# Date 2008-01-16 Time 05:49:18 PST -0800 (1200491358.33 s)
#phil __OFF__

Command line arguments: "../894.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15690
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 894

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.6953, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.98103
Completeness in resolution range: 0.963409
Completeness with d_max=infinity: 0.960481

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0608
                             d_min =   1.9810

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.98103
Completeness in resolution range: 0.963409
Completeness with d_max=infinity: 0.960481

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0612 -  4.2392 [2133/2159]  1922   211   9.9%
  bin  2:  4.2392 -  3.3773 [2046/2065]  1840   206  10.1%
  bin  3:  3.3773 -  2.9540 [2030/2049]  1825   205  10.1%
  bin  4:  2.9540 -  2.6856 [2010/2040]  1810   200  10.0%
  bin  5:  2.6856 -  2.4940 [1992/2011]  1798   194   9.7%
  bin  6:  2.4940 -  2.3476 [1980/2005]  1775   205  10.4%
  bin  7:  2.3476 -  2.2304 [1967/1995]  1770   197  10.0%
  bin  8:  2.2304 -  2.1336 [1975/2011]  1780   195   9.9%
  bin  9:  2.1336 -  2.0517 [1970/2012]  1771   199  10.1%
  bin 10:  2.0517 -  1.9810 [1486/1986]  1339   147   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_894/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 16
        2.42 -     3.04: 2199
        3.04 -     3.66: 4704
        3.66 -     4.28: 9065
        4.28 -     4.90: 12346
  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 113 " - " O   HOH Z 350 "  2.210 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.248 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.259 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28325 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_894/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_894/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.69535 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2933   r_free= 0.2963   ksol= 0.00   Bsol= 0.00   scale= 0.987    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.945798                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7284 0.99   1386  155 0.2733 0.2671      6.3133      6.2657|
|  2:  4.7284 -  3.7725 0.99   1340  146 0.2283 0.2274       6.314      6.3026|
|  3:  3.7725 -  3.3013 0.99   1306  144 0.2460 0.2336      6.1994      6.3049|
|  4:  3.3013 -  3.0021 0.99   1299  153 0.2584 0.2910      6.1029        6.14|
|  5:  3.0021 -  2.7884 0.99   1298  139 0.2930 0.2937      5.9969      6.0201|
|  6:  2.7884 -  2.6249 0.99   1277  143 0.3049 0.3185      5.9314      5.9301|
|  7:  2.6249 -  2.4940 0.99   1289  136 0.3108 0.3032      5.9245      5.8936|
|  8:  2.4940 -  2.3859 0.98   1266  151 0.3304 0.3187      5.8831      5.8693|
|  9:  2.3859 -  2.2944 0.98   1263  142 0.3107 0.3151      5.8079      5.7571|
| 10:  2.2944 -  2.2155 0.99   1274  137 0.3243 0.3695      5.8029      5.9124|
| 11:  2.2155 -  2.1464 0.98   1277  140 0.3480 0.3342      5.7932      5.8237|
| 12:  2.1464 -  2.0852 0.97   1239  143 0.3375 0.3592      5.7283      5.7953|
| 13:  2.0852 -  2.0305 1.00   1279  135 0.3457 0.3334      5.6423      5.5688|
| 14:  2.0305 -  1.9810 0.65    837   95 0.3547 0.3660       5.623      5.5819|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0612 -  4.7284  1386   155  0.81  24.43   0.87     0.82      37617.77|
|  2:  4.7284 -  3.7725  1340   146  0.86  19.86   0.99     0.93      38044.61|
|  3:  3.7725 -  3.3013  1306   144  0.83  23.32   1.01     0.98      36477.05|
|  4:  3.3013 -  3.0021  1299   153  0.81  25.56   1.02     0.97      32536.73|
|  5:  3.0021 -  2.7884  1298   139  0.76  29.87   1.00     0.94      27514.52|
|  6:  2.7884 -  2.6249  1277   143  0.76  30.44   1.02     0.94      23625.37|
|  7:  2.6249 -  2.4940  1289   136  0.77  29.39   1.02     0.96      20839.87|
|  8:  2.4940 -  2.3859  1266   151  0.75  31.00   1.02     0.97      19384.75|
|  9:  2.3859 -  2.2944  1263   142  0.76  30.51   1.05     0.98      18372.70|
| 10:  2.2944 -  2.2155  1274   137  0.73  32.95   1.07     0.98      18751.29|
| 11:  2.2155 -  2.1464  1277   140  0.71  34.60   1.08     0.97      18246.60|
| 12:  2.1464 -  2.0852  1239   143  0.72  33.99   1.07     0.98      17066.77|
| 13:  2.0852 -  2.0305  1279   135  0.70  35.85   1.06     0.96      14230.66|
| 14:  2.0305 -  1.9810   837    95  0.73  33.04   1.06     0.93      11127.16|
|alpha:            min =        0.82 max =            0.98 mean =         0.95|
|beta:             min =    11127.16 max =        38044.61 mean =     24354.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.77|
|phase err.(work): min =        0.00 max =           89.95 mean =        29.45|
|phase err.(test): min =        0.00 max =           89.81 mean =        29.40|
|-----------------------------------------------------------------------------|

============================== 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 = 4.151956              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.919   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.556164              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.381   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      203 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1996 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1851 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2853 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4665 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4400 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5629 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6717 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.156 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2933   r_free= 0.2963   ksol= 0.00   Bsol= 0.00   scale= 0.987    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.945798                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2789   r_free= 0.2833   ksol= 0.33   Bsol= 45.03   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.54,-2.37,-0.56,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.921411                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.608417              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.161   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.271781              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.209   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2789      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2833      final r-factor (free) = 0.1730          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8772 = 3.61 * 0.50 * 5.9397 + 1.00 * 0.1608                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1980 = 3.61 * 0.50 * 5.6207 + 1.00 * 0.0570                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1528      final r-factor (work) = 0.1438          |
| start r-factor (free) = 0.1730      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5342 = 0.27 * 1.00 * 5.6207 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5164 = 0.27 * 1.00 * 5.3178 + 1.00 * 0.0712                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.94   16.32    None  None   None       |
|    all(noH): 2823   0      0.00    77.94   16.32    None  None   None       |
|    Sol.    : 438    0      6.13    62.48   37.13    None  None   None       |
|    Mac.    : 2385   0      0.00    77.94   12.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.794:  376   |   5:    38.970 -  46.764:  111        |
|      1:     7.794 -  15.588: 1571   |   6:    46.764 -  54.558:   79        |
|      2:    15.588 -  23.382:  387   |   7:    54.558 -  62.352:   39        |
|      3:    23.382 -  31.176:  143   |   8:    62.352 -  70.146:    1        |
