# Date 2008-01-16 Time 05:59:46 PST -0800 (1200491986.09 s)
#phil __OFF__

Command line arguments: "../966.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21535
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 966

-------------------------------------------------------------------------------
  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, 48.1033, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, 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, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 2.02062
Completeness in resolution range: 0.963457
Completeness with d_max=infinity: 0.960433

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1841
                             d_min =   2.0206

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, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 2.02062
Completeness in resolution range: 0.963457
Completeness with d_max=infinity: 0.960433

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1845 -  4.3229 [2142/2169]  1927   215  10.0%
  bin  2:  4.3229 -  3.4444 [2040/2056]  1837   203  10.0%
  bin  3:  3.4444 -  3.0129 [2040/2059]  1838   202   9.9%
  bin  4:  3.0129 -  2.7392 [1995/2025]  1793   202  10.1%
  bin  5:  2.7392 -  2.5438 [1991/2010]  1789   202  10.1%
  bin  6:  2.5438 -  2.3945 [1980/2016]  1788   192   9.7%
  bin  7:  2.3945 -  2.2750 [1980/2013]  1779   201  10.2%
  bin  8:  2.2750 -  2.1762 [1959/1993]  1761   198  10.1%
  bin  9:  2.1762 -  2.0927 [1946/1974]  1753   193   9.9%
  bin 10:  2.0927 -  2.0206 [1516/2017]  1365   151  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_966/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.73 -     2.37: 13
        2.37 -     3.00: 1874
        3.00 -     3.63: 4463
        3.63 -     4.27: 8873
        4.27 -     4.90: 12352
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.733 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.828 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.934 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.067 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27570 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_966/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_966/model_refine_001.geo

CPU time processing inputs: 8.96


============================ 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 48.10325 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4782   r_free= 0.4666   ksol= 0.00   Bsol= 0.00   scale= 0.860    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.289055                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1845 -  4.8212 0.99   1387  153 0.3806 0.3779      6.5692       6.538|
|  2:  4.8212 -  3.8473 0.99   1328  150 0.4282 0.4503      6.8848      6.9118|
|  3:  3.8473 -  3.3670 0.99   1318  149 0.4620 0.4090      6.7181      6.6229|
|  4:  3.3670 -  3.0619 0.99   1296  134 0.4698 0.4788      6.5516      6.4948|
|  5:  3.0619 -  2.8440 0.99   1288  147 0.5059 0.4392      6.3855      6.3976|
|  6:  2.8440 -  2.6772 0.99   1287  145 0.5031 0.5100      6.2794      6.1954|
|  7:  2.6772 -  2.5438 0.99   1280  146 0.5091 0.4616      6.2551      6.1647|
|  8:  2.5438 -  2.4336 0.98   1288  136 0.5092 0.4801      6.1805      6.1847|
|  9:  2.4336 -  2.3402 0.98   1266  142 0.5166 0.5103      6.1098      6.1565|
| 10:  2.3402 -  2.2597 0.98   1254  137 0.5221 0.4807      6.1152      6.0741|
| 11:  2.2597 -  2.1893 1.00   1280  148 0.5301 0.5262      6.0467      6.0964|
| 12:  2.1893 -  2.1269 0.97   1267  135 0.5204 0.5649      5.9737      6.0364|
| 13:  2.1269 -  2.0710 0.98   1253  139 0.5176 0.5144      5.8913      5.8475|
| 14:  2.0710 -  2.0206 0.66    838   98 0.5119 0.5386      5.8585      5.7574|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1845 -  4.8212  1387   153  0.69  34.91   0.81     0.72      74256.74|
|  2:  4.8212 -  3.8473  1328   150  0.70  34.97   0.87     0.78     105912.40|
|  3:  3.8473 -  3.3670  1318   149  0.61  43.23   0.86     0.75     110863.75|
|  4:  3.3670 -  3.0619  1296   134  0.52  50.60   0.86     0.66     100391.26|
|  5:  3.0619 -  2.8440  1288   147  0.43  57.37   0.86     0.58      78411.27|
|  6:  2.8440 -  2.6772  1287   145  0.40  59.60   0.85     0.53      68987.77|
|  7:  2.6772 -  2.5438  1280   146  0.39  60.33   0.88     0.52      60966.44|
|  8:  2.5438 -  2.4336  1288   136  0.38  61.40   0.88     0.52      57788.55|
|  9:  2.4336 -  2.3402  1266   142  0.37  62.51   0.88     0.52      53565.67|
| 10:  2.3402 -  2.2597  1254   137  0.38  61.44   0.90     0.54      48785.56|
| 11:  2.2597 -  2.1893  1280   148  0.34  64.17   0.89     0.51      46389.89|
| 12:  2.1893 -  2.1269  1267   135  0.32  66.38   0.88     0.47      44770.12|
| 13:  2.1269 -  2.0710  1253   139  0.27  69.88   0.88     0.39      39675.68|
| 14:  2.0710 -  2.0206   838    98  0.27  70.04   0.92     0.33      30104.15|
|alpha:            min =        0.33 max =            0.78 mean =         0.57|
|beta:             min =    30104.15 max =       110863.75 mean =     67053.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.97 mean =        56.32|
|phase err.(test): min =        0.00 max =           89.90 mean =        56.62|
|-----------------------------------------------------------------------------|

