# Date 2008-01-16 Time 04:46:12 PST -0800 (1200487572.25 s)
#phil __OFF__

Command line arguments: "../455.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28802
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 455

-------------------------------------------------------------------------------
  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: (69.5475, 47.6339, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


================================== 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: (69.5475, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8941 1.9806
Completeness in resolution range: 0.958366
Completeness with d_max=infinity: 0.955375

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8941
                             d_min =   1.9806

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: (69.5475, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8941 1.9806
Completeness in resolution range: 0.958366
Completeness with d_max=infinity: 0.955375

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8945 -  4.2374 [2150/2178]  1935   215  10.0%
  bin  2:  4.2374 -  3.3762 [2046/2069]  1843   203   9.9%
  bin  3:  3.3762 -  2.9532 [2043/2065]  1837   206  10.1%
  bin  4:  2.9532 -  2.6849 [2010/2029]  1812   198   9.9%
  bin  5:  2.6849 -  2.4934 [2015/2044]  1806   209  10.4%
  bin  6:  2.4934 -  2.3470 [1976/2018]  1787   189   9.6%
  bin  7:  2.3470 -  2.2299 [1982/2018]  1785   197   9.9%
  bin  8:  2.2299 -  2.1331 [1981/2018]  1777   204  10.3%
  bin  9:  2.1331 -  2.0512 [1950/1982]  1754   196  10.1%
  bin 10:  2.0512 -  1.9806 [1436/2019]  1294   142   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_455/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 24
        2.42 -     3.04: 2193
        3.04 -     3.66: 4702
        3.66 -     4.28: 9017
        4.28 -     4.90: 12388
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.887 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  2.015 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.027 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  2.090 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28319 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_455/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_455/model_refine_001.geo

CPU time processing inputs: 9.83


============================ 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 = 69.5475 47.63395 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3594   r_free= 0.3518   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.130608                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.7258 0.99   1391  156 0.3009 0.3230      6.3955       6.431|
|  2:  4.7258 -  3.7711 0.99   1344  149 0.2907 0.2783      6.5572      6.5365|
|  3:  3.7711 -  3.3003 0.99   1317  150 0.3117 0.2984      6.4523       6.414|
|  4:  3.3003 -  3.0013 0.99   1308  133 0.3308 0.3083       6.316      6.1887|
|  5:  3.0013 -  2.7876 0.98   1286  147 0.3648 0.3229      6.2001      6.1441|
|  6:  2.7876 -  2.6242 0.98   1293  143 0.3833 0.3795      6.1294       6.031|
|  7:  2.6242 -  2.4934 0.99   1294  153 0.3869 0.3331      6.1123      5.9796|
|  8:  2.4934 -  2.3854 0.99   1284  133 0.3904 0.4334      6.0461      6.1018|
|  9:  2.3854 -  2.2939 0.98   1282  147 0.4164 0.4050      6.0209      6.0135|
| 10:  2.2939 -  2.2150 0.97   1254  141 0.4091 0.4383       6.003      6.0382|
| 11:  2.2150 -  2.1459 0.98   1270  142 0.4041 0.3655      5.9178      5.9223|
| 12:  2.1459 -  2.0848 0.99   1278  141 0.4200 0.4430      5.8929       5.934|
| 13:  2.0848 -  2.0300 0.97   1264  133 0.4405 0.4136      5.8247      5.7862|
| 14:  2.0300 -  1.9806 0.60    765   91 0.4109 0.4340      5.7356      5.6904|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8945 -  4.7258  1391   156  0.76  29.23   0.86     0.77      52173.61|
|  2:  4.7258 -  3.7711  1344   149  0.82  24.55   0.96     0.89      55832.33|
|  3:  3.7711 -  3.3003  1317   150  0.79  27.80   0.98     0.93      52347.36|
|  4:  3.3003 -  3.0013  1308   133  0.76  30.22   0.98     0.93      43608.08|
|  5:  3.0013 -  2.7876  1286   147  0.71  34.50   0.96     0.90      36369.48|
|  6:  2.7876 -  2.6242  1293   143  0.69  36.54   0.97     0.88      32544.29|
|  7:  2.6242 -  2.4934  1294   153  0.69  36.91   0.98     0.87      30930.54|
|  8:  2.4934 -  2.3854  1284   133  0.65  40.36   0.99     0.85      31888.71|
|  9:  2.3854 -  2.2939  1282   147  0.61  43.32   0.98     0.83      31198.46|
| 10:  2.2939 -  2.2150  1254   141  0.60  44.34   1.01     0.81      30419.60|
| 11:  2.2150 -  2.1459  1270   142  0.59  45.24   1.00     0.83      28386.48|
| 12:  2.1459 -  2.0848  1278   141  0.58  46.10   1.02     0.84      27215.70|
| 13:  2.0848 -  2.0300  1264   133  0.56  47.33   0.99     0.80      24003.43|
| 14:  2.0300 -  1.9806   765    91  0.56  47.60   1.01     0.74      20019.46|
|alpha:            min =        0.74 max =            0.93 mean =         0.85|
|beta:             min =    20019.46 max =        55832.33 mean =     36190.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.67|
|phase err.(work): min =        0.00 max =           89.97 mean =        37.71|
|phase err.(test): min =        0.00 max =           89.50 mean =        37.91|
|-----------------------------------------------------------------------------|