|      4:    31.176 -  38.970:  115   |   9:    70.146 -  77.940:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1438 r_free = 0.1749             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1432 r_free = 0.1752             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1432   r_free= 0.1752   ksol= 0.33   Bsol= 45.03   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.54,-2.37,-0.56,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.320743                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1431   r_free= 0.1736   ksol= 0.33   Bsol= 49.13   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.87,-1.67,-0.00,-0.00,-0.00); trace/3= -2.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.321229                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.844114              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.863  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.430758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.962   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1431      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1736      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9741 = 1.84 * 0.50 * 5.3327 + 1.00 * 0.0570                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8821 = 1.84 * 0.50 * 5.2361 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1529          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3170 = 0.43 * 1.00 * 5.2361 + 1.00 * 0.0616                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2228 = 0.43 * 1.00 * 5.1412 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    75.01   17.03    None  None   None       |
|    all(noH): 2823   0      1.52    75.01   17.03    None  None   None       |
|    Sol.    : 438    0      4.35    72.79   39.12    None  None   None       |
|    Mac.    : 2385   0      1.52    75.01   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.518 -   8.867:  681   |   5:    38.263 -  45.612:  108        |
|      1:     8.867 -  16.216: 1277   |   6:    45.612 -  52.961:   83        |
|      2:    16.216 -  23.565:  344   |   7:    52.961 -  60.310:   63        |
|      3:    23.565 -  30.914:  124   |   8:    60.310 -  67.659:   27        |
|      4:    30.914 -  38.263:  102   |   9:    67.659 -  75.008:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1529             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1142 r_free = 0.1528             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1528   ksol= 0.33   Bsol= 49.13   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.87,-1.67,-0.00,-0.00,-0.00); trace/3= -2.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.138854                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1528   ksol= 0.32   Bsol= 48.59   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.63,-1.63,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.138634                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.273700              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.364  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.374887              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.676  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8988 = 2.27 * 0.50 * 5.1411 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8769 = 2.27 * 0.50 * 5.1147 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1082      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9256 = 0.37 * 1.00 * 5.1147 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9229 = 0.37 * 1.00 * 5.1074 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.51    76.40   16.94    None  None   None       |
|    all(noH): 2823   0      1.51    76.40   16.94    None  None   None       |
|    Sol.    : 438    0      3.94    73.11   38.90    None  None   None       |
|    Mac.    : 2385   0      1.51    76.40   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.514 -   9.002:  761   |   5:    38.955 -  46.443:  110        |
|      1:     9.002 -  16.490: 1216   |   6:    46.443 -  53.931:   82        |
|      2:    16.490 -  23.979:  335   |   7:    53.931 -  61.419:   60        |
|      3:    23.979 -  31.467:  124   |   8:    61.419 -  68.907:   25        |
|      4:    31.467 -  38.955:  102   |   9:    68.907 -  76.395:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1076 r_free = 0.1525             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1075 r_free = 0.1525             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1525   ksol= 0.32   Bsol= 48.59   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.63,-1.63,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108459                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1526   ksol= 0.32   Bsol= 48.59   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.50,-1.57,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110323                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.701700              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.594  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.343461              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.094  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9622 = 2.70 * 0.50 * 5.1078 + 1.00 * 0.0623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9580 = 2.70 * 0.50 * 5.1023 + 1.00 * 0.0655                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1058      final r-factor (work) = 0.1054          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.2721 = 5.34 * 1.00 * 5.1023 + 1.00 * 0.0082                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.2712 = 5.34 * 1.00 * 5.1018 + 1.00 * 0.0096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    86.83   17.07    None  None   None       |
|    all(noH): 2823   0      0.36    86.83   17.07    None  None   None       |
|    Sol.    : 438    0      5.37    77.88   39.83    None  None   None       |
|    Mac.    : 2385   0      0.36    86.83   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.359 -   9.007:  817   |   5:    43.595 -  52.243:   99        |
|      1:     9.007 -  17.654: 1242   |   6:    52.243 -  60.890:   78        |
|      2:    17.654 -  26.301:  286   |   7:    60.890 -  69.537:   31        |
|      3:    26.301 -  34.948:  133   |   8:    69.537 -  78.184:   14        |
|      4:    34.948 -  43.595:  117   |   9:    78.184 -  86.832:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1054 r_free = 0.1559             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1053 r_free = 0.1559             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1559   ksol= 0.32   Bsol= 48.59   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.50,-1.57,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109610                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1559   ksol= 0.32   Bsol= 48.59   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.27,-1.36,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.109746                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.582329              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.635  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.157626              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.728  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1052      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1027 = 1.58 * 0.50 * 5.1028 + 1.00 * 0.0655                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1040 = 1.58 * 0.50 * 5.1204 + 1.00 * 0.0529                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1078      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8167 = 0.16 * 1.00 * 5.1204 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8163 = 0.16 * 1.00 * 5.1332 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.61    82.81   16.33    None  None   None       |
|    all(noH): 2823   0      1.61    82.81   16.33    None  None   None       |
|    Sol.    : 438    0      6.43    74.08   36.74    None  None   None       |
|    Mac.    : 2385   0      1.61    82.81   12.58    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:     1.606 -   9.726: 1000   |   5:    42.206 -  50.326:  101        |
|      1:     9.726 -  17.846: 1102   |   6:    50.326 -  58.446:   58        |