============================== 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 = 11.110129             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.262   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.862200              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.729   (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 |  1.733 -  2.050:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.050 -  2.366:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.366 -  2.683:       83 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.683 -  3.000:     1791 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.000 -  3.316:     1830 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.316 -  3.633:     2633 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.633 -  3.950:     4608 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.950 -  4.267:     4265 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.267 -  4.583:     5604 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.583 -  4.900:     6748 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.733 |       0.194 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.508)------------------------------------------|
|    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: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4782   r_free= 0.4666   ksol= 0.00   Bsol= 0.00   scale= 0.860    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.289055                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4705   r_free= 0.4586   ksol= 0.28   Bsol= 47.70   scale= 0.904   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,3.74,2.26,0.00,0.00,0.00); trace/3= 0.99                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.284545                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.330653              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.796   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.288239              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.332   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4705      final r-factor (work) = 0.3827          |
| start r-factor (free) = 0.4586      final r-factor (free) = 0.4145          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.4707 = 9.33 * 0.50 * 6.2812 + 1.00 * 0.1669                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.9656 = 9.33 * 0.50 * 6.1807 + 1.00 * 0.1308                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3827      final r-factor (work) = 0.3517          |
| start r-factor (free) = 0.4145      final r-factor (free) = 0.4252          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9681 = 1.29 * 1.00 * 6.1807 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8919 = 1.29 * 1.00 * 6.1091 + 1.00 * 0.0219                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.508)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.95  18.88    None  None   None       |
|    all(noH): 2823   0      0.00    111.95  18.88    None  None   None       |
|    Sol.    : 438    0      0.00    111.95  37.26    None  None   None       |
|    Mac.    : 2385   0      0.00    90.94   15.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.195: 1043   |   5:    55.973 -  67.167:   64        |
|      1:    11.195 -  22.389:  925   |   6:    67.167 -  78.362:   29        |
|      2:    22.389 -  33.584:  449   |   7:    78.362 -  89.556:    8        |
|      3:    33.584 -  44.778:  208   |   8:    89.556 - 100.751:    3        |
|      4:    44.778 -  55.973:   93   |   9:   100.751 - 111.945:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3517 r_free = 0.4252             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3514 r_free = 0.4242             target_work(ml) = 6.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3514   r_free= 0.4242   ksol= 0.28   Bsol= 47.70   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,3.74,2.26,0.00,0.00,0.00); trace/3= 0.99                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.113916                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3509   r_free= 0.4225   ksol= 0.30   Bsol= 62.63   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,2.62,1.64,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.115777                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.740109              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.948   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.814534              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.575  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3509      final r-factor (work) = 0.2979          |
| start r-factor (free) = 0.4225      final r-factor (free) = 0.3630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7835 = 7.74 * 0.50 * 6.1117 + 1.00 * 0.1308                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5203 = 7.74 * 0.50 * 6.0557 + 1.00 * 0.0844                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2979      final r-factor (work) = 0.2873          |
| start r-factor (free) = 0.3630      final r-factor (free) = 0.3579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9546 = 0.81 * 1.00 * 6.0557 + 1.00 * 0.0220                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8932 = 0.81 * 1.00 * 5.9755 + 1.00 * 0.0259                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.508)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    164.19  18.53    None  None   None       |
|    all(noH): 2823   0      0.00    164.19  18.53    None  None   None       |
|    Sol.    : 438    0      0.00    111.99  37.49    None  None   None       |
|    Mac.    : 2385   0      0.00    164.19  15.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  16.419: 1597   |   5:    82.094 -  98.513:    8        |
|      1:    16.419 -  32.838:  820   |   6:    98.513 - 114.931:    1        |
|      2:    32.838 -  49.256:  253   |   7:   114.931 - 131.350:    0        |
|      3:    49.256 -  65.675:  105   |   8:   131.350 - 147.769:    0        |
|      4:    65.675 -  82.094:   38   |   9:   147.769 - 164.188:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2873 r_free = 0.3579             target_work(ml) = 5.971         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2872 r_free = 0.3579             target_work(ml) = 5.971         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2872   r_free= 0.3579   ksol= 0.30   Bsol= 62.63   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,2.62,1.64,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.970722                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2873   r_free= 0.3577   ksol= 0.32   Bsol= 71.14   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,2.38,1.39,0.00,0.00,0.00); trace/3= 1.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.972235                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.052646             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.667  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.436232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.713  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2873      final r-factor (work) = 0.2280          |
| start r-factor (free) = 0.3577      final r-factor (free) = 0.2838          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1233 = 10.05 * 0.50 * 5.9763 + 1.00 * 0.0844                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.6714 = 10.05 * 0.50 * 5.8812 + 1.00 * 0.1106                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2280      final r-factor (work) = 0.1985          |
| start r-factor (free) = 0.2838      final r-factor (free) = 0.2572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.3546 = 2.44 * 1.00 * 5.8812 + 1.00 * 0.0266                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.8800 = 2.44 * 1.00 * 5.6887 + 1.00 * 0.0210                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.508)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.04  18.77    None  None   None       |
|    all(noH): 2823   0      0.00    122.04  18.77    None  None   None       |
|    Sol.    : 438    0      2.12    122.04  47.10    None  None   None       |
|    Mac.    : 2385   0      0.00    104.94  13.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.204: 1452   |   5:    61.022 -  73.226:   84        |
|      1:    12.204 -  24.409:  731   |   6:    73.226 -  85.431:   52        |
|      2:    24.409 -  36.613:  231   |   7:    85.431 -  97.635:   18        |
|      3:    36.613 -  48.818:  146   |   8:    97.635 - 109.839:    8        |
|      4:    48.818 -  61.022:   99   |   9:   109.839 - 122.044:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1985 r_free = 0.2572             target_work(ml) = 5.646         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1984 r_free = 0.2569             target_work(ml) = 5.645         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1984   r_free= 0.2569   ksol= 0.32   Bsol= 71.14   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,2.38,1.39,0.00,0.00,0.00); trace/3= 1.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.644604                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1982   r_free= 0.2566   ksol= 0.34   Bsol= 90.47   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,1.15,0.97,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.643757                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.036823              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.006   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.339314              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.147  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1982      final r-factor (work) = 0.1718          |
| start r-factor (free) = 0.2566      final r-factor (free) = 0.2195          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7503 = 3.04 * 0.50 * 5.6900 + 1.00 * 0.1106                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5427 = 3.04 * 0.50 * 5.5852 + 1.00 * 0.0621                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1718      final r-factor (work) = 0.1644          |