============================== 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 = 5.971203              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.844   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.822885              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.574   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      196 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1997 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1886 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2816 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4619 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4398 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5625 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6763 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.216 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3594   r_free= 0.3518   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.130608                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3470   r_free= 0.3364   ksol= 0.30   Bsol= 33.30   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,3.26,-1.47,0.00,-0.00,-0.00); trace/3= -0.20                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.110651                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.495469              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.692   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.460233              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.353   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3470      final r-factor (work) = 0.2094          |
| start r-factor (free) = 0.3364      final r-factor (free) = 0.2301          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9706 = 5.50 * 0.50 * 6.1162 + 1.00 * 0.1649                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1274 = 5.50 * 0.50 * 5.8380 + 1.00 * 0.0861                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2094      final r-factor (work) = 0.1911          |
| start r-factor (free) = 0.2301      final r-factor (free) = 0.2364          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6929 = 0.46 * 1.00 * 5.8380 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5867 = 0.46 * 1.00 * 5.5912 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.98   16.86    None  None   None       |
|    all(noH): 2823   0      0.00    63.98   16.86    None  None   None       |
|    Sol.    : 438    0      7.39    63.98   37.78    None  None   None       |
|    Mac.    : 2385   0      0.00    57.71   13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.398:  354   |   5:    31.992 -  38.390:  109        |
|      1:     6.398 -  12.797: 1098   |   6:    38.390 -  44.788:  109        |
|      2:    12.797 -  19.195:  619   |   7:    44.788 -  51.186:   80        |
|      3:    19.195 -  25.593:  242   |   8:    51.186 -  57.585:   64        |
|      4:    25.593 -  31.992:  129   |   9:    57.585 -  63.983:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1911 r_free = 0.2364             target_work(ml) = 5.604         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1908 r_free = 0.2367             target_work(ml) = 5.603         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1908   r_free= 0.2367   ksol= 0.30   Bsol= 33.30   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,3.26,-1.47,0.00,-0.00,-0.00); trace/3= -0.20                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.602845                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1884   r_free= 0.2345   ksol= 0.32   Bsol= 52.16   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-0.06,-1.50,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.595402                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.615550              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.906   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.196627              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.257   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1884      final r-factor (work) = 0.1357          |
| start r-factor (free) = 0.2345      final r-factor (free) = 0.1773          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9986 = 4.62 * 0.50 * 5.5952 + 1.00 * 0.0861                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6728 = 4.62 * 0.50 * 5.4631 + 1.00 * 0.0653                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1357      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1773      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0901 = 0.20 * 1.00 * 5.4631 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0428 = 0.20 * 1.00 * 5.2656 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    73.29   16.54    None  None   None       |
|    all(noH): 2823   0      1.69    73.29   16.54    None  None   None       |
|    Sol.    : 438    0      5.95    66.20   37.63    None  None   None       |
|    Mac.    : 2385   0      1.69    73.29   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.687 -   8.847:  758   |   5:    37.488 -  44.648:  110        |
|      1:     8.847 -  16.007: 1191   |   6:    44.648 -  51.808:   88        |
|      2:    16.007 -  23.167:  349   |   7:    51.808 -  58.969:   63        |
|      3:    23.167 -  30.328:  120   |   8:    58.969 -  66.129:   24        |
|      4:    30.328 -  37.488:  117   |   9:    66.129 -  73.289:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1269 r_free = 0.1657             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1267 r_free = 0.1656             target_work(ml) = 5.231         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1656   ksol= 0.32   Bsol= 52.16   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-0.06,-1.50,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.231017                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1649   ksol= 0.33   Bsol= 52.16   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.09,-1.25,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.230118                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.699196              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.274  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.227625              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.296  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1267      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1649      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5388 = 1.70 * 0.50 * 5.2655 + 1.00 * 0.0653                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4703 = 1.70 * 0.50 * 5.1974 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1905 = 0.23 * 1.00 * 5.1974 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1828 = 0.23 * 1.00 * 5.1627 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.85    75.90   16.42    None  None   None       |
|    all(noH): 2823   0      1.85    75.90   16.42    None  None   None       |
|    Sol.    : 438    0      3.47    68.51   37.71    None  None   None       |
|    Mac.    : 2385   0      1.85    75.90   12.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.847 -   9.252:  888   |   5:    38.873 -  46.278:  114        |
|      1:     9.252 -  16.657: 1125   |   6:    46.278 -  53.683:   90        |
|      2:    16.657 -  24.062:  309   |   7:    53.683 -  61.088:   49        |
|      3:    24.062 -  31.468:  118   |   8:    61.088 -  68.493:   16        |
|      4:    31.468 -  38.873:  111   |   9:    68.493 -  75.898:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1566             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1566             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1566   ksol= 0.33   Bsol= 52.16   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.09,-1.25,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159159                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1566   ksol= 0.33   Bsol= 52.16   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.38,-1.16,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158940                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.003251              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.693  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.570610              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.666  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2253 = 2.00 * 0.50 * 5.1623 + 1.00 * 0.0546                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2103 = 2.00 * 0.50 * 5.1408 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1108      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9411 = 0.57 * 1.00 * 5.1408 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9338 = 0.57 * 1.00 * 5.1261 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    84.06   16.49    None  None   None       |
|    all(noH): 2823   0      0.88    84.06   16.49    None  None   None       |
|    Sol.    : 438    0      3.57    72.60   38.59    None  None   None       |