|      2:    17.846 -  25.966:  261   |   7:    58.446 -  66.567:   18        |
|      3:    25.966 -  34.086:  137   |   8:    66.567 -  74.687:    9        |
|      4:    34.086 -  42.206:  132   |   9:    74.687 -  82.807:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1093 r_free = 0.1552             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1553             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1553   ksol= 0.32   Bsol= 48.59   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.27,-1.36,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127001                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7284 0.99   1386  155 0.0987 0.1289      5.3789      5.5246|
|  2:  4.7284 -  3.7725 0.99   1340  146 0.0863 0.1085      5.4419      5.6194|
|  3:  3.7725 -  3.3013 0.99   1306  144 0.1034 0.1513      5.4585      5.8733|
|  4:  3.3013 -  3.0021 0.99   1299  153 0.1176 0.1468      5.4425        5.55|
|  5:  3.0021 -  2.7884 0.99   1298  139 0.1295 0.1815      5.3159      5.5767|
|  6:  2.7884 -  2.6249 0.99   1277  143 0.1171 0.1743        5.19      5.4229|
|  7:  2.6249 -  2.4940 0.99   1289  136 0.1224 0.1565      5.1504      5.3407|
|  8:  2.4940 -  2.3859 0.98   1266  151 0.1123 0.1700      5.0223      5.3173|
|  9:  2.3859 -  2.2944 0.98   1263  142 0.1128 0.1812      5.0101      5.3279|
| 10:  2.2944 -  2.2155 0.99   1274  137 0.1098 0.1688      4.9377      5.1793|
| 11:  2.2155 -  2.1464 0.98   1277  140 0.1124 0.1779      4.9381      5.2894|
| 12:  2.1464 -  2.0852 0.97   1239  143 0.1086 0.1552      4.8713      5.0787|
| 13:  2.0852 -  2.0305 1.00   1279  135 0.1121 0.1784      4.7717      5.1135|
| 14:  2.0305 -  1.9810 0.65    837   95 0.1012 0.1577      4.6064      4.8383|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0612 -  4.7284  1386   155  0.94   9.06   0.98     0.95       6987.07|
|  2:  4.7284 -  3.7725  1340   146  0.95   7.84   1.01     1.00       8976.77|
|  3:  3.7725 -  3.3013  1306   144  0.94  11.11   1.02     1.01      10190.61|
|  4:  3.3013 -  3.0021  1299   153  0.92  13.55   1.00     0.98      10224.33|
|  5:  3.0021 -  2.7884  1298   139  0.90  15.76   0.99     0.96       8153.40|
|  6:  2.7884 -  2.6249  1277   143  0.91  15.44   0.98     0.96       6880.49|
|  7:  2.6249 -  2.4940  1289   136  0.91  15.01   0.99     0.96       5940.78|
|  8:  2.4940 -  2.3859  1266   151  0.91  14.41   0.99     0.97       4831.18|
|  9:  2.3859 -  2.2944  1263   142  0.91  14.61   1.00     0.98       4712.21|
| 10:  2.2944 -  2.2155  1274   137  0.91  14.97   0.99     0.96       4148.70|
| 11:  2.2155 -  2.1464  1277   140  0.90  16.31   1.00     0.96       4367.04|
| 12:  2.1464 -  2.0852  1239   143  0.92  14.62   1.00     0.99       3927.86|
| 13:  2.0852 -  2.0305  1279   135  0.90  15.70   1.00     1.00       3186.68|
| 14:  2.0305 -  1.9810   837    95  0.93  13.19   0.98     0.95       2168.34|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2168.34 max =        10224.33 mean =      6183.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.64|
|phase err.(test): min =        0.00 max =           89.83 mean =        13.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1553   ksol= 0.32   Bsol= 48.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.16,-1.23,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127035                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1553   ksol= 0.32   Bsol= 48.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.16,-1.23,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127035                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7284 0.99   1386  155 0.0987 0.1289      5.3791      5.5248|
|  2:  4.7284 -  3.7725 0.99   1340  146 0.0863 0.1084      5.4419      5.6193|
|  3:  3.7725 -  3.3013 0.99   1306  144 0.1034 0.1513      5.4584       5.873|
|  4:  3.3013 -  3.0021 0.99   1299  153 0.1176 0.1468      5.4425        5.55|
|  5:  3.0021 -  2.7884 0.99   1298  139 0.1295 0.1815      5.3159      5.5769|
|  6:  2.7884 -  2.6249 0.99   1277  143 0.1171 0.1741        5.19      5.4225|
|  7:  2.6249 -  2.4940 0.99   1289  136 0.1223 0.1564      5.1503      5.3404|
|  8:  2.4940 -  2.3859 0.98   1266  151 0.1123 0.1700      5.0222      5.3174|
|  9:  2.3859 -  2.2944 0.98   1263  142 0.1128 0.1812      5.0101      5.3277|
| 10:  2.2944 -  2.2155 0.99   1274  137 0.1098 0.1688      4.9378      5.1795|
| 11:  2.2155 -  2.1464 0.98   1277  140 0.1124 0.1781      4.9382      5.2897|
| 12:  2.1464 -  2.0852 0.97   1239  143 0.1086 0.1553      4.8715      5.0789|
| 13:  2.0852 -  2.0305 1.00   1279  135 0.1121 0.1785      4.7718      5.1138|
| 14:  2.0305 -  1.9810 0.65    837   95 0.1012 0.1577      4.6064      4.8381|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0612 -  4.7284  1386   155  0.94   9.07   0.98     0.95       6989.58|
|  2:  4.7284 -  3.7725  1340   146  0.95   7.84   1.01     1.00       8976.61|
|  3:  3.7725 -  3.3013  1306   144  0.94  11.10   1.02     1.01      10186.36|
|  4:  3.3013 -  3.0021  1299   153  0.92  13.55   1.00     0.98      10224.59|
|  5:  3.0021 -  2.7884  1298   139  0.90  15.76   0.99     0.96       8152.18|
|  6:  2.7884 -  2.6249  1277   143  0.91  15.44   0.98     0.96       6880.24|
|  7:  2.6249 -  2.4940  1289   136  0.91  15.01   0.99     0.96       5938.72|
|  8:  2.4940 -  2.3859  1266   151  0.91  14.42   0.99     0.97       4830.29|
|  9:  2.3859 -  2.2944  1263   142  0.91  14.61   1.01     0.98       4711.05|
| 10:  2.2944 -  2.2155  1274   137  0.91  14.97   1.00     0.96       4149.61|
| 11:  2.2155 -  2.1464  1277   140  0.90  16.32   1.00     0.96       4368.30|
| 12:  2.1464 -  2.0852  1239   143  0.92  14.62   1.00     0.99       3930.44|
| 13:  2.0852 -  2.0305  1279   135  0.90  15.70   1.00     1.00       3187.15|
| 14:  2.0305 -  1.9810   837    95  0.93  13.19   0.98     0.95       2168.22|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2168.22 max =        10224.59 mean =      6183.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.64|
|phase err.(test): min =        0.00 max =           89.83 mean =        13.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.55    82.75   16.27    None  None   None       |
|    all(noH): 2823   0      1.55    82.75   16.27    None  None   None       |
|    Sol.    : 438    0      6.37    74.03   36.68    None  None   None       |
|    Mac.    : 2385   0      1.55    82.75   12.53    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:     1.549 -   9.669: 1000   |   5:    42.149 -  50.269:  101        |
|      1:     9.669 -  17.789: 1102   |   6:    50.269 -  58.389:   58        |
|      2:    17.789 -  25.909:  261   |   7:    58.389 -  66.509:   18        |
|      3:    25.909 -  34.029:  137   |   8:    66.509 -  74.629:    9        |
|      4:    34.029 -  42.149:  132   |   9:    74.629 -  82.749:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 293         
Filter by distance & map next to the model:
   mapped sites are within: 0.593 - 4.571
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 293
   mapped sites are within: 0.709 - 4.571

peak=    5.652 closest distance to " CG  PRO A  54 " =    1.316
peak=    5.467 closest distance to " O   HOH Z 126 " =    1.881
peak=    5.449 closest distance to " NH2 ARG A  56 " =    2.172
peak=    5.210 closest distance to " CB  GLN A 223 " =    1.454
peak=    5.118 closest distance to " CB  SER A  63 " =    1.240
peak=    5.034 closest distance to " O   HOH Z 232 " =    2.297
peak=    5.000 closest distance to " NE2 GLN A  11 " =    1.156
peak=    4.989 closest distance to " CB  PRO A  54 " =    0.959
peak=    4.985 closest distance to " CB  ARG A 275 " =    0.904
peak=    4.725 closest distance to " CG  PRO A  90 " =    1.118
peak=    4.689 closest distance to " CB  GLN A 183 " =    1.161
peak=    4.643 closest distance to " ND2 ASN A 187 " =    1.513
peak=    4.634 closest distance to " CB  GLU A 152 " =    1.176
peak=    4.631 closest distance to " C   PRO A 198 " =    1.500
peak=    4.622 closest distance to " O   HOH Z 142 " =    1.740
