# Date 2008-01-16 Time 05:48:08 PST -0800 (1200491288.26 s)
#phil __OFF__

Command line arguments: "../886.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14570
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 886

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.4607, 86.822, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.98286
Completeness in resolution range: 0.956261
Completeness with d_max=infinity: 0.953375

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1235
                             d_min =   1.9829

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: (70.9525, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.98286
Completeness in resolution range: 0.956261
Completeness with d_max=infinity: 0.953375

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1239 -  4.2434 [2153/2178]  1938   215  10.0%
  bin  2:  4.2434 -  3.3805 [2053/2073]  1848   205  10.0%
  bin  3:  3.3805 -  2.9568 [2058/2077]  1849   209  10.2%
  bin  4:  2.9568 -  2.6881 [2006/2036]  1809   197   9.8%
  bin  5:  2.6881 -  2.4964 [2023/2042]  1824   199   9.8%
  bin  6:  2.4964 -  2.3498 [1998/2023]  1791   207  10.4%
  bin  7:  2.3498 -  2.2325 [1980/2008]  1784   196   9.9%
  bin  8:  2.2325 -  2.1356 [1992/2028]  1796   196   9.8%
  bin  9:  2.1356 -  2.0536 [1960/2002]  1759   201  10.3%
  bin 10:  2.0536 -  1.9829 [1366/2018]  1232   134   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_886/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2176
        3.04 -     3.66: 4679
        3.66 -     4.28: 9027
        4.28 -     4.90: 12289
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.293 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28183 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 =====================


==================== 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/noshake/run_886/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_886/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.4607 86.82195 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3164   r_free= 0.3106   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.023536                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7332 0.99   1397  155 0.2841 0.2698      6.3389       6.265|
|  2:  4.7332 -  3.7761 0.99   1346  152 0.2500 0.2316      6.4105      6.3219|
|  3:  3.7761 -  3.3045 0.99   1319  141 0.2591 0.2509      6.2706      6.3515|
|  4:  3.3045 -  3.0049 0.99   1312  152 0.2894 0.3165      6.2016      6.2337|
|  5:  3.0049 -  2.7910 0.99   1306  147 0.3322 0.2764      6.0909      6.0033|
|  6:  2.7910 -  2.6273 0.99   1302  136 0.3136 0.3243       5.973      5.9287|
|  7:  2.6273 -  2.4964 0.99   1286  142 0.3363 0.3237      5.9896       6.003|
|  8:  2.4964 -  2.3881 0.98   1274  145 0.3502 0.3458      5.9521      5.9596|
|  9:  2.3881 -  2.2965 0.98   1262  147 0.3448 0.3361      5.9006      5.8676|
| 10:  2.2965 -  2.2175 1.00   1300  144 0.3617 0.3660      5.8948      5.8364|
| 11:  2.2175 -  2.1484 0.98   1276  137 0.3734 0.3918      5.8625      5.9131|
| 12:  2.1484 -  2.0871 0.98   1249  139 0.3684 0.3672      5.8107      5.8288|
| 13:  2.0871 -  2.0323 0.99   1286  141 0.3822 0.3870      5.7043      5.6669|
| 14:  2.0323 -  1.9829 0.55    715   81 0.4014 0.4036      5.7382      5.6902|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7332  1397   155  0.81  24.24   0.86     0.83      37359.71|
|  2:  4.7332 -  3.7761  1346   152  0.86  20.31   0.97     0.93      39403.67|
|  3:  3.7761 -  3.3045  1319   141  0.82  24.23   1.00     0.97      39667.40|
|  4:  3.3045 -  3.0049  1312   152  0.80  26.71   0.99     0.95      35240.06|
|  5:  3.0049 -  2.7910  1306   147  0.75  31.44   0.99     0.93      30102.64|
|  6:  2.7910 -  2.6273  1302   136  0.75  31.32   0.99     0.92      25023.68|
|  7:  2.6273 -  2.4964  1286   142  0.74  32.56   1.01     0.91      24139.38|
|  8:  2.4964 -  2.3881  1274   145  0.72  33.68   1.01     0.91      22574.26|
|  9:  2.3881 -  2.2965  1262   147  0.72  33.81   1.03     0.92      21961.89|
| 10:  2.2965 -  2.2175  1300   144  0.71  35.17   1.04     0.94      20542.93|
| 11:  2.2175 -  2.1484  1276   137  0.68  37.17   1.04     0.94      21065.43|
| 12:  2.1484 -  2.0871  1249   139  0.68  37.38   1.04     0.91      19712.26|
| 13:  2.0871 -  2.0323  1286   141  0.64  41.05   1.03     0.90      17748.57|
| 14:  2.0323 -  1.9829   715    81  0.68  37.75   1.04     0.90      14489.16|
|alpha:            min =        0.83 max =            0.97 mean =         0.92|
|beta:             min =    14489.16 max =        39667.40 mean =     26919.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.74|
|phase err.(work): min =        0.00 max =           89.98 mean =        31.60|
|phase err.(test): min =        0.00 max =           89.77 mean =        31.22|
|-----------------------------------------------------------------------------|