|    Mac.    : 2385   0      0.88    84.06   12.44    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:     0.876 -   9.195:  924   |   5:    42.470 -  50.789:  110        |
|      1:     9.195 -  17.514: 1164   |   6:    50.789 -  59.108:   90        |
|      2:    17.514 -  25.833:  262   |   7:    59.108 -  67.427:   26        |
|      3:    25.833 -  34.152:  127   |   8:    67.427 -  75.746:    8        |
|      4:    34.152 -  42.470:  109   |   9:    75.746 -  84.065:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1097 r_free = 0.1559             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1097 r_free = 0.1560             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1560   ksol= 0.33   Bsol= 52.16   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.38,-1.16,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1560   ksol= 0.33   Bsol= 52.16   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-1.26,-0.91,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131208                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.633416              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.630  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.699603              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.759  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8119 = 2.63 * 0.50 * 5.1270 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8146 = 2.63 * 0.50 * 5.1242 + 1.00 * 0.0676                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1078      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7178 = 1.70 * 1.00 * 5.1242 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7112 = 1.70 * 1.00 * 5.1195 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.26    95.33   16.61    None  None   None       |
|    all(noH): 2823   0      0.26    95.33   16.61    None  None   None       |
|    Sol.    : 438    0      5.05    84.68   39.73    None  None   None       |
|    Mac.    : 2385   0      0.26    95.33   12.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.255 -   9.763: 1124   |   5:    47.793 -  57.301:   90        |
|      1:     9.763 -  19.270: 1054   |   6:    57.301 -  66.809:   69        |
|      2:    19.270 -  28.778:  212   |   7:    66.809 -  76.316:   13        |
|      3:    28.778 -  38.286:  133   |   8:    76.316 -  85.824:    5        |
|      4:    38.286 -  47.793:  119   |   9:    85.824 -  95.332:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1075 r_free = 0.1564             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1074 r_free = 0.1564             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1564   ksol= 0.33   Bsol= 52.16   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-1.26,-0.91,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122424                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.7258 0.99   1391  156 0.0950 0.1270      5.3487      5.5209|
|  2:  4.7258 -  3.7711 0.99   1344  149 0.0823 0.1079      5.4073      5.6174|
|  3:  3.7711 -  3.3003 0.99   1317  150 0.1016 0.1486      5.4476      5.8203|
|  4:  3.3003 -  3.0013 0.99   1308  133 0.1184 0.1566      5.4313      5.6128|
|  5:  3.0013 -  2.7876 0.98   1286  147 0.1254 0.1659      5.3005      5.5052|
|  6:  2.7876 -  2.6242 0.98   1293  143 0.1223 0.1949      5.2084      5.4585|
|  7:  2.6242 -  2.4934 0.99   1294  153 0.1139 0.1559        5.11      5.3295|
|  8:  2.4934 -  2.3854 0.99   1284  133 0.1114 0.1756       5.054      5.3267|
|  9:  2.3854 -  2.2939 0.98   1282  147 0.1121 0.1867       4.996       5.329|
| 10:  2.2939 -  2.2150 0.97   1254  141 0.1087 0.1728      4.9632      5.1805|
| 11:  2.2150 -  2.1459 0.98   1270  142 0.1107 0.1755      4.9164      5.2448|
| 12:  2.1459 -  2.0848 0.99   1278  141 0.1047 0.1656      4.8347      5.1326|
| 13:  2.0848 -  2.0300 0.97   1264  133 0.1061 0.1646      4.7691      5.0148|
| 14:  2.0300 -  1.9806 0.60    765   91 0.1040 0.1811      4.6933      4.9748|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8945 -  4.7258  1391   156  0.94   8.71   0.97     0.95       6667.71|
|  2:  4.7258 -  3.7711  1344   149  0.95   7.85   1.01     1.00       8641.37|
|  3:  3.7711 -  3.3003  1317   150  0.94  11.02   1.02     1.02      10017.75|
|  4:  3.3003 -  3.0013  1308   133  0.92  13.35   1.01     0.99       9976.83|
|  5:  3.0013 -  2.7876  1286   147  0.90  15.60   0.99     0.97       8099.57|
|  6:  2.7876 -  2.6242  1293   143  0.90  16.11   0.98     0.95       7008.59|
|  7:  2.6242 -  2.4934  1294   153  0.91  14.81   0.98     0.95       5694.52|
|  8:  2.4934 -  2.3854  1284   133  0.91  14.73   0.99     0.96       5301.07|
|  9:  2.3854 -  2.2939  1282   147  0.91  15.42   0.99     0.96       4777.38|
| 10:  2.2939 -  2.2150  1254   141  0.90  15.79   0.98     0.94       4551.47|
| 11:  2.2150 -  2.1459  1270   142  0.91  15.69   0.99     0.96       4240.28|
| 12:  2.1459 -  2.0848  1278   141  0.91  14.79   0.99     0.97       3686.49|
| 13:  2.0848 -  2.0300  1264   133  0.91  15.61   0.99     0.98       3287.13|
| 14:  2.0300 -  1.9806   765    91  0.91  15.28   0.96     0.92       2746.68|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2746.68 max =        10017.75 mean =      6180.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.81|
|phase err.(test): min =        0.00 max =           88.99 mean =        13.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1564   ksol= 0.32   Bsol= 51.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.02,-0.64,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1564   ksol= 0.32   Bsol= 51.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.02,-0.64,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122619                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.7258 0.99   1391  156 0.0950 0.1271      5.3496      5.5225|
|  2:  4.7258 -  3.7711 0.99   1344  149 0.0823 0.1078      5.4077      5.6169|
|  3:  3.7711 -  3.3003 0.99   1317  150 0.1016 0.1487      5.4475      5.8207|
|  4:  3.3003 -  3.0013 0.99   1308  133 0.1185 0.1567      5.4314      5.6132|
|  5:  3.0013 -  2.7876 0.98   1286  147 0.1254 0.1659      5.3006       5.505|
|  6:  2.7876 -  2.6242 0.98   1293  143 0.1223 0.1949      5.2084      5.4583|
|  7:  2.6242 -  2.4934 0.99   1294  153 0.1139 0.1560      5.1102      5.3299|
|  8:  2.4934 -  2.3854 0.99   1284  133 0.1114 0.1757      5.0543      5.3268|
|  9:  2.3854 -  2.2939 0.98   1282  147 0.1120 0.1867      4.9962      5.3289|
| 10:  2.2939 -  2.2150 0.97   1254  141 0.1087 0.1729      4.9635      5.1812|
| 11:  2.2150 -  2.1459 0.98   1270  142 0.1107 0.1754      4.9165      5.2447|
| 12:  2.1459 -  2.0848 0.99   1278  141 0.1047 0.1657      4.8347      5.1328|
| 13:  2.0848 -  2.0300 0.97   1264  133 0.1061 0.1646       4.769      5.0144|
| 14:  2.0300 -  1.9806 0.60    765   91 0.1040 0.1810      4.6934      4.9747|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8945 -  4.7258  1391   156  0.94   8.73   0.98     0.95       6684.10|
|  2:  4.7258 -  3.7711  1344   149  0.95   7.86   1.02     1.00       8650.96|
|  3:  3.7711 -  3.3003  1317   150  0.94  11.02   1.03     1.02      10017.33|
|  4:  3.3003 -  3.0013  1308   133  0.92  13.36   1.01     1.00       9979.62|
|  5:  3.0013 -  2.7876  1286   147  0.90  15.60   1.00     0.98       8098.33|
|  6:  2.7876 -  2.6242  1293   143  0.90  16.11   0.99     0.95       7007.03|
|  7:  2.6242 -  2.4934  1294   153  0.91  14.82   0.99     0.96       5695.69|
|  8:  2.4934 -  2.3854  1284   133  0.91  14.74   1.00     0.97       5303.59|
|  9:  2.3854 -  2.2939  1282   147  0.91  15.43   1.01     0.97       4781.60|
| 10:  2.2939 -  2.2150  1254   141  0.90  15.80   1.00     0.96       4552.63|
| 11:  2.2150 -  2.1459  1270   142  0.91  15.69   1.00     0.97       4241.07|
| 12:  2.1459 -  2.0848  1278   141  0.91  14.79   1.01     0.99       3685.96|
| 13:  2.0848 -  2.0300  1264   133  0.91  15.61   1.00     0.99       3286.08|
| 14:  2.0300 -  1.9806   765    91  0.91  15.28   0.98     0.93       2745.87|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2745.87 max =        10017.33 mean =      6183.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.00 mean =        13.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.25    95.33   16.61    None  None   None       |
|    all(noH): 2823   0      0.25    95.33   16.61    None  None   None       |
|    Sol.    : 438    0      5.04    84.67   39.73    None  None   None       |
|    Mac.    : 2385   0      0.25    95.33   12.36    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:     0.248 -   9.756: 1124   |   5:    47.787 -  57.294:   90        |
|      1:     9.756 -  19.264: 1054   |   6:    57.294 -  66.802:   69        |
|      2:    19.264 -  28.771:  212   |   7:    66.802 -  76.310:   13        |
|      3:    28.771 -  38.279:  133   |   8:    76.310 -  85.817:    5        |
|      4:    38.279 -  47.787:  119   |   9:    85.817 -  95.325:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 273         
Filter by distance & map next to the model:
   mapped sites are within: 0.470 - 4.622
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 273
   mapped sites are within: 0.747 - 4.622