peak=    4.571 closest distance to " O   HOH Z 236 " =    2.008
peak=    4.538 closest distance to " CB  ASN A 148 " =    1.418
peak=    4.529 closest distance to " CB  LEU A 228 " =    1.069
peak=    4.525 closest distance to " O   HOH Z  15 " =    2.249
peak=    4.441 closest distance to " CG  PRO A 198 " =    1.307
peak=    4.428 closest distance to " O   HOH Z  78 " =    1.666
peak=    4.406 closest distance to " CB  GLU A 128 " =    1.031
peak=    4.377 closest distance to " OD1 ASN A  69 " =    2.560
peak=    4.334 closest distance to " O   HOH Z 193 " =    1.914
peak=    4.321 closest distance to " O   HOH Z 369 " =    2.036
peak=    4.319 closest distance to " O   HOH Z 298 " =    1.864
peak=    4.317 closest distance to " O   HOH Z 234 " =    3.740
peak=    4.306 closest distance to " CA  TYR A  30 " =    0.931
peak=    4.296 closest distance to " CG  PRO A 243 " =    1.111
peak=    4.175 closest distance to " O   HOH Z 303 " =    2.066
peak=    4.133 closest distance to " CB  TYR A 169 " =    0.709
peak=    4.121 closest distance to " CB  SER A   3 " =    1.382
peak=    4.096 closest distance to " O   HOH Z 272 " =    1.874
peak=    4.089 closest distance to " CA  THR A 264 " =    0.877
peak=    4.079 closest distance to " CB  VAL A 265 " =    1.276
peak=    4.077 closest distance to " CG2 VAL A 257 " =    0.987
peak=    4.068 closest distance to " CB  ARG A  79 " =    1.369
peak=    4.057 closest distance to " O   HOH Z 144 " =    2.236
peak=    4.054 closest distance to " O   HOH Z  68 " =    2.121
peak=    4.046 closest distance to " O   HOH Z 427 " =    2.946
peak=    4.026 closest distance to " O   HOH Z 126 " =    2.101
peak=    4.012 closest distance to " OD2 ASP A 286 " =    2.851
peak=    3.998 closest distance to " O   HOH Z 250 " =    1.457
peak=    3.979 closest distance to " CA  ASN A 215 " =    1.157
peak=    3.972 closest distance to " CB  SER A 216 " =    0.783
peak=    3.971 closest distance to " O   HOH Z 346 " =    1.598
peak=    3.960 closest distance to " CD1 LEU A 300 " =    1.211
peak=    3.950 closest distance to " O   HOH Z 158 " =    3.070
peak=    3.944 closest distance to " O   HOH Z 203 " =    1.899
peak=    3.936 closest distance to " CB  TRP A 266 " =    0.947
peak=    3.932 closest distance to " O   HOH Z 368 " =    1.865
peak=    3.927 closest distance to " CZ  PHE A 218 " =    1.021
peak=    3.902 closest distance to " CA  ALA A  21 " =    1.183
peak=    3.888 closest distance to " NH1AARG A 145 " =    1.172
peak=    3.883 closest distance to " O   HOH Z 344 " =    3.107
peak=    3.876 closest distance to " O   HOH Z 316 " =    3.118
peak=    3.863 closest distance to " O   HOH Z 132 " =    2.512
peak=    3.858 closest distance to " O   HOH Z  61 " =    1.612
peak=    3.853 closest distance to " NZ  LYS A 117 " =    3.266
peak=    3.852 closest distance to " O   HOH Z 133 " =    1.643
peak=    3.852 closest distance to " O   HOH Z 193 " =    1.717
peak=    3.836 closest distance to " CB  LEU A 143 " =    1.122
peak=    3.831 closest distance to " CB  TRP A 179 " =    1.314
peak=    3.824 closest distance to " CE  LYS A  76 " =    0.896
peak=    3.814 closest distance to " O   HOH Z  10 " =    1.865
peak=    3.811 closest distance to " O   HOH Z 189 " =    2.261
peak=    3.801 closest distance to " O   HOH Z 389 " =    1.963
peak=    3.800 closest distance to " O   HOH Z 214 " =    2.032
peak=    3.783 closest distance to " CD  ARG A 159 " =    0.754
peak=    3.769 closest distance to " O   HOH Z  61 " =    1.548
peak=    3.767 closest distance to " CB  ARG A 190 " =    1.626
peak=    3.760 closest distance to " CG1 ILE A  33 " =    1.269
peak=    3.758 closest distance to " O   HOH Z 368 " =    3.618
peak=    3.748 closest distance to " O   HOH Z  43 " =    1.878
peak=    3.744 closest distance to " O   HOH Z  21 " =    1.752
peak=    3.742 closest distance to " CD  ARG A  66 " =    2.372
peak=    3.730 closest distance to " O   HOH Z   1 " =    1.854
peak=    3.722 closest distance to " O   HOH Z 207 " =    1.827
peak=    3.717 closest distance to " CB  SER A 212 " =    1.179
peak=    3.703 closest distance to " CG  LEU A 167 " =    1.219
peak=    3.694 closest distance to " OD1BASN A 224 " =    2.328
peak=    3.690 closest distance to " N   ARG A 156 " =    1.316
peak=    3.688 closest distance to " CB  ASN A  39 " =    0.917
peak=    3.687 closest distance to " O   HOH Z 197 " =    3.135
peak=    3.684 closest distance to " O   HOH Z 128 " =    2.205
peak=    3.681 closest distance to " O   SER A  87 " =    2.291
peak=    3.677 closest distance to " ND1 HIS A  86 " =    1.670
peak=    3.676 closest distance to " O   HOH Z 425 " =    2.013
peak=    3.670 closest distance to " O   HOH Z  59 " =    1.894
peak=    3.669 closest distance to " O   HOH Z 426 " =    1.601
peak=    3.667 closest distance to " O   HOH Z 273 " =    2.631
peak=    3.665 closest distance to " O   HOH Z  64 " =    2.181
peak=    3.663 closest distance to " O   HOH Z 403 " =    1.692
peak=    3.647 closest distance to " NH2BARG A 145 " =    2.155
peak=    3.640 closest distance to " CD BLYS A 290 " =    1.203
peak=    3.640 closest distance to " CG2 THR A 221 " =    1.096
peak=    3.640 closest distance to " O   HOH Z 419 " =    1.978
peak=    3.639 closest distance to " CG1BVAL A  72 " =    1.547
peak=    3.639 closest distance to " O   HOH Z 291 " =    1.560
peak=    3.636 closest distance to " O   HOH Z 219 " =    2.133
peak=    3.625 closest distance to " NH2 ARG A 156 " =    1.219
peak=    3.622 closest distance to " O   HOH Z 305 " =    3.633
peak=    3.615 closest distance to " O   HOH Z 128 " =    2.143
peak=    3.608 closest distance to " CB  VAL A 202 " =    1.612
peak=    3.607 closest distance to " O   HOH Z 135 " =    1.676
peak=    3.604 closest distance to " O   HOH Z 209 " =    2.255
peak=    3.597 closest distance to " CB  MET A  40 " =    0.814
peak=    3.588 closest distance to " O   MET A 105 " =    1.753
peak=    3.573 closest distance to " O   HOH Z  40 " =    1.689
peak=    3.570 closest distance to " CD  ARG A 269 " =    0.938
peak=    3.569 closest distance to " O   HOH Z 147 " =    1.744
peak=    3.568 closest distance to " O   HOH Z 213 " =    1.809
peak=    3.566 closest distance to " CB  GLU A 277 " =    3.583
peak=    3.561 closest distance to " CB  ASN A 142 " =    0.978
peak=    3.561 closest distance to " O   HOH Z 234 " =    1.712
peak=    3.558 closest distance to " CD2 LEU A 255 " =    1.480
peak=    3.547 closest distance to " CA  ALA A 233 " =    1.310
peak=    3.545 closest distance to " CA  ALA A  51 " =    0.891
peak=    3.543 closest distance to " O   HOH Z  88 " =    3.214
peak=    3.540 closest distance to " CD1 ILE A 106 " =    0.873
peak=    3.538 closest distance to " CA  THR A 221 " =    0.966
peak=    3.535 closest distance to " CG2 ILE A 120 " =    1.144
peak=    3.532 closest distance to " O   HOH Z 402 " =    1.452
peak=    3.523 closest distance to " O   HOH Z 295 " =    1.534
peak=    3.522 closest distance to " O   HOH Z 245 " =    1.353
peak=    3.514 closest distance to " CB  ASP A 140 " =    0.863
peak=    3.511 closest distance to " O   HOH Z  93 " =    2.533
peak=    3.503 closest distance to " O   HOH Z 406 " =    1.644
peak=    3.495 closest distance to " CB  ALA A  34 " =    1.025
peak=    3.490 closest distance to " CD  LYS A 166 " =    1.255
peak=    3.482 closest distance to " CG  GLN A  11 " =    1.857
peak=    3.470 closest distance to " CD  ARG A  66 " =    2.311
peak=    3.468 closest distance to " O   HOH Z 180 " =    2.140
peak=    3.467 closest distance to " O   HOH Z  44 " =    1.691
peak=    3.466 closest distance to " CD2 TRP A 179 " =    1.324
peak=    3.462 closest distance to " NH2AARG A 275 " =    3.689
peak=    3.461 closest distance to " CA  SER A  87 " =    1.029
peak=    3.460 closest distance to " O   HOH Z 193 " =    1.923
peak=    3.457 closest distance to " CG  MET A 113 " =    1.223
peak=    3.455 closest distance to " CD  LYS A 119 " =    1.356
peak=    3.436 closest distance to " O   HOH Z 407 " =    2.397
peak=    3.434 closest distance to " CB  ILE A 120 " =    1.157