============================== 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 = 3.961662              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.020   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664231              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.812   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      196 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1980 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1861 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2818 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4632 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4395 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5650 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6639 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.155 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3164   r_free= 0.3106   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.023536                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3036   r_free= 0.3016   ksol= 0.34   Bsol= 53.09   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,-0.06,-1.02,-0.00,-0.00,-0.00); trace/3= -0.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.003276                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.528622              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.216   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340033              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.693   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3036      final r-factor (work) = 0.1727          |
| start r-factor (free) = 0.3016      final r-factor (free) = 0.1955          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7645 = 3.53 * 0.50 * 6.0098 + 1.00 * 0.1613                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1171 = 3.53 * 0.50 * 5.6984 + 1.00 * 0.0633                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1727      final r-factor (work) = 0.1573          |
| start r-factor (free) = 0.1955      final r-factor (free) = 0.2033          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9437 = 0.34 * 1.00 * 5.6984 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8486 = 0.34 * 1.00 * 5.4106 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    73.45   17.09    None  None   None       |
|    all(noH): 2823   0      1.52    73.45   17.09    None  None   None       |
|    Sol.    : 438    0      5.00    73.45   39.23    None  None   None       |
|    Mac.    : 2385   0      1.52    69.11   13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.524 -   8.716:  667   |   5:    37.488 -  44.681:  105        |
|      1:     8.716 -  15.909: 1231   |   6:    44.681 -  51.874:   81        |
|      2:    15.909 -  23.102:  384   |   7:    51.874 -  59.067:   65        |
|      3:    23.102 -  30.295:  130   |   8:    59.067 -  66.259:   29        |
|      4:    30.295 -  37.488:  117   |   9:    66.259 -  73.452:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1573 r_free = 0.2033             target_work(ml) = 5.427         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1569 r_free = 0.2032             target_work(ml) = 5.426         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1569   r_free= 0.2032   ksol= 0.34   Bsol= 53.09   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,-0.06,-1.02,-0.00,-0.00,-0.00); trace/3= -0.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.425823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1560   r_free= 0.2008   ksol= 0.33   Bsol= 59.39   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.19,-1.49,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.423251                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.091326              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.467  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.122543              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.389  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1560      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.2008      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4521 = 3.09 * 0.50 * 5.4273 + 1.00 * 0.0633                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2782 = 3.09 * 0.50 * 5.3169 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6604 = 0.12 * 1.00 * 5.3169 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6446 = 0.12 * 1.00 * 5.2068 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.04    71.21   16.64    None  None   None       |
|    all(noH): 2823   0      2.04    71.21   16.64    None  None   None       |
|    Sol.    : 438    0      6.25    71.21   37.07    None  None   None       |
|    Mac.    : 2385   0      2.04    69.72   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.039 -   8.957:  667   |   5:    36.625 -  43.542:  106        |
|      1:     8.957 -  15.874: 1264   |   6:    43.542 -  50.459:   83        |
|      2:    15.874 -  22.791:  368   |   7:    50.459 -  57.376:   57        |
|      3:    22.791 -  29.708:  129   |   8:    57.376 -  64.293:   21        |
|      4:    29.708 -  36.625:  117   |   9:    64.293 -  71.211:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1186 r_free = 0.1593             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1185 r_free = 0.1594             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1594   ksol= 0.33   Bsol= 59.39   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.19,-1.49,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.180311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1587   ksol= 0.33   Bsol= 59.39   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.63,-1.40,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.179029                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.525820              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.711  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.445295              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.020  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0318 = 1.53 * 0.50 * 5.2060 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9951 = 1.53 * 0.50 * 5.1688 + 1.00 * 0.0518                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1155      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3081 = 0.45 * 1.00 * 5.1688 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3012 = 0.45 * 1.00 * 5.1499 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 36     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.18    73.83   16.90    None  None   None       |
|    all(noH): 2823   0      1.18    73.83   16.90    None  None   None       |
|    Sol.    : 438    0      6.25    72.69   38.62    None  None   None       |
|    Mac.    : 2385   0      1.18    73.83   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.180 -   8.446:  610   |   5:    37.507 -  44.772:  115        |
|      1:     8.446 -  15.711: 1306   |   6:    44.772 -  52.038:   82        |
|      2:    15.711 -  22.976:  363   |   7:    52.038 -  59.303:   67        |
|      3:    22.976 -  30.242:  139   |   8:    59.303 -  66.568:   25        |
|      4:    30.242 -  37.507:  104   |   9:    66.568 -  73.833:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1561             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1561             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1561   ksol= 0.33   Bsol= 59.39   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.63,-1.40,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151501                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1560   ksol= 0.33   Bsol= 59.39   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.63,-1.26,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151299                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.338438              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.163  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.258482              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.929  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0731 = 2.34 * 0.50 * 5.1499 + 1.00 * 0.0518                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0654 = 2.34 * 0.50 * 5.1340 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.0050 = 5.26 * 1.00 * 5.1340 + 1.00 * 0.0080                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.9617 = 5.26 * 1.00 * 5.1253 + 1.00 * 0.0102                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.11    89.12   17.32    None  None   None       |
|    all(noH): 2823   0      0.11    89.12   17.32    None  None   None       |
|    Sol.    : 438    0      6.14    86.25   40.95    None  None   None       |
|    Mac.    : 2385   0      0.11    89.12   12.98    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:     0.111 -   9.012:  826   |   5:    44.615 -  53.515:   95        |