peak=    5.734 closest distance to " NH2 ARG A  56 " =    2.366
peak=    5.556 closest distance to " CB  ARG A 275 " =    0.931
peak=    5.444 closest distance to " CB  GLN A 223 " =    1.377
peak=    5.011 closest distance to " CB  GLN A 183 " =    1.302
peak=    4.885 closest distance to " CB  SER A  63 " =    1.163
peak=    4.766 closest distance to " O   HOH Z 403 " =    1.779
peak=    4.749 closest distance to " CG  PRO A 213 " =    1.244
peak=    4.743 closest distance to " CA  TYR A  30 " =    0.923
peak=    4.711 closest distance to " O   HOH Z 232 " =    2.368
peak=    4.560 closest distance to " O   HOH Z 298 " =    1.883
peak=    4.555 closest distance to " O   HOH Z 234 " =    3.708
peak=    4.489 closest distance to " O   HOH Z 126 " =    1.843
peak=    4.460 closest distance to " O   HOH Z 402 " =    1.488
peak=    4.451 closest distance to " O   HOH Z 142 " =    1.579
peak=    4.439 closest distance to " O   HOH Z 193 " =    1.766
peak=    4.421 closest distance to " C   PRO A 198 " =    1.438
peak=    4.414 closest distance to " CB  GLU A 152 " =    1.147
peak=    4.398 closest distance to " O   HOH Z  97 " =    1.963
peak=    4.364 closest distance to " O   HOH Z  15 " =    2.090
peak=    4.364 closest distance to " CB  ARG A 190 " =    1.691
peak=    4.364 closest distance to " O   SER A  87 " =    2.201
peak=    4.343 closest distance to " O   HOH Z 209 " =    2.217
peak=    4.306 closest distance to " CB  ARG A  79 " =    1.295
peak=    4.283 closest distance to " CG  PRO A  90 " =    1.162
peak=    4.253 closest distance to " O   HOH Z 203 " =    1.757
peak=    4.245 closest distance to " O   HOH Z 369 " =    2.221
peak=    4.207 closest distance to " O   HOH Z  59 " =    2.341
peak=    4.204 closest distance to " O   HOH Z 368 " =    2.128
peak=    4.192 closest distance to " O   HOH Z  40 " =    1.931
peak=    4.166 closest distance to " CG1 ILE A  33 " =    1.163
peak=    4.144 closest distance to " CB  TYR A 169 " =    0.848
peak=    4.130 closest distance to " CG  PRO A 198 " =    1.230
peak=    4.129 closest distance to " O   HOH Z 272 " =    1.862
peak=    4.125 closest distance to " CA  ALA A  21 " =    1.255
peak=    4.111 closest distance to " NZ  LYS A 117 " =    3.193
peak=    4.083 closest distance to " NH2BARG A 145 " =    2.074
peak=    4.079 closest distance to " CB  GLU A 128 " =    1.210
peak=    4.052 closest distance to " O   HOH Z 284 " =    2.940
peak=    4.052 closest distance to " CG  ARG A  66 " =    2.669
peak=    4.035 closest distance to " O   HOH Z  78 " =    1.697
peak=    4.029 closest distance to " O   HOH Z 287 " =    2.013
peak=    4.028 closest distance to " O   HOH Z  43 " =    2.129
peak=    4.028 closest distance to " O   HOH Z  44 " =    2.010
peak=    4.021 closest distance to " O   HOH Z 158 " =    2.982
peak=    4.014 closest distance to " CA  ASN A 176 " =    1.218
peak=    4.013 closest distance to " OD1 ASN A  69 " =    2.518
peak=    4.001 closest distance to " O   HOH Z 346 " =    1.688
peak=    3.979 closest distance to " NE2 GLN A  11 " =    0.993
peak=    3.969 closest distance to " CD2 TRP A 179 " =    1.420
peak=    3.962 closest distance to " O   HOH Z 250 " =    1.425
peak=    3.952 closest distance to " CB  GLU A 277 " =    3.577
peak=    3.950 closest distance to " O   HOH Z 371 " =    3.354
peak=    3.937 closest distance to " O   HOH Z 423 " =    2.005
peak=    3.926 closest distance to " CG1BVAL A  72 " =    1.776
peak=    3.914 closest distance to " CD  ARG A 269 " =    1.006
peak=    3.912 closest distance to " O   HOH Z 147 " =    1.790
peak=    3.906 closest distance to " CG2 ILE A 120 " =    1.077
peak=    3.905 closest distance to " O   HOH Z  97 " =    2.392
peak=    3.904 closest distance to " CB  SER A   3 " =    1.175
peak=    3.903 closest distance to " CG  PRO A 243 " =    1.124
peak=    3.896 closest distance to " O   HOH Z 245 " =    1.375
peak=    3.893 closest distance to " O   HOH Z 128 " =    1.994
peak=    3.891 closest distance to " O   HOH Z 279 " =    2.130
peak=    3.887 closest distance to " O   HOH Z 189 " =    2.217
peak=    3.875 closest distance to " O   HOH Z 108 " =    2.665
peak=    3.871 closest distance to " O   HOH Z 357 " =    1.968
peak=    3.870 closest distance to " OD2 ASP A 286 " =    2.793
peak=    3.865 closest distance to " CA  ARG A  36 " =    1.056
peak=    3.862 closest distance to " O   HOH Z 427 " =    2.888
peak=    3.851 closest distance to " O   HOH Z 132 " =    2.641
peak=    3.828 closest distance to " CB  VAL A 265 " =    1.273
peak=    3.823 closest distance to " CB  TRP A 179 " =    1.260
peak=    3.822 closest distance to " ND2 ASN A 187 " =    1.472
peak=    3.816 closest distance to " O   HOH Z  61 " =    1.578
peak=    3.813 closest distance to " O   HOH Z 345 " =    2.878
peak=    3.799 closest distance to " O   HOH Z 389 " =    1.876
peak=    3.798 closest distance to " O   HOH Z 316 " =    3.050
peak=    3.791 closest distance to " CB  ASN A 148 " =    1.388
peak=    3.762 closest distance to " CA  LYS A 117 " =    1.281
peak=    3.762 closest distance to " O   HOH Z  80 " =    1.645
peak=    3.749 closest distance to " CA  ARG A 195 " =    1.330
peak=    3.749 closest distance to " O   HOH Z 265 " =    2.258
peak=    3.740 closest distance to " O   HOH Z 345 " =    1.622
peak=    3.728 closest distance to " OE1 GLU A   2 " =    2.200
peak=    3.725 closest distance to " O   HOH Z 134 " =    1.291
peak=    3.722 closest distance to " OD2 ASP A 298 " =    3.884
peak=    3.721 closest distance to " O   HOH Z  63 " =    2.016
peak=    3.714 closest distance to " O   HOH Z 214 " =    2.382
peak=    3.713 closest distance to " O   HOH Z 380 " =    1.860
peak=    3.704 closest distance to " CB  ASP A 140 " =    0.945
peak=    3.701 closest distance to " O   HOH Z 421 " =    1.764
peak=    3.696 closest distance to " CA  ALA A  51 " =    0.946
peak=    3.695 closest distance to " O   HOH Z 247 " =    1.320
peak=    3.684 closest distance to " O   HOH Z 261 " =    1.666
peak=    3.684 closest distance to " O   HOH Z 102 " =    1.253
peak=    3.682 closest distance to " O   HOH Z 227 " =    1.668
peak=    3.680 closest distance to " N   ASN A  39 " =    1.291
peak=    3.677 closest distance to " CZ  PHE A 218 " =    1.096
peak=    3.675 closest distance to " O   HOH Z 417 " =    3.011
peak=    3.668 closest distance to " O   HOH Z 411 " =    3.718
peak=    3.666 closest distance to " O   HOH Z 185 " =    1.727
peak=    3.663 closest distance to " O   HOH Z  54 " =    1.722
peak=    3.659 closest distance to " CG  GLN A  58 " =    2.639
peak=    3.657 closest distance to " CD2 LEU A 297 " =    0.908
peak=    3.654 closest distance to " O   HOH Z 327 " =    1.588
peak=    3.647 closest distance to " CB  SER A  62 " =    0.844
peak=    3.643 closest distance to " CA  THR A 221 " =    1.052
peak=    3.643 closest distance to " N   HIS A 108 " =    1.907
peak=    3.642 closest distance to " O   HOH Z 163 " =    1.477
peak=    3.638 closest distance to " O   HOH Z 197 " =    2.670
peak=    3.629 closest distance to " O   HOH Z 261 " =    1.962
peak=    3.623 closest distance to " O   HOH Z  21 " =    1.795
peak=    3.622 closest distance to " OG BSER A 164 " =    2.291
peak=    3.622 closest distance to " O   HOH Z 132 " =    2.626
peak=    3.619 closest distance to " CB  ASN A  39 " =    0.790
peak=    3.614 closest distance to " CB  ALA A 291 " =    1.295
peak=    3.608 closest distance to " O   HOH Z 426 " =    1.537
peak=    3.607 closest distance to " CB  TRP A 266 " =    0.955
peak=    3.607 closest distance to " O   HOH Z 305 " =    3.602
peak=    3.606 closest distance to " CG2 THR A 221 " =    1.166
peak=    3.602 closest distance to " O   HOH Z 126 " =    1.972
peak=    3.600 closest distance to " CB  SER A 141 " =    1.011
peak=    3.599 closest distance to " O   HOH Z 361 " =    3.590
peak=    3.595 closest distance to " O   HOH Z 250 " =    1.636
peak=    3.589 closest distance to " CB  VAL A 202 " =    1.477
peak=    3.584 closest distance to " CB  LEU A 228 " =    1.136
peak=    3.581 closest distance to " CB  TYR A 169 " =    1.020
peak=    3.570 closest distance to " O   HOH Z 126 " =    1.608
peak=    3.568 closest distance to " O   HOH Z 180 " =    2.314
peak=    3.568 closest distance to " O   HOH Z 359 " =    1.426
peak=    3.560 closest distance to " O   HOH Z 303 " =    2.149
peak=    3.554 closest distance to " CG2 ILE A  20 " =    1.384
peak=    3.553 closest distance to " CB  ARG A 139 " =    0.914
peak=    3.552 closest distance to " O   HOH Z 183 " =    1.467
peak=    3.550 closest distance to " O   HOH Z 416 " =    2.885