| start r-factor (free) = 0.2195      final r-factor (free) = 0.2091          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9162 = 0.34 * 1.00 * 5.5852 + 1.00 * 0.0211                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8792 = 0.34 * 1.00 * 5.4952 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.508)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.89  17.46    None  None   None       |
|    all(noH): 2823   0      0.00    119.89  17.46    None  None   None       |
|    Sol.    : 438    0      2.71    119.89  45.55    None  None   None       |
|    Mac.    : 2385   0      0.00    101.52  12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.989: 1595   |   5:    59.945 -  71.934:   73        |
|      1:    11.989 -  23.978:  665   |   6:    71.934 -  83.923:   47        |
|      2:    23.978 -  35.967:  183   |   7:    83.923 -  95.912:   17        |
|      3:    35.967 -  47.956:  136   |   8:    95.912 - 107.901:    5        |
|      4:    47.956 -  59.945:  100   |   9:   107.901 - 119.890:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1644 r_free = 0.2091             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1643 r_free = 0.2091             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1643   r_free= 0.2091   ksol= 0.34   Bsol= 90.47   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,1.15,0.97,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.469724                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1646   r_free= 0.2094   ksol= 0.34   Bsol= 87.10   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,0.61,0.92,0.00,0.00,0.00); trace/3= 0.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.470951                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.217339              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.051  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.201166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.116  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1646      final r-factor (work) = 0.1456          |
| start r-factor (free) = 0.2094      final r-factor (free) = 0.1904          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1546 = 2.22 * 0.50 * 5.4953 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0663 = 2.22 * 0.50 * 5.4128 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1456      final r-factor (work) = 0.1400          |
| start r-factor (free) = 0.1904      final r-factor (free) = 0.1905          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5160 = 1.20 * 1.00 * 5.4128 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4343 = 1.20 * 1.00 * 5.3433 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.508)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.59  17.13    None  None   None       |
|    all(noH): 2823   0      0.00    124.59  17.13    None  None   None       |
|    Sol.    : 438    0      3.14    124.59  46.51    None  None   None       |
|    Mac.    : 2385   0      0.00    103.25  11.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.459: 1715   |   5:    62.293 -  74.751:   73        |
|      1:    12.459 -  24.917:  595   |   6:    74.751 -  87.210:   41        |
|      2:    24.917 -  37.376:  163   |   7:    87.210 -  99.669:   18        |
|      3:    37.376 -  49.834:  116   |   8:    99.669 - 112.127:    5        |
|      4:    49.834 -  62.293:   96   |   9:   112.127 - 124.586:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1400 r_free = 0.1905             target_work(ml) = 5.339         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1399 r_free = 0.1905             target_work(ml) = 5.339         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1399   r_free= 0.1905   ksol= 0.34   Bsol= 87.10   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,0.61,0.92,0.00,0.00,0.00); trace/3= 0.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.339067                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1845 -  4.8212 0.99   1387  153 0.1064 0.1422      5.4654      5.6062|
|  2:  4.8212 -  3.8473 0.99   1328  150 0.0953 0.1115      5.5335      5.6986|
|  3:  3.8473 -  3.3670 0.99   1318  149 0.1236 0.1791      5.6183      6.0185|
|  4:  3.3670 -  3.0619 0.99   1296  134 0.1474 0.1981      5.6232      5.7846|
|  5:  3.0619 -  2.8440 0.99   1288  147 0.1723 0.1891      5.5553      5.6727|
|  6:  2.8440 -  2.6772 0.99   1287  145 0.1586 0.2584      5.4215      5.6872|
|  7:  2.6772 -  2.5438 0.99   1280  146 0.1633 0.2037      5.3953      5.5418|
|  8:  2.5438 -  2.4336 0.98   1288  136 0.1608 0.2154      5.3276      5.5772|
|  9:  2.4336 -  2.3402 0.98   1266  142 0.1630 0.2260      5.2838      5.5019|
| 10:  2.3402 -  2.2597 0.98   1254  137 0.1515 0.2047      5.2096      5.3858|
| 11:  2.2597 -  2.1893 1.00   1280  148 0.1487 0.2287      5.1513      5.4741|
| 12:  2.1893 -  2.1269 0.97   1267  135 0.1398 0.1967      5.0465      5.3392|
| 13:  2.1269 -  2.0710 0.98   1253  139 0.1440 0.2000      4.9943      5.1585|
| 14:  2.0710 -  2.0206 0.66    838   98 0.1443 0.2328      4.9382      5.2322|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1845 -  4.8212  1387   153  0.93  10.58   0.95     0.92       8849.74|
|  2:  4.8212 -  3.8473  1328   150  0.94   9.44   1.00     0.98      10910.39|
|  3:  3.8473 -  3.3670  1318   149  0.92  13.42   1.02     1.01      13581.52|
|  4:  3.3670 -  3.0619  1296   134  0.89  16.83   1.01     0.97      14423.78|
|  5:  3.0619 -  2.8440  1288   147  0.86  20.22   1.00     0.98      12926.42|
|  6:  2.8440 -  2.6772  1287   145  0.87  19.77   0.97     0.94      10244.98|
|  7:  2.6772 -  2.5438  1280   146  0.87  20.08   0.99     0.96       9779.05|
|  8:  2.5438 -  2.4336  1288   136  0.86  20.20   0.98     0.93       8696.91|
|  9:  2.4336 -  2.3402  1266   142  0.86  21.05   0.98     0.92       8114.68|
| 10:  2.3402 -  2.2597  1254   137  0.86  20.55   0.98     0.92       7065.28|
| 11:  2.2597 -  2.1893  1280   148  0.86  20.31   0.97     0.91       6517.39|
| 12:  2.1893 -  2.1269  1267   135  0.88  18.83   0.98     0.97       5560.78|
| 13:  2.1269 -  2.0710  1253   139  0.87  19.73   0.95     0.92       4900.82|
| 14:  2.0710 -  2.0206   838    98  0.86  20.20   0.92     0.87       4343.62|
|alpha:            min =        0.87 max =            1.01 mean =         0.94|
|beta:             min =     4343.62 max =        14423.78 mean =      9144.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.80|
|phase err.(test): min =        0.00 max =           88.91 mean =        17.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1399   r_free= 0.1903   ksol= 0.33   Bsol= 85.31   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.18,0.76,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.339003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1399   r_free= 0.1903   ksol= 0.33   Bsol= 85.31   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.18,0.76,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.339003                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1845 -  4.8212 0.99   1387  153 0.1064 0.1424      5.4657      5.6072|
|  2:  4.8212 -  3.8473 0.99   1328  150 0.0952 0.1113      5.5336      5.6976|
|  3:  3.8473 -  3.3670 0.99   1318  149 0.1237 0.1791      5.6185      6.0188|
|  4:  3.3670 -  3.0619 0.99   1296  134 0.1474 0.1982      5.6236      5.7851|
|  5:  3.0619 -  2.8440 0.99   1288  147 0.1725 0.1890      5.5556      5.6725|
|  6:  2.8440 -  2.6772 0.99   1287  145 0.1584 0.2579      5.4211      5.6859|
|  7:  2.6772 -  2.5438 0.99   1280  146 0.1633 0.2040      5.3951      5.5418|
|  8:  2.5438 -  2.4336 0.98   1288  136 0.1608 0.2153      5.3275      5.5768|
|  9:  2.4336 -  2.3402 0.98   1266  142 0.1629 0.2260      5.2836      5.5024|
| 10:  2.3402 -  2.2597 0.98   1254  137 0.1515 0.2057      5.2095      5.3865|
| 11:  2.2597 -  2.1893 1.00   1280  148 0.1487 0.2285      5.1508      5.4732|
| 12:  2.1893 -  2.1269 0.97   1267  135 0.1399 0.1972      5.0463      5.3396|
| 13:  2.1269 -  2.0710 0.98   1253  139 0.1441 0.1998      4.9939      5.1581|
| 14:  2.0710 -  2.0206 0.66    838   98 0.1443 0.2327      4.9378      5.2311|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1845 -  4.8212  1387   153  0.93  10.60   0.95     0.92       8863.19|
|  2:  4.8212 -  3.8473  1328   150  0.94   9.45   1.00     0.98      10914.85|
|  3:  3.8473 -  3.3670  1318   149  0.92  13.42   1.02     1.02      13584.84|
|  4:  3.3670 -  3.0619  1296   134  0.89  16.84   1.01     0.98      14431.83|
|  5:  3.0619 -  2.8440  1288   147  0.86  20.21   1.01     0.99      12919.93|
|  6:  2.8440 -  2.6772  1287   145  0.87  19.75   0.98     0.94      10238.96|
|  7:  2.6772 -  2.5438  1280   146  0.87  20.07   1.00     0.97       9766.28|
|  8:  2.5438 -  2.4336  1288   136  0.86  20.20   0.99     0.94       8692.70|
|  9:  2.4336 -  2.3402  1266   142  0.86  21.04   0.99     0.93       8112.33|
| 10:  2.3402 -  2.2597  1254   137  0.86  20.55   0.99     0.93       7064.01|
| 11:  2.2597 -  2.1893  1280   148  0.86  20.31   0.98     0.92       6519.13|
| 12:  2.1893 -  2.1269  1267   135  0.88  18.83   1.00     0.98       5559.40|
| 13:  2.1269 -  2.0710  1253   139  0.87  19.73   0.97     0.94       4895.19|
| 14:  2.0710 -  2.0206   838    98  0.86  20.18   0.94     0.88       4332.70|
|alpha:            min =        0.88 max =            1.02 mean =         0.95|
|beta:             min =     4332.70 max =        14431.83 mean =      9143.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.94 mean =        17.80|
|phase err.(test): min =        0.00 max =           88.89 mean =        17.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.508)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.47    125.06  17.60    None  None   None       |
|    all(noH): 2823   0      0.47    125.06  17.60    None  None   None       |
|    Sol.    : 438    0      3.61    125.06  46.98    None  None   None       |
|    Mac.    : 2385   0      0.47    103.72  12.21    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:     0.470 -  12.928: 1715   |   5:    62.762 -  75.221:   73        |
|      1:    12.928 -  25.387:  595   |   6:    75.221 -  87.679:   41        |
|      2:    25.387 -  37.845:  163   |   7:    87.679 - 100.138:   18        |
|      3:    37.845 -  50.304:  116   |   8:   100.138 - 112.597:    5        |
|      4:    50.304 -  62.762:   96   |   9:   112.597 - 125.055:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.538 - 5.326
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 337
   mapped sites are within: 0.713 - 5.326

