# Date 2008-01-16 Time 05:53:07 PST -0800 (1200491587.38 s)
#phil __OFF__

Command line arguments: "../917.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2447
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 917

-------------------------------------------------------------------------------
  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, 47.1647, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.9911
Completeness in resolution range: 0.963125
Completeness with d_max=infinity: 0.960151

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9911

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, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.9911
Completeness in resolution range: 0.963125
Completeness with d_max=infinity: 0.960151

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2605 [2129/2157]  1918   211   9.9%
  bin  2:  4.2605 -  3.3943 [2051/2067]  1844   207  10.1%
  bin  3:  3.3943 -  2.9690 [2021/2040]  1817   204  10.1%
  bin  4:  2.9690 -  2.6992 [2017/2047]  1820   197   9.8%
  bin  5:  2.6992 -  2.5067 [1992/2011]  1792   200  10.0%
  bin  6:  2.5067 -  2.3595 [1981/2006]  1781   200  10.1%
  bin  7:  2.3595 -  2.2417 [1954/1987]  1761   193   9.9%
  bin  8:  2.2417 -  2.1444 [1975/2006]  1779   196   9.9%
  bin  9:  2.1444 -  2.0621 [1983/2025]  1783   200  10.1%
  bin 10:  2.0621 -  1.9911 [1486/1993]  1335   151  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_917/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: 11
        2.42 -     3.04: 2189
        3.04 -     3.66: 4636
        3.66 -     4.28: 8988
        4.28 -     4.90: 12311
  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 207 " - " O   HOH Z 341 "  1.940 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.341 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28130 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_917/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_917/model_refine_001.geo

CPU time processing inputs: 9.25


============================ 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 47.16465 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2574   r_free= 0.2552   ksol= 0.00   Bsol= 0.00   scale= 0.993    |
|                                                                             |
| 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:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.832370                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7519 0.99   1385  154 0.2583 0.2529      6.2712      6.1974|
|  2:  4.7519 -  3.7915 0.99   1340  146 0.1897 0.1928      6.1645      6.1542|
|  3:  3.7915 -  3.3180 0.99   1303  147 0.2111 0.2021      6.0593      6.1293|
|  4:  3.3180 -  3.0173 0.99   1305  147 0.2305 0.2254      5.9867      5.9543|
|  5:  3.0173 -  2.8025 0.99   1292  140 0.2473 0.2422      5.8505      5.9015|
|  6:  2.8025 -  2.6382 0.99   1280  148 0.2632 0.2615      5.8084       5.795|
|  7:  2.6382 -  2.5067 0.99   1286  137 0.2732 0.2421       5.809      5.7479|
|  8:  2.5067 -  2.3980 0.98   1266  147 0.2885 0.2833      5.7664      5.7709|
|  9:  2.3980 -  2.3061 0.98   1275  142 0.2785 0.2895      5.7082      5.7535|
| 10:  2.3061 -  2.2267 0.99   1261  135 0.2889 0.2936      5.7048      5.7089|
| 11:  2.2267 -  2.1573 0.99   1270  143 0.2949 0.3032      5.6685      5.7348|
| 12:  2.1573 -  2.0958 0.97   1247  138 0.3034 0.2813      5.6437      5.6444|
| 13:  2.0958 -  2.0408 0.99   1266  139 0.3011 0.3145      5.5541       5.462|
| 14:  2.0408 -  1.9911 0.66    854   96 0.2908 0.2866      5.4642      5.4344|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7519  1385   154  0.82  23.57   0.87     0.82      35111.26|
|  2:  4.7519 -  3.7915  1340   146  0.88  17.46   0.99     0.93      29122.03|
|  3:  3.7915 -  3.3180  1303   147  0.87  19.18   1.01     0.98      24854.74|
|  4:  3.3180 -  3.0173  1305   147  0.86  20.58   1.01     0.98      21532.19|
|  5:  3.0173 -  2.8025  1292   140  0.82  24.79   1.02     0.97      18481.97|
|  6:  2.8025 -  2.6382  1280   148  0.83  24.26   1.03     0.97      15825.28|
|  7:  2.6382 -  2.5067  1286   137  0.82  24.42   1.03     0.98      14439.40|
|  8:  2.5067 -  2.3980  1266   147  0.81  26.13   1.03     0.99      14265.77|
|  9:  2.3980 -  2.3061  1275   142  0.80  26.86   1.06     0.99      13901.63|
| 10:  2.3061 -  2.2267  1261   135  0.78  28.26   1.08     0.99      13745.44|
| 11:  2.2267 -  2.1573  1270   143  0.78  28.47   1.09     1.01      12962.36|
| 12:  2.1573 -  2.0958  1247   138  0.79  27.60   1.07     1.05      11953.66|
| 13:  2.0958 -  2.0408  1266   139  0.79  27.90   1.07     1.05       9869.10|
| 14:  2.0408 -  1.9911   854    96  0.82  25.60   1.07     1.01       7344.04|
|alpha:            min =        0.82 max =            1.05 mean =         0.98|
|beta:             min =     7344.04 max =        35111.26 mean =     17815.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.82|
|phase err.(work): min =        0.00 max =           89.99 mean =        24.57|
|phase err.(test): min =        0.00 max =           89.34 mean =        24.10|
|-----------------------------------------------------------------------------|

============================== 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 = 2.221952              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.795   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.442963              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.203   (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:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      183 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2006 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1824 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2812 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4627 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4361 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5592 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6719 |
|-----------------------------------------------------------------------------|
|-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 |   4.114    4.900  1.806 |       0.143 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    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: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2574   r_free= 0.2552   ksol= 0.00   Bsol= 0.00   scale= 0.993    |
|                                                                             |
| 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:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.832370                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2423   r_free= 0.2407   ksol= 0.31   Bsol= 49.47   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,-1.67,-1.48,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.801079                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.027280              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.056   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.222478              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.978   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2423      final r-factor (work) = 0.1522          |
| start r-factor (free) = 0.2407      final r-factor (free) = 0.1674          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0732 = 2.03 * 0.50 * 5.8328 + 1.00 * 0.1608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6479 = 2.03 * 0.50 * 5.5188 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1522      final r-factor (work) = 0.1417          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2344 = 0.22 * 1.00 * 5.5188 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2472 = 0.22 * 1.00 * 5.3019 + 1.00 * 0.0676                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.05   16.37    None  None   None       |
|    all(noH): 2823   0      0.00    81.05   16.37    None  None   None       |