peak=    3.544 closest distance to " CD  LYS A 166 " =    1.361
peak=    3.542 closest distance to " O   HOH Z 406 " =    1.508
peak=    3.540 closest distance to " CB  ALA A 248 " =    1.395
peak=    3.529 closest distance to " CG2 VAL A 197 " =    1.167
peak=    3.525 closest distance to " O   HOH Z 299 " =    4.418
peak=    3.524 closest distance to " NZ  LYS A 166 " =    3.013
peak=    3.524 closest distance to " O   HOH Z  68 " =    1.900
peak=    3.517 closest distance to " O   TRP A 274 " =    1.942
peak=    3.516 closest distance to " CA  ALA A  84 " =    1.194
peak=    3.516 closest distance to " O   HOH Z 365 " =    2.766
peak=    3.503 closest distance to " NH2AARG A 275 " =    3.655
peak=    3.500 closest distance to " O   HOH Z 425 " =    1.981
peak=    3.495 closest distance to " CA  ASN A 215 " =    1.117
peak=    3.494 closest distance to " O   HOH Z 427 " =    3.152
peak=    3.493 closest distance to " O   HOH Z 173 " =    2.090
peak=    3.491 closest distance to " O   HOH Z 344 " =    3.099
peak=    3.490 closest distance to " O   HOH Z 325 " =    2.017
peak=    3.480 closest distance to " CG  ARG A  66 " =    0.974
peak=    3.467 closest distance to " CA  ALA A 160 " =    0.835
peak=    3.464 closest distance to " CG  ARG A 219 " =    1.212
peak=    3.454 closest distance to " O   HOH Z 374 " =    2.662
peak=    3.454 closest distance to " O   HOH Z 291 " =    1.423
peak=    3.451 closest distance to " O   ALA A 165 " =    1.418
peak=    3.450 closest distance to " CE  LYS A  76 " =    0.854
peak=    3.450 closest distance to " O   HOH Z 281 " =    4.622
peak=    3.447 closest distance to " CD1 LEU A  96 " =    0.747
peak=    3.439 closest distance to " NE2 GLN A  77 " =    3.192
peak=    3.430 closest distance to " NH2 ARG A 156 " =    1.172
peak=    3.425 closest distance to " O   HOH Z 403 " =    1.416
peak=    3.421 closest distance to " O   HOH Z  49 " =    2.296
peak=    3.421 closest distance to " CG2BVAL A  41 " =    0.842
peak=    3.419 closest distance to " O   HOH Z  35 " =    2.307
peak=    3.417 closest distance to " ND1 HIS A  81 " =    1.598
peak=    3.416 closest distance to " CA  ASP A 162 " =    1.159
peak=    3.407 closest distance to " O   HOH Z   1 " =    2.442
peak=    3.405 closest distance to " NH1AARG A 145 " =    1.232
peak=    3.404 closest distance to " N   TYR A 116 " =    1.564
peak=    3.403 closest distance to " OG1 THR A 294 " =    2.399
peak=    3.402 closest distance to " CB  ILE A 120 " =    1.317
peak=    3.401 closest distance to " O   HOH Z 193 " =    2.175
peak=    3.395 closest distance to " CD  ARG A 159 " =    0.755
peak=    3.395 closest distance to " CD1 ILE A 106 " =    0.873
peak=    3.385 closest distance to " O   HOH Z  66 " =    2.211
peak=    3.377 closest distance to " CA  ASP A 140 " =    1.129
peak=    3.375 closest distance to " O   HOH Z 383 " =    2.080
peak=    3.370 closest distance to " CG1 VAL A 153 " =    0.989
peak=    3.367 closest distance to " O   HOH Z 422 " =    2.621
peak=    3.366 closest distance to " CZ2 TRP A 179 " =    1.748
peak=    3.363 closest distance to " O   HOH Z 258 " =    2.261
peak=    3.358 closest distance to " O   THR A 251 " =    1.204
peak=    3.352 closest distance to " O   HOH Z 135 " =    1.761
peak=    3.352 closest distance to " CB  THR A  31 " =    1.743
peak=    3.348 closest distance to " O   HOH Z 128 " =    2.248
peak=    3.348 closest distance to " O   HOH Z 156 " =    2.506
peak=    3.348 closest distance to " O   HOH Z 336 " =    1.654
peak=    3.347 closest distance to " CG  PRO A  54 " =    1.327
peak=    3.343 closest distance to " CD1 LEU A 300 " =    1.248
peak=    3.339 closest distance to " O   HOH Z 435 " =    1.890
peak=    3.339 closest distance to " CB  SER A  26 " =    1.732
peak=    3.333 closest distance to " OG  SER A  62 " =    2.809
peak=    3.330 closest distance to " O   HOH Z 298 " =    2.421
peak=    3.329 closest distance to " CG AARG A 275 " =    1.225
peak=    3.325 closest distance to " CA  MET A 105 " =    1.086
peak=    3.318 closest distance to " O   HOH Z  19 " =    1.660
peak=    3.317 closest distance to " CE  LYS A 119 " =    1.116
peak=    3.298 closest distance to " O   HOH Z 435 " =    3.019
peak=    3.282 closest distance to " CG2 VAL A 257 " =    0.798
peak=    3.278 closest distance to " OE1 GLN A  11 " =    1.862
peak=    3.272 closest distance to " O   HOH Z 313 " =    1.776
peak=    3.267 closest distance to " CB  TYR A 116 " =    0.824
peak=    3.267 closest distance to " CD2 HIS A  81 " =    1.086
peak=    3.265 closest distance to " O   HOH Z 423 " =    3.415
peak=    3.262 closest distance to " CA  ALA A 291 " =    0.820
peak=    3.249 closest distance to " CB  PRO A 163 " =    4.030
peak=    3.243 closest distance to " CA  MET A  40 " =    1.067
peak=    3.241 closest distance to " NH2 ARG A  79 " =    1.333
peak=    3.238 closest distance to " CG1 ILE A 151 " =    0.954
peak=    3.232 closest distance to " O   HOH Z 273 " =    2.931
peak=    3.219 closest distance to " CB  ALA A   9 " =    1.539
peak=    3.218 closest distance to " O   HOH Z 414 " =    1.612
peak=    3.217 closest distance to " CB  ASN A 215 " =    1.165
peak=    3.216 closest distance to " CA  TYR A 116 " =    1.396
peak=    3.214 closest distance to " O   HOH Z 148 " =    3.225
peak=    3.209 closest distance to " CB  SER A 212 " =    1.052
peak=    3.205 closest distance to " CB  ASN A 285 " =    0.946
peak=    3.201 closest distance to " CA  SER A  32 " =    1.570
peak=    3.200 closest distance to " O   THR A 220 " =    1.175
peak=    3.197 closest distance to " O   HOH Z  61 " =    1.516
peak=    3.196 closest distance to " O   HOH Z 124 " =    1.288
peak=    3.193 closest distance to " CD2 LEU A 255 " =    1.308
peak=    3.191 closest distance to " CD  ARG A  66 " =    2.888
peak=    3.190 closest distance to " CG2 VAL A  78 " =    0.875
peak=    3.189 closest distance to " CA  GLY A  80 " =    0.953
peak=    3.186 closest distance to " CG  MET A 185 " =    1.138
peak=    3.183 closest distance to " O   HOH Z 409 " =    3.294
peak=    3.181 closest distance to " CA  VAL A 125 " =    1.179
peak=    3.178 closest distance to " CZ  PHE A  38 " =    1.344
peak=    3.173 closest distance to " O   HOH Z  89 " =    2.165
peak=    3.170 closest distance to " CB  GLN A 278 " =    0.865
peak=    3.163 closest distance to " O   HOH Z 298 " =    2.754
peak=    3.161 closest distance to " O   HOH Z 438 " =    1.913
peak=    3.160 closest distance to " CB  ARG A  79 " =    0.791
peak=    3.155 closest distance to " CA  ASP A 191 " =    0.881
peak=    3.151 closest distance to " CB  MET A  40 " =    0.847
peak=    3.150 closest distance to " CD  LYS A  76 " =    1.948
peak=    3.148 closest distance to " O   HOH Z  46 " =    1.391
peak=    3.146 closest distance to " CB  ALA A  71 " =    1.305
peak=    3.145 closest distance to " O   HOH Z 353 " =    2.816
peak=    3.139 closest distance to " CG2 VAL A 202 " =    1.192
peak=    3.138 closest distance to " N   ARG A 156 " =    1.375
peak=    3.137 closest distance to " O   HOH Z  85 " =    2.170
peak=    3.134 closest distance to " O   HOH Z 419 " =    1.491
peak=    3.127 closest distance to " O   ASN A  74 " =    1.503
peak=    3.125 closest distance to " O   HOH Z 425 " =    1.233
peak=    3.122 closest distance to " O   HOH Z  88 " =    3.448
peak=    3.122 closest distance to " O   HOH Z 350 " =    1.840
peak=    3.121 closest distance to " O   HOH Z 152 " =    1.857
peak=    3.121 closest distance to " CE  LYS A  48 " =    1.085
peak=    3.113 closest distance to " CB  ALA A 100 " =    1.171
peak=    3.111 closest distance to " O   HOH Z  10 " =    1.750
peak=    3.111 closest distance to " O   HOH Z 163 " =    1.652
peak=    3.109 closest distance to " O   HOH Z 251 " =    1.559
peak=    3.094 closest distance to " CA  GLU A 152 " =    0.860
peak=    3.087 closest distance to " CG  LYS A  76 " =    1.039
peak=    3.084 closest distance to " OE1 GLU A   2 " =    1.650
peak=    3.084 closest distance to " C   SER A  32 " =    1.097
peak=    3.079 closest distance to " OE1 GLN A 240 " =    1.519
peak=    3.075 closest distance to " C   ALA A 299 " =    0.954
peak=    3.074 closest distance to " ND2 ASN A 110 " =    1.534
peak=    3.068 closest distance to " O   HOH Z 329 " =    3.839
peak=    3.059 closest distance to " O   HOH Z 417 " =    2.036
peak=    3.044 closest distance to " CB  LYS A 289 " =    1.034
peak=    3.036 closest distance to " O   HOH Z 189 " =    2.529
peak=    3.031 closest distance to " O   HOH Z 145 " =    2.421