peak=    3.434 closest distance to " CB  SER A  62 " =    1.199
peak=    3.432 closest distance to " O   HOH Z 280 " =    3.053
peak=    3.428 closest distance to " CB  ARG A 139 " =    0.921
peak=    3.428 closest distance to " O   HOH Z  40 " =    1.847
peak=    3.426 closest distance to " CA  MET A  40 " =    1.122
peak=    3.408 closest distance to " CB  MET A  47 " =    0.997
peak=    3.406 closest distance to " CB  ALA A 291 " =    1.335
peak=    3.406 closest distance to " CA  ALA A 158 " =    1.159
peak=    3.402 closest distance to " N   ASN A  39 " =    1.275
peak=    3.400 closest distance to " O   HOH Z 345 " =    3.418
peak=    3.399 closest distance to " CD2 LEU A 297 " =    0.867
peak=    3.398 closest distance to " O   HOH Z 172 " =    3.269
peak=    3.398 closest distance to " O   HOH Z 327 " =    1.714
peak=    3.395 closest distance to " OG  SER A 206 " =    1.341
peak=    3.394 closest distance to " CA  ALA A 154 " =    0.934
peak=    3.391 closest distance to " O   HOH Z 411 " =    3.905
peak=    3.390 closest distance to " CB  ALA A   1 " =    4.571
peak=    3.384 closest distance to " OG  SER A  22 " =    2.694
peak=    3.381 closest distance to " O   HOH Z 248 " =    1.755
peak=    3.381 closest distance to " CA  ASP A 140 " =    1.187
peak=    3.376 closest distance to " CB  SER A 141 " =    0.986
peak=    3.374 closest distance to " O   HOH Z  97 " =    1.944
peak=    3.374 closest distance to " CD  ARG A 219 " =    1.047
peak=    3.373 closest distance to " CG1 VAL A 153 " =    0.907
peak=    3.372 closest distance to " O   HOH Z 258 " =    1.792
peak=    3.367 closest distance to " CZ  PHE A 192 " =    0.886
peak=    3.366 closest distance to " CB  ALA A 248 " =    1.319
peak=    3.366 closest distance to " OD1 ASN A 217 " =    1.697
peak=    3.365 closest distance to " O   HOH Z  54 " =    1.633
peak=    3.360 closest distance to " O   HOH Z 371 " =    3.021
peak=    3.359 closest distance to " CA  ALA A  84 " =    1.376
peak=    3.359 closest distance to " CB  ALA A 242 " =    0.864
peak=    3.358 closest distance to " O   HOH Z 263 " =    1.669
peak=    3.353 closest distance to " CA  ALA A 291 " =    0.935
peak=    3.353 closest distance to " O   HOH Z 411 " =    1.782
peak=    3.350 closest distance to " CB  THR A 157 " =    1.120
peak=    3.347 closest distance to " CB  TYR A 116 " =    0.842
peak=    3.346 closest distance to " CG  LYS A  76 " =    0.957
peak=    3.336 closest distance to " CB  GLU A  46 " =    0.987
peak=    3.334 closest distance to " N   ASN A 127 " =    1.251
peak=    3.327 closest distance to " O   HOH Z 144 " =    1.810
peak=    3.326 closest distance to " O   HOH Z  54 " =    2.503
peak=    3.324 closest distance to " CB  PHE A  16 " =    1.043
peak=    3.323 closest distance to " O   HOH Z   1 " =    1.714
peak=    3.322 closest distance to " O   HOH Z 437 " =    1.514
peak=    3.321 closest distance to " N   VAL A 126 " =    1.358
peak=    3.317 closest distance to " O   HOH Z  44 " =    3.215
peak=    3.316 closest distance to " O   HOH Z  19 " =    2.553
peak=    3.309 closest distance to " CD  PRO A 243 " =    1.557
peak=    3.304 closest distance to " CB  HIS A 108 " =    0.777
peak=    3.302 closest distance to " CB  GLN A  88 " =    1.245
peak=    3.302 closest distance to " O   HOH Z 425 " =    1.246
peak=    3.302 closest distance to " O   HOH Z 108 " =    2.319
peak=    3.299 closest distance to " OE1 GLU A   2 " =    2.188
peak=    3.293 closest distance to " ND1 HIS A  81 " =    1.600
peak=    3.289 closest distance to " O   HOH Z 329 " =    3.699
peak=    3.286 closest distance to " CB  ASN A 224 " =    1.080
peak=    3.283 closest distance to " O   HOH Z  66 " =    2.100
peak=    3.282 closest distance to " CB  ALA A   9 " =    1.555
peak=    3.282 closest distance to " CB  LEU A 255 " =    0.785
peak=    3.280 closest distance to " O   HOH Z 175 " =    2.131
peak=    3.278 closest distance to " O   HOH Z 409 " =    2.774
peak=    3.272 closest distance to " O   HOH Z 261 " =    2.122
peak=    3.272 closest distance to " N   PHE A 130 " =    1.241
peak=    3.267 closest distance to " O   HOH Z 163 " =    1.853
peak=    3.266 closest distance to " OG BSER A 164 " =    2.353
peak=    3.257 closest distance to " CB  ILE A 234 " =    0.995
peak=    3.257 closest distance to " CA  ARG A 195 " =    1.174
peak=    3.251 closest distance to " N   GLN A 278 " =    1.024
peak=    3.245 closest distance to " CG  ARG A 159 " =    0.908
peak=    3.242 closest distance to " CZ  PHE A 208 " =    1.144
peak=    3.242 closest distance to " NH1BARG A 145 " =    1.165
peak=    3.239 closest distance to " CB  ALA A 248 " =    0.903
peak=    3.237 closest distance to " O   HOH Z 423 " =    1.779
peak=    3.237 closest distance to " O   HOH Z 294 " =    1.506
peak=    3.236 closest distance to " O   HOH Z 128 " =    2.099
peak=    3.234 closest distance to " O   HOH Z 271 " =    2.374
peak=    3.231 closest distance to " O   TRP A 274 " =    1.824
peak=    3.231 closest distance to " O   HOH Z 345 " =    1.750
peak=    3.230 closest distance to " O   HOH Z 353 " =    2.696
peak=    3.229 closest distance to " CD2 HIS A  81 " =    1.207
peak=    3.229 closest distance to " CB  ALA A 233 " =    1.441
peak=    3.223 closest distance to " OG  SER A  97 " =    3.563
peak=    3.223 closest distance to " O   HOH Z 173 " =    1.784
peak=    3.222 closest distance to " CG AARG A 275 " =    1.192
peak=    3.221 closest distance to " O   HOH Z 281 " =    4.068
peak=    3.220 closest distance to " NZ  LYS A  76 " =    1.280
peak=    3.219 closest distance to " O   HOH Z 227 " =    2.183
peak=    3.218 closest distance to " CB  GLU A 152 " =    1.379
peak=    3.218 closest distance to " O   HOH Z  49 " =    2.866
peak=    3.216 closest distance to " O   HOH Z 133 " =    2.423
peak=    3.209 closest distance to " CB  LYS A 193 " =    0.998
peak=    3.206 closest distance to " CB  PRO A 198 " =    0.954
peak=    3.204 closest distance to " CE BLYS A 290 " =    1.104
peak=    3.202 closest distance to " O   HOH Z 433 " =    1.839
peak=    3.199 closest distance to " CA  ILE A 234 " =    0.917
peak=    3.197 closest distance to " CB  GLN A  89 " =    1.268
peak=    3.196 closest distance to " O   HOH Z 163 " =    1.825
peak=    3.195 closest distance to " O   TYR A 116 " =    1.311
peak=    3.194 closest distance to " N   SER A 135 " =    1.299
peak=    3.190 closest distance to " O   HOH Z 292 " =    1.814
peak=    3.187 closest distance to " O   ALA A   1 " =    1.508
peak=    3.180 closest distance to " CG1 ILE A 151 " =    0.996
peak=    3.167 closest distance to " O   THR A 220 " =    1.360
peak=    3.164 closest distance to " CA  ASN A 217 " =    1.295
peak=    3.164 closest distance to " O   HOH Z 383 " =    1.732
peak=    3.162 closest distance to " O   HOH Z 166 " =    3.796
peak=    3.161 closest distance to " CB  TRP A 150 " =    1.445
peak=    3.156 closest distance to " O   HOH Z 175 " =    2.183
peak=    3.155 closest distance to " CG  MET A 185 " =    1.010
peak=    3.153 closest distance to " CZ2 TRP A 179 " =    1.711
peak=    3.153 closest distance to " CA  ARG A  36 " =    1.088
peak=    3.152 closest distance to " O   HOH Z 171 " =    2.098
peak=    3.150 closest distance to " O   HOH Z 287 " =    2.169
peak=    3.148 closest distance to " O   HOH Z 148 " =    3.279
peak=    3.147 closest distance to " CB  TRP A 179 " =    1.448
peak=    3.146 closest distance to " O   HOH Z 334 " =    1.516
peak=    3.139 closest distance to " N   ASN A 252 " =    1.376
peak=    3.136 closest distance to " O   HOH Z  49 " =    2.142
peak=    3.135 closest distance to " CB  SER A  26 " =    1.602
peak=    3.132 closest distance to " OD1 ASN A 187 " =    1.757
peak=    3.121 closest distance to " O   THR A 251 " =    1.129
peak=    3.118 closest distance to " OG1 THR A 294 " =    2.469
peak=    3.116 closest distance to " O   ALA A 158 " =    1.279
peak=    3.113 closest distance to " NH2AARG A 190 " =    1.254
peak=    3.111 closest distance to " O  BHOH Z  74 " =    1.322
peak=    3.111 closest distance to " CB  ALA A 114 " =    1.158