|    Sol.    : 438    0      5.70    62.73   37.06    None  None   None       |
|    Mac.    : 2385   0      0.00    81.05   12.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.105:  459   |   5:    40.525 -  48.630:  103        |
|      1:     8.105 -  16.210: 1528   |   6:    48.630 -  56.735:   74        |
|      2:    16.210 -  24.315:  360   |   7:    56.735 -  64.840:   23        |
|      3:    24.315 -  32.420:  155   |   8:    64.840 -  72.945:    0        |
|      4:    32.420 -  40.525:  120   |   9:    72.945 -  81.050:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1417 r_free = 0.1690             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1411 r_free = 0.1687             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1411   r_free= 0.1687   ksol= 0.31   Bsol= 49.47   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,-1.67,-1.48,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.305142                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1409   r_free= 0.1674   ksol= 0.33   Bsol= 55.45   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.43,-1.82,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.305349                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.336921              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.552  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.413938              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.942   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1409      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6048 = 1.34 * 0.50 * 5.3121 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5479 = 1.34 * 0.50 * 5.2293 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3515 = 0.41 * 1.00 * 5.2293 + 1.00 * 0.1869                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1440 = 0.41 * 1.00 * 5.1591 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.44    76.36   16.92    None  None   None       |
|    all(noH): 2823   0      1.44    76.36   16.92    None  None   None       |
|    Sol.    : 438    0      2.67    67.50   38.88    None  None   None       |
|    Mac.    : 2385   0      1.44    76.36   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:     1.439 -   8.931:  731   |   5:    38.901 -  46.394:  109        |
|      1:     8.931 -  16.424: 1254   |   6:    46.394 -  53.886:   89        |
|      2:    16.424 -  23.916:  314   |   7:    53.886 -  61.378:   69        |
|      3:    23.916 -  31.409:  131   |   8:    61.378 -  68.871:   21        |
|      4:    31.409 -  38.901:  102   |   9:    68.871 -  76.363:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1542             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1540             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1540   ksol= 0.33   Bsol= 55.45   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.43,-1.82,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.157322                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1539   ksol= 0.33   Bsol= 55.45   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.20,-1.51,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157413                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.556413              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.957  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.210582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.885  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6480 = 2.56 * 0.50 * 5.1601 + 1.00 * 0.0523                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6197 = 2.56 * 0.50 * 5.1258 + 1.00 * 0.0678                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2136 = 1.21 * 1.00 * 5.1258 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1998 = 1.21 * 1.00 * 5.1134 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.60    88.07   17.04    None  None   None       |
|    all(noH): 2823   0      0.60    88.07   17.04    None  None   None       |
|    Sol.    : 438    0      2.88    76.01   39.74    None  None   None       |
|    Mac.    : 2385   0      0.60    88.07   12.87    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:     0.600 -   9.348:  886   |   5:    44.336 -  53.084:  103        |
|      1:     9.348 -  18.095: 1207   |   6:    53.084 -  61.831:   79        |
|      2:    18.095 -  26.842:  255   |   7:    61.831 -  70.578:   31        |
|      3:    26.842 -  35.589:  143   |   8:    70.578 -  79.325:    6        |
|      4:    35.589 -  44.336:  109   |   9:    79.325 -  88.073:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1078 r_free = 0.1545             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1077 r_free = 0.1545             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1545   ksol= 0.33   Bsol= 55.45   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.20,-1.51,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117754                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1541   ksol= 0.32   Bsol= 55.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.02,-1.31,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.119307                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.650276              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.069  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.163617              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.399  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2884 = 1.65 * 0.50 * 5.1150 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2863 = 1.65 * 0.50 * 5.1279 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8485 = 0.16 * 1.00 * 5.1279 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8489 = 0.16 * 1.00 * 5.1429 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.39    84.56   16.34    None  None   None       |
|    all(noH): 2823   0      1.39    84.56   16.34    None  None   None       |
|    Sol.    : 438    0      4.59    71.19   36.89    None  None   None       |
|    Mac.    : 2385   0      1.39    84.56   12.56    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:     1.392 -   9.709:  997   |   5:    42.976 -  51.293:   96        |
|      1:     9.709 -  18.025: 1123   |   6:    51.293 -  59.609:   58        |
|      2:    18.025 -  26.342:  247   |   7:    59.609 -  67.926:   19        |
|      3:    26.342 -  34.659:  134   |   8:    67.926 -  76.243:    4        |
|      4:    34.659 -  42.976:  141   |   9:    76.243 -  84.560:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1550             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1551             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1551   ksol= 0.32   Bsol= 55.45   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.02,-1.31,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138980                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1551   ksol= 0.32   Bsol= 51.32   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.95,-1.20,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.139165                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.102585              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.595  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.416192              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.428  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0333 = 3.10 * 0.50 * 5.1430 + 1.00 * 0.0550                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0167 = 3.10 * 0.50 * 5.1218 + 1.00 * 0.0713                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1390 = 0.42 * 1.00 * 5.1218 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1365 = 0.42 * 1.00 * 5.1136 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    85.45   16.36    None  None   None       |