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.870 - 5.913
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 213
   mapped sites are within: 0.870 - 5.913

peak=   -5.081 closest distance to " O   HOH Z 266 " =    4.713
peak=   -4.678 closest distance to " C   HIS A 108 " =    1.109
peak=   -4.304 closest distance to " CD  ARG A 156 " =    2.080
peak=   -4.291 closest distance to " O   HOH Z  13 " =    1.672
peak=   -4.262 closest distance to " SG  CYS A 254 " =    3.409
peak=   -4.208 closest distance to " OXT GLY A 302 " =    2.806
peak=   -4.192 closest distance to " CD  GLN A  58 " =    1.142
peak=   -4.140 closest distance to " OE1 GLN A 223 " =    2.091
peak=   -4.133 closest distance to " CB  ALA A 161 " =    2.602
peak=   -4.090 closest distance to " CD1 LEU A 101 " =    2.422
peak=   -4.076 closest distance to " CB  PRO A 243 " =    2.670
peak=   -4.062 closest distance to " O   HOH Z 165 " =    1.907
peak=   -4.058 closest distance to " O   HOH Z 372 " =    2.311
peak=   -4.058 closest distance to " CG  ASP A 132 " =    2.352
peak=   -4.052 closest distance to " O   PRO A 163 " =    2.089
peak=   -4.047 closest distance to " O   HOH Z 377 " =    2.125
peak=   -4.036 closest distance to " O   VAL A  67 " =    2.686
peak=   -4.013 closest distance to " CA  ASP A 298 " =    1.035
peak=   -4.000 closest distance to " OG  SER A  97 " =    2.192
peak=   -3.983 closest distance to " OG BSER A 134 " =    1.280
peak=   -3.973 closest distance to " O   HOH Z 196 " =    1.945
peak=   -3.960 closest distance to " O   HOH Z 231 " =    2.380
peak=   -3.923 closest distance to " O   HOH Z 394 " =    1.554
peak=   -3.889 closest distance to " O   HOH Z  10 " =    1.590
peak=   -3.865 closest distance to " CE2 TYR A  30 " =    2.705
peak=   -3.857 closest distance to " O   HOH Z 353 " =    2.187
peak=   -3.851 closest distance to " CD1 LEU A  25 " =    2.486
peak=   -3.816 closest distance to " CB  ASN A  39 " =    2.327
peak=   -3.800 closest distance to " O   HOH Z 198 " =    2.062
peak=   -3.788 closest distance to " O   VAL A  67 " =    2.865
peak=   -3.749 closest distance to " N   ALA A  43 " =    2.773
peak=   -3.743 closest distance to " CB  ALA A 291 " =    2.301
peak=   -3.739 closest distance to " O   HOH Z 292 " =    4.517
peak=   -3.736 closest distance to " ND2 ASN A  45 " =    1.048
peak=   -3.727 closest distance to " O   HOH Z 407 " =    3.015
peak=   -3.724 closest distance to " N   ALA A 248 " =    1.713
peak=   -3.689 closest distance to " CD  ARG A 195 " =    5.130
peak=   -3.673 closest distance to " CD  ARG A 139 " =    1.549
peak=   -3.670 closest distance to " CZ  TYR A 169 " =    1.825
peak=   -3.667 closest distance to " O   HOH Z 166 " =    1.855
peak=   -3.659 closest distance to " O   HOH Z 389 " =    1.747
peak=   -3.647 closest distance to " CB  PHE A 192 " =    2.035
peak=   -3.646 closest distance to " O   SER A 210 " =    1.910
peak=   -3.642 closest distance to " CZ3 TRP A 179 " =    1.279
peak=   -3.637 closest distance to " OD2 ASP A 171 " =    2.433
peak=   -3.633 closest distance to " NE2 GLN A  88 " =    1.749
peak=   -3.622 closest distance to " O   PHE A 218 " =    1.610
peak=   -3.618 closest distance to " OD1 ASN A 148 " =    1.505
peak=   -3.614 closest distance to " OD1 ASN A  39 " =    2.225
peak=   -3.612 closest distance to " O   HOH Z 311 " =    3.685
peak=   -3.600 closest distance to " O   HOH Z 126 " =    1.879
peak=   -3.599 closest distance to " O   HOH Z 234 " =    4.110
peak=   -3.583 closest distance to " O   HOH Z 252 " =    3.563
peak=   -3.580 closest distance to " CG2 ILE A 263 " =    2.276
peak=   -3.578 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.573 closest distance to " O   HOH Z 114 " =    3.382
peak=   -3.548 closest distance to " CG1 VAL A 112 " =    2.742
peak=   -3.545 closest distance to " O   HOH Z  52 " =    1.525
peak=   -3.539 closest distance to " CD1 PHE A  59 " =    1.966
peak=   -3.539 closest distance to " O   TRP A  92 " =    1.880
peak=   -3.538 closest distance to " OG BSER A 134 " =    1.731
peak=   -3.533 closest distance to " N   GLN A  58 " =    1.629
peak=   -3.530 closest distance to " N   THR A 235 " =    1.380
peak=   -3.526 closest distance to " CG1 VAL A 125 " =    2.302
peak=   -3.523 closest distance to " O   HOH Z  11 " =    2.037
peak=   -3.522 closest distance to " CB  PHE A 208 " =    2.269
peak=   -3.521 closest distance to " NH1 ARG A 195 " =    2.584
peak=   -3.515 closest distance to " O   HOH Z 290 " =    1.187
peak=   -3.502 closest distance to " O   HOH Z  71 " =    1.813
peak=   -3.495 closest distance to " CB  ASP A 286 " =    1.890
peak=   -3.487 closest distance to " O   ALA A  34 " =    2.154
peak=   -3.485 closest distance to " O   HOH Z   6 " =    1.721
peak=   -3.482 closest distance to " O   HOH Z 283 " =    2.114
peak=   -3.477 closest distance to " O   HOH Z 166 " =    1.649
peak=   -3.475 closest distance to " CG1 VAL A 250 " =    2.695
peak=   -3.470 closest distance to " O   HOH Z 414 " =    1.499
peak=   -3.458 closest distance to " CA  GLY A 133 " =    2.357
peak=   -3.457 closest distance to " O   HOH Z 102 " =    1.605
peak=   -3.457 closest distance to " ND2 ASN A 187 " =    1.533
peak=   -3.451 closest distance to " O   ALA A 160 " =    1.496
peak=   -3.450 closest distance to " CD1 TYR A 247 " =    2.521
peak=   -3.439 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.438 closest distance to " O   VAL A 189 " =    2.634
peak=   -3.434 closest distance to " NE1 TRP A 266 " =    2.374
peak=   -3.434 closest distance to " O   HOH Z 377 " =    1.822
peak=   -3.432 closest distance to " O   HOH Z 185 " =    2.407
peak=   -3.431 closest distance to " OG  SER A   3 " =    1.793
peak=   -3.418 closest distance to " N   THR A  52 " =    1.679
peak=   -3.417 closest distance to " O   LEU A 167 " =    1.591
peak=   -3.412 closest distance to " CB  ALA A 248 " =    2.183
peak=   -3.412 closest distance to " CZ  PHE A  59 " =    1.708
peak=   -3.406 closest distance to " CG  ASP A 231 " =    0.870
peak=   -3.402 closest distance to " CG1AVAL A  41 " =    2.636
peak=   -3.396 closest distance to " CB  ALA A  43 " =    2.453
peak=   -3.394 closest distance to " C   LEU A 143 " =    1.079
peak=   -3.390 closest distance to " O   HOH Z  15 " =    1.491
peak=   -3.389 closest distance to " CB  ALA A  10 " =    2.288
peak=   -3.388 closest distance to " CD1 LEU A 228 " =    2.144
peak=   -3.380 closest distance to " O   HOH Z 171 " =    2.081
peak=   -3.380 closest distance to " O   GLY A  80 " =    2.452
peak=   -3.377 closest distance to " O   HOH Z 123 " =    2.314
peak=   -3.368 closest distance to " O   HOH Z 377 " =    1.769
peak=   -3.367 closest distance to " N   VAL A 189 " =    1.663
peak=   -3.363 closest distance to " CG  PRO A 243 " =    1.746
peak=   -3.359 closest distance to " ND2 ASN A  69 " =    1.583