peak=    7.696 closest distance to " O   HOH Z 400 " =    0.999
peak=    7.234 closest distance to " O   GLN A  11 " =    1.132
peak=    6.151 closest distance to " O   HOH Z 203 " =    0.991
peak=    5.603 closest distance to " O   HOH Z 210 " =    1.429
peak=    5.583 closest distance to " O   HOH Z  54 " =    1.388
peak=    5.457 closest distance to " O   HOH Z  41 " =    1.131
peak=    5.352 closest distance to " O   HOH Z 117 " =    1.430
peak=    5.051 closest distance to " OD1 ASN A 301 " =    1.075
peak=    4.989 closest distance to " OD1 ASN A  69 " =    0.901
peak=    4.938 closest distance to " O   HOH Z 113 " =    2.135
peak=    4.926 closest distance to " CB  GLN A 223 " =    1.466
peak=    4.901 closest distance to " CB  SER A  63 " =    1.386
peak=    4.838 closest distance to " O   HOH Z  65 " =    1.121
peak=    4.823 closest distance to " O   HOH Z 425 " =    1.738
peak=    4.750 closest distance to " CG  PRO A  54 " =    1.418
peak=    4.702 closest distance to " N   SER A 164 " =    0.982
peak=    4.657 closest distance to " O   HOH Z 412 " =    3.408
peak=    4.641 closest distance to " O   HOH Z  49 " =    1.355
peak=    4.481 closest distance to " CB  GLN A 183 " =    1.197
peak=    4.440 closest distance to " O   HOH Z 422 " =    1.108
peak=    4.386 closest distance to " NH1AARG A 145 " =    1.368
peak=    4.361 closest distance to " CB  GLU A 128 " =    1.034
peak=    4.328 closest distance to " O   HOH Z  82 " =    0.954
peak=    4.324 closest distance to " O   HOH Z 139 " =    1.457
peak=    4.324 closest distance to " CA  TYR A  30 " =    0.971
peak=    4.284 closest distance to " O   HOH Z 234 " =    3.891
peak=    4.267 closest distance to " CG AARG A 275 " =    1.208
peak=    4.259 closest distance to " CG  PRO A 280 " =    0.951
peak=    4.258 closest distance to " O   PRO A 198 " =    1.645
peak=    4.235 closest distance to " NE2 GLN A  11 " =    1.164
peak=    4.223 closest distance to " NH2 ARG A 156 " =    1.205
peak=    4.222 closest distance to " O   HOH Z  69 " =    1.362
peak=    4.215 closest distance to " CG1AVAL A 121 " =    0.768
peak=    4.213 closest distance to " O   HOH Z 248 " =    1.623
peak=    4.200 closest distance to " NH2AARG A 145 " =    1.117
peak=    4.182 closest distance to " CZ  PHE A 218 " =    1.096
peak=    4.175 closest distance to " CG  PRO A 198 " =    1.159
peak=    4.168 closest distance to " O   HOH Z 261 " =    2.161
peak=    4.156 closest distance to " CG  GLN A  77 " =    0.849
peak=    4.152 closest distance to " O   HOH Z 176 " =    1.975
peak=    4.146 closest distance to " OH  TYR A  68 " =    0.925
peak=    4.144 closest distance to " OE1 GLN A  88 " =    0.871
peak=    4.143 closest distance to " O   HOH Z  18 " =    2.330
peak=    4.127 closest distance to " CG1 ILE A 120 " =    1.186
peak=    4.123 closest distance to " O   HOH Z 214 " =    1.982
peak=    4.083 closest distance to " CB  TRP A 179 " =    1.374
peak=    4.082 closest distance to " CA  GLN A  11 " =    1.078
peak=    4.079 closest distance to " CD2 TRP A 179 " =    1.255
peak=    4.067 closest distance to " CZ  PHE A  38 " =    1.163
peak=    4.060 closest distance to " CB  ARG A 275 " =    0.839
peak=    4.059 closest distance to " O   HOH Z 196 " =    1.701
peak=    4.039 closest distance to " O   HOH Z 418 " =    2.010
peak=    4.037 closest distance to " NE2 GLN A  77 " =    3.077
peak=    4.033 closest distance to " CB  SER A  62 " =    0.916
peak=    4.026 closest distance to " CG2BVAL A  41 " =    1.009
peak=    4.019 closest distance to " O   HOH Z 134 " =    2.025
peak=    4.011 closest distance to " CD  ARG A  66 " =    2.692
peak=    4.002 closest distance to " CE1 HIS A 115 " =    1.116
peak=    3.999 closest distance to " CD  ARG A 269 " =    0.818
peak=    3.997 closest distance to " CB  MET A  47 " =    0.977
peak=    3.996 closest distance to " O   HOH Z 147 " =    1.449
peak=    3.973 closest distance to " O   HOH Z 415 " =    1.180
peak=    3.962 closest distance to " CB  ASN A 148 " =    1.598
peak=    3.949 closest distance to " CB  VAL A 202 " =    1.482
peak=    3.939 closest distance to " CB  PRO A  54 " =    0.939
peak=    3.929 closest distance to " O   HOH Z 149 " =    2.182
peak=    3.928 closest distance to " O   ASP A 200 " =    1.614
peak=    3.924 closest distance to " O   HOH Z 389 " =    2.134
peak=    3.920 closest distance to " O   HOH Z 394 " =    1.757
peak=    3.903 closest distance to " O   HOH Z  67 " =    1.206
peak=    3.898 closest distance to " O   HOH Z 126 " =    1.599
peak=    3.898 closest distance to " CA  ARG A 195 " =    1.133
peak=    3.882 closest distance to " O   HOH Z  76 " =    1.238
peak=    3.875 closest distance to " O   HOH Z  48 " =    1.926
peak=    3.867 closest distance to " O   HOH Z 159 " =    1.267
peak=    3.864 closest distance to " CB  ASP A 140 " =    0.923
peak=    3.832 closest distance to " CB  ASN A  39 " =    0.800
peak=    3.821 closest distance to " O   HOH Z 437 " =    1.782
peak=    3.813 closest distance to " CA  ILE A 106 " =    0.830
peak=    3.810 closest distance to " CA  ALA A 291 " =    0.901
peak=    3.804 closest distance to " CB  GLU A  37 " =    0.902
peak=    3.802 closest distance to " CB  MET A  40 " =    1.002
peak=    3.798 closest distance to " N   ALA A   1 " =    2.382
peak=    3.787 closest distance to " O   HOH Z 141 " =    1.750
peak=    3.770 closest distance to " O   HOH Z  80 " =    2.177
peak=    3.761 closest distance to " O   HOH Z 174 " =    2.055
peak=    3.759 closest distance to " N   THR A  52 " =    1.211
peak=    3.755 closest distance to " CA  ALA A 160 " =    1.025
peak=    3.751 closest distance to " CB  ALA A 114 " =    0.793
peak=    3.749 closest distance to " O   HOH Z 369 " =    1.823
peak=    3.745 closest distance to " O   HOH Z 431 " =    1.113
peak=    3.739 closest distance to " CA  ALA A  51 " =    1.032
peak=    3.738 closest distance to " CE  LYS A  76 " =    0.814
peak=    3.733 closest distance to " OE1 GLN A  58 " =    3.531
peak=    3.725 closest distance to " CB  ASN A  45 " =    1.148
peak=    3.719 closest distance to " O   HOH Z 403 " =    1.477
peak=    3.714 closest distance to " CB  ARG A 190 " =    1.838
peak=    3.713 closest distance to " NH1 ARG A  36 " =    1.330
peak=    3.711 closest distance to " O   HOH Z 301 " =    1.523
peak=    3.706 closest distance to " CD1 LEU A  96 " =    0.793
peak=    3.705 closest distance to " O   HOH Z 377 " =    1.471
peak=    3.703 closest distance to " O   THR A 251 " =    1.218
peak=    3.691 closest distance to " CB  ALA A 248 " =    1.396
peak=    3.687 closest distance to " CA  GLU A 152 " =    0.974
peak=    3.686 closest distance to " CB  TRP A 266 " =    1.076
peak=    3.684 closest distance to " O   SER A  87 " =    2.340
peak=    3.682 closest distance to " N   TYR A 116 " =    1.764
peak=    3.671 closest distance to " CD  ARG A  36 " =    0.976
peak=    3.665 closest distance to " CB  ASN A 285 " =    0.821
peak=    3.656 closest distance to " CG  ARG A 138 " =    1.443
peak=    3.653 closest distance to " CG  PRO A 243 " =    1.136
peak=    3.653 closest distance to " CA  ALA A 100 " =    1.100
peak=    3.649 closest distance to " CA  ARG A  36 " =    1.067
peak=    3.645 closest distance to " CG  GLN A  11 " =    1.199
peak=    3.637 closest distance to " CA  ASN A 217 " =    1.309
peak=    3.636 closest distance to " O   HOH Z 199 " =    1.512
peak=    3.634 closest distance to " O   ALA A 165 " =    1.398
peak=    3.630 closest distance to " O   HOH Z 350 " =    1.011
peak=    3.628 closest distance to " O   HOH Z   7 " =    1.595
peak=    3.624 closest distance to " CA  TRP A 274 " =    0.959
peak=    3.622 closest distance to " CB  LEU A 101 " =    1.281
peak=    3.616 closest distance to " ND2 ASN A  69 " =    1.355
peak=    3.615 closest distance to " CA  GLY A 196 " =    0.982
peak=    3.612 closest distance to " O   HOH Z 417 " =    2.922
peak=    3.608 closest distance to " CB  THR A  52 " =    0.861
peak=    3.600 closest distance to " O   HOH Z 133 " =    2.864
peak=    3.598 closest distance to " CB  ALA A  43 " =    1.183
peak=    3.596 closest distance to " CZ3 TRP A 266 " =    1.144
peak=    3.590 closest distance to " OE1 GLU A   2 " =    1.402
peak=    3.588 closest distance to " CB  GLN A  88 " =    1.280
peak=    3.580 closest distance to " ND2 ASN A 301 " =    0.927
peak=    3.575 closest distance to " O   HOH Z 346 " =    1.615
peak=    3.572 closest distance to " CG2 VAL A 197 " =    1.263
peak=    3.568 closest distance to " CB  SER A  26 " =    0.857
peak=    3.565 closest distance to " OE1 GLN A  58 " =    0.964
peak=    3.563 closest distance to " NE2 GLN A 278 " =    2.361
peak=    3.562 closest distance to " O   HOH Z 177 " =    1.506
peak=    3.560 closest distance to " CD  ARG A  24 " =    1.280
peak=    3.559 closest distance to " O   HOH Z 250 " =    2.491
peak=    3.557 closest distance to " CG  LEU A 167 " =    0.982
peak=    3.556 closest distance to " CB  ASP A 124 " =    0.787
peak=    3.554 closest distance to " O   HOH Z 176 " =    2.051
peak=    3.554 closest distance to " O   HOH Z 343 " =    2.391
peak=    3.545 closest distance to " O   HOH Z 197 " =    5.326
peak=    3.540 closest distance to " CA  VAL A 125 " =    1.280
peak=    3.534 closest distance to " CB  GLN A 194 " =    0.963
peak=    3.532 closest distance to " O  BHOH Z 338 " =    0.985
peak=    3.526 closest distance to " CD2 TYR A  68 " =    0.831
peak=    3.525 closest distance to " CA  THR A 246 " =    1.039
peak=    3.523 closest distance to " O   HOH Z  27 " =    1.192
peak=    3.511 closest distance to " CA  ASN A 249 " =    1.284
peak=    3.509 closest distance to " CD1 LEU A 300 " =    1.053
peak=    3.508 closest distance to " NH2 ARG A  56 " =    1.132
peak=    3.488 closest distance to " CA  SER A  12 " =    1.579
peak=    3.486 closest distance to " O   HOH Z 281 " =    2.532
peak=    3.485 closest distance to " O   HOH Z 146 " =    1.761
peak=    3.480 closest distance to " O   HOH Z 406 " =    1.730
peak=    3.472 closest distance to " O   HOH Z  73 " =    2.307
peak=    3.466 closest distance to " CD1 LEU A 255 " =    1.695
peak=    3.464 closest distance to " CE3 TRP A  85 " =    1.209
peak=    3.463 closest distance to " O   HOH Z 395 " =    1.552
peak=    3.463 closest distance to " O   HOH Z 394 " =    4.109
peak=    3.462 closest distance to " O   HOH Z 298 " =    2.022
peak=    3.460 closest distance to " NH1 ARG A  14 " =    1.344
peak=    3.459 closest distance to " O   HOH Z 404 " =    1.507
peak=    3.459 closest distance to " CA  ARG A 139 " =    1.422