|    all(noH): 2823   0      0.81    85.45   16.36    None  None   None       |
|    Sol.    : 438    0      5.88    71.25   37.68    None  None   None       |
|    Mac.    : 2385   0      0.81    85.45   12.45    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:     0.812 -   9.276:  940   |   5:    43.130 -  51.594:  106        |
|      1:     9.276 -  17.739: 1159   |   6:    51.594 -  60.057:   68        |
|      2:    17.739 -  26.203:  258   |   7:    60.057 -  68.521:   18        |
|      3:    26.203 -  34.666:  134   |   8:    68.521 -  76.984:    5        |
|      4:    34.666 -  43.130:  131   |   9:    76.984 -  85.448:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1557             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1064 r_free = 0.1557             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1557   ksol= 0.32   Bsol= 51.32   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.95,-1.20,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116794                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7519 0.99   1385  154 0.0972 0.1278      5.3644      5.5069|
|  2:  4.7519 -  3.7915 0.99   1340  146 0.0835 0.1085      5.4174      5.6122|
|  3:  3.7915 -  3.3180 0.99   1303  147 0.1010 0.1474      5.4445      5.8444|
|  4:  3.3180 -  3.0173 0.99   1305  147 0.1152 0.1506      5.4266       5.564|
|  5:  3.0173 -  2.8025 0.99   1292  140 0.1275 0.1767      5.3035      5.5531|
|  6:  2.8025 -  2.6382 0.99   1280  148 0.1141 0.1783       5.183      5.4337|
|  7:  2.6382 -  2.5067 0.99   1286  137 0.1184 0.1623      5.1385      5.3538|
|  8:  2.5067 -  2.3980 0.98   1266  147 0.1099 0.1721      5.0309      5.3185|
|  9:  2.3980 -  2.3061 0.98   1275  142 0.1108 0.1705      5.0035      5.3056|
| 10:  2.3061 -  2.2267 0.99   1261  135 0.1057 0.1783      4.9332      5.1915|
| 11:  2.2267 -  2.1573 0.99   1270  143 0.1078 0.1801      4.9204      5.2838|
| 12:  2.1573 -  2.0958 0.97   1247  138 0.1048 0.1525      4.8569       5.099|
| 13:  2.0958 -  2.0408 0.99   1266  139 0.1068 0.1761      4.7651      5.0909|
| 14:  2.0408 -  1.9911 0.66    854   96 0.0985 0.1723      4.6164      4.8941|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7519  1385   154  0.94   8.89   0.97     0.95       6796.19|
|  2:  4.7519 -  3.7915  1340   146  0.95   7.71   1.01     0.99       8682.10|
|  3:  3.7915 -  3.3180  1303   147  0.94  11.02   1.01     1.01      10004.10|
|  4:  3.3180 -  3.0173  1305   147  0.92  13.40   1.00     0.98      10056.60|
|  5:  3.0173 -  2.8025  1292   140  0.90  15.88   0.99     0.96       8099.97|
|  6:  2.8025 -  2.6382  1280   148  0.91  15.48   0.98     0.95       6884.20|
|  7:  2.6382 -  2.5067  1286   137  0.91  14.88   0.98     0.96       5948.70|
|  8:  2.5067 -  2.3980  1266   147  0.91  14.80   0.98     0.97       5097.89|
|  9:  2.3980 -  2.3061  1275   142  0.91  14.86   0.99     0.96       4777.87|
| 10:  2.3061 -  2.2267  1261   135  0.91  15.09   0.99     0.95       4224.22|
| 11:  2.2267 -  2.1573  1270   143  0.90  16.39   0.98     0.95       4322.62|
| 12:  2.1573 -  2.0958  1247   138  0.92  14.49   0.99     0.98       3878.11|
| 13:  2.0958 -  2.0408  1266   139  0.91  15.72   0.99     0.98       3282.82|
| 14:  2.0408 -  1.9911   854    96  0.92  14.09   0.96     0.93       2351.50|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2351.50 max =        10056.60 mean =      6154.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.70|
|phase err.(test): min =        0.00 max =           89.90 mean =        13.26|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1557   ksol= 0.32   Bsol= 51.29   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.74,-0.98,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116871                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1557   ksol= 0.32   Bsol= 51.29   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.74,-0.98,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116871                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7519 0.99   1385  154 0.0973 0.1280      5.3651       5.508|
|  2:  4.7519 -  3.7915 0.99   1340  146 0.0835 0.1084      5.4177      5.6119|
|  3:  3.7915 -  3.3180 0.99   1303  147 0.1010 0.1474      5.4445      5.8445|
|  4:  3.3180 -  3.0173 0.99   1305  147 0.1152 0.1506      5.4265       5.564|
|  5:  3.0173 -  2.8025 0.99   1292  140 0.1275 0.1767      5.3034      5.5529|
|  6:  2.8025 -  2.6382 0.99   1280  148 0.1141 0.1783      5.1829      5.4336|
|  7:  2.6382 -  2.5067 0.99   1286  137 0.1184 0.1623      5.1386      5.3541|
|  8:  2.5067 -  2.3980 0.98   1266  147 0.1099 0.1721      5.0308      5.3183|
|  9:  2.3980 -  2.3061 0.98   1275  142 0.1108 0.1705      5.0036      5.3057|
| 10:  2.3061 -  2.2267 0.99   1261  135 0.1057 0.1783      4.9334      5.1916|
| 11:  2.2267 -  2.1573 0.99   1270  143 0.1078 0.1801      4.9205      5.2838|
| 12:  2.1573 -  2.0958 0.97   1247  138 0.1048 0.1525      4.8568      5.0992|
| 13:  2.0958 -  2.0408 0.99   1266  139 0.1068 0.1761      4.7649      5.0906|
| 14:  2.0408 -  1.9911 0.66    854   96 0.0985 0.1723      4.6164       4.894|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7519  1385   154  0.94   8.90   0.98     0.95       6808.73|
|  2:  4.7519 -  3.7915  1340   146  0.95   7.72   1.01     1.00       8690.03|
|  3:  3.7915 -  3.3180  1303   147  0.94  11.02   1.02     1.01      10003.58|
|  4:  3.3180 -  3.0173  1305   147  0.92  13.40   1.01     0.99      10055.75|
|  5:  3.0173 -  2.8025  1292   140  0.90  15.88   0.99     0.96       8098.19|
|  6:  2.8025 -  2.6382  1280   148  0.91  15.48   0.98     0.95       6883.23|
|  7:  2.6382 -  2.5067  1286   137  0.91  14.88   0.99     0.96       5948.16|
|  8:  2.5067 -  2.3980  1266   147  0.91  14.80   0.99     0.97       5097.40|
|  9:  2.3980 -  2.3061  1275   142  0.91  14.86   1.00     0.97       4778.02|
| 10:  2.3061 -  2.2267  1261   135  0.91  15.09   0.99     0.95       4224.46|
| 11:  2.2267 -  2.1573  1270   143  0.90  16.39   0.99     0.96       4322.71|
| 12:  2.1573 -  2.0958  1247   138  0.92  14.49   1.00     0.99       3877.39|
| 13:  2.0958 -  2.0408  1266   139  0.91  15.72   1.00     0.99       3281.77|
| 14:  2.0408 -  1.9911   854    96  0.92  14.09   0.98     0.94       2351.12|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2351.12 max =        10055.75 mean =      6155.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.70|
|phase err.(test): min =        0.00 max =           89.90 mean =        13.26|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    85.42   16.34    None  None   None       |
|    all(noH): 2823   0      0.78    85.42   16.34    None  None   None       |
|    Sol.    : 438    0      5.86    71.22   37.65    None  None   None       |
|    Mac.    : 2385   0      0.78    85.42   12.42    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:     0.785 -   9.248:  940   |   5:    43.102 -  51.566:  106        |
|      1:     9.248 -  17.712: 1159   |   6:    51.566 -  60.030:   68        |
|      2:    17.712 -  26.175:  258   |   7:    60.030 -  68.493:   18        |
|      3:    26.175 -  34.639:  134   |   8:    68.493 -  76.957:    5        |
|      4:    34.639 -  43.102:  131   |   9:    76.957 -  85.420:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 287         
Filter by distance & map next to the model:
   mapped sites are within: 0.541 - 4.731
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 287
   mapped sites are within: 0.731 - 4.731

peak=    5.931 closest distance to " NH2 ARG A  56 " =    2.292
peak=    5.413 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.188 closest distance to " O   HOH Z 126 " =    1.857
peak=    5.119 closest distance to " CB  SER A  63 " =    1.223
peak=    5.027 closest distance to " O   HOH Z 232 " =    2.326
peak=    4.749 closest distance to " CB  GLN A 183 " =    1.229
peak=    4.748 closest distance to " CB  ARG A 275 " =    0.892