peak=    3.106 closest distance to " OG1 THR A 246 " =    3.212
peak=    3.103 closest distance to " CB  ARG A 138 " =    0.980
peak=    3.101 closest distance to " CG BARG A 102 " =    1.845
peak=    3.100 closest distance to " CB  PHE A 283 " =    0.733
peak=    3.093 closest distance to " CB  ASN A 215 " =    1.082
peak=    3.093 closest distance to " CA  LYS A 290 " =    1.260
peak=    3.083 closest distance to " CZ3 TRP A 123 " =    1.206
peak=    3.081 closest distance to " O   HOH Z 152 " =    1.850
peak=    3.081 closest distance to " CG  GLN A  89 " =    1.466
peak=    3.079 closest distance to " O   HOH Z 291 " =    1.792
peak=    3.068 closest distance to " CB  LYS A 117 " =    1.170
peak=    3.067 closest distance to " OD1 ASP A 238 " =    1.004
peak=    3.066 closest distance to " CB  GLN A 278 " =    0.850
peak=    3.064 closest distance to " O   HOH Z 336 " =    1.887
peak=    3.055 closest distance to " CA  MET A 105 " =    0.945
peak=    3.049 closest distance to " O   ALA A   1 " =    1.676
peak=    3.026 closest distance to " O   HOH Z 366 " =    3.041
peak=    3.021 closest distance to " O   HOH Z 391 " =    2.937
peak=    3.007 closest distance to " O   HOH Z  88 " =    1.970

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.681 - 5.559
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 195
   mapped sites are within: 0.774 - 5.559

peak=   -4.654 closest distance to " O   HOH Z 290 " =    1.067
peak=   -4.616 closest distance to " CB  PRO A 243 " =    2.615
peak=   -4.533 closest distance to " O   HOH Z 266 " =    4.813
peak=   -4.358 closest distance to " CD  ARG A 156 " =    2.026
peak=   -4.345 closest distance to " CG  GLN A 223 " =    1.752
peak=   -4.179 closest distance to " O   VAL A  67 " =    2.689
peak=   -4.109 closest distance to " O   HOH Z 377 " =    1.985
peak=   -4.067 closest distance to " CB  ALA A 161 " =    2.625
peak=   -4.039 closest distance to " N   ALA A  43 " =    2.491
peak=   -4.036 closest distance to " O   HOH Z 372 " =    2.433
peak=   -4.034 closest distance to " ND2 ASN A  45 " =    1.551
peak=   -3.990 closest distance to " C   HIS A 108 " =    1.082
peak=   -3.987 closest distance to " CZ3 TRP A 179 " =    1.160
peak=   -3.974 closest distance to " O   HOH Z 389 " =    1.886
peak=   -3.955 closest distance to " O   HOH Z 118 " =    3.171
peak=   -3.932 closest distance to " SG  CYS A 254 " =    3.333
peak=   -3.926 closest distance to " O   HOH Z 231 " =    2.182
peak=   -3.914 closest distance to " O   HOH Z 126 " =    1.866
peak=   -3.911 closest distance to " O   HOH Z 185 " =    2.281
peak=   -3.897 closest distance to " OG BSER A 134 " =    1.209
peak=   -3.894 closest distance to " O   HOH Z 435 " =    2.783
peak=   -3.892 closest distance to " O   HOH Z 198 " =    2.112
peak=   -3.891 closest distance to " CE2 TYR A  30 " =    2.809
peak=   -3.845 closest distance to " CZ  TYR A 169 " =    1.680
peak=   -3.813 closest distance to " O   HOH Z 351 " =    1.426
peak=   -3.797 closest distance to " O   HOH Z 353 " =    2.197
peak=   -3.793 closest distance to " O   PRO A 198 " =    1.233
peak=   -3.787 closest distance to " C   ALA A 158 " =    1.386
peak=   -3.752 closest distance to " CB  CYS A 201 " =    2.642
peak=   -3.752 closest distance to " ND2 ASN A  45 " =    1.088
peak=   -3.744 closest distance to " CG1 VAL A 112 " =    2.871
peak=   -3.741 closest distance to " CG  ASP A 231 " =    0.774
peak=   -3.736 closest distance to " CG  MET A 105 " =    0.979
peak=   -3.731 closest distance to " CD1 LEU A 228 " =    2.315
peak=   -3.727 closest distance to " CG  PHE A 283 " =    2.796
peak=   -3.709 closest distance to " O   HOH Z  43 " =    1.603
peak=   -3.697 closest distance to " O   HOH Z 211 " =    1.631
peak=   -3.687 closest distance to " NH2AARG A 275 " =    5.396
peak=   -3.687 closest distance to " O   VAL A  67 " =    2.675
peak=   -3.684 closest distance to " CE  MET A 105 " =    2.274
peak=   -3.682 closest distance to " O   HOH Z  10 " =    1.495
peak=   -3.675 closest distance to " O   HOH Z 313 " =    2.009
peak=   -3.660 closest distance to " N   GLN A  58 " =    1.866
peak=   -3.644 closest distance to " CD2 PHE A 192 " =    2.073
peak=   -3.635 closest distance to " CB  ALA A 291 " =    2.208
peak=   -3.632 closest distance to " CD1 PHE A  59 " =    1.837
peak=   -3.627 closest distance to " N   SER A 212 " =    1.991
peak=   -3.614 closest distance to " CD  GLN A  58 " =    1.038
peak=   -3.605 closest distance to " OG  SER A  97 " =    2.187
peak=   -3.604 closest distance to " CZ  PHE A  59 " =    1.588
peak=   -3.599 closest distance to " CD2 LEU A 300 " =    2.987
peak=   -3.598 closest distance to " CG  GLU A 152 " =    0.830
peak=   -3.595 closest distance to " C   ASN A 285 " =    2.482
peak=   -3.594 closest distance to " CB  PRO A 163 " =    2.544
peak=   -3.586 closest distance to " O   HOH Z 198 " =    1.256
peak=   -3.577 closest distance to " O   HOH Z  47 " =    1.571
peak=   -3.559 closest distance to " CE2 PHE A 218 " =    2.497
peak=   -3.559 closest distance to " CG2 ILE A 263 " =    2.293
peak=   -3.547 closest distance to " OE1 GLN A  88 " =    1.185
peak=   -3.545 closest distance to " O   GLY A 211 " =    1.422
peak=   -3.544 closest distance to " CA  GLY A  98 " =    1.912
peak=   -3.529 closest distance to " OXT GLY A 302 " =    2.816
peak=   -3.526 closest distance to " NH1 ARG A 195 " =    2.549
peak=   -3.525 closest distance to " O   PRO A 163 " =    2.022
peak=   -3.513 closest distance to " CD  ARG A 139 " =    1.574
peak=   -3.511 closest distance to " O   HOH Z 222 " =    1.106
peak=   -3.510 closest distance to " O   HOH Z  38 " =    1.513
peak=   -3.507 closest distance to " O   HOH Z  52 " =    1.237
peak=   -3.483 closest distance to " O   HOH Z 407 " =    3.166
peak=   -3.475 closest distance to " CA  GLY A 241 " =    2.349
peak=   -3.471 closest distance to " CB  ASN A  39 " =    2.253
peak=   -3.467 closest distance to " O   HOH Z  11 " =    1.793
peak=   -3.457 closest distance to " O   GLY A 196 " =    1.102
peak=   -3.447 closest distance to " CD1 LEU A 101 " =    2.369
peak=   -3.442 closest distance to " O   VAL A 189 " =    2.542
peak=   -3.441 closest distance to " O   ALA A 161 " =    1.583
peak=   -3.437 closest distance to " OD1 ASN A 148 " =    1.689
peak=   -3.435 closest distance to " SG ACYS A 201 " =    1.871
peak=   -3.423 closest distance to " CD1 ILE A 239 " =    2.098
peak=   -3.420 closest distance to " O   GLN A 240 " =    2.091
peak=   -3.417 closest distance to " OD1 ASP A 171 " =    1.581
peak=   -3.417 closest distance to " NH2 ARG A  79 " =    1.940
peak=   -3.413 closest distance to " C   LEU A 143 " =    1.242
peak=   -3.413 closest distance to " OG BSER A 134 " =    1.713
peak=   -3.408 closest distance to " CB  ALA A 291 " =    2.275
peak=   -3.402 closest distance to " O   HOH Z 417 " =    2.426
peak=   -3.398 closest distance to " O   HOH Z 282 " =    1.091
peak=   -3.395 closest distance to " CB  ALA A 248 " =    2.482
peak=   -3.393 closest distance to " CG1 VAL A 197 " =    2.211
peak=   -3.391 closest distance to " CA  GLY A 203 " =    2.236
peak=   -3.390 closest distance to " OD1 ASP A 191 " =    1.650
peak=   -3.384 closest distance to " CB  TYR A  15 " =    2.156
peak=   -3.384 closest distance to " N   THR A 235 " =    1.342
peak=   -3.382 closest distance to " CG  GLN A  88 " =    0.895
peak=   -3.367 closest distance to " OD1 ASN A 187 " =    1.528
peak=   -3.363 closest distance to " O   HOH Z 193 " =    1.919
peak=   -3.363 closest distance to " O   HOH Z 395 " =    5.222
peak=   -3.357 closest distance to " O   HOH Z 311 " =    3.574
peak=   -3.349 closest distance to " CD1 LEU A 297 " =    2.382
peak=   -3.349 closest distance to " CG1 VAL A 250 " =    2.657
peak=   -3.345 closest distance to " O   HOH Z 111 " =    2.143
peak=   -3.340 closest distance to " O   HOH Z  51 " =    1.222
peak=   -3.339 closest distance to " CG  GLU A 277 " =    1.198
peak=   -3.335 closest distance to " CD1 ILE A 199 " =    2.561
peak=   -3.328 closest distance to " CG  ARG A 269 " =    2.414