|      1:     9.012 -  17.912: 1253   |   6:    53.515 -  62.416:   72        |
|      2:    17.912 -  26.813:  271   |   7:    62.416 -  71.317:   37        |
|      3:    26.813 -  35.714:  137   |   8:    71.317 -  80.218:   21        |
|      4:    35.714 -  44.615:  106   |   9:    80.218 -  89.118:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1085 r_free = 0.1560             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1084 r_free = 0.1560             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1560   ksol= 0.33   Bsol= 59.39   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.63,-1.26,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127496                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1560   ksol= 0.32   Bsol= 59.39   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.40,-0.99,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127423                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.385924              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.539  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.275214              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.092  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6151 = 1.39 * 0.50 * 5.1265 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6114 = 1.39 * 0.50 * 5.1384 + 1.00 * 0.0507                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4244 = 0.28 * 1.00 * 5.1384 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4250 = 0.28 * 1.00 * 5.1470 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.90    87.87   16.78    None  None   None       |
|    all(noH): 2823   0      0.90    87.87   16.78    None  None   None       |
|    Sol.    : 438    0      6.05    83.35   38.92    None  None   None       |
|    Mac.    : 2385   0      0.90    87.87   12.71    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:     0.901 -   9.598:  980   |   5:    44.386 -  53.083:   88        |
|      1:     9.598 -  18.295: 1137   |   6:    53.083 -  61.780:   65        |
|      2:    18.295 -  26.992:  247   |   7:    61.780 -  70.477:   23        |
|      3:    26.992 -  35.689:  143   |   8:    70.477 -  79.175:   13        |
|      4:    35.689 -  44.386:  122   |   9:    79.175 -  87.872:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1562             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1562             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1562   ksol= 0.32   Bsol= 59.39   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.40,-0.99,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143001                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7332 0.99   1397  155 0.0994 0.1256      5.3866      5.5261|
|  2:  4.7332 -  3.7761 0.99   1346  152 0.0863 0.1094      5.4407      5.6068|
|  3:  3.7761 -  3.3045 0.99   1319  141 0.1057 0.1509       5.468      5.8647|
|  4:  3.3045 -  3.0049 0.99   1312  152 0.1191 0.1637      5.4547      5.5892|
|  5:  3.0049 -  2.7910 0.99   1306  147 0.1337 0.1757      5.3295      5.5802|
|  6:  2.7910 -  2.6273 0.99   1302  136 0.1201 0.1811      5.2001      5.4417|
|  7:  2.6273 -  2.4964 0.99   1286  142 0.1261 0.1608      5.1655      5.3576|
|  8:  2.4964 -  2.3881 0.98   1274  145 0.1154 0.1663      5.0495      5.2997|
|  9:  2.3881 -  2.2965 0.98   1262  147 0.1154 0.1747      5.0225      5.2987|
| 10:  2.2965 -  2.2175 1.00   1300  144 0.1117 0.1696      4.9418      5.2109|
| 11:  2.2175 -  2.1484 0.98   1276  137 0.1137 0.1782       4.943      5.2646|
| 12:  2.1484 -  2.0871 0.98   1249  139 0.1103 0.1704      4.8773      5.1772|
| 13:  2.0871 -  2.0323 0.99   1286  141 0.1136 0.1750      4.7801      5.0428|
| 14:  2.0323 -  1.9829 0.55    715   81 0.1051 0.1577      4.6691      4.8778|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7332  1397   155  0.94   9.19   0.97     0.94       7136.75|
|  2:  4.7332 -  3.7761  1346   152  0.95   7.85   1.01     1.00       8926.62|
|  3:  3.7761 -  3.3045  1319   141  0.94  11.12   1.02     1.01      10057.38|
|  4:  3.3045 -  3.0049  1312   152  0.92  13.72   1.00     0.98      10431.64|
|  5:  3.0049 -  2.7910  1306   147  0.90  15.90   0.99     0.97       8403.62|
|  6:  2.7910 -  2.6273  1302   136  0.90  16.12   0.99     0.96       6986.78|
|  7:  2.6273 -  2.4964  1286   142  0.91  15.40   0.99     0.96       6149.12|
|  8:  2.4964 -  2.3881  1274   145  0.91  14.79   0.99     0.97       5015.55|
|  9:  2.3881 -  2.2965  1262   147  0.91  14.87   1.00     0.96       4818.37|
| 10:  2.2965 -  2.2175  1300   144  0.90  15.53   1.00     0.97       4277.96|
| 11:  2.2175 -  2.1484  1276   137  0.90  16.01   0.98     0.94       4273.98|
| 12:  2.1484 -  2.0871  1249   139  0.91  14.92   1.00     0.99       3966.60|
| 13:  2.0871 -  2.0323  1286   141  0.90  16.23   0.99     0.97       3289.09|
| 14:  2.0323 -  1.9829   715    81  0.92  13.90   0.97     0.94       2546.15|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2546.15 max =        10431.64 mean =      6319.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.91|
|phase err.(test): min =        0.00 max =           89.66 mean =        13.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1562   ksol= 0.33   Bsol= 59.35   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.30,-0.85,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143057                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1562   ksol= 0.33   Bsol= 59.35   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.30,-0.85,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143057                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7332 0.99   1397  155 0.0994 0.1257      5.3872      5.5268|
|  2:  4.7332 -  3.7761 0.99   1346  152 0.0863 0.1094      5.4408      5.6066|
|  3:  3.7761 -  3.3045 0.99   1319  141 0.1057 0.1509      5.4679      5.8646|
|  4:  3.3045 -  3.0049 0.99   1312  152 0.1191 0.1637      5.4546      5.5892|
|  5:  3.0049 -  2.7910 0.99   1306  147 0.1337 0.1757      5.3296      5.5803|
|  6:  2.7910 -  2.6273 0.99   1302  136 0.1201 0.1810      5.2001      5.4414|
|  7:  2.6273 -  2.4964 0.99   1286  142 0.1261 0.1608      5.1655      5.3576|
|  8:  2.4964 -  2.3881 0.98   1274  145 0.1154 0.1663      5.0494      5.2997|
|  9:  2.3881 -  2.2965 0.98   1262  147 0.1154 0.1747      5.0225      5.2985|
| 10:  2.2965 -  2.2175 1.00   1300  144 0.1117 0.1697      4.9419      5.2113|
| 11:  2.2175 -  2.1484 0.98   1276  137 0.1136 0.1783      4.9432      5.2648|
| 12:  2.1484 -  2.0871 0.98   1249  139 0.1103 0.1704      4.8774      5.1773|
| 13:  2.0871 -  2.0323 0.99   1286  141 0.1136 0.1750        4.78      5.0426|
| 14:  2.0323 -  1.9829 0.55    715   81 0.1051 0.1577      4.6689      4.8774|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7332  1397   155  0.94   9.19   0.97     0.94       7146.32|
|  2:  4.7332 -  3.7761  1346   152  0.95   7.85   1.01     1.00       8930.95|
|  3:  3.7761 -  3.3045  1319   141  0.94  11.12   1.02     1.01      10055.32|
|  4:  3.3045 -  3.0049  1312   152  0.92  13.72   1.01     0.98      10431.48|
|  5:  3.0049 -  2.7910  1306   147  0.90  15.90   1.00     0.97       8402.35|
|  6:  2.7910 -  2.6273  1302   136  0.90  16.12   0.99     0.96       6986.47|
|  7:  2.6273 -  2.4964  1286   142  0.91  15.40   0.99     0.96       6148.28|
|  8:  2.4964 -  2.3881  1274   145  0.91  14.79   0.99     0.97       5014.65|
|  9:  2.3881 -  2.2965  1262   147  0.91  14.87   1.00     0.96       4817.40|
| 10:  2.2965 -  2.2175  1300   144  0.90  15.53   1.00     0.97       4279.37|
| 11:  2.2175 -  2.1484  1276   137  0.90  16.02   0.99     0.94       4276.11|
| 12:  2.1484 -  2.0871  1249   139  0.91  14.92   1.01     1.00       3967.83|
| 13:  2.0871 -  2.0323  1286   141  0.90  16.23   0.99     0.97       3288.45|
| 14:  2.0323 -  1.9829   715    81  0.92  13.89   0.97     0.94       2544.84|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2544.84 max =        10431.48 mean =      6320.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.92|
|phase err.(test): min =        0.00 max =           89.67 mean =        13.43|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    87.84   16.75    None  None   None       |
|    all(noH): 2823   0      0.87    87.84   16.75    None  None   None       |
|    Sol.    : 438    0      6.01    83.32   38.89    None  None   None       |
|    Mac.    : 2385   0      0.87    87.84   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.870 -   9.567:  980   |   5:    44.355 -  53.052:   88        |
|      1:     9.567 -  18.264: 1137   |   6:    53.052 -  61.750:   65        |
|      2:    18.264 -  26.961:  247   |   7:    61.750 -  70.447:   23        |
|      3:    26.961 -  35.658:  143   |   8:    70.447 -  79.144:   13        |
|      4:    35.658 -  44.355:  122   |   9:    79.144 -  87.841:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.513 - 4.628
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 302
   mapped sites are within: 0.707 - 4.628