peak=    4.649 closest distance to " C   PRO A 198 " =    1.491
peak=    4.638 closest distance to " NE2 GLN A  11 " =    1.095
peak=    4.636 closest distance to " O   HOH Z 298 " =    1.957
peak=    4.565 closest distance to " CB  GLU A 152 " =    1.202
peak=    4.530 closest distance to " CA  TYR A  30 " =    0.933
peak=    4.445 closest distance to " O   HOH Z 369 " =    2.108
peak=    4.437 closest distance to " O   HOH Z  78 " =    1.637
peak=    4.413 closest distance to " O   HOH Z  15 " =    2.176
peak=    4.355 closest distance to " CB  LEU A 228 " =    1.067
peak=    4.345 closest distance to " CG  PRO A 213 " =    1.184
peak=    4.340 closest distance to " O   HOH Z 142 " =    1.601
peak=    4.314 closest distance to " O   HOH Z 236 " =    2.042
peak=    4.302 closest distance to " CB  ARG A  79 " =    1.376
peak=    4.294 closest distance to " OD1 ASN A  69 " =    2.592
peak=    4.294 closest distance to " CB  TYR A 169 " =    0.764
peak=    4.290 closest distance to " O   HOH Z 193 " =    1.860
peak=    4.282 closest distance to " O   HOH Z 303 " =    2.058
peak=    4.276 closest distance to " O   HOH Z 261 " =    2.175
peak=    4.226 closest distance to " CB  ASN A 148 " =    1.467
peak=    4.206 closest distance to " O   HOH Z 368 " =    2.040
peak=    4.149 closest distance to " O   HOH Z 158 " =    3.025
peak=    4.136 closest distance to " O   HOH Z 427 " =    2.991
peak=    4.106 closest distance to " O   HOH Z 403 " =    1.707
peak=    4.093 closest distance to " O   HOH Z 197 " =    3.025
peak=    4.091 closest distance to " O   HOH Z 234 " =    3.741
peak=    4.089 closest distance to " CB  GLU A 277 " =    3.614
peak=    4.088 closest distance to " O   HOH Z 209 " =    2.308
peak=    4.056 closest distance to " ND2 ASN A 187 " =    1.435
peak=    4.046 closest distance to " O   HOH Z  43 " =    1.910
peak=    4.038 closest distance to " CB  GLU A 128 " =    1.068
peak=    4.031 closest distance to " O   HOH Z 203 " =    1.806
peak=    4.017 closest distance to " O   HOH Z 250 " =    1.434
peak=    4.007 closest distance to " O   HOH Z  40 " =    1.778
peak=    4.005 closest distance to " O   MET A 105 " =    1.852
peak=    3.999 closest distance to " CB  ARG A 190 " =    1.658
peak=    3.998 closest distance to " O   HOH Z  61 " =    1.587
peak=    3.982 closest distance to " CB  VAL A 265 " =    1.277
peak=    3.953 closest distance to " O   HOH Z 214 " =    2.047
peak=    3.933 closest distance to " CB  SER A   3 " =    1.330
peak=    3.904 closest distance to " CB  ASP A 140 " =    0.928
peak=    3.898 closest distance to " O   HOH Z 344 " =    3.181
peak=    3.892 closest distance to " CB  TRP A 266 " =    0.943
peak=    3.860 closest distance to " CB  VAL A 202 " =    1.555
peak=    3.859 closest distance to " CZ  PHE A 218 " =    1.071
peak=    3.853 closest distance to " CD1 LEU A 300 " =    1.240
peak=    3.852 closest distance to " NH2 ARG A 156 " =    1.168
peak=    3.849 closest distance to " CD  ARG A  66 " =    2.451
peak=    3.848 closest distance to " O   HOH Z  66 " =    2.205
peak=    3.847 closest distance to " O   HOH Z  92 " =    2.506
peak=    3.837 closest distance to " CA  ASN A 215 " =    1.149
peak=    3.825 closest distance to " O   HOH Z 346 " =    1.663
peak=    3.816 closest distance to " CG1 ILE A  33 " =    1.191
peak=    3.810 closest distance to " O   SER A  87 " =    2.190
peak=    3.809 closest distance to " OD2 ASP A 286 " =    2.876
peak=    3.807 closest distance to " CG2 VAL A 257 " =    0.919
peak=    3.802 closest distance to " O   HOH Z 316 " =    3.147
peak=    3.798 closest distance to " CG  PRO A 243 " =    1.127
peak=    3.794 closest distance to " O   HOH Z  10 " =    1.829
peak=    3.789 closest distance to " CA  ALA A  21 " =    1.250
peak=    3.782 closest distance to " CG  PRO A 198 " =    1.261
peak=    3.778 closest distance to " O   HOH Z 423 " =    1.882
peak=    3.775 closest distance to " O   HOH Z   1 " =    2.036
peak=    3.774 closest distance to " O   HOH Z 128 " =    2.077
peak=    3.769 closest distance to " O   HOH Z 189 " =    2.334
peak=    3.760 closest distance to " O   HOH Z 147 " =    1.780
peak=    3.755 closest distance to " O   HOH Z 272 " =    1.830
peak=    3.741 closest distance to " O   HOH Z  63 " =    2.066
peak=    3.729 closest distance to " NH1AARG A 145 " =    1.199
peak=    3.723 closest distance to " CG2 THR A 221 " =    1.102
peak=    3.713 closest distance to " CA  THR A 221 " =    0.984
peak=    3.703 closest distance to " CB  SER A 212 " =    1.117
peak=    3.702 closest distance to " O   HOH Z 193 " =    1.683
peak=    3.693 closest distance to " NZ  LYS A 117 " =    3.251
peak=    3.688 closest distance to " O   HOH Z 425 " =    1.956
peak=    3.683 closest distance to " CB  TRP A 179 " =    1.397
peak=    3.683 closest distance to " CB  ASN A  39 " =    0.865
peak=    3.681 closest distance to " O   HOH Z  21 " =    1.741
peak=    3.680 closest distance to " O   HOH Z  54 " =    2.374
peak=    3.670 closest distance to " CG  PRO A  90 " =    1.086
peak=    3.663 closest distance to " O   HOH Z 180 " =    2.134
peak=    3.659 closest distance to " CA  ARG A 195 " =    1.222
peak=    3.654 closest distance to " ND2 ASN A 110 " =    1.724
peak=    3.653 closest distance to " CB  TYR A 169 " =    0.844
peak=    3.650 closest distance to " CG1BVAL A  72 " =    1.655
peak=    3.645 closest distance to " ND1 HIS A  81 " =    1.657
peak=    3.644 closest distance to " O   HOH Z 132 " =    2.635
peak=    3.643 closest distance to " O   HOH Z 280 " =    2.958
peak=    3.628 closest distance to " CE  LYS A  76 " =    0.850
peak=    3.624 closest distance to " O   TRP A 274 " =    1.865
peak=    3.624 closest distance to " CA  ALA A  51 " =    0.917
peak=    3.623 closest distance to " ND2 ASN A 249 " =    1.924
peak=    3.622 closest distance to " O   HOH Z 108 " =    2.664
peak=    3.620 closest distance to " CA  THR A 264 " =    0.884
peak=    3.597 closest distance to " O   HOH Z 135 " =    1.681
peak=    3.588 closest distance to " O   HOH Z 133 " =    1.620
peak=    3.586 closest distance to " O   HOH Z 133 " =    2.409
peak=    3.584 closest distance to " O   HOH Z 245 " =    1.308
peak=    3.584 closest distance to " CD1 ILE A 106 " =    0.817
peak=    3.577 closest distance to " O   HOH Z  97 " =    2.701
peak=    3.576 closest distance to " O   HOH Z 426 " =    1.549
peak=    3.575 closest distance to " O   HOH Z  97 " =    1.919
peak=    3.574 closest distance to " O   HOH Z 305 " =    3.678
peak=    3.570 closest distance to " CB  ILE A 120 " =    1.258
peak=    3.568 closest distance to " CD2 TRP A 179 " =    1.341
peak=    3.564 closest distance to " O   HOH Z 406 " =    1.589
peak=    3.549 closest distance to " CD  ARG A 159 " =    0.760
peak=    3.544 closest distance to " NH2AARG A 275 " =    3.585
peak=    3.528 closest distance to " CA  ALA A 291 " =    0.875
peak=    3.519 closest distance to " N   ARG A 156 " =    1.358
peak=    3.517 closest distance to " CB  ARG A 139 " =    0.970
peak=    3.508 closest distance to " O   HOH Z  44 " =    1.760
peak=    3.502 closest distance to " O   HOH Z 371 " =    3.295
peak=    3.495 closest distance to " O   HOH Z 172 " =    3.618
peak=    3.495 closest distance to " CA  ARG A  36 " =    1.106
peak=    3.488 closest distance to " NH2BARG A 145 " =    2.015
peak=    3.487 closest distance to " CG2 ILE A 120 " =    1.051
peak=    3.484 closest distance to " CD  ARG A  66 " =    2.408
peak=    3.481 closest distance to " ND1 HIS A  86 " =    1.706
peak=    3.476 closest distance to " O   HOH Z  61 " =    1.489
peak=    3.471 closest distance to " O   ALA A 165 " =    1.464
peak=    3.470 closest distance to " OG1 THR A 294 " =    2.442
peak=    3.467 closest distance to " O   HOH Z 213 " =    1.926
peak=    3.461 closest distance to " CD  ARG A 269 " =    0.937
peak=    3.453 closest distance to " CG  LEU A 167 " =    1.240