peak=   -3.358 closest distance to " CG1 VAL A  78 " =    3.154
peak=   -3.355 closest distance to " CG  GLN A  58 " =    1.031
peak=   -3.353 closest distance to " OD2 ASP A 191 " =    1.513
peak=   -3.350 closest distance to " CE  MET A 105 " =    2.157
peak=   -3.350 closest distance to " C   ALA A 158 " =    1.277
peak=   -3.350 closest distance to " O   ALA A  10 " =    1.826
peak=   -3.346 closest distance to " O   HOH Z 111 " =    1.866
peak=   -3.344 closest distance to " OE2 GLU A   2 " =    1.678
peak=   -3.343 closest distance to " CG2 VAL A 189 " =    2.196
peak=   -3.341 closest distance to " NE2 GLN A 103 " =    1.710
peak=   -3.335 closest distance to " CG  GLN A  11 " =    1.871
peak=   -3.334 closest distance to " CG1 VAL A 112 " =    2.867
peak=   -3.334 closest distance to " O   HOH Z 435 " =    2.680
peak=   -3.330 closest distance to " CZ  ARG A  66 " =    1.274
peak=   -3.329 closest distance to " OE1 GLN A 223 " =    1.972
peak=   -3.327 closest distance to " N   SER A 276 " =    1.436
peak=   -3.325 closest distance to " OD1 ASP A 171 " =    1.574
peak=   -3.322 closest distance to " CE3 TRP A 150 " =    2.110
peak=   -3.318 closest distance to " NH2 ARG A  79 " =    2.079
peak=   -3.317 closest distance to " CD2 LEU A 300 " =    2.804
peak=   -3.312 closest distance to " CD  LYS A 289 " =    2.386
peak=   -3.312 closest distance to " CB  ALA A 248 " =    2.024
peak=   -3.309 closest distance to " O   HOH Z 193 " =    1.835
peak=   -3.308 closest distance to " CD1 ILE A 239 " =    2.088
peak=   -3.302 closest distance to " OG  SER A  62 " =    1.599
peak=   -3.293 closest distance to " SG ACYS A 201 " =    2.131
peak=   -3.293 closest distance to " CG1 VAL A  78 " =    2.572
peak=   -3.292 closest distance to " CD2 LEU A 237 " =    2.479
peak=   -3.291 closest distance to " CB  ALA A 291 " =    2.291
peak=   -3.287 closest distance to " O   HOH Z  37 " =    1.767
peak=   -3.287 closest distance to " O   GLY A  80 " =    2.572
peak=   -3.285 closest distance to " OG  SER A  26 " =    1.302
peak=   -3.284 closest distance to " N   ALA A 226 " =    1.955
peak=   -3.279 closest distance to " OG BSER A 210 " =    2.137
peak=   -3.277 closest distance to " O   HOH Z  43 " =    1.647
peak=   -3.276 closest distance to " OG BSER A 210 " =    1.293
peak=   -3.271 closest distance to " CG  GLU A  53 " =    1.464
peak=   -3.267 closest distance to " CB  PHE A  16 " =    2.613
peak=   -3.265 closest distance to " ND2 ASN A  39 " =    1.228
peak=   -3.264 closest distance to " N   ALA A 248 " =    2.249
peak=   -3.262 closest distance to " O   HOH Z 150 " =    1.929
peak=   -3.260 closest distance to " O   HOH Z  19 " =    1.988
peak=   -3.258 closest distance to " CA  GLY A 203 " =    2.305
peak=   -3.257 closest distance to " O   ILE A 234 " =    1.337
peak=   -3.256 closest distance to " CD2 TYR A 293 " =    1.964
peak=   -3.252 closest distance to " O   HOH Z 422 " =    1.540
peak=   -3.249 closest distance to " NH2 ARG A  66 " =    1.868
peak=   -3.247 closest distance to " O   HOH Z  11 " =    1.841
peak=   -3.244 closest distance to " O   HOH Z  90 " =    2.919
peak=   -3.240 closest distance to " NH2AARG A 275 " =    5.118
peak=   -3.238 closest distance to " O   ASN A 187 " =    1.517
peak=   -3.234 closest distance to " CG1 VAL A 112 " =    2.574
peak=   -3.233 closest distance to " NE2 GLN A 194 " =    1.795
peak=   -3.231 closest distance to " O   HOH Z 361 " =    3.368
peak=   -3.227 closest distance to " O   TYR A 186 " =    1.631
peak=   -3.226 closest distance to " O   HOH Z 252 " =    4.203
peak=   -3.226 closest distance to " CB  PRO A 163 " =    2.566
peak=   -3.218 closest distance to " OE1 GLN A 183 " =    1.449
peak=   -3.217 closest distance to " NH2 ARG A 159 " =    2.399
peak=   -3.216 closest distance to " CE2 PHE A  61 " =    2.545
peak=   -3.216 closest distance to " CA  GLY A 241 " =    2.338
peak=   -3.210 closest distance to " O   GLY A 196 " =    1.062
peak=   -3.209 closest distance to " O   HOH Z 418 " =    1.432
peak=   -3.197 closest distance to " O   HOH Z  38 " =    1.675
peak=   -3.197 closest distance to " OD1 ASP A 191 " =    1.558
peak=   -3.193 closest distance to " O   ILE A 106 " =    1.693
peak=   -3.189 closest distance to " NH2 ARG A  66 " =    5.448
peak=   -3.188 closest distance to " O   HOH Z 351 " =    1.366
peak=   -3.183 closest distance to " N   GLY A 133 " =    1.978
peak=   -3.182 closest distance to " O   HOH Z 385 " =    1.930
peak=   -3.179 closest distance to " O   HOH Z 412 " =    4.563
peak=   -3.175 closest distance to " O   HOH Z 191 " =    5.913
peak=   -3.170 closest distance to " C   SER A 206 " =    1.578
peak=   -3.169 closest distance to " CD2 TYR A 247 " =    2.373
peak=   -3.169 closest distance to " OG  SER A  97 " =    2.341
peak=   -3.165 closest distance to " CD1 LEU A  83 " =    2.345
peak=   -3.165 closest distance to " O   HOH Z  90 " =    2.017
peak=   -3.161 closest distance to " O   HOH Z  44 " =    2.212
peak=   -3.161 closest distance to " NE2 GLN A  88 " =    1.083
peak=   -3.158 closest distance to " O   SER A  95 " =    1.588
peak=   -3.158 closest distance to " O   HOH Z  41 " =    2.179
peak=   -3.153 closest distance to " CG  ARG A 219 " =    2.552
peak=   -3.150 closest distance to " C   ASN A 285 " =    2.260
peak=   -3.147 closest distance to " O   HOH Z 213 " =    1.546
peak=   -3.136 closest distance to " O   PRO A 198 " =    1.314
peak=   -3.134 closest distance to " O   MET A  40 " =    2.713
peak=   -3.132 closest distance to " C   GLN A 205 " =    1.819
peak=   -3.130 closest distance to " OD2 ASP A 171 " =    1.751
peak=   -3.125 closest distance to " O   HOH Z 298 " =    1.333
peak=   -3.114 closest distance to " O  BHOH Z 338 " =    1.448
peak=   -3.114 closest distance to " CG  PRO A 163 " =    2.612
peak=   -3.114 closest distance to " CD1 TRP A 179 " =    1.177
peak=   -3.111 closest distance to " O   HOH Z 251 " =    1.443
peak=   -3.106 closest distance to " O   SER A   3 " =    1.150
peak=   -3.104 closest distance to " O   HOH Z 174 " =    4.064
peak=   -3.089 closest distance to " O   HOH Z 111 " =    3.643
peak=   -3.087 closest distance to " O   SER A 135 " =    1.534
peak=   -3.080 closest distance to " CA  SER A  62 " =    2.575
peak=   -3.079 closest distance to " O   HOH Z 297 " =    2.809
peak=   -3.076 closest distance to " O   ASP A 171 " =    2.025
peak=   -3.070 closest distance to " CZ  PHE A  38 " =    1.968
peak=   -3.065 closest distance to " O   HOH Z 134 " =    2.687
peak=   -3.063 closest distance to " O   HOH Z 263 " =    2.931
peak=   -3.056 closest distance to " CE3 TRP A 274 " =    2.442
peak=   -3.041 closest distance to " O   HOH Z  77 " =    2.122
peak=   -3.031 closest distance to " O   ASN A 301 " =    1.357
peak=   -3.021 closest distance to " O   PRO A 198 " =    1.699