peak=    5.661 closest distance to " NH2 ARG A  56 " =    2.181
peak=    5.539 closest distance to " CG  PRO A  54 " =    1.342
peak=    5.355 closest distance to " NE2 GLN A  11 " =    1.165
peak=    5.318 closest distance to " CB  GLN A 223 " =    1.418
peak=    5.176 closest distance to " CG  PRO A 213 " =    1.256
peak=    5.139 closest distance to " O   HOH Z 232 " =    2.345
peak=    4.956 closest distance to " O   HOH Z 126 " =    1.877
peak=    4.950 closest distance to " O   HOH Z 144 " =    1.809
peak=    4.876 closest distance to " CB  PRO A  54 " =    1.014
peak=    4.857 closest distance to " CB  ARG A 275 " =    0.905
peak=    4.778 closest distance to " CG  PRO A 198 " =    1.254
peak=    4.726 closest distance to " CB  GLN A 183 " =    1.218
peak=    4.714 closest distance to " O   HOH Z 298 " =    1.996
peak=    4.678 closest distance to " CB  SER A  63 " =    1.235
peak=    4.589 closest distance to " O   HOH Z  78 " =    1.778
peak=    4.557 closest distance to " CB  ASN A 148 " =    1.401
peak=    4.461 closest distance to " CB  LEU A 228 " =    1.096
peak=    4.433 closest distance to " O   HOH Z 287 " =    2.213
peak=    4.430 closest distance to " O   HOH Z 369 " =    2.104
peak=    4.429 closest distance to " CG2 VAL A 257 " =    0.969
peak=    4.389 closest distance to " ND2 ASN A 187 " =    1.503
peak=    4.374 closest distance to " CB  ARG A  79 " =    1.374
peak=    4.333 closest distance to " C   PRO A 198 " =    1.547
peak=    4.324 closest distance to " CA  TYR A  30 " =    0.966
peak=    4.317 closest distance to " CB  ARG A 190 " =    1.604
peak=    4.301 closest distance to " O   HOH Z 427 " =    2.873
peak=    4.294 closest distance to " O   HOH Z   9 " =    2.254
peak=    4.286 closest distance to " CZ  PHE A 218 " =    1.027
peak=    4.247 closest distance to " CG  PRO A 243 " =    1.096
peak=    4.241 closest distance to " CB  GLU A 128 " =    0.981
peak=    4.222 closest distance to " O   HOH Z 303 " =    2.175
peak=    4.198 closest distance to " O   HOH Z 250 " =    1.520
peak=    4.195 closest distance to " CD  ARG A 159 " =    0.766
peak=    4.185 closest distance to " CB  VAL A 265 " =    1.275
peak=    4.160 closest distance to " CB  ASN A 187 " =    1.192
peak=    4.127 closest distance to " CB  TRP A 266 " =    1.007
peak=    4.095 closest distance to " O   HOH Z 234 " =    3.774
peak=    4.068 closest distance to " O   HOH Z 189 " =    2.594
peak=    4.065 closest distance to " OD1 ASN A  69 " =    2.650
peak=    4.060 closest distance to " O   HOH Z 193 " =    1.866
peak=    4.038 closest distance to " CG  LEU A 167 " =    1.252
peak=    4.030 closest distance to " CB  SER A 212 " =    1.185
peak=    4.020 closest distance to " O   HOH Z 423 " =    1.488
peak=    4.020 closest distance to " ND1 HIS A  86 " =    1.731
peak=    4.002 closest distance to " CA  ASN A 215 " =    1.154
peak=    3.996 closest distance to " NH1AARG A 145 " =    1.248
peak=    3.989 closest distance to " O   HOH Z 316 " =    3.085
peak=    3.974 closest distance to " CB  SER A 216 " =    0.839
peak=    3.974 closest distance to " O   HOH Z 158 " =    3.020
peak=    3.973 closest distance to " CE  LYS A  76 " =    0.854
peak=    3.945 closest distance to " O   HOH Z   1 " =    1.972
peak=    3.939 closest distance to " O   HOH Z 272 " =    1.816
peak=    3.924 closest distance to " O   HOH Z 133 " =    2.441
peak=    3.924 closest distance to " O   HOH Z 261 " =    1.999
peak=    3.920 closest distance to " CA  SER A  87 " =    1.008
peak=    3.919 closest distance to " CA  THR A 264 " =    0.857
peak=    3.915 closest distance to " CD  ARG A  66 " =    2.265
peak=    3.900 closest distance to " O   HOH Z  61 " =    1.614
peak=    3.899 closest distance to " NZ  LYS A 117 " =    3.179
peak=    3.898 closest distance to " CB  GLU A 152 " =    1.286
peak=    3.897 closest distance to " CB  ASP A 124 " =    0.762
peak=    3.892 closest distance to " O   HOH Z 346 " =    1.647
peak=    3.865 closest distance to " O   HOH Z 368 " =    2.010
peak=    3.855 closest distance to " CB  SER A   3 " =    1.310
peak=    3.837 closest distance to " CB  ASN A  39 " =    0.900
peak=    3.836 closest distance to " CB  ASN A 142 " =    0.954
peak=    3.825 closest distance to " O   HOH Z 419 " =    2.108
peak=    3.810 closest distance to " CD1 LEU A 300 " =    1.182
peak=    3.790 closest distance to " O   HOH Z 132 " =    2.463
peak=    3.788 closest distance to " O   HOH Z 209 " =    2.297
peak=    3.769 closest distance to " CD  ARG A 269 " =    0.953
peak=    3.764 closest distance to " O   HOH Z 214 " =    2.116
peak=    3.761 closest distance to " CG2 THR A 221 " =    0.996
peak=    3.750 closest distance to " O   HOH Z  40 " =    1.919
peak=    3.746 closest distance to " O   HOH Z  21 " =    1.725
peak=    3.723 closest distance to " O   HOH Z 437 " =    1.456
peak=    3.722 closest distance to " CB  VAL A 202 " =    1.621
peak=    3.722 closest distance to " O   HOH Z 352 " =    1.849
peak=    3.718 closest distance to " O   HOH Z 193 " =    1.696
peak=    3.700 closest distance to " O   HOH Z 180 " =    2.119
peak=    3.698 closest distance to " CD BLYS A 290 " =    1.074
peak=    3.687 closest distance to " O   HOH Z 389 " =    1.905
peak=    3.683 closest distance to " O   HOH Z 285 " =    2.652
peak=    3.666 closest distance to " O   HOH Z   9 " =    1.923
peak=    3.654 closest distance to " O   HOH Z 329 " =    3.860
peak=    3.650 closest distance to " O   HOH Z 353 " =    2.638
peak=    3.649 closest distance to " O   HOH Z  68 " =    2.181
peak=    3.649 closest distance to " N   PHE A 130 " =    1.196
peak=    3.647 closest distance to " CB  MET A  40 " =    0.799
peak=    3.631 closest distance to " O   HOH Z  10 " =    1.846
peak=    3.631 closest distance to " CD2 TRP A 179 " =    1.298
peak=    3.630 closest distance to " O   HOH Z 371 " =    1.828
peak=    3.626 closest distance to " CB  ASP A 140 " =    0.933
peak=    3.623 closest distance to " CB  SER A 210 " =    0.729
peak=    3.620 closest distance to " CB  GLU A 277 " =    3.634
peak=    3.616 closest distance to " O   HOH Z  40 " =    1.956
peak=    3.615 closest distance to " CB  ALA A  34 " =    1.007
peak=    3.610 closest distance to " CB  TYR A 116 " =    0.827
peak=    3.609 closest distance to " O   HOH Z 371 " =    2.886
peak=    3.608 closest distance to " N   ASN A 127 " =    1.271
peak=    3.600 closest distance to " CA  ALA A 233 " =    1.250
peak=    3.597 closest distance to " O   HOH Z 368 " =    3.607
peak=    3.592 closest distance to " CD  LYS A 166 " =    1.273
peak=    3.592 closest distance to " CB  LEU A 143 " =    1.123
peak=    3.575 closest distance to " O   HOH Z 344 " =    3.178
peak=    3.574 closest distance to " N   ARG A 156 " =    1.344
peak=    3.572 closest distance to " CB  GLN A  88 " =    1.229
peak=    3.569 closest distance to " O   HOH Z 213 " =    2.072
peak=    3.567 closest distance to " O   HOH Z  54 " =    2.464
peak=    3.562 closest distance to " CB  GLU A  46 " =    0.966
peak=    3.559 closest distance to " O   HOH Z   1 " =    1.750
peak=    3.556 closest distance to " O   HOH Z 172 " =    3.103
peak=    3.552 closest distance to " CB  ASN A 110 " =    1.079
peak=    3.551 closest distance to " CG1 ILE A  33 " =    1.257
peak=    3.550 closest distance to " O   TYR A 116 " =    1.292
peak=    3.542 closest distance to " O   HOH Z 291 " =    1.531
peak=    3.540 closest distance to " N   ASN A  39 " =    1.255
peak=    3.540 closest distance to " O   HOH Z 411 " =    3.796
peak=    3.539 closest distance to " O   HOH Z 386 " =    3.079
peak=    3.535 closest distance to " CG  MET A 113 " =    1.244
peak=    3.528 closest distance to " CG2 ILE A 120 " =    1.142
peak=    3.525 closest distance to " ND2 ASN A 249 " =    0.881
peak=    3.520 closest distance to " O   SER A  87 " =    2.185
peak=    3.512 closest distance to " CA  ARG A 195 " =    1.272
peak=    3.507 closest distance to " CG1 VAL A 153 " =    0.893
peak=    3.504 closest distance to " O   HOH Z 234 " =    1.763
peak=    3.500 closest distance to " O   HOH Z 219 " =    1.926
peak=    3.499 closest distance to " CB  MET A  47 " =    1.018
peak=    3.497 closest distance to " O   HOH Z 313 " =    1.917
peak=    3.491 closest distance to " O   HOH Z 426 " =    1.892
peak=    3.487 closest distance to " NE2 HIS A 207 " =    1.304
peak=    3.486 closest distance to " O   HOH Z 327 " =    1.792
peak=    3.482 closest distance to " CA  THR A 221 " =    0.974
peak=    3.479 closest distance to " O   ASN A 209 " =    1.331
peak=    3.478 closest distance to " OD1BASN A 224 " =    2.332
peak=    3.478 closest distance to " CA  ALA A  51 " =    0.923
peak=    3.476 closest distance to " OD2 ASP A 286 " =    2.882
peak=    3.469 closest distance to " O   THR A 251 " =    1.108
peak=    3.469 closest distance to " O   HOH Z 305 " =    3.602
peak=    3.468 closest distance to " NH2BARG A 145 " =    2.125
peak=    3.468 closest distance to " O   HOH Z 135 " =    1.666
peak=    3.467 closest distance to " CB  ALA A   1 " =    4.628
peak=    3.456 closest distance to " CD2 LEU A 255 " =    1.660
peak=    3.454 closest distance to " CB  LYS A 117 " =    1.243
peak=    3.447 closest distance to " O   HOH Z  61 " =    1.491
peak=    3.443 closest distance to " O   HOH Z 273 " =    2.754
peak=    3.442 closest distance to " O   HOH Z 391 " =    2.859
peak=    3.437 closest distance to " CG1BVAL A  72 " =    1.596
peak=    3.431 closest distance to " O   HOH Z 128 " =    2.288