peak=    3.448 closest distance to " CB  GLU A  46 " =    1.000
peak=    3.446 closest distance to " O   HOH Z  88 " =    3.450
peak=    3.446 closest distance to " O   HOH Z 193 " =    2.103
peak=    3.444 closest distance to " CD2 LEU A 297 " =    0.826
peak=    3.442 closest distance to " CD BLYS A 290 " =    1.003
peak=    3.442 closest distance to " CD  LYS A 166 " =    1.243
peak=    3.437 closest distance to " N   VAL A 126 " =    1.380
peak=    3.435 closest distance to " O   HOH Z 419 " =    1.912
peak=    3.435 closest distance to " CA  MET A  40 " =    1.122
peak=    3.434 closest distance to " OE1 GLU A   2 " =    2.231
peak=    3.433 closest distance to " CB  MET A  40 " =    0.830
peak=    3.433 closest distance to " CB  ALA A   1 " =    4.731
peak=    3.427 closest distance to " CA  ALA A  84 " =    1.348
peak=    3.424 closest distance to " CB  ASN A 142 " =    1.043
peak=    3.422 closest distance to " O   HOH Z 425 " =    1.261
peak=    3.413 closest distance to " O   HOH Z 295 " =    1.476
peak=    3.411 closest distance to " CB  ALA A  34 " =    1.050
peak=    3.410 closest distance to " O   HOH Z 411 " =    3.838
peak=    3.409 closest distance to " CG2 ILE A  20 " =    1.364
peak=    3.405 closest distance to " CB  ALA A 291 " =    1.373
peak=    3.404 closest distance to " O   HOH Z 148 " =    3.259
peak=    3.404 closest distance to " CZ2 TRP A 179 " =    1.735
peak=    3.401 closest distance to " CE1 TYR A 186 " =    1.276
peak=    3.400 closest distance to " O   HOH Z 368 " =    3.591
peak=    3.399 closest distance to " O   HOH Z 175 " =    2.135
peak=    3.397 closest distance to " CD1 LEU A  96 " =    0.731
peak=    3.381 closest distance to " CA  ASN A 176 " =    1.837
peak=    3.379 closest distance to " O   HOH Z 299 " =    4.462
peak=    3.379 closest distance to " O   HOH Z 248 " =    1.734
peak=    3.370 closest distance to " CB  MET A  47 " =    1.003
peak=    3.368 closest distance to " CB  TYR A 116 " =    0.842
peak=    3.365 closest distance to " O   HOH Z 281 " =    3.998
peak=    3.360 closest distance to " O   HOH Z 258 " =    1.675
peak=    3.359 closest distance to " OG BSER A 164 " =    2.382
peak=    3.356 closest distance to " CB  SER A 141 " =    0.947
peak=    3.356 closest distance to " O   HOH Z 291 " =    1.550
peak=    3.351 closest distance to " O   HOH Z 383 " =    2.016
peak=    3.341 closest distance to " O   HOH Z  54 " =    1.614
peak=    3.338 closest distance to " CA  ILE A  33 " =    1.473
peak=    3.335 closest distance to " CG2BVAL A  41 " =    0.835
peak=    3.330 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.327 closest distance to " O   HOH Z 411 " =    1.774
peak=    3.326 closest distance to " O   HOH Z 185 " =    1.766
peak=    3.319 closest distance to " O   HOH Z 359 " =    1.471
peak=    3.318 closest distance to " O   HOH Z 171 " =    2.205
peak=    3.318 closest distance to " O   HOH Z 166 " =    3.708
peak=    3.318 closest distance to " O   HOH Z  66 " =    2.148
peak=    3.317 closest distance to " N   ASN A 127 " =    1.285
peak=    3.317 closest distance to " CG  GLN A  58 " =    2.700
peak=    3.312 closest distance to " O   HOH Z 345 " =    3.389
peak=    3.312 closest distance to " CZ  PHE A 192 " =    0.959
peak=    3.312 closest distance to " CA  ASP A 140 " =    1.169
peak=    3.308 closest distance to " O   HOH Z  85 " =    2.263
peak=    3.306 closest distance to " CG  LYS A  76 " =    0.970
peak=    3.297 closest distance to " O   HOH Z 329 " =    3.798
peak=    3.297 closest distance to " CA  MET A 105 " =    0.977
peak=    3.294 closest distance to " CB  THR A  31 " =    1.777
peak=    3.293 closest distance to " O   HOH Z 128 " =    2.226
peak=    3.292 closest distance to " CG1 ILE A 151 " =    0.978
peak=    3.290 closest distance to " O   THR A 251 " =    1.237
peak=    3.288 closest distance to " CA  ALA A 233 " =    1.399
peak=    3.286 closest distance to " CG  MET A 185 " =    1.049
peak=    3.286 closest distance to " CD2 LEU A 255 " =    1.493
peak=    3.282 closest distance to " OG  SER A  22 " =    2.718
peak=    3.278 closest distance to " O   HOH Z 402 " =    1.445
peak=    3.270 closest distance to " CD  LYS A 119 " =    1.377
peak=    3.268 closest distance to " CB  ALA A   9 " =    1.533
peak=    3.268 closest distance to " N   ASN A  39 " =    1.320
peak=    3.263 closest distance to " O   HOH Z 327 " =    1.756
peak=    3.262 closest distance to " CA  ASP A 162 " =    1.129
peak=    3.261 closest distance to " CB  ASN A 224 " =    1.101
peak=    3.260 closest distance to " O   HOH Z 199 " =    1.525
peak=    3.260 closest distance to " CD  ARG A 219 " =    1.066
peak=    3.259 closest distance to " CG  MET A 185 " =    1.126
peak=    3.258 closest distance to " CB  ALA A 248 " =    0.930
peak=    3.257 closest distance to " CG1 VAL A 153 " =    0.875
peak=    3.257 closest distance to " CA  TYR A 116 " =    1.385
peak=    3.256 closest distance to " O   HOH Z 273 " =    2.739
peak=    3.254 closest distance to " O   HOH Z 263 " =    1.725
peak=    3.252 closest distance to " CB  ALA A 100 " =    1.188
peak=    3.251 closest distance to " O   HOH Z 174 " =    2.657
peak=    3.245 closest distance to " CG BARG A 275 " =    1.401
peak=    3.244 closest distance to " O   HOH Z 391 " =    2.935
peak=    3.242 closest distance to " O  BHOH Z 338 " =    2.298
peak=    3.241 closest distance to " CA  GLY A 267 " =    1.119
peak=    3.240 closest distance to " O   HOH Z 410 " =    1.942
peak=    3.238 closest distance to " CB  GLN A  88 " =    1.230
peak=    3.235 closest distance to " O   HOH Z 173 " =    1.866
peak=    3.233 closest distance to " O   HOH Z 261 " =    2.157
peak=    3.233 closest distance to " CB  SER A 216 " =    0.798
peak=    3.233 closest distance to " O   HOH Z  59 " =    2.216
peak=    3.231 closest distance to " N   SER A 135 " =    1.319
peak=    3.224 closest distance to " CB  GLN A 103 " =    0.843
peak=    3.223 closest distance to " O   HOH Z 345 " =    1.677
peak=    3.223 closest distance to " CG AARG A 275 " =    1.157
peak=    3.220 closest distance to " O   HOH Z 250 " =    1.457
peak=    3.220 closest distance to " O   ALA A 158 " =    1.280
peak=    3.219 closest distance to " CB  ASN A 110 " =    1.197
peak=    3.218 closest distance to " CA  ALA A 158 " =    1.167
peak=    3.216 closest distance to " O   HOH Z 403 " =    1.334
peak=    3.216 closest distance to " CA  ASN A 217 " =    1.279
peak=    3.216 closest distance to " O   HOH Z 417 " =    3.172
peak=    3.210 closest distance to " O   HOH Z 234 " =    1.768
peak=    3.205 closest distance to " NH2 ARG A 219 " =    1.791
peak=    3.202 closest distance to " CD1AILE A 234 " =    0.940
peak=    3.201 closest distance to " CA  ALA A 154 " =    0.930
peak=    3.199 closest distance to " CB  GLN A  89 " =    1.225
peak=    3.196 closest distance to " O   HOH Z 144 " =    1.844
peak=    3.193 closest distance to " O   HOH Z  88 " =    2.955
peak=    3.193 closest distance to " CB  HIS A 108 " =    0.828
peak=    3.192 closest distance to " NE2 GLN A  77 " =    3.327
peak=    3.191 closest distance to " OE1 GLN A  11 " =    2.166
peak=    3.189 closest distance to " CG  GLN A  77 " =    1.933
peak=    3.187 closest distance to " O   HOH Z  49 " =    3.037
peak=    3.184 closest distance to " O   HOH Z 219 " =    1.877
peak=    3.183 closest distance to " CB  THR A 157 " =    1.122
peak=    3.183 closest distance to " CA  ALA A 248 " =    1.232
peak=    3.175 closest distance to " O   HOH Z 163 " =    1.565
peak=    3.174 closest distance to " OD1BASN A 224 " =    2.341
peak=    3.172 closest distance to " O   HOH Z 285 " =    3.036
peak=    3.162 closest distance to " CA  SER A  87 " =    1.052
peak=    3.154 closest distance to " O   HOH Z 435 " =    1.951
peak=    3.145 closest distance to " CG2 VAL A 197 " =    1.083
peak=    3.145 closest distance to " O   HOH Z  20 " =    1.570
