
   5_bss:   8.871  0.068  0.245 83.345  0.035  2.312   5.6790e-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:  79.05   0.00  16.02  78.13   0.00  14.86  79.05   0.00  22.31
   1_occ:  79.05   0.00  16.02  78.13   0.00  14.86  79.05   0.00  22.31
   2_bss:  79.05   0.00  16.02  78.13   0.00  14.86  79.05   0.00  22.31
   2_xyz:  79.05   0.00  16.02  78.13   0.00  14.86  79.05   0.00  22.31
   2_adp:  78.14   0.00  15.94  76.40   0.00  14.41  78.14   0.00  24.28
   2_occ:  78.14   0.00  15.94  76.40   0.00  14.41  78.14   0.00  24.28
   3_bss:  78.14   0.00  15.94  76.40   0.00  14.41  78.14   0.00  24.28
   3_xyz:  78.14   0.00  15.94  76.40   0.00  14.41  78.14   0.00  24.28
   3_adp:  78.72   0.00  15.95  70.33   0.00  13.19  78.72   0.00  31.00
   3_occ:  78.72   0.00  15.95  70.33   0.00  13.19  78.72   0.00  31.00
   4_bss:  78.72   0.00  15.95  70.33   0.00  13.19  78.72   0.00  31.00
   4_xyz:  78.72   0.00  15.95  70.33   0.00  13.19  78.72   0.00  31.00
   4_adp:  83.97   0.00  16.17  74.94   0.00  11.84  83.97   2.02  39.77
   4_occ:  83.97   0.00  16.17  74.94   0.00  11.84  83.97   2.02  39.77
   5_bss:  83.97   0.00  16.17  74.94   0.00  11.84  83.97   2.02  39.77
   5_xyz:  83.97   0.00  16.17  74.94   0.00  11.84  83.97   2.02  39.77
   5_adp:  87.54   0.00  15.95  87.54   0.00  11.07  85.95   3.57  42.54
   5_occ:  87.54   0.00  15.95  87.54   0.00  11.07  85.95   3.57  42.54
   5_bss:  88.02   0.48  16.43  88.02   0.48  11.55  86.43   4.05  43.02
------------------------------------------------------------------------
 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:    1.288    0.020    0.412
   1_adp:    1.288    0.020    0.412
   1_occ:    1.288    0.020    0.412
   2_bss:    1.288    0.020    0.412
   2_xyz:    1.616    0.023    0.591
   2_adp:    1.616    0.023    0.591
   2_occ:    1.616    0.023    0.591
   3_bss:    1.616    0.023    0.591
   3_xyz:    1.733    0.080    0.706
   3_adp:    1.733    0.080    0.706
   3_occ:    1.733    0.080    0.706
   4_bss:    1.733    0.080    0.706
   4_xyz:    2.135    0.046    0.842
   4_adp:    2.135    0.046    0.842
   4_occ:    2.135    0.046    0.842
   5_bss:    2.135    0.046    0.842
   5_xyz:    2.273    0.055    0.913
   5_adp:    2.273    0.055    0.913
   5_occ:    2.273    0.055    0.913
   5_bss:    2.273    0.055    0.913
------------------------------------------------------------------------

CPU time actual refinement: 353.70


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1094/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_1094/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1094/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1094/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1094/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.55 
  Macro-tasks:
    bulk solvent and scale       = 40.01  
    individual site refinement   = 147.05 
    weights calculation          = 33.18  
    collect and process          = 6.13   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 226.48 
  Micro-tasks:
    mask                            = 3.23   
    f_calc                          = 114.29 
    alpha_beta                      = 8.20   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 122.32 
    fmodel                         = 6.96   
    r_factors                      = 0.26   
    phase_errors                   = 9.46   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 266.09 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.039 micro seconds
Total CPU time: 6.12 minutes
from_scatterers_fft:    632 calls, 114.01 s
gradients_fft:          578 calls, 109.76 s

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

# Date 2008-01-16 Time 03:09:57 PST -0800 (1200481797.42 s)
Start R-work = 0.5065, R-free = 0.5037 (no bulk solvent and anisotropic scale)
Final R-work = 0.1614, R-free = 0.2156 (no bulk solvent and anisotropic scale)

Start R-work = 0.4979, R-free = 0.4920
Final R-work = 0.1465, R-free = 0.2017