peak=    3.423 closest distance to " O  BHOH Z 338 " =    2.412
peak=    3.419 closest distance to " O   HOH Z 193 " =    2.028
peak=    3.418 closest distance to " O   HOH Z  43 " =    1.863
peak=    3.417 closest distance to " CA  ARG A  36 " =    1.065
peak=    3.416 closest distance to " CA  MET A  40 " =    1.138
peak=    3.415 closest distance to " CB  ARG A 139 " =    0.925
peak=    3.415 closest distance to " CB  TRP A 179 " =    1.441
peak=    3.408 closest distance to " NH2 ARG A 156 " =    1.195
peak=    3.407 closest distance to " O   HOH Z 280 " =    3.040
peak=    3.400 closest distance to " CE1 PHE A 218 " =    0.989
peak=    3.400 closest distance to " CB  ALA A 114 " =    0.832
peak=    3.400 closest distance to " CG  ARG A 159 " =    0.869
peak=    3.395 closest distance to " CB  PRO A  90 " =    1.162
peak=    3.394 closest distance to " O   HOH Z 409 " =    2.566
peak=    3.392 closest distance to " O   MET A 105 " =    1.831
peak=    3.392 closest distance to " CA  ALA A  21 " =    1.155
peak=    3.392 closest distance to " CB  ALA A 291 " =    1.281
peak=    3.383 closest distance to " OG BSER A 164 " =    2.393
peak=    3.382 closest distance to " CA  ARG A 102 " =    1.143
peak=    3.378 closest distance to " CD  ARG A 219 " =    1.118
peak=    3.378 closest distance to " ND2 ASN A 110 " =    1.778
peak=    3.376 closest distance to " O   HOH Z 175 " =    2.143
peak=    3.375 closest distance to " CA  LYS A 290 " =    1.283
peak=    3.367 closest distance to " O   HOH Z 302 " =    1.875
peak=    3.361 closest distance to " CB  THR A  82 " =    1.379
peak=    3.360 closest distance to " N   GLN A 278 " =    1.216
peak=    3.359 closest distance to " CA  ILE A 234 " =    0.973
peak=    3.359 closest distance to " O   HOH Z 425 " =    2.089
peak=    3.357 closest distance to " CG1 ILE A 151 " =    1.050
peak=    3.357 closest distance to " NH1 ARG A 138 " =    1.086
peak=    3.346 closest distance to " O   HOH Z  88 " =    3.977
peak=    3.344 closest distance to " CB  SER A  62 " =    1.149
peak=    3.340 closest distance to " CA  ALA A 158 " =    1.149
peak=    3.339 closest distance to " O   HOH Z 406 " =    1.604
peak=    3.336 closest distance to " O   HOH Z 294 " =    1.514
peak=    3.330 closest distance to " CA  ASN A 217 " =    1.237
peak=    3.330 closest distance to " CZ  PHE A  38 " =    1.251
peak=    3.327 closest distance to " CG  GLN A  89 " =    1.517
peak=    3.327 closest distance to " O   HOH Z 116 " =    3.026
peak=    3.323 closest distance to " O   HOH Z 405 " =    1.183
peak=    3.320 closest distance to " O   HOH Z 133 " =    1.652
peak=    3.308 closest distance to " CD2 LEU A 297 " =    0.887
peak=    3.308 closest distance to " O   HOH Z 402 " =    1.421
peak=    3.305 closest distance to " NE2 GLN A  73 " =    3.816
peak=    3.302 closest distance to " O   HOH Z 345 " =    1.746
peak=    3.301 closest distance to " CB  ILE A 120 " =    1.212
peak=    3.301 closest distance to " CB  HIS A 108 " =    0.761
peak=    3.300 closest distance to " CB  THR A 157 " =    1.129
peak=    3.299 closest distance to " N   SER A 146 " =    1.698
peak=    3.297 closest distance to " CA  ALA A 154 " =    0.985
peak=    3.294 closest distance to " CD1 ILE A 106 " =    0.792
peak=    3.294 closest distance to " O   HOH Z 403 " =    1.634
peak=    3.291 closest distance to " OG  SER A  22 " =    2.786
peak=    3.288 closest distance to " CE1 TYR A 186 " =    1.342
peak=    3.287 closest distance to " O   HOH Z 261 " =    2.327
peak=    3.287 closest distance to " O   HOH Z  88 " =    3.133
peak=    3.283 closest distance to " O   HOH Z 109 " =    2.573
peak=    3.283 closest distance to " CZ3 TRP A 266 " =    1.107
peak=    3.280 closest distance to " O   HOH Z 245 " =    1.284
peak=    3.278 closest distance to " CB  ALA A 248 " =    1.283
peak=    3.276 closest distance to " O   HOH Z 325 " =    3.879
peak=    3.272 closest distance to " O   HOH Z 108 " =    2.476
peak=    3.272 closest distance to " O   HOH Z 379 " =    3.538
peak=    3.271 closest distance to " O   HOH Z 148 " =    3.437
peak=    3.268 closest distance to " CG1 VAL A 189 " =    1.849
peak=    3.261 closest distance to " OE1 GLU A 236 " =    1.217
peak=    3.256 closest distance to " CD  PRO A 243 " =    1.579
peak=    3.251 closest distance to " O   HOH Z 238 " =    3.712
peak=    3.250 closest distance to " O   HOH Z 345 " =    3.554
peak=    3.250 closest distance to " O   HOH Z 425 " =    1.246
peak=    3.243 closest distance to " CB  PRO A 243 " =    1.270
peak=    3.242 closest distance to " CD1 LEU A  96 " =    0.783
peak=    3.241 closest distance to " O   HOH Z 218 " =    4.473
peak=    3.227 closest distance to " O   HOH Z 373 " =    1.559
peak=    3.227 closest distance to " CA  TYR A 116 " =    1.337
peak=    3.223 closest distance to " O   HOH Z 422 " =    2.672
peak=    3.221 closest distance to " CA  ALA A 291 " =    0.829
peak=    3.219 closest distance to " CA  MET A 105 " =    0.938
peak=    3.219 closest distance to " CA  GLU A  46 " =    0.806
peak=    3.214 closest distance to " CB  THR A 235 " =    1.101
peak=    3.212 closest distance to " O   HOH Z 185 " =    1.816
peak=    3.211 closest distance to " CG  GLN A 278 " =    1.309
peak=    3.210 closest distance to " CB  ALA A   9 " =    1.588
peak=    3.209 closest distance to " CG1 ILE A 120 " =    1.058
peak=    3.209 closest distance to " O   HOH Z  53 " =    2.540
peak=    3.209 closest distance to " CB  GLN A  89 " =    1.306
peak=    3.206 closest distance to " O   HOH Z 227 " =    1.685
peak=    3.203 closest distance to " CB  ALA A 248 " =    0.960
peak=    3.203 closest distance to " CA  ASN A 127 " =    1.073
peak=    3.201 closest distance to " O   HOH Z 152 " =    2.722
peak=    3.198 closest distance to " O   HOH Z  64 " =    2.084
peak=    3.197 closest distance to " O   HOH Z  93 " =    2.742
peak=    3.192 closest distance to " O   HOH Z 290 " =    1.016
peak=    3.191 closest distance to " OD1 ASP A 238 " =    0.990
peak=    3.191 closest distance to " O   HOH Z 365 " =    2.907
peak=    3.189 closest distance to " CB  VAL A 265 " =    1.962
peak=    3.189 closest distance to " OG  SER A  62 " =    2.968
peak=    3.186 closest distance to " O   HOH Z 126 " =    1.548
peak=    3.182 closest distance to " O   HOH Z  44 " =    2.947
peak=    3.181 closest distance to " CD1 ILE A 263 " =    1.324
peak=    3.177 closest distance to " O   ASN A  74 " =    1.540
peak=    3.170 closest distance to " O   HOH Z 325 " =    2.461
peak=    3.167 closest distance to " O   HOH Z 128 " =    2.157
peak=    3.160 closest distance to " N   VAL A 296 " =    1.708
peak=    3.154 closest distance to " CB  ALA A 242 " =    0.845
peak=    3.152 closest distance to " O   HOH Z 271 " =    2.437
peak=    3.150 closest distance to " CA  GLY A 267 " =    1.201
peak=    3.150 closest distance to " OG  SER A 206 " =    1.178
peak=    3.148 closest distance to " O   HOH Z 188 " =    2.010
peak=    3.144 closest distance to " CB  LEU A  83 " =    0.747
peak=    3.144 closest distance to " NH1 ARG A  14 " =    1.032
peak=    3.143 closest distance to " O   HOH Z 130 " =    3.805
peak=    3.142 closest distance to " O   HOH Z 227 " =    1.992
peak=    3.140 closest distance to " O   HOH Z 163 " =    1.791
peak=    3.140 closest distance to " CB  LYS A 193 " =    1.018
peak=    3.139 closest distance to " CA  ALA A  84 " =    1.361
peak=    3.138 closest distance to " O   HOH Z  59 " =    1.657
peak=    3.133 closest distance to " CG  GLN A 144 " =    0.853
peak=    3.121 closest distance to " N   GLY A  98 " =    1.053
peak=    3.117 closest distance to " O   HOH Z 407 " =    2.340
peak=    3.115 closest distance to " O   HOH Z 423 " =    2.575
peak=    3.114 closest distance to " CB  VAL A 268 " =    0.852
peak=    3.114 closest distance to " N   TYR A  15 " =    0.707
peak=    3.110 closest distance to " CB  ARG A 138 " =    0.991
peak=    3.106 closest distance to " CG2BVAL A  41 " =    0.907
peak=    3.104 closest distance to " CG BARG A 102 " =    1.877
peak=    3.100 closest distance to " CB  ASN A 215 " =    1.069
peak=    3.099 closest distance to " CB  GLN A 103 " =    0.855
peak=    3.095 closest distance to " O   HOH Z 359 " =    4.140
peak=    3.091 closest distance to " O   HOH Z 211 " =    2.842
peak=    3.090 closest distance to " CB  TRP A 150 " =    1.328
peak=    3.089 closest distance to " O   HOH Z 285 " =    1.811
peak=    3.088 closest distance to " O   HOH Z 386 " =    2.922
peak=    3.086 closest distance to " CA  ALA A 299 " =    0.905
peak=    3.085 closest distance to " O   HOH Z 298 " =    2.436
peak=    3.081 closest distance to " CA  SER A  95 " =    1.033
peak=    3.076 closest distance to " O   THR A 294 " =    1.023
peak=    3.076 closest distance to " CG2 ILE A 151 " =    0.861
peak=    3.073 closest distance to " O   HOH Z  88 " =    1.972
peak=    3.072 closest distance to " CB  ASP A 171 " =    0.828
peak=    3.070 closest distance to " CG  LYS A  76 " =    0.968
peak=    3.069 closest distance to " CD1AILE A 234 " =    0.985
peak=    3.066 closest distance to " CA  ASP A 140 " =    1.273
peak=    3.064 closest distance to " NH1BARG A 145 " =    1.063
peak=    3.060 closest distance to " OG BSER A 134 " =    2.973
peak=    3.057 closest distance to " O   ALA A 158 " =    1.316
peak=    3.048 closest distance to " ND1 HIS A  81 " =    1.649
peak=    3.031 closest distance to " O   HOH Z 188 " =    2.465
peak=    3.028 closest distance to " CA  GLY A 136 " =    1.002