peak=    3.144 closest distance to " O   HOH Z 421 " =    1.721
peak=    3.142 closest distance to " O   HOH Z 423 " =    3.095
peak=    3.139 closest distance to " O   HOH Z 417 " =    2.004
peak=    3.138 closest distance to " O   HOH Z  30 " =    2.162
peak=    3.138 closest distance to " CG1 ILE A  49 " =    1.443
peak=    3.132 closest distance to " C   TYR A 214 " =    1.488
peak=    3.129 closest distance to " CB  GLN A 205 " =    1.112
peak=    3.120 closest distance to " O   HOH Z 387 " =    3.219
peak=    3.117 closest distance to " CB  GLN A 278 " =    0.848
peak=    3.113 closest distance to " O   HOH Z 359 " =    3.893
peak=    3.112 closest distance to " O   HOH Z 374 " =    2.714
peak=    3.104 closest distance to " OD1 ASP A 231 " =    1.910
peak=    3.094 closest distance to " N   GLY A  98 " =    1.119
peak=    3.094 closest distance to " O   HOH Z 365 " =    3.027
peak=    3.093 closest distance to " O   HOH Z 384 " =    2.924
peak=    3.092 closest distance to " O   HOH Z 353 " =    2.696
peak=    3.092 closest distance to " CG2 ILE A 234 " =    0.834
peak=    3.090 closest distance to " O   HOH Z 116 " =    1.740
peak=    3.089 closest distance to " CB  ALA A 114 " =    1.188
peak=    3.086 closest distance to " CB  ASN A 215 " =    1.148
peak=    3.085 closest distance to " O   HOH Z 409 " =    3.096
peak=    3.081 closest distance to " CB  TRP A 150 " =    1.370
peak=    3.077 closest distance to " O   HOH Z 358 " =    3.685
peak=    3.048 closest distance to " N   TYR A  15 " =    0.759
peak=    3.022 closest distance to " O   HOH Z  88 " =    2.067
peak=    3.009 closest distance to " CB  ARG A 138 " =    1.004

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.690 - 5.386
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 203
   mapped sites are within: 0.796 - 5.386

peak=   -4.665 closest distance to " O   HOH Z 266 " =    4.882
peak=   -4.493 closest distance to " CB  PRO A 243 " =    2.626
peak=   -4.434 closest distance to " CD  ARG A 156 " =    2.031
peak=   -4.375 closest distance to " O   VAL A  67 " =    2.769
peak=   -4.351 closest distance to " CG  GLN A 223 " =    2.032
peak=   -4.274 closest distance to " C   HIS A 108 " =    1.122
peak=   -4.234 closest distance to " O   ILE A 109 " =    2.607
peak=   -4.171 closest distance to " O   HOH Z 372 " =    2.398
peak=   -4.095 closest distance to " O   HOH Z 290 " =    1.160
peak=   -4.065 closest distance to " SG  CYS A 254 " =    3.436
peak=   -4.043 closest distance to " CG1 VAL A 112 " =    2.782
peak=   -4.037 closest distance to " O   HOH Z 377 " =    2.149
peak=   -4.023 closest distance to " O   HOH Z 126 " =    1.884
peak=   -4.020 closest distance to " N   ALA A  43 " =    2.581
peak=   -3.984 closest distance to " O   HOH Z  10 " =    1.564
peak=   -3.983 closest distance to " OG  SER A  97 " =    2.185
peak=   -3.969 closest distance to " O   HOH Z 114 " =    3.308
peak=   -3.957 closest distance to " CD  GLN A  58 " =    1.025
peak=   -3.934 closest distance to " O   HOH Z 389 " =    1.833
peak=   -3.903 closest distance to " OG BSER A 134 " =    1.196
peak=   -3.871 closest distance to " CZ3 TRP A 179 " =    1.153
peak=   -3.864 closest distance to " O   PRO A 163 " =    2.150
peak=   -3.861 closest distance to " O   HOH Z 196 " =    2.038
peak=   -3.855 closest distance to " O   HOH Z 353 " =    2.126
peak=   -3.838 closest distance to " NH2AARG A 275 " =    5.386
peak=   -3.837 closest distance to " O   HOH Z 198 " =    2.152
peak=   -3.815 closest distance to " ND2 ASN A  45 " =    1.820
peak=   -3.790 closest distance to " O   HOH Z 311 " =    3.735
peak=   -3.771 closest distance to " O   HOH Z 231 " =    2.281
peak=   -3.762 closest distance to " CG  ASP A 231 " =    0.796
peak=   -3.756 closest distance to " CE2 TYR A  30 " =    2.766
peak=   -3.748 closest distance to " CG2 ILE A 263 " =    2.334
peak=   -3.737 closest distance to " CA  ASP A 298 " =    1.073
peak=   -3.732 closest distance to " CA  VAL A  67 " =    2.736
peak=   -3.732 closest distance to " O   HOH Z 435 " =    2.783
peak=   -3.712 closest distance to " CD1 PHE A  59 " =    1.863
peak=   -3.706 closest distance to " CB  ALA A 291 " =    2.361
peak=   -3.697 closest distance to " SG ACYS A 201 " =    1.885
peak=   -3.691 closest distance to " O   HOH Z  43 " =    1.579
peak=   -3.681 closest distance to " CD2 LEU A 300 " =    2.925
peak=   -3.675 closest distance to " O   PRO A 198 " =    1.284
peak=   -3.674 closest distance to " CD  ARG A 139 " =    1.544
peak=   -3.673 closest distance to " O   HOH Z 185 " =    2.340
peak=   -3.664 closest distance to " CD1 LEU A 101 " =    2.455
peak=   -3.662 closest distance to " CG  ASP A 132 " =    2.315
peak=   -3.642 closest distance to " CG  PHE A 283 " =    2.764
peak=   -3.639 closest distance to " CD1 LEU A 228 " =    2.298
peak=   -3.637 closest distance to " O   HOH Z 407 " =    3.183
peak=   -3.637 closest distance to " OD1 ASN A 148 " =    1.587
peak=   -3.632 closest distance to " O   HOH Z  73 " =    2.287
peak=   -3.631 closest distance to " OG BSER A 134 " =    1.793
peak=   -3.622 closest distance to " OXT GLY A 302 " =    2.884
peak=   -3.608 closest distance to " O   HOH Z 211 " =    1.674
peak=   -3.605 closest distance to " CA  GLY A 203 " =    2.387
peak=   -3.594 closest distance to " N   GLN A  58 " =    1.620
peak=   -3.593 closest distance to " CG1 VAL A 250 " =    2.673
peak=   -3.571 closest distance to " O   HOH Z  52 " =    1.411
peak=   -3.566 closest distance to " O   HOH Z 292 " =    4.579
peak=   -3.566 closest distance to " OD1 ASP A 171 " =    1.597
peak=   -3.565 closest distance to " NH1 ARG A 195 " =    2.574
peak=   -3.559 closest distance to " CB  PRO A 163 " =    2.525
peak=   -3.555 closest distance to " O   HOH Z 198 " =    1.333
peak=   -3.555 closest distance to " CB  ASN A  39 " =    2.298
peak=   -3.548 closest distance to " ND2 ASN A  45 " =    1.123
peak=   -3.536 closest distance to " O   HOH Z  38 " =    1.477
peak=   -3.535 closest distance to " CG1 VAL A 112 " =    2.613
peak=   -3.533 closest distance to " C   LEU A 143 " =    1.132
peak=   -3.528 closest distance to " CD2 PHE A 192 " =    2.056
peak=   -3.527 closest distance to " OG  SER A  62 " =    1.655
peak=   -3.515 closest distance to " C   ALA A 158 " =    1.290
peak=   -3.509 closest distance to " CB  ALA A 291 " =    2.249
peak=   -3.499 closest distance to " O   HOH Z  13 " =    1.546
peak=   -3.497 closest distance to " C   ASN A 285 " =    2.451
peak=   -3.490 closest distance to " O   GLY A 211 " =    1.529
peak=   -3.489 closest distance to " O   HOH Z 394 " =    1.441
peak=   -3.488 closest distance to " CB  CYS A 201 " =    2.618
peak=   -3.485 closest distance to " N   SER A 212 " =    2.022
peak=   -3.480 closest distance to " CB  TYR A  15 " =    2.185
peak=   -3.474 closest distance to " CG  ARG A 269 " =    2.403
peak=   -3.467 closest distance to " CZ  PHE A  59 " =    1.638
peak=   -3.464 closest distance to " CD  ARG A 195 " =    5.166
peak=   -3.458 closest distance to " NE2 GLN A  88 " =    1.879
peak=   -3.455 closest distance to " O   VAL A 189 " =    2.606
peak=   -3.453 closest distance to " O   HOH Z 166 " =    1.559
peak=   -3.452 closest distance to " CA  GLY A 241 " =    3.119
peak=   -3.448 closest distance to " O   HOH Z 253 " =    3.961
peak=   -3.447 closest distance to " O   HOH Z 351 " =    1.501
peak=   -3.444 closest distance to " CB  ALA A  43 " =    2.501
peak=   -3.439 closest distance to " O   HOH Z  11 " =    1.786
peak=   -3.437 closest distance to " N   MET A 105 " =    2.856
peak=   -3.437 closest distance to " CD1 LEU A 297 " =    2.357
peak=   -3.423 closest distance to " NH2 ARG A  79 " =    1.970
peak=   -3.420 closest distance to " CZ  TYR A 169 " =    1.772
peak=   -3.414 closest distance to " O   HOH Z 313 " =    2.020
peak=   -3.404 closest distance to " CD2 LEU A 237 " =    2.715
peak=   -3.404 closest distance to " O   HOH Z 298 " =    2.588