peak=    3.454 closest distance to " CG  PRO A 213 " =    1.314
peak=    3.454 closest distance to " O   HOH Z 401 " =    1.064
peak=    3.449 closest distance to " OG BSER A  99 " =    2.830
peak=    3.448 closest distance to " O   HOH Z 221 " =    1.120
peak=    3.438 closest distance to " O   HOH Z 393 " =    3.884
peak=    3.436 closest distance to " O   HOH Z 139 " =    4.968
peak=    3.432 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.429 closest distance to " CB  MET A 105 " =    1.128
peak=    3.426 closest distance to " CG1 VAL A 153 " =    1.102
peak=    3.424 closest distance to " CA  ARG A 156 " =    1.037
peak=    3.423 closest distance to " O   THR A 220 " =    1.193
peak=    3.422 closest distance to " O   HOH Z 272 " =    1.377
peak=    3.419 closest distance to " CA  TRP A  92 " =    0.980
peak=    3.411 closest distance to " CA  CYS A 260 " =    1.500
peak=    3.409 closest distance to " CB  SER A 288 " =    0.903
peak=    3.404 closest distance to " CG2 THR A  42 " =    0.942
peak=    3.403 closest distance to " CB  GLU A 152 " =    1.038
peak=    3.400 closest distance to " CB  PRO A 198 " =    1.153
peak=    3.391 closest distance to " O   HOH Z  44 " =    1.921
peak=    3.387 closest distance to " CB  SER A 210 " =    1.006
peak=    3.387 closest distance to " CB  GLU A  46 " =    1.081
peak=    3.386 closest distance to " O   HOH Z 316 " =    3.050
peak=    3.383 closest distance to " O   HOH Z 126 " =    2.404
peak=    3.379 closest distance to " CA  ALA A  21 " =    1.469
peak=    3.379 closest distance to " CB  PHE A 283 " =    0.885
peak=    3.375 closest distance to " CD  LYS A 166 " =    1.621
peak=    3.368 closest distance to " N   HIS A 108 " =    1.807
peak=    3.364 closest distance to " O   HOH Z  88 " =    3.418
peak=    3.359 closest distance to " CB  ALA A 299 " =    0.721
peak=    3.358 closest distance to " CB  ALA A 256 " =    1.444
peak=    3.357 closest distance to " O  BHOH Z  74 " =    1.238
peak=    3.357 closest distance to " CB  GLU A 277 " =    3.822
peak=    3.356 closest distance to " N   SER A 271 " =    1.163
peak=    3.354 closest distance to " CD  ARG A 195 " =    1.030
peak=    3.352 closest distance to " O   HOH Z 435 " =    2.766
peak=    3.352 closest distance to " O   HOH Z 359 " =    1.447
peak=    3.351 closest distance to " N   ILE A  33 " =    0.971
peak=    3.350 closest distance to " O   HOH Z 258 " =    2.197
peak=    3.348 closest distance to " CA  LEU A  83 " =    1.326
peak=    3.348 closest distance to " O   HOH Z 265 " =    2.030
peak=    3.345 closest distance to " NZ  LYS A 117 " =    2.761
peak=    3.343 closest distance to " N   TYR A  15 " =    0.938
peak=    3.341 closest distance to " CA  GLY A 267 " =    1.188
peak=    3.340 closest distance to " N   GLY A 262 " =    1.228
peak=    3.339 closest distance to " ND2 ASN A 176 " =    0.944
peak=    3.338 closest distance to " CA  ARG A 102 " =    1.209
peak=    3.338 closest distance to " O   HOH Z 132 " =    3.271
peak=    3.332 closest distance to " CG  GLU A  37 " =    0.934
peak=    3.330 closest distance to " O   HOH Z 421 " =    1.612
peak=    3.327 closest distance to " ND2 ASN A  45 " =    1.319
peak=    3.326 closest distance to " O   HOH Z 200 " =    1.677
peak=    3.325 closest distance to " ND2 ASN A 187 " =    1.487
peak=    3.323 closest distance to " CA  TYR A 116 " =    1.477
peak=    3.320 closest distance to " O   HOH Z 250 " =    1.224
peak=    3.319 closest distance to " CB  ARG A  79 " =    0.922
peak=    3.315 closest distance to " CA  ALA A 248 " =    1.325
peak=    3.310 closest distance to " O   HOH Z  15 " =    2.455
peak=    3.309 closest distance to " O   HOH Z  89 " =    3.715
peak=    3.306 closest distance to " O   HOH Z 434 " =    1.723
peak=    3.297 closest distance to " CE1 TYR A 186 " =    1.440
peak=    3.296 closest distance to " O   HOH Z 213 " =    1.647
peak=    3.296 closest distance to " O   HOH Z 298 " =    2.347
peak=    3.296 closest distance to " O   THR A 182 " =    1.463
peak=    3.294 closest distance to " CG2 VAL A 257 " =    0.851
peak=    3.292 closest distance to " N   GLU A  44 " =    1.280
peak=    3.292 closest distance to " C   GLN A  88 " =    1.653
peak=    3.291 closest distance to " CG2 VAL A 126 " =    0.878
peak=    3.289 closest distance to " CD  ARG A 159 " =    0.845
peak=    3.287 closest distance to " CA  GLY A 229 " =    0.940
peak=    3.287 closest distance to " O   HOH Z 368 " =    2.225
peak=    3.285 closest distance to " N   VAL A 126 " =    1.689
peak=    3.283 closest distance to " O   PRO A  90 " =    1.443
peak=    3.282 closest distance to " CG2 THR A  29 " =    1.427
peak=    3.281 closest distance to " O   HOH Z 189 " =    2.892
peak=    3.279 closest distance to " NH1 ARG A 269 " =    0.735
peak=    3.272 closest distance to " O   VAL A  72 " =    0.950
peak=    3.265 closest distance to " O   HOH Z 344 " =    1.994
peak=    3.262 closest distance to " N   ASN A  39 " =    1.226
peak=    3.260 closest distance to " O   HOH Z 362 " =    3.241
peak=    3.258 closest distance to " CB  ASN A 187 " =    1.204
peak=    3.258 closest distance to " CB  SER A 141 " =    1.077
peak=    3.256 closest distance to " CA  GLY A   6 " =    0.839
peak=    3.256 closest distance to " O   HOH Z 426 " =    1.336
peak=    3.255 closest distance to " CA  ALA A 295 " =    1.038
peak=    3.254 closest distance to " OE1 GLU A 152 " =    0.905
peak=    3.253 closest distance to " O   HOH Z  22 " =    2.382
peak=    3.250 closest distance to " CG2AVAL A 121 " =    1.964
peak=    3.249 closest distance to " N   TYR A 247 " =    1.264
peak=    3.247 closest distance to " CB  GLN A  89 " =    1.176
peak=    3.246 closest distance to " O   ARG A 275 " =    0.726
peak=    3.245 closest distance to " O   HOH Z 234 " =    1.766
peak=    3.244 closest distance to " N   ALA A  10 " =    1.636
peak=    3.241 closest distance to " O   HOH Z  54 " =    1.631
peak=    3.240 closest distance to " O   HOH Z 193 " =    2.074
peak=    3.239 closest distance to " CD1 LEU A 222 " =    0.816
peak=    3.238 closest distance to " O   HOH Z 367 " =    1.624
peak=    3.237 closest distance to " O   HOH Z 144 " =    1.260
peak=    3.235 closest distance to " NZ  LYS A 117 " =    0.833
peak=    3.234 closest distance to " O   HOH Z 358 " =    1.408
peak=    3.234 closest distance to " ND2 ASN A 249 " =    0.854
peak=    3.232 closest distance to " CB  SER A  28 " =    1.161
peak=    3.227 closest distance to " O   HOH Z 369 " =    2.750
peak=    3.219 closest distance to " O   HOH Z  68 " =    1.950
peak=    3.218 closest distance to " CG  LYS A  76 " =    1.190
peak=    3.215 closest distance to " CB  LEU A 228 " =    1.168
peak=    3.211 closest distance to " CA  ASP A 162 " =    1.054
peak=    3.203 closest distance to " O   HOH Z 415 " =    1.566
peak=    3.202 closest distance to " CA  ASP A 191 " =    1.007
peak=    3.201 closest distance to " CA  GLN A 223 " =    0.863
peak=    3.200 closest distance to " CD1 LEU A 167 " =    1.224
peak=    3.190 closest distance to " CB  ALA A  71 " =    1.289
peak=    3.188 closest distance to " CB  LEU A  83 " =    0.753
peak=    3.186 closest distance to " NE1 TRP A  92 " =    1.724
peak=    3.186 closest distance to " CA  HIS A 115 " =    1.013
peak=    3.176 closest distance to " O   ASN A 217 " =    1.725
peak=    3.175 closest distance to " OD1 ASN A 148 " =    2.073
peak=    3.173 closest distance to " N   ASN A 252 " =    1.339
peak=    3.173 closest distance to " OD2 ASP A 298 " =    3.368
peak=    3.171 closest distance to " O   HOH Z  44 " =    1.874
peak=    3.168 closest distance to " O   HOH Z 297 " =    4.503
peak=    3.167 closest distance to " CB  ARG A 156 " =    1.138
peak=    3.167 closest distance to " O   VAL A 121 " =    0.943
peak=    3.166 closest distance to " CD  LYS A  76 " =    1.794
peak=    3.160 closest distance to " CB  PRO A 243 " =    1.554
peak=    3.159 closest distance to " O   HOH Z 408 " =    3.223
peak=    3.159 closest distance to " CB  TRP A 150 " =    1.607
peak=    3.156 closest distance to " CA  MET A 105 " =    1.492
peak=    3.152 closest distance to " O   HOH Z 156 " =    2.787
peak=    3.151 closest distance to " O   HOH Z  78 " =    2.286
peak=    3.147 closest distance to " O   THR A 294 " =    1.792
peak=    3.145 closest distance to " CB  ALA A   1 " =    1.118
peak=    3.145 closest distance to " NE2 GLN A  58 " =    4.923
peak=    3.144 closest distance to " CB  SER A  62 " =    1.240
peak=    3.143 closest distance to " O   HOH Z 371 " =    2.155
peak=    3.142 closest distance to " O   HOH Z 316 " =    2.971
peak=    3.137 closest distance to " CB  TYR A 247 " =    0.869
peak=    3.132 closest distance to " CA  ALA A 154 " =    1.089
peak=    3.128 closest distance to " O   HOH Z 435 " =    1.795
peak=    3.128 closest distance to " O   HOH Z  90 " =    3.718
peak=    3.127 closest distance to " NE  ARG A 138 " =    1.220
peak=    3.126 closest distance to " O   HOH Z 345 " =    3.517
peak=    3.123 closest distance to " CZ3 TRP A 274 " =    4.507
peak=    3.121 closest distance to " CB  ASN A 142 " =    1.154
peak=    3.117 closest distance to " O   HOH Z  40 " =    1.710
peak=    3.113 closest distance to " O   ASP A 124 " =    1.178
peak=    3.112 closest distance to " O   HOH Z 271 " =    1.948
peak=    3.108 closest distance to " O   HOH Z 139 " =    4.142
peak=    3.100 closest distance to " CA  SER A  87 " =    0.993
peak=    3.100 closest distance to " O   HOH Z  50 " =    3.630
peak=    3.097 closest distance to " O   GLN A  58 " =    1.971
peak=    3.094 closest distance to " O   ALA A  84 " =    1.410
peak=    3.092 closest distance to " O   HOH Z 135 " =    2.152
peak=    3.090 closest distance to " O   GLY A  91 " =    1.149
peak=    3.090 closest distance to " N   GLN A 278 " =    1.394
peak=    3.090 closest distance to " O   HOH Z 303 " =    1.890
peak=    3.087 closest distance to " C   PRO A  54 " =    0.713
peak=    3.082 closest distance to " N   GLU A   2 " =    0.991
peak=    3.073 closest distance to " O   HOH Z  85 " =    1.973
peak=    3.067 closest distance to " OE2 GLU A   2 " =    2.048
peak=    3.061 closest distance to " N   LYS A 166 " =    0.874
peak=    3.058 closest distance to " O   HOH Z  39 " =    1.192
peak=    3.055 closest distance to " CG1 VAL A 257 " =    1.190
peak=    3.044 closest distance to " O   ASN A  74 " =    1.641
peak=    3.037 closest distance to " CB  SER A 212 " =    1.035
peak=    3.036 closest distance to " NZ  LYS A  76 " =    1.381
peak=    3.013 closest distance to " O   HOH Z  20 " =    2.961