================= 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    :  0.3594 0.3518   6.130608e+00   6.102515e+00
   1_bss:  0.3470 0.3364   6.110651e+00   6.076032e+00
   1_xyz:  0.2094 0.2301   5.653047e+00   5.743009e+00
   1_adp:  0.1911 0.2364   5.603628e+00   5.773736e+00
   1_occ:  0.1908 0.2367   5.602845e+00   5.773586e+00
   2_bss:  0.1884 0.2345   5.595402e+00   5.765368e+00
   2_xyz:  0.1357 0.1773   5.296831e+00   5.506251e+00
   2_adp:  0.1269 0.1657   5.231662e+00   5.441457e+00
   2_occ:  0.1267 0.1656   5.231017e+00   5.441078e+00
   3_bss:  0.1267 0.1649   5.230118e+00   5.438258e+00
   3_xyz:  0.1172 0.1577   5.171441e+00   5.392202e+00
   3_adp:  0.1155 0.1566   5.159348e+00   5.384057e+00
   3_occ:  0.1155 0.1566   5.159159e+00   5.384139e+00
   4_bss:  0.1154 0.1566   5.158940e+00   5.384069e+00
   4_xyz:  0.1108 0.1549   5.132111e+00   5.369714e+00
   4_adp:  0.1097 0.1559   5.131092e+00   5.375857e+00
   4_occ:  0.1097 0.1560   5.131122e+00   5.376119e+00
   5_bss:  0.1096 0.1560   5.131208e+00   5.376229e+00
   5_xyz:  0.1078 0.1557   5.122564e+00   5.373798e+00
   5_adp:  0.1075 0.1564   5.122247e+00   5.376598e+00
   5_occ:  0.1074 0.1564   5.122424e+00   5.376942e+00
   5_bss:  0.1073 0.1564   5.122619e+00   5.377126e+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:  0.301  33.298  -2.394   3.261  -1.469   0.000  -0.000  -0.000
   1_xyz:  0.301  33.298  -2.394   3.261  -1.469   0.000  -0.000  -0.000
   1_adp:  0.301  33.298  -2.394   3.261  -1.469   0.000  -0.000  -0.000
   1_occ:  0.301  33.298  -2.394   3.261  -1.469   0.000  -0.000  -0.000
   2_bss:  0.321  52.155  -2.916  -0.062  -1.500  -0.000  -0.000  -0.000
   2_xyz:  0.321  52.155  -2.916  -0.062  -1.500  -0.000  -0.000  -0.000
   2_adp:  0.321  52.155  -2.916  -0.062  -1.500  -0.000  -0.000  -0.000
   2_occ:  0.321  52.155  -2.916  -0.062  -1.500  -0.000  -0.000  -0.000
   3_bss:  0.327  52.155  -2.741  -1.088  -1.252  -0.000  -0.000  -0.000
   3_xyz:  0.327  52.155  -2.741  -1.088  -1.252  -0.000  -0.000  -0.000
   3_adp:  0.327  52.155  -2.741  -1.088  -1.252  -0.000  -0.000  -0.000
   3_occ:  0.327  52.155  -2.741  -1.088  -1.252  -0.000  -0.000  -0.000
   4_bss:  0.327  52.155  -2.665  -1.384  -1.157  -0.000  -0.000  -0.000
   4_xyz:  0.327  52.155  -2.665  -1.384  -1.157  -0.000  -0.000  -0.000
   4_adp:  0.327  52.155  -2.665  -1.384  -1.157  -0.000  -0.000  -0.000
   4_occ:  0.327  52.155  -2.665  -1.384  -1.157  -0.000  -0.000  -0.000
   5_bss:  0.326  52.155  -2.408  -1.257  -0.910  -0.000  -0.000  -0.000
   5_xyz:  0.326  52.155  -2.408  -1.257  -0.910  -0.000  -0.000  -0.000
   5_adp:  0.326  52.155  -2.408  -1.257  -0.910  -0.000  -0.000  -0.000
   5_occ:  0.326  52.155  -2.408  -1.257  -0.910  -0.000  -0.000  -0.000
   5_bss:  0.325  51.498  -2.109  -1.018  -0.636  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.727 0.6723  0.8502    36187.917
   1_bss:  36.570 0.6841  0.8569    32663.618
   1_xyz:  22.855 0.8344  0.9899    13816.425
   1_adp:  23.922 0.8225  0.9746    14712.345
   1_occ:  23.935 0.8223  0.9742    14714.707
   2_bss:  23.528 0.8265  0.9388    14351.909
   2_xyz:  16.851 0.8900  0.9801     7980.767
   2_adp:  15.293 0.9040  0.9807     7052.607
   2_occ:  15.289 0.9041  0.9805     7045.023
   3_bss:  15.230 0.9045  0.9747     7004.618
   3_xyz:  14.135 0.9139  0.9785     6389.344
   3_adp:  13.940 0.9157  0.9734     6325.602
   3_occ:  13.942 0.9157  0.9734     6324.603
   4_bss:  13.935 0.9158  0.9724     6324.179
   4_xyz:  13.644 0.9180  0.9737     6123.101
   4_adp:  13.748 0.9172  0.9670     6180.481
   4_occ:  13.753 0.9172  0.9670     6183.532
   5_bss:  13.755 0.9172  0.9744     6185.088
   5_xyz:  13.704 0.9176  0.9745     6158.759
   5_adp:  13.753 0.9172  0.9667     6175.029
   5_occ:  13.761 0.9172  0.9666     6179.470
   5_bss:  13.766 0.9171  0.9759     6182.031
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6493e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6493e-01
   1_xyz:   1.246  0.010  0.077 15.458  0.005  4.112   8.6051e-02
   1_adp:   1.246  0.010  0.077 15.458  0.005  4.112   8.6051e-02
   1_occ:   1.246  0.010  0.077 15.458  0.005  4.112   8.6051e-02
   2_bss:   1.246  0.010  0.077 15.458  0.005  4.112   8.6051e-02
   2_xyz:   1.065  0.008  0.073 15.014  0.004  4.123   6.5272e-02
   2_adp:   1.065  0.008  0.073 15.014  0.004  4.123   6.5272e-02
   2_occ:   1.065  0.008  0.073 15.014  0.004  4.123   6.5272e-02
   3_bss:   1.065  0.008  0.073 15.014  0.004  4.123   6.5272e-02
   3_xyz:   0.944  0.006  0.071 14.886  0.004  4.126   5.4571e-02
   3_adp:   0.944  0.006  0.071 14.886  0.004  4.126   5.4571e-02
   3_occ:   0.944  0.006  0.071 14.886  0.004  4.126   5.4571e-02
   4_bss:   0.944  0.006  0.071 14.886  0.004  4.126   5.4571e-02
   4_xyz:   1.016  0.007  0.076 14.940  0.004  4.128   6.1081e-02
   4_adp:   1.016  0.007  0.076 14.940  0.004  4.128   6.1081e-02
   4_occ:   1.016  0.007  0.076 14.940  0.004  4.128   6.1081e-02
   5_bss:   1.016  0.007  0.076 14.940  0.004  4.128   6.1081e-02
   5_xyz:   1.064  0.009  0.080 14.983  0.005  4.111   6.7601e-02
   5_adp:   1.064  0.009  0.080 14.983  0.005  4.111   6.7601e-02
   5_occ:   1.064  0.009  0.080 14.983  0.005  4.111   6.7601e-02
   5_bss:   1.064  0.009  0.080 14.983  0.005  4.111   6.7601e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4085e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4085e-01
   1_xyz:   7.599  0.099  0.307 86.801  0.039  2.256   1.0459e-01
   1_adp:   7.599  0.099  0.307 86.801  0.039  2.256   1.0459e-01
   1_occ:   7.599  0.099  0.307 86.801  0.039  2.256   1.0459e-01
   2_bss:   7.599  0.099  0.307 86.801  0.039  2.256   1.0459e-01
   2_xyz:   7.489  0.063  0.228 82.424  0.042  2.290   4.8995e-02
   2_adp:   7.489  0.063  0.228 82.424  0.042  2.290   4.8995e-02
   2_occ:   7.489  0.063  0.228 82.424  0.042  2.290   4.8995e-02
   3_bss:   7.489  0.063  0.228 82.424  0.042  2.290   4.8995e-02
   3_xyz:   7.241  0.044  0.236 83.042  0.038  2.375   3.4305e-02
   3_adp:   7.241  0.044  0.236 83.042  0.038  2.375   3.4305e-02
   3_occ:   7.241  0.044  0.236 83.042  0.038  2.375   3.4305e-02
   4_bss:   7.241  0.044  0.236 83.042  0.038  2.375   3.4305e-02
   4_xyz:   7.778  0.050  0.247 82.252  0.035  2.312   3.9864e-02
   4_adp:   7.778  0.050  0.247 82.252  0.035  2.312   3.9864e-02
   4_occ:   7.778  0.050  0.247 82.252  0.035  2.312   3.9864e-02
   5_bss:   7.778  0.050  0.247 82.252  0.035  2.312   3.9864e-02
   5_xyz:   7.766  0.050  0.267 82.767  0.038  2.319   4.9336e-02
   5_adp:   7.766  0.050  0.267 82.767  0.038  2.319   4.9336e-02
   5_occ:   7.766  0.050  0.267 82.767  0.038  2.319   4.9336e-02
   5_bss:   7.766  0.050  0.267 82.767  0.038  2.319   4.9336e-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:  63.98   0.00  16.86  57.71   0.00  13.02  63.98   7.39  37.78
   1_occ:  63.98   0.00  16.86  57.71   0.00  13.02  63.98   7.39  37.78
   2_bss:  63.98   0.00  16.86  57.71   0.00  13.02  63.98   7.39  37.78
   2_xyz:  63.98   0.00  16.86  57.71   0.00  13.02  63.98   7.39  37.78
   2_adp:  73.29   1.69  16.54  73.29   1.69  12.67  66.20   5.95  37.63
   2_occ:  73.29   1.69  16.54  73.29   1.69  12.67  66.20   5.95  37.63
   3_bss:  73.29   1.69  16.54  73.29   1.69  12.67  66.20   5.95  37.63
   3_xyz:  73.29   1.69  16.54  73.29   1.69  12.67  66.20   5.95  37.63
   3_adp:  75.90   1.85  16.42  75.90   1.85  12.52  68.51   3.47  37.71
   3_occ:  75.90   1.85  16.42  75.90   1.85  12.52  68.51   3.47  37.71
   4_bss:  75.90   1.85  16.42  75.90   1.85  12.52  68.51   3.47  37.71
   4_xyz:  75.90   1.85  16.42  75.90   1.85  12.52  68.51   3.47  37.71
   4_adp:  84.06   0.88  16.49  84.06   0.88  12.44  72.60   3.57  38.59
   4_occ:  84.06   0.88  16.49  84.06   0.88  12.44  72.60   3.57  38.59
   5_bss:  84.06   0.88  16.49  84.06   0.88  12.44  72.60   3.57  38.59
   5_xyz:  84.06   0.88  16.49  84.06   0.88  12.44  72.60   3.57  38.59
   5_adp:  95.33   0.26  16.61  95.33   0.26  12.37  84.68   5.05  39.73
   5_occ:  95.33   0.26  16.61  95.33   0.26  12.37  84.68   5.05  39.73
   5_bss:  95.33   0.25  16.61  95.33   0.25  12.36  84.67   5.04  39.73
------------------------------------------------------------------------
 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:    1.407    0.026    0.366
   1_adp:    1.407    0.026    0.366
   1_occ:    1.407    0.026    0.366
   2_bss:    1.407    0.026    0.366
   2_xyz:    0.968    0.043    0.453
   2_adp:    0.968    0.043    0.453
   2_occ:    0.968    0.043    0.453
   3_bss:    0.968    0.043    0.453
   3_xyz:    1.044    0.048    0.491
   3_adp:    1.044    0.048    0.491
   3_occ:    1.044    0.048    0.491
   4_bss:    1.044    0.048    0.491
   4_xyz:    1.065    0.053    0.508
   4_adp:    1.065    0.053    0.508
   4_occ:    1.065    0.053    0.508
   5_bss:    1.065    0.053    0.508
   5_xyz:    1.105    0.048    0.509
   5_adp:    1.105    0.048    0.509
   5_occ:    1.105    0.048    0.509
   5_bss:    1.105    0.048    0.509
------------------------------------------------------------------------

CPU time actual refinement: 325.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_455/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_455/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_455/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_455/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_455/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.58 
  Macro-tasks:
    bulk solvent and scale       = 37.57  
    individual site refinement   = 130.42 
    weights calculation          = 29.44  
    collect and process          = 6.63   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 204.18 
  Micro-tasks:
    mask                            = 1.26   
    f_calc                          = 104.87 
    alpha_beta                      = 8.16   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 112.07 
    fmodel                         = 6.59   
    r_factors                      = 0.21   
    phase_errors                   = 10.80  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 245.29 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.698 micro seconds
Total CPU time: 5.66 minutes
from_scatterers_fft:    629 calls, 104.51 s
gradients_fft:          574 calls,  99.22 s

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

# Date 2008-01-16 Time 04:51:50 PST -0800 (1200487910.96 s)
Start R-work = 0.3594, R-free = 0.3518 (no bulk solvent and anisotropic scale)
Final R-work = 0.1288, R-free = 0.1737 (no bulk solvent and anisotropic scale)

Start R-work = 0.3470, R-free = 0.3364
Final R-work = 0.1073, R-free = 0.1564