peak=   -3.399 closest distance to " N   ALA A 226 " =    2.132
peak=   -3.399 closest distance to " CD2 TYR A 293 " =    2.051
peak=   -3.379 closest distance to " O   HOH Z 111 " =    2.171
peak=   -3.372 closest distance to " O   HOH Z   6 " =    1.530
peak=   -3.371 closest distance to " CG  ARG A  66 " =    2.392
peak=   -3.371 closest distance to " O   HOH Z  60 " =    2.488
peak=   -3.364 closest distance to " NH2 ARG A  79 " =    1.610
peak=   -3.352 closest distance to " OD1 ASN A 187 " =    1.606
peak=   -3.349 closest distance to " CB  ASP A 286 " =    2.155
peak=   -3.348 closest distance to " N   THR A 235 " =    1.318
peak=   -3.336 closest distance to " CG  GLU A 277 " =    1.154
peak=   -3.334 closest distance to " CE  MET A 105 " =    2.257
peak=   -3.329 closest distance to " ND2 ASN A  60 " =    1.438
peak=   -3.328 closest distance to " CB  PHE A 208 " =    2.272
peak=   -3.325 closest distance to " CD2 PHE A  61 " =    2.489
peak=   -3.324 closest distance to " CG2 VAL A 189 " =    2.143
peak=   -3.323 closest distance to " CD  PRO A 213 " =    2.232
peak=   -3.323 closest distance to " ND2 ASN A 249 " =    2.351
peak=   -3.321 closest distance to " O   HOH Z 426 " =    1.643
peak=   -3.315 closest distance to " CG1 VAL A 197 " =    2.274
peak=   -3.314 closest distance to " CE2 PHE A 218 " =    2.452
peak=   -3.304 closest distance to " CE3 TRP A 150 " =    2.092
peak=   -3.301 closest distance to " O   HOH Z  47 " =    1.621
peak=   -3.292 closest distance to " OE1 GLN A 223 " =    2.124
peak=   -3.290 closest distance to " O   HOH Z  76 " =    1.925
peak=   -3.283 closest distance to " O   HOH Z  37 " =    1.883
peak=   -3.279 closest distance to " NH2 ARG A 159 " =    2.429
peak=   -3.276 closest distance to " O   HOH Z 165 " =    1.918
peak=   -3.269 closest distance to " CG  PRO A 163 " =    2.567
peak=   -3.267 closest distance to " O   HOH Z  93 " =    2.160
peak=   -3.266 closest distance to " OD2 ASP A 171 " =    1.867
peak=   -3.265 closest distance to " O   HOH Z  44 " =    2.178
peak=   -3.265 closest distance to " CD1 ILE A 239 " =    2.106
peak=   -3.258 closest distance to " NH2BARG A 275 " =    1.998
peak=   -3.255 closest distance to " CG  TRP A 266 " =    1.809
peak=   -3.253 closest distance to " O   HOH Z  51 " =    1.641
peak=   -3.252 closest distance to " CD1 ILE A 151 " =    2.367
peak=   -3.245 closest distance to " CE BMET A  47 " =    2.078
peak=   -3.245 closest distance to " CG  MET A 105 " =    0.972
peak=   -3.243 closest distance to " OG1 THR A 178 " =    1.353
peak=   -3.243 closest distance to " O   HOH Z 317 " =    1.624
peak=   -3.237 closest distance to " CH2 TRP A 177 " =    2.077
peak=   -3.236 closest distance to " CG  GLU A  53 " =    1.478
peak=   -3.235 closest distance to " OG  SER A  26 " =    1.302
peak=   -3.233 closest distance to " CB  ALA A 248 " =    2.422
peak=   -3.232 closest distance to " O   MET A  40 " =    2.756
peak=   -3.232 closest distance to " O   GLY A  80 " =    2.546
peak=   -3.226 closest distance to " O   HOH Z 281 " =    2.660
peak=   -3.220 closest distance to " O   HOH Z 174 " =    3.078
peak=   -3.220 closest distance to " NE2 GLN A 103 " =    1.706
peak=   -3.218 closest distance to " O   HOH Z 385 " =    1.996
peak=   -3.217 closest distance to " CB  ALA A 248 " =    2.037
peak=   -3.214 closest distance to " O   PHE A 218 " =    1.660
peak=   -3.210 closest distance to " CG2 THR A 221 " =    2.236
peak=   -3.208 closest distance to " O   PRO A 198 " =    2.056
peak=   -3.207 closest distance to " CD2 PHE A 225 " =    1.180
peak=   -3.201 closest distance to " O   HOH Z 177 " =    1.694
peak=   -3.200 closest distance to " O   PRO A 198 " =    1.333
peak=   -3.200 closest distance to " O   HOH Z 357 " =    2.039
peak=   -3.199 closest distance to " O   HOH Z 298 " =    1.275
peak=   -3.196 closest distance to " O   HOH Z 234 " =    4.192
peak=   -3.196 closest distance to " O   ALA A  10 " =    1.713
peak=   -3.189 closest distance to " OG BSER A 210 " =    2.238
peak=   -3.185 closest distance to " CB  LEU A  83 " =    2.412
peak=   -3.181 closest distance to " O   HOH Z 166 " =    1.809
peak=   -3.179 closest distance to " NH1 ARG A  36 " =    2.083
peak=   -3.177 closest distance to " CZ  PHE A  38 " =    2.323
peak=   -3.176 closest distance to " O   PHE A 218 " =    1.650
peak=   -3.176 closest distance to " O   HOH Z 322 " =    1.589
peak=   -3.175 closest distance to " O   HOH Z 264 " =    1.854
peak=   -3.174 closest distance to " O   HOH Z 414 " =    1.630
peak=   -3.172 closest distance to " O   HOH Z 241 " =    1.333
peak=   -3.170 closest distance to " O   ASN A 301 " =    1.574
peak=   -3.164 closest distance to " CD1 ILE A 199 " =    2.504
peak=   -3.160 closest distance to " CA  GLY A 241 " =    2.299
peak=   -3.158 closest distance to " CD2 TYR A 247 " =    2.438
peak=   -3.156 closest distance to " OH  TYR A 247 " =    2.046
peak=   -3.155 closest distance to " OE1 GLN A  88 " =    1.229
peak=   -3.150 closest distance to " O   HOH Z 252 " =    4.267
peak=   -3.148 closest distance to " OE2 GLU A   2 " =    1.678
peak=   -3.144 closest distance to " O   ALA A  34 " =    2.546
peak=   -3.143 closest distance to " O   ALA A 292 " =    2.008
peak=   -3.139 closest distance to " O   HOH Z 134 " =    2.814
peak=   -3.139 closest distance to " C   MET A 188 " =    1.430
peak=   -3.120 closest distance to " CB  TRP A  85 " =    2.440
peak=   -3.117 closest distance to " N   ASP A 171 " =    2.446
peak=   -3.117 closest distance to " O   HOH Z  51 " =    1.438
peak=   -3.110 closest distance to " SD  MET A 188 " =    2.273
peak=   -3.110 closest distance to " CA  GLY A 133 " =    2.100
peak=   -3.108 closest distance to " CG2 ILE A  20 " =    2.784
peak=   -3.102 closest distance to " O   TRP A  70 " =    1.547
peak=   -3.101 closest distance to " O   HOH Z  41 " =    2.499
peak=   -3.098 closest distance to " N   ALA A 248 " =    1.581
peak=   -3.096 closest distance to " O   HOH Z 393 " =    1.400
peak=   -3.080 closest distance to " O   HOH Z 323 " =    1.374
peak=   -3.080 closest distance to " O   HOH Z 193 " =    1.809
peak=   -3.078 closest distance to " CG  ASN A 301 " =    1.982
peak=   -3.073 closest distance to " O   HOH Z 421 " =    3.075
peak=   -3.071 closest distance to " N   TYR A  68 " =    3.090
peak=   -3.070 closest distance to " CA  GLY A 241 " =    2.796
peak=   -3.068 closest distance to " CD2 PHE A  59 " =    2.513
peak=   -3.054 closest distance to " O   HOH Z 350 " =    1.690
peak=   -3.040 closest distance to " CD  GLN A  88 " =    0.860
peak=   -3.038 closest distance to " CB  ASP A 132 " =    2.351
peak=   -3.014 closest distance to " OD2 ASP A  50 " =    2.272

================= 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    :  0.2574 0.2552   5.832370e+00   5.827707e+00
   1_bss:  0.2423 0.2407   5.801079e+00   5.788063e+00
   1_xyz:  0.1522 0.1674   5.358009e+00   5.452846e+00
   1_adp:  0.1417 0.1690   5.307862e+00   5.468557e+00
   1_occ:  0.1411 0.1687   5.305142e+00   5.466432e+00
   2_bss:  0.1409 0.1674   5.305349e+00   5.463722e+00
   2_xyz:  0.1217 0.1548   5.184568e+00   5.378207e+00
   2_adp:  0.1164 0.1542   5.157571e+00   5.373333e+00
   2_occ:  0.1163 0.1540   5.157322e+00   5.373331e+00
   3_bss:  0.1162 0.1539   5.157413e+00   5.373375e+00
   3_xyz:  0.1089 0.1533   5.118967e+00   5.363038e+00
   3_adp:  0.1078 0.1545   5.117611e+00   5.367308e+00
   3_occ:  0.1077 0.1545   5.117754e+00   5.367705e+00
   4_bss:  0.1080 0.1541   5.119307e+00   5.367481e+00
   4_xyz:  0.1100 0.1563   5.137251e+00   5.383030e+00
   4_adp:  0.1113 0.1550   5.138826e+00   5.378247e+00
   4_occ:  0.1113 0.1551   5.138980e+00   5.378692e+00
   5_bss:  0.1112 0.1551   5.139165e+00   5.378926e+00
   5_xyz:  0.1071 0.1549   5.117813e+00   5.373355e+00
   5_adp:  0.1065 0.1557   5.116784e+00   5.376329e+00
   5_occ:  0.1064 0.1557   5.116794e+00   5.376396e+00