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 231         
Filter by distance & map next to the model:
   mapped sites are within: 0.617 - 5.980
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 230 from: 231
   mapped sites are within: 0.759 - 5.980

peak=   -4.842 closest distance to " O   HOH Z 418 " =    1.223
peak=   -4.768 closest distance to " O   HOH Z 203 " =    0.935
peak=   -4.539 closest distance to " CD  GLN A 223 " =    1.430
peak=   -4.357 closest distance to " O   HOH Z 400 " =    1.257
peak=   -4.290 closest distance to " O   HOH Z 166 " =    1.304
peak=   -4.289 closest distance to " CD2 LEU A 237 " =    2.586
peak=   -4.247 closest distance to " O   HOH Z 407 " =    0.936
peak=   -4.246 closest distance to " O   HOH Z 411 " =    5.392
peak=   -4.215 closest distance to " O   GLN A  11 " =    1.065
peak=   -4.209 closest distance to " N   ARG A 275 " =    0.986
peak=   -4.164 closest distance to " OD2 ASP A 171 " =    1.824
peak=   -4.117 closest distance to " N   ALA A  43 " =    2.732
peak=   -4.086 closest distance to " CD1 PHE A  59 " =    1.967
peak=   -4.027 closest distance to " O   PRO A 198 " =    1.293
peak=   -3.982 closest distance to " O   HOH Z 400 " =    0.996
peak=   -3.980 closest distance to " CG  PRO A 243 " =    1.747
peak=   -3.961 closest distance to " CG2 VAL A 202 " =    2.278
peak=   -3.949 closest distance to " CE2 PHE A  61 " =    2.784
peak=   -3.943 closest distance to " CG  ARG A 269 " =    2.409
peak=   -3.939 closest distance to " OE1 GLN A  88 " =    1.071
peak=   -3.936 closest distance to " CA  GLU A 277 " =    1.069
peak=   -3.934 closest distance to " O   ASP A 171 " =    1.035
peak=   -3.882 closest distance to " CD  ARG A  14 " =    3.275
peak=   -3.875 closest distance to " O   HOH Z 114 " =    1.201
peak=   -3.855 closest distance to " O   HOH Z 128 " =    2.778
peak=   -3.847 closest distance to " OD1 ASN A 148 " =    1.374
peak=   -3.847 closest distance to " OD1 ASN A 301 " =    0.870
peak=   -3.843 closest distance to " CD1 LEU A 167 " =    2.001
peak=   -3.817 closest distance to " O   HOH Z 211 " =    1.120
peak=   -3.816 closest distance to " O   HOH Z 166 " =    2.324
peak=   -3.804 closest distance to " CD1 PHE A 130 " =    2.393
peak=   -3.783 closest distance to " CD2 PHE A  61 " =    2.129
peak=   -3.770 closest distance to " C   ASN A 285 " =    2.276
peak=   -3.766 closest distance to " CE3 TRP A 150 " =    1.877
peak=   -3.746 closest distance to " O   HOH Z 133 " =    1.645
peak=   -3.745 closest distance to " CA  GLY A 203 " =    2.407
peak=   -3.744 closest distance to " O   HOH Z 184 " =    1.621
peak=   -3.734 closest distance to " O   HOH Z 150 " =    1.997
peak=   -3.720 closest distance to " O   HOH Z  60 " =    1.495
peak=   -3.711 closest distance to " CD  GLN A  58 " =    0.782
peak=   -3.704 closest distance to " CA  VAL A 197 " =    0.985
peak=   -3.703 closest distance to " N   ILE A 120 " =    0.957
peak=   -3.701 closest distance to " O   HOH Z 155 " =    1.773
peak=   -3.696 closest distance to " O   HOH Z 221 " =    1.087
peak=   -3.688 closest distance to " O   VAL A  67 " =    2.782
peak=   -3.684 closest distance to " NH2 ARG A  66 " =    1.837
peak=   -3.680 closest distance to " O   SER A 206 " =    1.305
peak=   -3.665 closest distance to " CB  PRO A 243 " =    2.905
peak=   -3.651 closest distance to " C   LEU A 101 " =    1.164
peak=   -3.638 closest distance to " O   VAL A 189 " =    2.523
peak=   -3.629 closest distance to " SD  MET A  93 " =    1.922
peak=   -3.627 closest distance to " O   HOH Z 225 " =    1.453
peak=   -3.625 closest distance to " O   HOH Z 234 " =    4.583
peak=   -3.617 closest distance to " CB  SER A 146 " =    2.144
peak=   -3.599 closest distance to " O   HOH Z 369 " =    2.442
peak=   -3.598 closest distance to " O   HOH Z  10 " =    1.681
peak=   -3.589 closest distance to " O   HOH Z 331 " =    0.988
peak=   -3.578 closest distance to " CA  ASP A 298 " =    1.085
peak=   -3.566 closest distance to " O   HOH Z  67 " =    1.319
peak=   -3.566 closest distance to " NE  ARG A  79 " =    1.288
peak=   -3.560 closest distance to " O   HOH Z  37 " =    1.536
peak=   -3.548 closest distance to " O   HOH Z 174 " =    1.643
peak=   -3.547 closest distance to " O   HOH Z 122 " =    1.243
peak=   -3.546 closest distance to " N   SER A 134 " =    1.173
peak=   -3.539 closest distance to " CE3 TRP A 274 " =    2.213
peak=   -3.538 closest distance to " O   HOH Z  19 " =    2.084
peak=   -3.531 closest distance to " O   HOH Z 377 " =    0.759
peak=   -3.529 closest distance to " SD  MET A 105 " =    2.426
peak=   -3.529 closest distance to " CG  ARG A 259 " =    2.500
peak=   -3.529 closest distance to " O   HOH Z 196 " =    1.737
peak=   -3.528 closest distance to " CB  PRO A  54 " =    2.614
peak=   -3.524 closest distance to " O   HOH Z  54 " =    1.321
peak=   -3.521 closest distance to " O   HOH Z 340 " =    1.502
peak=   -3.520 closest distance to " O   HOH Z 183 " =    1.676
peak=   -3.519 closest distance to " O   HOH Z  41 " =    2.274
peak=   -3.518 closest distance to " O   HOH Z 151 " =    1.427
peak=   -3.517 closest distance to " C   VAL A 265 " =    0.876
peak=   -3.515 closest distance to " CG  ASN A  45 " =    0.857
peak=   -3.513 closest distance to " CZ  TYR A  68 " =    1.073
peak=   -3.513 closest distance to " CB  ALA A 291 " =    2.505
peak=   -3.511 closest distance to " CG2 ILE A  20 " =    2.564
peak=   -3.511 closest distance to " O   HOH Z 207 " =    1.474
peak=   -3.510 closest distance to " O   HOH Z 216 " =    1.034
peak=   -3.509 closest distance to " O   HOH Z 185 " =    2.603
peak=   -3.503 closest distance to " O   HOH Z 109 " =    3.785
peak=   -3.499 closest distance to " O   HOH Z 134 " =    2.256
peak=   -3.498 closest distance to " O   HOH Z 191 " =    5.980
peak=   -3.494 closest distance to " O   HOH Z 394 " =    1.793
peak=   -3.483 closest distance to " CG1 VAL A 112 " =    2.769
peak=   -3.477 closest distance to " CZ  PHE A  38 " =    1.095
peak=   -3.472 closest distance to " CG  LEU A 281 " =    1.963
peak=   -3.472 closest distance to " O   HOH Z  15 " =    1.631
peak=   -3.471 closest distance to " CD1 ILE A 263 " =    2.045
peak=   -3.467 closest distance to " O   HOH Z 368 " =    2.074
peak=   -3.464 closest distance to " NH2 ARG A  36 " =    1.125
peak=   -3.464 closest distance to " CB  ALA A  43 " =    2.827
peak=   -3.447 closest distance to " O   HOH Z 438 " =    3.036
peak=   -3.439 closest distance to " OG  SER A  63 " =    1.233
peak=   -3.438 closest distance to " O   HOH Z   7 " =    1.031
peak=   -3.438 closest distance to " O   HOH Z  37 " =    2.320
peak=   -3.438 closest distance to " CD  GLN A  88 " =    0.945
peak=   -3.437 closest distance to " O   HOH Z   6 " =    1.136
peak=   -3.436 closest distance to " O   HOH Z 156 " =    3.640
peak=   -3.435 closest distance to " OD2 ASP A 298 " =    1.039
peak=   -3.433 closest distance to " CD2 TYR A 293 " =    1.818
peak=   -3.433 closest distance to " O   HOH Z 250 " =    2.136
peak=   -3.432 closest distance to " CG  GLN A  58 " =    1.181
peak=   -3.432 closest distance to " N   GLN A 223 " =    1.009
peak=   -3.430 closest distance to " CG  GLU A  53 " =    1.486
peak=   -3.430 closest distance to " O   ARG A 275 " =    1.874
peak=   -3.430 closest distance to " O   HOH Z  52 " =    1.805
peak=   -3.430 closest distance to " CD  GLN A  77 " =    1.059
peak=   -3.424 closest distance to " CG2 THR A 221 " =    2.367