peak=   -3.324 closest distance to " CD2 LEU A 237 " =    2.724
peak=   -3.322 closest distance to " NH2BARG A 275 " =    1.860
peak=   -3.320 closest distance to " O   HOH Z 426 " =    1.643
peak=   -3.318 closest distance to " CD2 LEU A 300 " =    2.886
peak=   -3.315 closest distance to " C   MET A 188 " =    1.465
peak=   -3.311 closest distance to " CB  ASP A 286 " =    2.134
peak=   -3.309 closest distance to " O   HOH Z 210 " =    1.025
peak=   -3.307 closest distance to " O   HOH Z 322 " =    1.499
peak=   -3.305 closest distance to " O   HOH Z  13 " =    1.452
peak=   -3.301 closest distance to " O   HOH Z 348 " =    2.234
peak=   -3.298 closest distance to " CB  ALA A 248 " =    2.000
peak=   -3.296 closest distance to " O   HOH Z 196 " =    2.095
peak=   -3.295 closest distance to " CG1 VAL A 112 " =    2.604
peak=   -3.282 closest distance to " O   SER A 135 " =    1.460
peak=   -3.282 closest distance to " CD  GLU A 236 " =    1.025
peak=   -3.281 closest distance to " CG  TRP A 266 " =    1.817
peak=   -3.280 closest distance to " O   PRO A 198 " =    1.230
peak=   -3.280 closest distance to " OD2 ASP A 171 " =    2.166
peak=   -3.278 closest distance to " CA  GLY A 241 " =    3.037
peak=   -3.274 closest distance to " O   HOH Z  93 " =    2.107
peak=   -3.270 closest distance to " NH2 ARG A  79 " =    1.586
peak=   -3.270 closest distance to " ND2 ASN A 249 " =    2.327
peak=   -3.268 closest distance to " CB  ALA A  43 " =    2.455
peak=   -3.266 closest distance to " O   HOH Z 385 " =    2.063
peak=   -3.263 closest distance to " O   TRP A  70 " =    1.511
peak=   -3.258 closest distance to " N   ALA A 248 " =    1.587
peak=   -3.255 closest distance to " CD2 PHE A  61 " =    2.516
peak=   -3.250 closest distance to " CB  ASP A 132 " =    2.352
peak=   -3.248 closest distance to " CD1 ILE A 239 " =    2.544
peak=   -3.248 closest distance to " N   THR A 157 " =    1.501
peak=   -3.245 closest distance to " O   VAL A 174 " =    2.037
peak=   -3.242 closest distance to " CE3 TRP A 274 " =    2.439
peak=   -3.241 closest distance to " O   HOH Z  73 " =    2.258
peak=   -3.240 closest distance to " CE  MET A  93 " =    1.211
peak=   -3.239 closest distance to " O   HOH Z  63 " =    1.482
peak=   -3.233 closest distance to " O   LYS A 117 " =    1.808
peak=   -3.233 closest distance to " N   ALA A 226 " =    2.127
peak=   -3.231 closest distance to " O   MET A  40 " =    2.764
peak=   -3.229 closest distance to " O   PHE A 218 " =    1.539
peak=   -3.229 closest distance to " O   HOH Z  60 " =    2.562
peak=   -3.226 closest distance to " NE2 GLN A 278 " =    1.729
peak=   -3.224 closest distance to " O   HOH Z  76 " =    1.848
peak=   -3.223 closest distance to " O   HOH Z 241 " =    1.356
peak=   -3.219 closest distance to " C   LEU A 222 " =    0.807
peak=   -3.216 closest distance to " O   HOH Z 253 " =    3.909
peak=   -3.207 closest distance to " CE  LYS A  76 " =    2.790
peak=   -3.206 closest distance to " N   MET A 105 " =    2.759
peak=   -3.195 closest distance to " N   GLY A  23 " =    2.377
peak=   -3.192 closest distance to " CB  CYS A 254 " =    2.318
peak=   -3.189 closest distance to " O   HOH Z 359 " =    3.258
peak=   -3.188 closest distance to " O   HOH Z 323 " =    1.217
peak=   -3.183 closest distance to " CD2 TYR A 293 " =    2.001
peak=   -3.183 closest distance to " CE3 TRP A 150 " =    2.047
peak=   -3.178 closest distance to " O   HOH Z 317 " =    1.598
peak=   -3.176 closest distance to " O   HOH Z  51 " =    1.528
peak=   -3.176 closest distance to " O   HOH Z 394 " =    1.421
peak=   -3.173 closest distance to " CA  ASP A 298 " =    1.074
peak=   -3.167 closest distance to " O   HOH Z 298 " =    2.573
peak=   -3.165 closest distance to " CE BMET A  47 " =    2.044
peak=   -3.155 closest distance to " O   HOH Z 298 " =    1.218
peak=   -3.140 closest distance to " O   HOH Z 191 " =    5.559
peak=   -3.136 closest distance to " CB  ALA A   7 " =    2.130
peak=   -3.133 closest distance to " CG  ARG A  66 " =    2.351
peak=   -3.132 closest distance to " O   GLY A  80 " =    2.440
peak=   -3.129 closest distance to " OD2 ASP A  50 " =    1.627
peak=   -3.125 closest distance to " CG  ASN A 301 " =    1.907
peak=   -3.120 closest distance to " NH1 ARG A  36 " =    2.108
peak=   -3.120 closest distance to " O   HOH Z 388 " =    2.017
peak=   -3.116 closest distance to " O   GLN A 240 " =    2.368
peak=   -3.116 closest distance to " CB  TRP A  85 " =    2.411
peak=   -3.109 closest distance to " ND2 ASN A  60 " =    1.357
peak=   -3.108 closest distance to " OD2 ASP A 171 " =    1.834
peak=   -3.101 closest distance to " N   ALA A 248 " =    1.867
peak=   -3.097 closest distance to " NE2 GLN A  88 " =    1.882
peak=   -3.094 closest distance to " CD  PRO A  90 " =    1.606
peak=   -3.089 closest distance to " O   HOH Z  44 " =    2.212
peak=   -3.086 closest distance to " O   HOH Z 423 " =    1.096
peak=   -3.081 closest distance to " O   ALA A 292 " =    1.932
peak=   -3.079 closest distance to " O   HOH Z 357 " =    1.967
peak=   -3.077 closest distance to " O   HOH Z 166 " =    1.515
peak=   -3.073 closest distance to " O   HOH Z 281 " =    3.212
peak=   -3.071 closest distance to " O   LYS A 289 " =    3.054
peak=   -3.067 closest distance to " O   HOH Z 281 " =    2.678
peak=   -3.053 closest distance to " CA  GLY A 241 " =    2.780
peak=   -3.050 closest distance to " O   HOH Z 166 " =    1.973
peak=   -3.032 closest distance to " O   HOH Z 137 " =    1.548
peak=   -3.024 closest distance to " O   ALA A  34 " =    2.853
peak=   -3.023 closest distance to " CG  GLU A 152 " =    1.321

================= 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    :  0.2933 0.2963   5.945798e+00   5.954515e+00
   1_bss:  0.2789 0.2833   5.921411e+00   5.921174e+00
   1_xyz:  0.1528 0.1730   5.366549e+00   5.481518e+00
   1_adp:  0.1438 0.1749   5.323581e+00   5.498452e+00
   1_occ:  0.1432 0.1752   5.320743e+00   5.496784e+00
   2_bss:  0.1431 0.1736   5.321229e+00   5.495055e+00
   2_xyz:  0.1205 0.1533   5.170457e+00   5.369617e+00
   2_adp:  0.1142 0.1529   5.139096e+00   5.363631e+00
   2_occ:  0.1142 0.1528   5.138854e+00   5.363669e+00
   3_bss:  0.1141 0.1528   5.138634e+00   5.363483e+00
   3_xyz:  0.1082 0.1525   5.110617e+00   5.355840e+00
   3_adp:  0.1076 0.1525   5.108405e+00   5.356348e+00
   3_occ:  0.1075 0.1525   5.108459e+00   5.356674e+00
   4_bss:  0.1077 0.1526   5.110323e+00   5.357864e+00
   4_xyz:  0.1058 0.1539   5.105211e+00   5.363805e+00
   4_adp:  0.1054 0.1559   5.109606e+00   5.373965e+00
   4_occ:  0.1053 0.1559   5.109610e+00   5.374122e+00
   5_bss:  0.1052 0.1559   5.109746e+00   5.374192e+00
   5_xyz:  0.1078 0.1569   5.126901e+00   5.385110e+00
   5_adp:  0.1093 0.1552   5.127004e+00   5.377196e+00
   5_occ:  0.1092 0.1553   5.127001e+00   5.377431e+00
   5_bss:  0.1092 0.1553   5.127035e+00   5.377436e+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:  0.325  45.031  -1.543  -2.369  -0.558  -0.000  -0.000  -0.000
   1_xyz:  0.325  45.031  -1.543  -2.369  -0.558  -0.000  -0.000  -0.000
   1_adp:  0.325  45.031  -1.543  -2.369  -0.558  -0.000  -0.000  -0.000
   1_occ:  0.325  45.031  -1.543  -2.369  -0.558  -0.000  -0.000  -0.000
   2_bss:  0.330  49.127  -2.482  -2.871  -1.674  -0.000  -0.000  -0.000
   2_xyz:  0.330  49.127  -2.482  -2.871  -1.674  -0.000  -0.000  -0.000
   2_adp:  0.330  49.127  -2.482  -2.871  -1.674  -0.000  -0.000  -0.000
   2_occ:  0.330  49.127  -2.482  -2.871  -1.674  -0.000  -0.000  -0.000
   3_bss:  0.324  48.589  -2.424  -2.625  -1.628  -0.000  -0.000  -0.000
   3_xyz:  0.324  48.589  -2.424  -2.625  -1.628  -0.000  -0.000  -0.000
   3_adp:  0.324  48.589  -2.424  -2.625  -1.628  -0.000  -0.000  -0.000
   3_occ:  0.324  48.589  -2.424  -2.625  -1.628  -0.000  -0.000  -0.000
   4_bss:  0.324  48.589  -2.333  -2.501  -1.566  -0.000  -0.000  -0.000
   4_xyz:  0.324  48.589  -2.333  -2.501  -1.566  -0.000  -0.000  -0.000
   4_adp:  0.324  48.589  -2.333  -2.501  -1.566  -0.000  -0.000  -0.000
   4_occ:  0.324  48.589  -2.333  -2.501  -1.566  -0.000  -0.000  -0.000