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.756 - 5.589
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.756 - 5.589

peak=   -4.594 closest distance to " CD  ARG A 156 " =    2.040
peak=   -4.551 closest distance to " CB  PRO A 243 " =    2.631
peak=   -4.399 closest distance to " O   HOH Z 377 " =    2.009
peak=   -4.275 closest distance to " O   HOH Z 266 " =    5.192
peak=   -4.232 closest distance to " O   PRO A 198 " =    1.212
peak=   -4.196 closest distance to " CG  GLN A 223 " =    1.947
peak=   -4.189 closest distance to " CD  ARG A  14 " =    3.478
peak=   -4.165 closest distance to " OG BSER A 134 " =    1.240
peak=   -4.143 closest distance to " O   HOH Z 231 " =    2.163
peak=   -4.107 closest distance to " CG1 VAL A 112 " =    2.896
peak=   -4.083 closest distance to " O   HOH Z 389 " =    2.005
peak=   -4.071 closest distance to " CZ3 TRP A 179 " =    1.162
peak=   -4.060 closest distance to " O   HOH Z 435 " =    2.838
peak=   -4.049 closest distance to " O   VAL A  67 " =    2.607
peak=   -4.013 closest distance to " O   HOH Z 290 " =    1.189
peak=   -4.010 closest distance to " N   ALA A  43 " =    2.618
peak=   -4.009 closest distance to " O   HOH Z 351 " =    1.478
peak=   -3.851 closest distance to " C   HIS A 108 " =    1.146
peak=   -3.847 closest distance to " CD  GLN A  58 " =    1.013
peak=   -3.826 closest distance to " ND2 ASN A  45 " =    1.828
peak=   -3.800 closest distance to " O   HOH Z  38 " =    1.436
peak=   -3.788 closest distance to " O   HOH Z 313 " =    1.849
peak=   -3.774 closest distance to " O   HOH Z 185 " =    2.247
peak=   -3.774 closest distance to " CE2 TYR A  30 " =    2.798
peak=   -3.757 closest distance to " CG  MET A 105 " =    0.957
peak=   -3.747 closest distance to " O   HOH Z 372 " =    2.461
peak=   -3.743 closest distance to " CB  ALA A  43 " =    2.559
peak=   -3.729 closest distance to " CB  ALA A 291 " =    2.234
peak=   -3.728 closest distance to " O   HOH Z 407 " =    3.235
peak=   -3.705 closest distance to " O   HOH Z 198 " =    2.079
peak=   -3.700 closest distance to " ND2 ASN A  45 " =    1.162
peak=   -3.698 closest distance to " CE  MET A 105 " =    2.349
peak=   -3.678 closest distance to " CD  ARG A 139 " =    1.567
peak=   -3.663 closest distance to " O   HOH Z 114 " =    3.035
peak=   -3.650 closest distance to " NH2AARG A 275 " =    5.442
peak=   -3.649 closest distance to " N   THR A 157 " =    1.511
peak=   -3.642 closest distance to " OD1 ASN A 148 " =    1.530
peak=   -3.639 closest distance to " CG1 VAL A 112 " =    2.631
peak=   -3.629 closest distance to " O   VAL A 189 " =    2.543
peak=   -3.625 closest distance to " O   HOH Z  52 " =    1.242
peak=   -3.623 closest distance to " ND2 ASN A 249 " =    2.362
peak=   -3.621 closest distance to " CD1 PHE A  59 " =    1.856
peak=   -3.593 closest distance to " O   TYR A 247 " =    2.842
peak=   -3.593 closest distance to " CA  GLY A 241 " =    2.290
peak=   -3.578 closest distance to " O   HOH Z  10 " =    1.493
peak=   -3.578 closest distance to " O   HOH Z  60 " =    2.395
peak=   -3.577 closest distance to " CD2 TYR A 293 " =    1.959
peak=   -3.575 closest distance to " CB  PHE A 192 " =    1.993
peak=   -3.567 closest distance to " C   LEU A 222 " =    0.756
peak=   -3.563 closest distance to " O   HOH Z 394 " =    1.451
peak=   -3.559 closest distance to " CB  ALA A 291 " =    2.087
peak=   -3.553 closest distance to " O   HOH Z  73 " =    2.145
peak=   -3.539 closest distance to " CA  ASN A 110 " =    2.553
peak=   -3.539 closest distance to " CB  ASN A  39 " =    2.212
peak=   -3.536 closest distance to " CE BMET A  47 " =    1.478
peak=   -3.534 closest distance to " CG  PHE A 283 " =    2.668
peak=   -3.530 closest distance to " CZ  PHE A  59 " =    1.536
peak=   -3.523 closest distance to " O   HOH Z 377 " =    0.803
peak=   -3.523 closest distance to " C   ALA A 158 " =    1.583
peak=   -3.520 closest distance to " N   ASP A 171 " =    2.387
peak=   -3.517 closest distance to " O   HOH Z 198 " =    1.537
peak=   -3.516 closest distance to " OG  SER A  97 " =    2.181
peak=   -3.513 closest distance to " CA  GLY A  98 " =    1.869
peak=   -3.506 closest distance to " O   HOH Z  43 " =    1.676
peak=   -3.503 closest distance to " CA  GLY A 203 " =    2.323
peak=   -3.491 closest distance to " CB  PRO A 163 " =    2.536
peak=   -3.488 closest distance to " CB  TRP A  85 " =    2.436
peak=   -3.488 closest distance to " N   ASP A 286 " =    2.456
peak=   -3.487 closest distance to " O   HOH Z 253 " =    3.998
peak=   -3.487 closest distance to " CD2 TYR A 247 " =    2.535
peak=   -3.485 closest distance to " O   HOH Z 298 " =    1.168
peak=   -3.474 closest distance to " CD  ARG A 195 " =    5.216
peak=   -3.470 closest distance to " OD1 ASP A 171 " =    1.607
peak=   -3.460 closest distance to " OH  TYR A 172 " =    1.784
peak=   -3.459 closest distance to " CG2 THR A 178 " =    2.295
peak=   -3.458 closest distance to " O   PRO A 163 " =    2.005
peak=   -3.457 closest distance to " O   VAL A  67 " =    2.817
peak=   -3.449 closest distance to " CZ  TYR A 169 " =    1.647
peak=   -3.448 closest distance to " CE2 PHE A 218 " =    2.437
peak=   -3.447 closest distance to " O   HOH Z 126 " =    1.914
peak=   -3.445 closest distance to " OE1 GLN A  88 " =    1.127
peak=   -3.427 closest distance to " CA  ASP A  27 " =    2.437
peak=   -3.419 closest distance to " O   HOH Z 102 " =    1.579
peak=   -3.417 closest distance to " O   HOH Z 359 " =    3.302
peak=   -3.415 closest distance to " CB  TYR A  15 " =    2.221
peak=   -3.411 closest distance to " CG2 ILE A 263 " =    2.331
peak=   -3.410 closest distance to " O   GLY A  17 " =    1.263
peak=   -3.408 closest distance to " CZ BARG A 275 " =    1.810
peak=   -3.406 closest distance to " O   HOH Z 211 " =    1.548
peak=   -3.404 closest distance to " O   ARG A 145 " =    1.601
peak=   -3.402 closest distance to " CG  ASP A 231 " =    0.764
peak=   -3.398 closest distance to " OD1 ASP A 191 " =    1.741
peak=   -3.384 closest distance to " CB  ALA A 131 " =    2.095
peak=   -3.380 closest distance to " O   HOH Z 174 " =    2.663
peak=   -3.376 closest distance to " CB  ALA A 248 " =    2.469
peak=   -3.376 closest distance to " CD1 LEU A 101 " =    2.315
peak=   -3.357 closest distance to " O   SER A 135 " =    1.387
peak=   -3.356 closest distance to " O   GLY A 211 " =    1.297
peak=   -3.353 closest distance to " CA  GLY A 133 " =    2.031
peak=   -3.353 closest distance to " CB  CYS A 254 " =    2.278