peak=   -3.423 closest distance to " CA  GLY A 241 " =    3.314
peak=   -3.422 closest distance to " CZ  ARG A 259 " =    0.938
peak=   -3.414 closest distance to " CZ  TYR A 169 " =    1.958
peak=   -3.412 closest distance to " O   HOH Z 109 " =    3.482
peak=   -3.406 closest distance to " O   MET A 113 " =    1.286
peak=   -3.403 closest distance to " O   HOH Z 424 " =    2.912
peak=   -3.400 closest distance to " ND2 ASN A  60 " =    2.222
peak=   -3.398 closest distance to " ND2 ASN A  60 " =    1.365
peak=   -3.389 closest distance to " O   HOH Z 243 " =    2.308
peak=   -3.384 closest distance to " O   MET A  47 " =    2.508
peak=   -3.383 closest distance to " NE2 GLN A 223 " =    1.268
peak=   -3.378 closest distance to " CG  LEU A  83 " =    2.085
peak=   -3.376 closest distance to " CG  GLN A  11 " =    1.259
peak=   -3.375 closest distance to " NE2 GLN A 194 " =    2.152
peak=   -3.374 closest distance to " ND2 ASN A  45 " =    1.819
peak=   -3.373 closest distance to " SD  MET A  40 " =    2.012
peak=   -3.371 closest distance to " CB  PRO A 280 " =    1.012
peak=   -3.365 closest distance to " O   SER A 276 " =    1.675
peak=   -3.364 closest distance to " O   HOH Z 198 " =    1.585
peak=   -3.363 closest distance to " CG  ARG A 259 " =    1.538
peak=   -3.363 closest distance to " O   HOH Z 164 " =    2.631
peak=   -3.358 closest distance to " OE2 GLU A  53 " =    1.173
peak=   -3.355 closest distance to " O   HOH Z  33 " =    2.166
peak=   -3.351 closest distance to " CB  ALA A  10 " =    2.148
peak=   -3.350 closest distance to " CG  HIS A  86 " =    1.193
peak=   -3.348 closest distance to " O   SER A 271 " =    2.252
peak=   -3.343 closest distance to " N   TYR A  68 " =    2.949
peak=   -3.340 closest distance to " SG  CYS A 254 " =    3.303
peak=   -3.337 closest distance to " OG1 THR A  82 " =    1.276
peak=   -3.336 closest distance to " O   HOH Z 366 " =    1.833
peak=   -3.335 closest distance to " O   HOH Z 283 " =    2.426
peak=   -3.320 closest distance to " CB  PHE A 130 " =    1.129
peak=   -3.319 closest distance to " CG2 ILE A  49 " =    2.711
peak=   -3.317 closest distance to " O   HOH Z 209 " =    0.976
peak=   -3.311 closest distance to " CG1 VAL A 112 " =    2.678
peak=   -3.309 closest distance to " O   HOH Z 292 " =    4.770
peak=   -3.308 closest distance to " OD1 ASP A 272 " =    1.533
peak=   -3.304 closest distance to " O   HOH Z 388 " =    1.948
peak=   -3.296 closest distance to " O   SER A   3 " =    1.031
peak=   -3.296 closest distance to " OG  SER A  62 " =    4.588
peak=   -3.296 closest distance to " O   HOH Z 111 " =    1.527
peak=   -3.296 closest distance to " O   HOH Z  38 " =    1.053
peak=   -3.296 closest distance to " CZ  ARG A  79 " =    1.926
peak=   -3.293 closest distance to " CG2BVAL A  41 " =    1.440
peak=   -3.292 closest distance to " CA  GLY A 241 " =    2.270
peak=   -3.289 closest distance to " CG  TYR A 169 " =    2.159
peak=   -3.284 closest distance to " CE  MET A  93 " =    1.927
peak=   -3.271 closest distance to " CA  THR A  18 " =    1.211
peak=   -3.267 closest distance to " O   HOH Z 401 " =    1.491
peak=   -3.267 closest distance to " NE1 TRP A 177 " =    2.098
peak=   -3.262 closest distance to " O   GLN A 240 " =    3.534
peak=   -3.260 closest distance to " O   ALA A  43 " =    1.908
peak=   -3.258 closest distance to " CD  GLU A 236 " =    1.124
peak=   -3.252 closest distance to " O   HOH Z 423 " =    1.425
peak=   -3.251 closest distance to " ND2 ASN A  60 " =    2.091
peak=   -3.245 closest distance to " O   HOH Z 211 " =    1.543
peak=   -3.240 closest distance to " O   SER A 210 " =    1.807
peak=   -3.231 closest distance to " O   HOH Z 109 " =    1.698
peak=   -3.222 closest distance to " CB  ALA A 256 " =    2.674
peak=   -3.218 closest distance to " O   HOH Z 287 " =    1.706
peak=   -3.217 closest distance to " O   HOH Z 171 " =    2.387
peak=   -3.216 closest distance to " CD2 HIS A 115 " =    1.082
peak=   -3.212 closest distance to " N   ASP A 191 " =    1.334
peak=   -3.211 closest distance to " N   GLN A  11 " =    1.301
peak=   -3.209 closest distance to " N   ALA A 242 " =    1.534
peak=   -3.207 closest distance to " CD1 TRP A  70 " =    1.035
peak=   -3.206 closest distance to " O   HOH Z 200 " =    1.201
peak=   -3.205 closest distance to " CD1 TYR A 214 " =    1.655
peak=   -3.202 closest distance to " CB  ALA A 100 " =    2.050
peak=   -3.202 closest distance to " O   HOH Z 189 " =    1.812
peak=   -3.201 closest distance to " O   HOH Z   7 " =    1.536
peak=   -3.201 closest distance to " CG2BVAL A 121 " =    1.406
peak=   -3.189 closest distance to " O   VAL A 174 " =    2.106
peak=   -3.188 closest distance to " CD1 LEU A 101 " =    2.524
peak=   -3.188 closest distance to " O   HOH Z 138 " =    0.989
peak=   -3.187 closest distance to " O   HOH Z 140 " =    1.907
peak=   -3.181 closest distance to " O   HOH Z 345 " =    3.160
peak=   -3.180 closest distance to " CG  ASP A 231 " =    0.828
peak=   -3.178 closest distance to " OE2 GLU A 128 " =    1.761
peak=   -3.178 closest distance to " N   ASP A 272 " =    1.422
peak=   -3.177 closest distance to " O   HOH Z 252 " =    4.028
peak=   -3.172 closest distance to " O   HOH Z 348 " =    2.259
peak=   -3.170 closest distance to " O   MET A  40 " =    2.699
peak=   -3.168 closest distance to " NH2 ARG A 159 " =    2.420
peak=   -3.163 closest distance to " NH2 ARG A  66 " =    1.587
peak=   -3.159 closest distance to " O   HOH Z 428 " =    1.287
peak=   -3.155 closest distance to " CB  GLN A  55 " =    1.627
peak=   -3.154 closest distance to " SG  CYS A 260 " =    2.439
peak=   -3.154 closest distance to " O   HOH Z 281 " =    2.264
peak=   -3.143 closest distance to " O   HOH Z 426 " =    1.805
peak=   -3.141 closest distance to " OG BSER A 210 " =    2.368
peak=   -3.140 closest distance to " CA  SER A 164 " =    2.164
peak=   -3.134 closest distance to " O   HOH Z  90 " =    3.424
peak=   -3.131 closest distance to " O   ALA A   1 " =    2.177
peak=   -3.127 closest distance to " C   ILE A 239 " =    2.235
peak=   -3.126 closest distance to " CD2 PHE A 225 " =    1.382
peak=   -3.124 closest distance to " O   HOH Z 108 " =    1.775
peak=   -3.119 closest distance to " OE1 GLN A 223 " =    2.475
peak=   -3.117 closest distance to " O   ARG A  79 " =    1.221
peak=   -3.106 closest distance to " CA  ASN A 127 " =    1.074
peak=   -3.101 closest distance to " O   HOH Z  53 " =    1.989
peak=   -3.101 closest distance to " CE3 TRP A 150 " =    1.259
peak=   -3.099 closest distance to " O   HOH Z 378 " =    1.255
peak=   -3.097 closest distance to " O   HOH Z 412 " =    1.788
peak=   -3.097 closest distance to " O   HOH Z 346 " =    1.899
peak=   -3.095 closest distance to " O   HOH Z 137 " =    1.410
peak=   -3.095 closest distance to " CD  LYS A 289 " =    2.262
peak=   -3.082 closest distance to " O   HOH Z  48 " =    0.945
peak=   -3.072 closest distance to " CD1 TRP A  85 " =    1.118
peak=   -3.060 closest distance to " CA  VAL A 232 " =    2.339
peak=   -3.060 closest distance to " CD  PRO A 213 " =    2.357
peak=   -3.059 closest distance to " O   HOH Z 325 " =    2.114
peak=   -3.059 closest distance to " OH  TYR A 169 " =    0.962
peak=   -3.052 closest distance to " CG2 VAL A 189 " =    1.998
peak=   -3.035 closest distance to " OG  SER A  97 " =    2.212
peak=   -3.033 closest distance to " O   HOH Z 340 " =    1.942
peak=   -3.033 closest distance to " CD1 ILE A 109 " =    2.826