   5_bss:  0.324  48.589  -2.100  -2.267  -1.355  -0.000  -0.000  -0.000
   5_xyz:  0.324  48.589  -2.100  -2.267  -1.355  -0.000  -0.000  -0.000
   5_adp:  0.324  48.589  -2.100  -2.267  -1.355  -0.000  -0.000  -0.000
   5_occ:  0.324  48.589  -2.100  -2.267  -1.355  -0.000  -0.000  -0.000
   5_bss:  0.324  48.532  -2.027  -2.162  -1.235  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  29.447 0.7677  0.9497    24355.292
   1_bss:  28.134 0.7798  0.9178    21246.228
   1_xyz:  15.655 0.9025  1.0009     7827.258
   1_adp:  16.049 0.8989  0.9980     8052.031
   1_occ:  16.015 0.8991  0.9979     7998.854
   2_bss:  15.985 0.8993  0.9676     7963.378
   2_xyz:  13.469 0.9194  0.9774     6128.694
   2_adp:  13.403 0.9198  0.9765     6007.042
   2_occ:  13.403 0.9198  0.9764     6005.123
   3_bss:  13.403 0.9198  0.9803     6000.927
   3_xyz:  13.235 0.9211  0.9798     5917.942
   3_adp:  13.235 0.9212  0.9756     5921.876
   3_occ:  13.244 0.9212  0.9755     5924.998
   4_bss:  13.289 0.9208  0.9784     5950.189
   4_xyz:  13.390 0.9200  0.9781     6032.823
   4_adp:  13.606 0.9183  0.9713     6130.275
   4_occ:  13.609 0.9183  0.9713     6133.030
   5_bss:  13.613 0.9183  0.9792     6134.972
   5_xyz:  13.794 0.9170  0.9780     6260.819
   5_adp:  13.597 0.9185  0.9750     6184.811
   5_occ:  13.603 0.9185  0.9750     6184.315
   5_bss:  13.604 0.9185  0.9765     6184.165
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6080e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6080e-01
   1_xyz:   0.962  0.007  0.070 14.984  0.004  4.111   5.7021e-02
   1_adp:   0.962  0.007  0.070 14.984  0.004  4.111   5.7021e-02
   1_occ:   0.962  0.007  0.070 14.984  0.004  4.111   5.7021e-02
   2_bss:   0.962  0.007  0.070 14.984  0.004  4.111   5.7021e-02
   2_xyz:   0.940  0.006  0.071 14.809  0.004  4.116   5.4110e-02
   2_adp:   0.940  0.006  0.071 14.809  0.004  4.116   5.4110e-02
   2_occ:   0.940  0.006  0.071 14.809  0.004  4.116   5.4110e-02
   3_bss:   0.940  0.006  0.071 14.809  0.004  4.116   5.4110e-02
   3_xyz:   1.005  0.008  0.076 15.016  0.004  4.118   6.2258e-02
   3_adp:   1.005  0.008  0.076 15.016  0.004  4.118   6.2258e-02
   3_occ:   1.005  0.008  0.076 15.016  0.004  4.118   6.2258e-02
   4_bss:   1.005  0.008  0.076 15.016  0.004  4.118   6.2258e-02
   4_xyz:   1.032  0.008  0.079 15.040  0.004  4.120   6.5548e-02
   4_adp:   1.032  0.008  0.079 15.040  0.004  4.120   6.5548e-02
   4_occ:   1.032  0.008  0.079 15.040  0.004  4.120   6.5548e-02
   5_bss:   1.032  0.008  0.079 15.040  0.004  4.120   6.5548e-02
   5_xyz:   0.918  0.006  0.070 14.782  0.004  4.119   5.2913e-02
   5_adp:   0.918  0.006  0.070 14.782  0.004  4.119   5.2913e-02
   5_occ:   0.918  0.006  0.070 14.782  0.004  4.119   5.2913e-02
   5_bss:   0.918  0.006  0.070 14.782  0.004  4.119   5.2913e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4066e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4066e-01
   1_xyz:   8.162  0.040  0.301 83.979  0.036  2.348   5.7825e-02
   1_adp:   8.162  0.040  0.301 83.979  0.036  2.348   5.7825e-02
   1_occ:   8.162  0.040  0.301 83.979  0.036  2.348   5.7825e-02
   2_bss:   8.162  0.040  0.301 83.979  0.036  2.348   5.7825e-02
   2_xyz:   7.617  0.034  0.207 84.493  0.041  2.335   4.3993e-02
   2_adp:   7.617  0.034  0.207 84.493  0.041  2.335   4.3993e-02
   2_occ:   7.617  0.034  0.207 84.493  0.041  2.335   4.3993e-02
   3_bss:   7.617  0.034  0.207 84.493  0.041  2.335   4.3993e-02
   3_xyz:   7.210  0.041  0.244 83.860  0.038  2.292   4.7617e-02
   3_adp:   7.210  0.041  0.244 83.860  0.038  2.292   4.7617e-02
   3_occ:   7.210  0.041  0.244 83.860  0.038  2.292   4.7617e-02
   4_bss:   7.210  0.041  0.244 83.860  0.038  2.292   4.7617e-02
   4_xyz:   6.811  0.041  0.246 83.545  0.038  2.273   5.1478e-02
   4_adp:   6.811  0.041  0.246 83.545  0.038  2.273   5.1478e-02
   4_occ:   6.811  0.041  0.246 83.545  0.038  2.273   5.1478e-02
   5_bss:   6.811  0.041  0.246 83.545  0.038  2.273   5.1478e-02
   5_xyz:   7.098  0.039  0.220 83.650  0.036  2.363   3.4277e-02
   5_adp:   7.098  0.039  0.220 83.650  0.036  2.363   3.4277e-02
   5_occ:   7.098  0.039  0.220 83.650  0.036  2.363   3.4277e-02
   5_bss:   7.098  0.039  0.220 83.650  0.036  2.363   3.4277e-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:  77.94   0.00  16.32  77.94   0.00  12.50  62.48   6.13  37.13
   1_occ:  77.94   0.00  16.32  77.94   0.00  12.50  62.48   6.13  37.13
   2_bss:  77.94   0.00  16.32  77.94   0.00  12.50  62.48   6.13  37.13
   2_xyz:  77.94   0.00  16.32  77.94   0.00  12.50  62.48   6.13  37.13
   2_adp:  75.01   1.52  17.03  75.01   1.52  12.98  72.79   4.35  39.12
   2_occ:  75.01   1.52  17.03  75.01   1.52  12.98  72.79   4.35  39.12
   3_bss:  75.01   1.52  17.03  75.01   1.52  12.98  72.79   4.35  39.12
   3_xyz:  75.01   1.52  17.03  75.01   1.52  12.98  72.79   4.35  39.12
   3_adp:  76.40   1.51  16.94  76.40   1.51  12.91  73.11   3.94  38.90
   3_occ:  76.40   1.51  16.94  76.40   1.51  12.91  73.11   3.94  38.90
   4_bss:  76.40   1.51  16.94  76.40   1.51  12.91  73.11   3.94  38.90
   4_xyz:  76.40   1.51  16.94  76.40   1.51  12.91  73.11   3.94  38.90
   4_adp:  86.83   0.36  17.07  86.83   0.36  12.89  77.88   5.37  39.83
   4_occ:  86.83   0.36  17.07  86.83   0.36  12.89  77.88   5.37  39.83
   5_bss:  86.83   0.36  17.07  86.83   0.36  12.89  77.88   5.37  39.83
   5_xyz:  86.83   0.36  17.07  86.83   0.36  12.89  77.88   5.37  39.83
   5_adp:  82.81   1.61  16.33  82.81   1.61  12.58  74.08   6.43  36.74
   5_occ:  82.81   1.61  16.33  82.81   1.61  12.58  74.08   6.43  36.74
   5_bss:  82.75   1.55  16.27  82.75   1.55  12.53  74.03   6.37  36.68
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.958    0.016    0.266
   1_adp:    0.958    0.016    0.266
   1_occ:    0.958    0.016    0.266
   2_bss:    0.958    0.016    0.266
   2_xyz:    0.663    0.017    0.303
   2_adp:    0.663    0.017    0.303
   2_occ:    0.663    0.017    0.303
   3_bss:    0.663    0.017    0.303
   3_xyz:    0.736    0.028    0.323
   3_adp:    0.736    0.028    0.323
   3_occ:    0.736    0.028    0.323
   4_bss:    0.736    0.028    0.323
   4_xyz:    0.882    0.036    0.335
   4_adp:    0.882    0.036    0.335
   4_occ:    0.882    0.036    0.335
   5_bss:    0.882    0.036    0.335
   5_xyz:    0.966    0.031    0.337
   5_adp:    0.966    0.031    0.337
   5_occ:    0.966    0.031    0.337
   5_bss:    0.966    0.031    0.337
------------------------------------------------------------------------

CPU time actual refinement: 330.81


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_894/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_894/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_894/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_894/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_894/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.66 
  Macro-tasks:
    bulk solvent and scale       = 37.15  
    individual site refinement   = 136.05 
    weights calculation          = 29.04  
    collect and process          = 6.62   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 208.97 
  Micro-tasks:
    mask                            = 1.22   
    f_calc                          = 106.28 
    alpha_beta                      = 8.19   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 115.34 
    fmodel                         = 6.88   
    r_factors                      = 0.20   
    phase_errors                   = 11.38  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 251.00 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.663 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    663 calls, 105.90 s
gradients_fft:          608 calls, 101.56 s

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

# Date 2008-01-16 Time 05:55:02 PST -0800 (1200491702.32 s)
Start R-work = 0.2933, R-free = 0.2963 (no bulk solvent and anisotropic scale)
Final R-work = 0.1336, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.2789, R-free = 0.2833
Final R-work = 0.1092, R-free = 0.1553