peak=   -3.352 closest distance to " O   HOH Z 353 " =    2.143
peak=   -3.352 closest distance to " O   HOH Z 298 " =    2.473
peak=   -3.345 closest distance to " O   PHE A 218 " =    1.517
peak=   -3.342 closest distance to " OXT GLY A 302 " =    2.967
peak=   -3.340 closest distance to " CG  ARG A 269 " =    2.404
peak=   -3.336 closest distance to " O   PRO A 198 " =    1.332
peak=   -3.333 closest distance to " CG  TRP A 266 " =    1.806
peak=   -3.330 closest distance to " O   ALA A  10 " =    1.620
peak=   -3.329 closest distance to " O   TRP A  70 " =    1.419
peak=   -3.329 closest distance to " CB  ALA A 248 " =    2.022
peak=   -3.324 closest distance to " CG1 VAL A 250 " =    2.655
peak=   -3.322 closest distance to " O   ALA A 180 " =    1.236
peak=   -3.322 closest distance to " ND2 ASN A 187 " =    1.536
peak=   -3.322 closest distance to " OD1 ASN A 187 " =    1.536
peak=   -3.320 closest distance to " C   LEU A 143 " =    1.315
peak=   -3.320 closest distance to " CG1 VAL A 125 " =    1.847
peak=   -3.315 closest distance to " N   SER A 212 " =    1.916
peak=   -3.314 closest distance to " CB  PRO A  54 " =    2.504
peak=   -3.312 closest distance to " CB  PHE A 208 " =    2.268
peak=   -3.311 closest distance to " O   HOH Z 426 " =    1.614
peak=   -3.308 closest distance to " O   HOH Z 176 " =    0.807
peak=   -3.303 closest distance to " CD1 LEU A 228 " =    2.335
peak=   -3.295 closest distance to " O   HOH Z 196 " =    2.195
peak=   -3.294 closest distance to " O   VAL A 189 " =    1.627
peak=   -3.292 closest distance to " O   HOH Z 281 " =    2.682
peak=   -3.291 closest distance to " CG  GLU A 277 " =    1.257
peak=   -3.287 closest distance to " CD2 PHE A  61 " =    2.086
peak=   -3.285 closest distance to " NE2 GLN A 278 " =    1.721
peak=   -3.282 closest distance to " OG BSER A 134 " =    1.762
peak=   -3.278 closest distance to " O   HOH Z 140 " =    1.494
peak=   -3.271 closest distance to " O   HOH Z  11 " =    1.809
peak=   -3.269 closest distance to " CB  ASP A 286 " =    2.068
peak=   -3.268 closest distance to " O   HOH Z 345 " =    2.173
peak=   -3.264 closest distance to " NH2 ARG A  79 " =    1.536
peak=   -3.261 closest distance to " O   HOH Z  51 " =    1.520
peak=   -3.252 closest distance to " CA  GLY A 241 " =    3.275
peak=   -3.251 closest distance to " N   SER A 276 " =    1.246
peak=   -3.250 closest distance to " O   GLN A 240 " =    2.136
peak=   -3.250 closest distance to " O   MET A  40 " =    2.801
peak=   -3.242 closest distance to " OG  SER A  87 " =    1.391
peak=   -3.242 closest distance to " O   HOH Z 244 " =    2.007
peak=   -3.239 closest distance to " O   HOH Z 292 " =    1.757
peak=   -3.237 closest distance to " O   HOH Z 111 " =    1.840
peak=   -3.235 closest distance to " C   PHE A  59 " =    1.326
peak=   -3.233 closest distance to " CE1 TYR A 169 " =    2.555
peak=   -3.226 closest distance to " CD1 LEU A 297 " =    2.529
peak=   -3.225 closest distance to " ND2BASN A 224 " =    1.784
peak=   -3.223 closest distance to " ND2BASN A 224 " =    1.735
peak=   -3.222 closest distance to " NE  ARG A  36 " =    2.050
peak=   -3.222 closest distance to " C   GLY A  13 " =    0.964
peak=   -3.218 closest distance to " CB  ALA A   9 " =    2.509
peak=   -3.218 closest distance to " CE  MET A 105 " =    2.310
peak=   -3.215 closest distance to " NE2 GLN A 194 " =    1.742
peak=   -3.210 closest distance to " CA  ASP A 298 " =    1.061
peak=   -3.206 closest distance to " OD2 ASP A 171 " =    1.790
peak=   -3.203 closest distance to " CD  GLU A 236 " =    1.087
peak=   -3.200 closest distance to " NH1AARG A 275 " =    1.869
peak=   -3.193 closest distance to " CE3 TRP A 274 " =    2.414
peak=   -3.192 closest distance to " CA  SER A 135 " =    1.300
peak=   -3.189 closest distance to " O   HOH Z 184 " =    1.757
peak=   -3.187 closest distance to " CA  TRP A 274 " =    1.366
peak=   -3.184 closest distance to " OD2 ASP A 171 " =    2.186
peak=   -3.180 closest distance to " O   HOH Z 317 " =    1.538
peak=   -3.176 closest distance to " CG  GLN A  88 " =    0.797
peak=   -3.176 closest distance to " O   HOH Z 128 " =    2.555
peak=   -3.174 closest distance to " O   HOH Z 282 " =    4.968
peak=   -3.173 closest distance to " O   HOH Z  13 " =    1.621
peak=   -3.169 closest distance to " O   ALA A  34 " =    2.540
peak=   -3.167 closest distance to " O   ALA A 292 " =    2.125
peak=   -3.153 closest distance to " O   HOH Z  63 " =    1.644
peak=   -3.152 closest distance to " O   SER A  62 " =    2.184
peak=   -3.151 closest distance to " N   GLN A  58 " =    1.868
peak=   -3.150 closest distance to " C   MET A 188 " =    1.436
peak=   -3.149 closest distance to " CB  ALA A 100 " =    2.249
peak=   -3.140 closest distance to " O   HOH Z 111 " =    1.290
peak=   -3.138 closest distance to " NH2 ARG A  79 " =    2.035
peak=   -3.135 closest distance to " CG1 VAL A 197 " =    2.248
peak=   -3.133 closest distance to " N   ALA A 248 " =    1.582
peak=   -3.132 closest distance to " O   HOH Z 357 " =    2.039
peak=   -3.124 closest distance to " O   SER A  22 " =    2.473
peak=   -3.121 closest distance to " CB  CYS A 201 " =    2.532
peak=   -3.118 closest distance to " CB  GLN A  11 " =    1.671
peak=   -3.116 closest distance to " NH1 ARG A 195 " =    2.620
peak=   -3.114 closest distance to " O   ALA A 161 " =    1.632
peak=   -3.113 closest distance to " O   HOH Z 417 " =    2.769
peak=   -3.113 closest distance to " O   HOH Z 350 " =    2.205
peak=   -3.113 closest distance to " O   HOH Z 266 " =    4.873
peak=   -3.112 closest distance to " O   HOH Z 283 " =    5.589
peak=   -3.112 closest distance to " O   HOH Z 423 " =    1.251
peak=   -3.107 closest distance to " N   ALA A 226 " =    2.171
peak=   -3.104 closest distance to " ND2 ASN A  60 " =    1.431
peak=   -3.094 closest distance to " SD  MET A 188 " =    2.325
peak=   -3.094 closest distance to " CD1 LEU A   5 " =    2.574
peak=   -3.092 closest distance to " CB  ASP A 132 " =    2.371
peak=   -3.091 closest distance to " CG2 VAL A 189 " =    1.958
peak=   -3.090 closest distance to " OD2 ASP A 191 " =    1.441
peak=   -3.076 closest distance to " O   HOH Z 318 " =    2.020
peak=   -3.067 closest distance to " OG  SER A 206 " =    1.824
peak=   -3.057 closest distance to " CA  GLY A 241 " =    2.833
peak=   -3.057 closest distance to " CE3 TRP A 150 " =    1.656
peak=   -3.057 closest distance to " CE  LYS A  76 " =    2.661
peak=   -3.052 closest distance to " CD1 ILE A 199 " =    2.622