================= 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    :  0.4782 0.4666   6.289055e+00   6.265806e+00
   1_bss:  0.4705 0.4586   6.284545e+00   6.257580e+00
   1_xyz:  0.3827 0.4145   6.155605e+00   6.192679e+00
   1_adp:  0.3517 0.4252   6.114509e+00   6.203374e+00
   1_occ:  0.3514 0.4242   6.113916e+00   6.203047e+00
   2_bss:  0.3509 0.4225   6.115777e+00   6.204083e+00
   2_xyz:  0.2979 0.3630   5.988835e+00   6.118270e+00
   2_adp:  0.2873 0.3579   5.971087e+00   6.107617e+00
   2_occ:  0.2872 0.3579   5.970722e+00   6.107792e+00
   3_bss:  0.2873 0.3577   5.972235e+00   6.108055e+00
   3_xyz:  0.2280 0.2838   5.752914e+00   5.920730e+00
   3_adp:  0.1985 0.2572   5.645503e+00   5.839377e+00
   3_occ:  0.1984 0.2569   5.644604e+00   5.838400e+00
   4_bss:  0.1982 0.2566   5.643757e+00   5.836579e+00
   4_xyz:  0.1718 0.2195   5.512127e+00   5.710656e+00
   4_adp:  0.1644 0.2091   5.470383e+00   5.660539e+00
   4_occ:  0.1643 0.2091   5.469724e+00   5.660187e+00
   5_bss:  0.1646 0.2094   5.470951e+00   5.661356e+00
   5_xyz:  0.1456 0.1904   5.363253e+00   5.570545e+00
   5_adp:  0.1400 0.1905   5.339047e+00   5.558885e+00
   5_occ:  0.1399 0.1905   5.339067e+00   5.559173e+00
   5_bss:  0.1399 0.1903   5.339003e+00   5.559060e+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:  0.279  47.698  -3.053   3.744   2.264   0.000   0.000   0.000
   1_xyz:  0.279  47.698  -3.053   3.744   2.264   0.000   0.000   0.000
   1_adp:  0.279  47.698  -3.053   3.744   2.264   0.000   0.000   0.000
   1_occ:  0.279  47.698  -3.053   3.744   2.264   0.000   0.000   0.000
   2_bss:  0.302  62.633  -1.016   2.620   1.639   0.000   0.000   0.000
   2_xyz:  0.302  62.633  -1.016   2.620   1.639   0.000   0.000   0.000
   2_adp:  0.302  62.633  -1.016   2.620   1.639   0.000   0.000   0.000
   2_occ:  0.302  62.633  -1.016   2.620   1.639   0.000   0.000   0.000
   3_bss:  0.322  71.141  -0.486   2.376   1.390   0.000   0.000   0.000
   3_xyz:  0.322  71.141  -0.486   2.376   1.390   0.000   0.000   0.000
   3_adp:  0.322  71.141  -0.486   2.376   1.390   0.000   0.000   0.000
   3_occ:  0.322  71.141  -0.486   2.376   1.390   0.000   0.000   0.000
   4_bss:  0.338  90.466  -0.631   1.146   0.972   0.000   0.000   0.000
   4_xyz:  0.338  90.466  -0.631   1.146   0.972   0.000   0.000   0.000
   4_adp:  0.338  90.466  -0.631   1.146   0.972   0.000   0.000   0.000
   4_occ:  0.338  90.466  -0.631   1.146   0.972   0.000   0.000   0.000
   5_bss:  0.335  87.101  -0.785   0.610   0.920   0.000   0.000   0.000
   5_xyz:  0.335  87.101  -0.785   0.610   0.920   0.000   0.000   0.000
   5_adp:  0.335  87.101  -0.785   0.610   0.920   0.000   0.000   0.000
   5_occ:  0.335  87.101  -0.785   0.610   0.920   0.000   0.000   0.000
   5_bss:  0.333  85.314  -0.936   0.179   0.757   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.354 0.4408  0.5673    67044.255
   1_bss:  55.182 0.4548  0.6104    64591.736
   1_xyz:  48.141 0.5427  0.7132    50509.525
   1_adp:  48.891 0.5333  0.6986    52343.047
   1_occ:  48.889 0.5333  0.6984    52377.517
   2_bss:  48.694 0.5359  0.7068    52252.067
   2_xyz:  40.355 0.6380  0.8298    38108.201
   2_adp:  39.368 0.6500  0.8280    36837.324
   2_occ:  39.363 0.6501  0.8275    36809.439
   3_bss:  39.342 0.6504  0.8287    36890.433
   3_xyz:  29.592 0.7616  0.9442    21461.070
   3_adp:  26.140 0.7994  0.9450    17369.053
   3_occ:  26.100 0.7998  0.9452    17310.428
   4_bss:  25.998 0.8008  0.9275    17187.714
   4_xyz:  22.018 0.8415  0.9501    12575.387
   4_adp:  20.304 0.8591  0.9465    11310.069
   4_occ:  20.290 0.8592  0.9465    11305.662
   5_bss:  20.303 0.8592  0.9383    11340.894
   5_xyz:  18.054 0.8802  0.9539     9311.737
   5_adp:  17.715 0.8835  0.9444     9132.671
   5_occ:  17.722 0.8834  0.9445     9142.769
   5_bss:  17.720 0.8834  0.9520     9141.696
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6693e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6693e-01
   1_xyz:   1.575  0.012  0.097 15.897  0.006  4.115   1.3083e-01
   1_adp:   1.575  0.012  0.097 15.897  0.006  4.115   1.3083e-01
   1_occ:   1.575  0.012  0.097 15.897  0.006  4.115   1.3083e-01
   2_bss:   1.575  0.012  0.097 15.897  0.006  4.115   1.3083e-01
   2_xyz:   1.242  0.009  0.082 14.965  0.005  4.111   8.4408e-02
   2_adp:   1.242  0.009  0.082 14.965  0.005  4.111   8.4408e-02
   2_occ:   1.242  0.009  0.082 14.965  0.005  4.111   8.4408e-02
   3_bss:   1.242  0.009  0.082 14.965  0.005  4.111   8.4408e-02
   3_xyz:   1.324  0.012  0.085 15.285  0.005  4.114   1.1059e-01
   3_adp:   1.324  0.012  0.085 15.285  0.005  4.114   1.1059e-01
   3_occ:   1.324  0.012  0.085 15.285  0.005  4.114   1.1059e-01
   4_bss:   1.324  0.012  0.085 15.285  0.005  4.114   1.1059e-01
   4_xyz:   1.021  0.007  0.074 14.587  0.004  4.127   6.2104e-02
   4_adp:   1.021  0.007  0.074 14.587  0.004  4.127   6.2104e-02
   4_occ:   1.021  0.007  0.074 14.587  0.004  4.127   6.2104e-02
   5_bss:   1.021  0.007  0.074 14.587  0.004  4.127   6.2104e-02
   5_xyz:   1.056  0.009  0.075 14.466  0.004  4.117   6.5311e-02
   5_adp:   1.056  0.009  0.075 14.466  0.004  4.117   6.5311e-02
   5_occ:   1.056  0.009  0.075 14.466  0.004  4.117   6.5311e-02
   5_bss:   1.056  0.009  0.075 14.466  0.004  4.117   6.5311e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.733   2.4599e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.733   2.4599e-01
   1_xyz:  10.836  0.067  0.314 83.817  0.052  2.048   9.5629e-02
   1_adp:  10.836  0.067  0.314 83.817  0.052  2.048   9.5629e-02
   1_occ:  10.836  0.067  0.314 83.817  0.052  2.048   9.5629e-02
   2_bss:  10.836  0.067  0.314 83.817  0.052  2.048   9.5629e-02
   2_xyz:   8.718  0.046  0.275 84.078  0.020  2.308   8.1238e-02
   2_adp:   8.718  0.046  0.275 84.078  0.020  2.308   8.1238e-02
   2_occ:   8.718  0.046  0.275 84.078  0.020  2.308   8.1238e-02
   3_bss:   8.718  0.046  0.275 84.078  0.020  2.308   8.1238e-02
   3_xyz:   9.281  0.089  0.242 81.870  0.041  2.122   2.2109e-01
   3_adp:   9.281  0.089  0.242 81.870  0.041  2.122   2.2109e-01
   3_occ:   9.281  0.089  0.242 81.870  0.041  2.122   2.2109e-01
   4_bss:   9.281  0.089  0.242 81.870  0.041  2.122   2.2109e-01
   4_xyz:   7.734  0.057  0.225 87.531  0.044  2.252   4.3019e-02
   4_adp:   7.734  0.057  0.225 87.531  0.044  2.252   4.3019e-02
   4_occ:   7.734  0.057  0.225 87.531  0.044  2.252   4.3019e-02
   5_bss:   7.734  0.057  0.225 87.531  0.044  2.252   4.3019e-02
   5_xyz:   7.889  0.036  0.237 82.586  0.036  2.282   5.6326e-02
   5_adp:   7.889  0.036  0.237 82.586  0.036  2.282   5.6326e-02
   5_occ:   7.889  0.036  0.237 82.586  0.036  2.282   5.6326e-02
   5_bss:   7.889  0.036  0.237 82.586  0.036  2.282   5.6326e-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: 111.95   0.00  18.88  90.94   0.00  15.50 111.95   0.00  37.26
   1_occ: 111.95   0.00  18.88  90.94   0.00  15.50 111.95   0.00  37.26
   2_bss: 111.95   0.00  18.88  90.94   0.00  15.50 111.95   0.00  37.26
   2_xyz: 111.95   0.00  18.88  90.94   0.00  15.50 111.95   0.00  37.26
   2_adp: 164.19   0.00  18.53 164.19   0.00  15.05 111.99   0.00  37.49
   2_occ: 164.19   0.00  18.53 164.19   0.00  15.05 111.99   0.00  37.49
   3_bss: 164.19   0.00  18.53 164.19   0.00  15.05 111.99   0.00  37.49
   3_xyz: 164.19   0.00  18.53 164.19   0.00  15.05 111.99   0.00  37.49
   3_adp: 122.04   0.00  18.77 104.94   0.00  13.57 122.04   2.12  47.10
   3_occ: 122.04   0.00  18.77 104.94   0.00  13.57 122.04   2.12  47.10
   4_bss: 122.04   0.00  18.77 104.94   0.00  13.57 122.04   2.12  47.10
   4_xyz: 122.04   0.00  18.77 104.94   0.00  13.57 122.04   2.12  47.10
   4_adp: 119.89   0.00  17.46 101.52   0.00  12.30 119.89   2.71  45.55
   4_occ: 119.89   0.00  17.46 101.52   0.00  12.30 119.89   2.71  45.55
   5_bss: 119.89   0.00  17.46 101.52   0.00  12.30 119.89   2.71  45.55
   5_xyz: 119.89   0.00  17.46 101.52   0.00  12.30 119.89   2.71  45.55
   5_adp: 124.59   0.00  17.13 103.25   0.00  11.74 124.59   3.14  46.51
   5_occ: 124.59   0.00  17.13 103.25   0.00  11.74 124.59   3.14  46.51
   5_bss: 125.06   0.47  17.60 103.72   0.47  12.21 125.06   3.61  46.98
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.718    0.017    0.361
   1_adp:    1.718    0.017    0.361
   1_occ:    1.718    0.017    0.361
   2_bss:    1.718    0.017    0.361
   2_xyz:    1.331    0.033    0.503
   2_adp:    1.331    0.033    0.503
   2_occ:    1.331    0.033    0.503
   3_bss:    1.331    0.033    0.503
   3_xyz:    1.752    0.037    0.747
   3_adp:    1.752    0.037    0.747
   3_occ:    1.752    0.037    0.747
   4_bss:    1.752    0.037    0.747
   4_xyz:    1.686    0.073    0.803
   4_adp:    1.686    0.073    0.803
   4_occ:    1.686    0.073    0.803
   5_bss:    1.686    0.073    0.803
   5_xyz:    1.718    0.106    0.855
   5_adp:    1.718    0.106    0.855
   5_occ:    1.718    0.106    0.855
   5_bss:    1.718    0.106    0.855
------------------------------------------------------------------------

CPU time actual refinement: 344.44


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_966/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_966/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_966/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_966/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_966/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.30 
  Macro-tasks:
    bulk solvent and scale       = 50.19  
    individual site refinement   = 137.36 
    weights calculation          = 29.30  
    collect and process          = 6.48   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 223.44 
  Micro-tasks:
    mask                            = 2.31   
    f_calc                          = 105.65 
    alpha_beta                      = 8.42   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 114.82 
    fmodel                         = 8.08   
    r_factors                      = 0.29   
    phase_errors                   = 10.25  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 251.22 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.900 micro seconds
Total CPU time: 5.96 minutes
from_scatterers_fft:    641 calls, 105.36 s
gradients_fft:          588 calls, 101.81 s

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

# Date 2008-01-16 Time 06:05:44 PST -0800 (1200492344.29 s)
Start R-work = 0.4782, R-free = 0.4666 (no bulk solvent and anisotropic scale)
Final R-work = 0.1550, R-free = 0.2035 (no bulk solvent and anisotropic scale)

Start R-work = 0.4705, R-free = 0.4586
Final R-work = 0.1399, R-free = 0.1903