================= 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    :  0.3164 0.3106   6.023536e+00   6.004944e+00
   1_bss:  0.3036 0.3016   6.003276e+00   5.981023e+00
   1_xyz:  0.1727 0.1955   5.479864e+00   5.575425e+00
   1_adp:  0.1573 0.2033   5.427192e+00   5.612733e+00
   1_occ:  0.1569 0.2032   5.425823e+00   5.611673e+00
   2_bss:  0.1560 0.2008   5.423251e+00   5.605639e+00
   2_xyz:  0.1219 0.1680   5.216779e+00   5.444716e+00
   2_adp:  0.1186 0.1593   5.180627e+00   5.399250e+00
   2_occ:  0.1185 0.1594   5.180311e+00   5.399606e+00
   3_bss:  0.1187 0.1587   5.179029e+00   5.396879e+00
   3_xyz:  0.1155 0.1556   5.160601e+00   5.383304e+00
   3_adp:  0.1134 0.1561   5.151349e+00   5.384039e+00
   3_occ:  0.1133 0.1561   5.151501e+00   5.384436e+00
   4_bss:  0.1133 0.1560   5.151299e+00   5.384246e+00
   4_xyz:  0.1093 0.1552   5.130396e+00   5.379018e+00
   4_adp:  0.1085 0.1560   5.127350e+00   5.379757e+00
   4_occ:  0.1084 0.1560   5.127496e+00   5.380121e+00
   5_bss:  0.1083 0.1560   5.127423e+00   5.380016e+00
   5_xyz:  0.1109 0.1576   5.145247e+00   5.391796e+00
   5_adp:  0.1114 0.1562   5.142935e+00   5.385733e+00
   5_occ:  0.1114 0.1562   5.143001e+00   5.385982e+00
   5_bss:  0.1113 0.1562   5.143057e+00   5.385999e+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:  0.338  53.088  -1.424  -0.058  -1.016  -0.000  -0.000  -0.000
   1_xyz:  0.338  53.088  -1.424  -0.058  -1.016  -0.000  -0.000  -0.000
   1_adp:  0.338  53.088  -1.424  -0.058  -1.016  -0.000  -0.000  -0.000
   1_occ:  0.338  53.088  -1.424  -0.058  -1.016  -0.000  -0.000  -0.000
   2_bss:  0.333  59.386  -2.407  -2.194  -1.490  -0.000  -0.000  -0.000
   2_xyz:  0.333  59.386  -2.407  -2.194  -1.490  -0.000  -0.000  -0.000
   2_adp:  0.333  59.386  -2.407  -2.194  -1.490  -0.000  -0.000  -0.000
   2_occ:  0.333  59.386  -2.407  -2.194  -1.490  -0.000  -0.000  -0.000
   3_bss:  0.333  59.386  -2.575  -2.630  -1.403  -0.000  -0.000  -0.000
   3_xyz:  0.333  59.386  -2.575  -2.630  -1.403  -0.000  -0.000  -0.000
   3_adp:  0.333  59.386  -2.575  -2.630  -1.403  -0.000  -0.000  -0.000
   3_occ:  0.333  59.386  -2.575  -2.630  -1.403  -0.000  -0.000  -0.000
   4_bss:  0.329  59.386  -2.475  -2.633  -1.256  -0.000  -0.000  -0.000
   4_xyz:  0.329  59.386  -2.475  -2.633  -1.256  -0.000  -0.000  -0.000
   4_adp:  0.329  59.386  -2.475  -2.633  -1.256  -0.000  -0.000  -0.000
   4_occ:  0.329  59.386  -2.475  -2.633  -1.256  -0.000  -0.000  -0.000
   5_bss:  0.325  59.386  -2.192  -2.403  -0.990  -0.000  -0.000  -0.000
   5_xyz:  0.325  59.386  -2.192  -2.403  -0.990  -0.000  -0.000  -0.000
   5_adp:  0.325  59.386  -2.192  -2.403  -0.990  -0.000  -0.000  -0.000
   5_occ:  0.325  59.386  -2.192  -2.403  -0.990  -0.000  -0.000  -0.000
   5_bss:  0.325  59.355  -2.086  -2.297  -0.852  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.563 0.7440  0.9185    26920.051
   1_bss:  30.601 0.7528  0.9049    24515.131
   1_xyz:  17.989 0.8819  1.0061     9599.640
   1_adp:  18.989 0.8719  1.0015    10275.286
   1_occ:  18.969 0.8721  1.0011    10232.986
   2_bss:  18.794 0.8737  0.9610    10091.577
   2_xyz:  15.313 0.9038  0.9784     7091.831
   2_adp:  14.291 0.9125  0.9804     6532.883
   2_occ:  14.296 0.9125  0.9802     6530.154
   3_bss:  14.261 0.9127  0.9741     6477.930
   3_xyz:  13.843 0.9166  0.9745     6298.563
   3_adp:  13.846 0.9166  0.9693     6281.003
   3_occ:  13.854 0.9165  0.9692     6284.404
   4_bss:  13.851 0.9165  0.9720     6281.593
   4_xyz:  13.775 0.9170  0.9726     6235.679
   4_adp:  13.813 0.9166  0.9663     6219.747
   4_occ:  13.819 0.9166  0.9662     6223.243
   5_bss:  13.820 0.9166  0.9752     6221.460
   5_xyz:  14.001 0.9154  0.9739     6381.773
   5_adp:  13.860 0.9165  0.9692     6318.707
   5_occ:  13.865 0.9165  0.9691     6319.411
   5_bss:  13.867 0.9164  0.9721     6320.267
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6135e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6135e-01
   1_xyz:   1.028  0.008  0.072 15.244  0.005  4.111   6.3281e-02
   1_adp:   1.028  0.008  0.072 15.244  0.005  4.111   6.3281e-02
   1_occ:   1.028  0.008  0.072 15.244  0.005  4.111   6.3281e-02
   2_bss:   1.028  0.008  0.072 15.244  0.005  4.111   6.3281e-02
   2_xyz:   1.006  0.007  0.075 14.868  0.003  4.121   6.0074e-02
   2_adp:   1.006  0.007  0.075 14.868  0.003  4.121   6.0074e-02
   2_occ:   1.006  0.007  0.075 14.868  0.003  4.121   6.0074e-02
   3_bss:   1.006  0.007  0.075 14.868  0.003  4.121   6.0074e-02
   3_xyz:   0.901  0.006  0.071 14.702  0.003  4.113   5.1752e-02
   3_adp:   0.901  0.006  0.071 14.702  0.003  4.113   5.1752e-02
   3_occ:   0.901  0.006  0.071 14.702  0.003  4.113   5.1752e-02
   4_bss:   0.901  0.006  0.071 14.702  0.003  4.113   5.1752e-02
   4_xyz:   1.015  0.008  0.077 14.890  0.004  4.114   6.2626e-02
   4_adp:   1.015  0.008  0.077 14.890  0.004  4.114   6.2626e-02
   4_occ:   1.015  0.008  0.077 14.890  0.004  4.114   6.2626e-02
   5_bss:   1.015  0.008  0.077 14.890  0.004  4.114   6.2626e-02
   5_xyz:   0.893  0.006  0.070 14.649  0.003  4.114   5.0705e-02
   5_adp:   0.893  0.006  0.070 14.649  0.003  4.114   5.0705e-02
   5_occ:   0.893  0.006  0.070 14.649  0.003  4.114   5.0705e-02
   5_bss:   0.893  0.006  0.070 14.649  0.003  4.114   5.0705e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4160e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4160e-01
   1_xyz:   8.738  0.045  0.254 84.798  0.045  2.249   5.9828e-02
   1_adp:   8.738  0.045  0.254 84.798  0.045  2.249   5.9828e-02
   1_occ:   8.738  0.045  0.254 84.798  0.045  2.249   5.9828e-02
   2_bss:   8.738  0.045  0.254 84.798  0.045  2.249   5.9828e-02
   2_xyz:   7.890  0.039  0.229 82.676  0.030  2.335   5.2361e-02
   2_adp:   7.890  0.039  0.229 82.676  0.030  2.335   5.2361e-02
   2_occ:   7.890  0.039  0.229 82.676  0.030  2.335   5.2361e-02
   3_bss:   7.890  0.039  0.229 82.676  0.030  2.335   5.2361e-02
   3_xyz:   7.778  0.039  0.215 84.065  0.033  2.361   3.1042e-02
   3_adp:   7.778  0.039  0.215 84.065  0.033  2.361   3.1042e-02
   3_occ:   7.778  0.039  0.215 84.065  0.033  2.361   3.1042e-02
   4_bss:   7.778  0.039  0.215 84.065  0.033  2.361   3.1042e-02
   4_xyz:   7.289  0.041  0.247 84.523  0.036  2.324   4.4794e-02
   4_adp:   7.289  0.041  0.247 84.523  0.036  2.324   4.4794e-02
   4_occ:   7.289  0.041  0.247 84.523  0.036  2.324   4.4794e-02
   5_bss:   7.289  0.041  0.247 84.523  0.036  2.324   4.4794e-02
   5_xyz:   7.403  0.040  0.211 83.810  0.035  2.396   3.2112e-02
   5_adp:   7.403  0.040  0.211 83.810  0.035  2.396   3.2112e-02
   5_occ:   7.403  0.040  0.211 83.810  0.035  2.396   3.2112e-02
   5_bss:   7.403  0.040  0.211 83.810  0.035  2.396   3.2112e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  73.45   1.52  17.09  69.11   1.52  13.02  73.45   5.00  39.23
   1_occ:  73.45   1.52  17.09  69.11   1.52  13.02  73.45   5.00  39.23
   2_bss:  73.45   1.52  17.09  69.11   1.52  13.02  73.45   5.00  39.23
   2_xyz:  73.45   1.52  17.09  69.11   1.52  13.02  73.45   5.00  39.23
   2_adp:  71.21   2.04  16.64  69.72   2.04  12.89  71.21   6.25  37.07
   2_occ:  71.21   2.04  16.64  69.72   2.04  12.89  71.21   6.25  37.07
   3_bss:  71.21   2.04  16.64  69.72   2.04  12.89  71.21   6.25  37.07
   3_xyz:  71.21   2.04  16.64  69.72   2.04  12.89  71.21   6.25  37.07
   3_adp:  73.83   1.18  16.90  73.83   1.18  12.91  72.69   6.25  38.62
   3_occ:  73.83   1.18  16.90  73.83   1.18  12.91  72.69   6.25  38.62
   4_bss:  73.83   1.18  16.90  73.83   1.18  12.91  72.69   6.25  38.62
   4_xyz:  73.83   1.18  16.90  73.83   1.18  12.91  72.69   6.25  38.62
   4_adp:  89.12   0.11  17.32  89.12   0.11  12.98  86.25   6.14  40.95
   4_occ:  89.12   0.11  17.32  89.12   0.11  12.98  86.25   6.14  40.95
   5_bss:  89.12   0.11  17.32  89.12   0.11  12.98  86.25   6.14  40.95
   5_xyz:  89.12   0.11  17.32  89.12   0.11  12.98  86.25   6.14  40.95
   5_adp:  87.87   0.90  16.78  87.87   0.90  12.71  83.35   6.05  38.92
   5_occ:  87.87   0.90  16.78  87.87   0.90  12.71  83.35   6.05  38.92
   5_bss:  87.84   0.87  16.75  87.84   0.87  12.68  83.32   6.01  38.89
------------------------------------------------------------------------
 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:    0.941    0.019    0.297
   1_adp:    0.941    0.019    0.297
   1_occ:    0.941    0.019    0.297
   2_bss:    0.941    0.019    0.297
   2_xyz:    0.870    0.032    0.355
   2_adp:    0.870    0.032    0.355
   2_occ:    0.870    0.032    0.355
   3_bss:    0.870    0.032    0.355
   3_xyz:    1.000    0.035    0.372
   3_adp:    1.000    0.035    0.372
   3_occ:    1.000    0.035    0.372
   4_bss:    1.000    0.035    0.372
   4_xyz:    1.079    0.029    0.384
   4_adp:    1.079    0.029    0.384
   4_occ:    1.079    0.029    0.384
   5_bss:    1.079    0.029    0.384
   5_xyz:    1.140    0.028    0.386
   5_adp:    1.140    0.028    0.386
   5_occ:    1.140    0.028    0.386
   5_bss:    1.140    0.028    0.386
------------------------------------------------------------------------

CPU time actual refinement: 318.55


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_886/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/noshake/run_886/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_886/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_886/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_886/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 318.40 
  Macro-tasks:
    bulk solvent and scale       = 35.29  
    individual site refinement   = 135.34 
    weights calculation          = 28.95  
    collect and process          = 6.62   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 206.30 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 100.60 
    alpha_beta                      = 8.00   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 110.82 
    fmodel                         = 6.48   
    r_factors                      = 0.23   
    phase_errors                   = 11.38  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 240.12 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.472 micro seconds
Total CPU time: 5.53 minutes
from_scatterers_fft:    649 calls, 100.15 s
gradients_fft:          594 calls,  96.70 s

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

# Date 2008-01-16 Time 05:53:39 PST -0800 (1200491619.75 s)
Start R-work = 0.3164, R-free = 0.3106 (no bulk solvent and anisotropic scale)
Final R-work = 0.1343, R-free = 0.1758 (no bulk solvent and anisotropic scale)

Start R-work = 0.3036, R-free = 0.3016
Final R-work = 0.1113, R-free = 0.1562