   5_bss:  0.1064 0.1557   5.116871e+00   5.376446e+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:  0.312  49.469  -1.420  -1.670  -1.478  -0.000  -0.000  -0.000
   1_xyz:  0.312  49.469  -1.420  -1.670  -1.478  -0.000  -0.000  -0.000
   1_adp:  0.312  49.469  -1.420  -1.670  -1.478  -0.000  -0.000  -0.000
   1_occ:  0.312  49.469  -1.420  -1.670  -1.478  -0.000  -0.000  -0.000
   2_bss:  0.328  55.449  -2.531  -2.430  -1.821  -0.000  -0.000  -0.000
   2_xyz:  0.328  55.449  -2.531  -2.430  -1.821  -0.000  -0.000  -0.000
   2_adp:  0.328  55.449  -2.531  -2.430  -1.821  -0.000  -0.000  -0.000
   2_occ:  0.328  55.449  -2.531  -2.430  -1.821  -0.000  -0.000  -0.000
   3_bss:  0.328  55.449  -2.374  -2.198  -1.512  -0.000  -0.000  -0.000
   3_xyz:  0.328  55.449  -2.374  -2.198  -1.512  -0.000  -0.000  -0.000
   3_adp:  0.328  55.449  -2.374  -2.198  -1.512  -0.000  -0.000  -0.000
   3_occ:  0.328  55.449  -2.374  -2.198  -1.512  -0.000  -0.000  -0.000
   4_bss:  0.323  55.449  -2.175  -2.017  -1.308  -0.000  -0.000  -0.000
   4_xyz:  0.323  55.449  -2.175  -2.017  -1.308  -0.000  -0.000  -0.000
   4_adp:  0.323  55.449  -2.175  -2.017  -1.308  -0.000  -0.000  -0.000
   4_occ:  0.323  55.449  -2.175  -2.017  -1.308  -0.000  -0.000  -0.000
   5_bss:  0.321  51.319  -2.128  -1.946  -1.198  -0.000  -0.000  -0.000
   5_xyz:  0.321  51.319  -2.128  -1.946  -1.198  -0.000  -0.000  -0.000
   5_adp:  0.321  51.319  -2.128  -1.946  -1.198  -0.000  -0.000  -0.000
   5_occ:  0.321  51.319  -2.128  -1.946  -1.198  -0.000  -0.000  -0.000
   5_bss:  0.321  51.292  -1.906  -1.736  -0.979  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  24.520 0.8207  0.9781    17815.456
   1_bss:  23.273 0.8315  0.9421    15102.533
   1_xyz:  15.081 0.9073  0.9929     7286.552
   1_adp:  15.502 0.9034  0.9875     7448.054
   1_occ:  15.465 0.9036  0.9875     7398.802
   2_bss:  15.404 0.9040  0.9620     7322.366
   2_xyz:  13.683 0.9179  0.9682     6209.198
   2_adp:  13.568 0.9188  0.9646     6072.666
   2_occ:  13.573 0.9188  0.9644     6071.757
   3_bss:  13.576 0.9187  0.9725     6072.118
   3_xyz:  13.385 0.9201  0.9738     5977.000
   3_adp:  13.485 0.9193  0.9677     6025.924
   3_occ:  13.491 0.9193  0.9676     6030.918
   4_bss:  13.510 0.9191  0.9737     6030.356
   4_xyz:  13.793 0.9170  0.9718     6213.614
   4_adp:  13.648 0.9181  0.9677     6174.182
   4_occ:  13.660 0.9181  0.9676     6178.745
   5_bss:  13.668 0.9180  0.9701     6178.401
   5_xyz:  13.576 0.9186  0.9712     6134.475
   5_adp:  13.649 0.9180  0.9656     6153.582
   5_occ:  13.653 0.9180  0.9656     6154.463
   5_bss:  13.655 0.9180  0.9721     6155.561
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6081e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6081e-01
   1_xyz:   0.952  0.006  0.066 15.000  0.004  4.113   5.3848e-02
   1_adp:   0.952  0.006  0.066 15.000  0.004  4.113   5.3848e-02
   1_occ:   0.952  0.006  0.066 15.000  0.004  4.113   5.3848e-02
   2_bss:   0.952  0.006  0.066 15.000  0.004  4.113   5.3848e-02
   2_xyz:   0.922  0.006  0.071 14.645  0.004  4.120   5.2346e-02
   2_adp:   0.922  0.006  0.071 14.645  0.004  4.120   5.2346e-02
   2_occ:   0.922  0.006  0.071 14.645  0.004  4.120   5.2346e-02
   3_bss:   0.922  0.006  0.071 14.645  0.004  4.120   5.2346e-02
   3_xyz:   1.054  0.009  0.080 15.049  0.004  4.123   6.7796e-02
   3_adp:   1.054  0.009  0.080 15.049  0.004  4.123   6.7796e-02
   3_occ:   1.054  0.009  0.080 15.049  0.004  4.123   6.7796e-02
   4_bss:   1.054  0.009  0.080 15.049  0.004  4.123   6.7796e-02
   4_xyz:   0.942  0.007  0.073 14.765  0.004  4.123   5.5021e-02
   4_adp:   0.942  0.007  0.073 14.765  0.004  4.123   5.5021e-02
   4_occ:   0.942  0.007  0.073 14.765  0.004  4.123   5.5021e-02
   5_bss:   0.942  0.007  0.073 14.765  0.004  4.123   5.5021e-02
   5_xyz:   1.079  0.010  0.083 15.074  0.004  4.126   7.1301e-02
   5_adp:   1.079  0.010  0.083 15.074  0.004  4.126   7.1301e-02
   5_occ:   1.079  0.010  0.083 15.074  0.004  4.126   7.1301e-02
   5_bss:   1.079  0.010  0.083 15.074  0.004  4.126   7.1301e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4199e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4199e-01
   1_xyz:   8.218  0.035  0.225 84.229  0.030  2.352   4.5699e-02
   1_adp:   8.218  0.035  0.225 84.229  0.030  2.352   4.5699e-02
   1_occ:   8.218  0.035  0.225 84.229  0.030  2.352   4.5699e-02
   2_bss:   8.218  0.035  0.225 84.229  0.030  2.352   4.5699e-02
   2_xyz:   6.858  0.037  0.205 84.143  0.036  2.400   4.0190e-02
   2_adp:   6.858  0.037  0.205 84.143  0.036  2.400   4.0190e-02
   2_occ:   6.858  0.037  0.205 84.143  0.036  2.400   4.0190e-02
   3_bss:   6.858  0.037  0.205 84.143  0.036  2.400   4.0190e-02
   3_xyz:   7.268  0.044  0.252 82.701  0.038  2.301   5.0954e-02
   3_adp:   7.268  0.044  0.252 82.701  0.038  2.301   5.0954e-02
   3_occ:   7.268  0.044  0.252 82.701  0.038  2.301   5.0954e-02
   4_bss:   7.268  0.044  0.252 82.701  0.038  2.301   5.0954e-02
   4_xyz:   7.115  0.040  0.224 82.836  0.036  2.391   4.0547e-02
   4_adp:   7.115  0.040  0.224 82.836  0.036  2.391   4.0547e-02
   4_occ:   7.115  0.040  0.224 82.836  0.036  2.391   4.0547e-02
   5_bss:   7.115  0.040  0.224 82.836  0.036  2.391   4.0547e-02
   5_xyz:   7.380  0.047  0.261 83.120  0.038  2.260   5.5617e-02
   5_adp:   7.380  0.047  0.261 83.120  0.038  2.260   5.5617e-02
   5_occ:   7.380  0.047  0.261 83.120  0.038  2.260   5.5617e-02
   5_bss:   7.380  0.047  0.261 83.120  0.038  2.260   5.5617e-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:  81.05   0.00  16.37  81.05   0.00  12.57  62.73   5.70  37.06
   1_occ:  81.05   0.00  16.37  81.05   0.00  12.57  62.73   5.70  37.06
   2_bss:  81.05   0.00  16.37  81.05   0.00  12.57  62.73   5.70  37.06
   2_xyz:  81.05   0.00  16.37  81.05   0.00  12.57  62.73   5.70  37.06
   2_adp:  76.36   1.44  16.92  76.36   1.44  12.89  67.50   2.67  38.88
   2_occ:  76.36   1.44  16.92  76.36   1.44  12.89  67.50   2.67  38.88
   3_bss:  76.36   1.44  16.92  76.36   1.44  12.89  67.50   2.67  38.88
   3_xyz:  76.36   1.44  16.92  76.36   1.44  12.89  67.50   2.67  38.88
   3_adp:  88.07   0.60  17.04  88.07   0.60  12.87  76.01   2.88  39.74
   3_occ:  88.07   0.60  17.04  88.07   0.60  12.87  76.01   2.88  39.74
   4_bss:  88.07   0.60  17.04  88.07   0.60  12.87  76.01   2.88  39.74
   4_xyz:  88.07   0.60  17.04  88.07   0.60  12.87  76.01   2.88  39.74
   4_adp:  84.56   1.39  16.34  84.56   1.39  12.56  71.19   4.59  36.89
   4_occ:  84.56   1.39  16.34  84.56   1.39  12.56  71.19   4.59  36.89
   5_bss:  84.56   1.39  16.34  84.56   1.39  12.56  71.19   4.59  36.89
   5_xyz:  84.56   1.39  16.34  84.56   1.39  12.56  71.19   4.59  36.89
   5_adp:  85.45   0.81  16.36  85.45   0.81  12.45  71.25   5.88  37.68
   5_occ:  85.45   0.81  16.36  85.45   0.81  12.45  71.25   5.88  37.68
   5_bss:  85.42   0.78  16.34  85.42   0.78  12.42  71.22   5.86  37.65
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.014    0.011    0.211
   1_adp:    1.014    0.011    0.211
   1_occ:    1.014    0.011    0.211
   2_bss:    1.014    0.011    0.211
   2_xyz:    0.716    0.009    0.248
   2_adp:    0.716    0.009    0.248
   2_occ:    0.716    0.009    0.248
   3_bss:    0.716    0.009    0.248
   3_xyz:    0.654    0.014    0.269
   3_adp:    0.654    0.014    0.269
   3_occ:    0.654    0.014    0.269
   4_bss:    0.654    0.014    0.269
   4_xyz:    0.772    0.022    0.278
   4_adp:    0.772    0.022    0.278
   4_occ:    0.772    0.022    0.278
   5_bss:    0.772    0.022    0.278
   5_xyz:    0.785    0.014    0.284
   5_adp:    0.785    0.014    0.284
   5_occ:    0.785    0.014    0.284
   5_bss:    0.785    0.014    0.284
------------------------------------------------------------------------

CPU time actual refinement: 318.49


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_917/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_917/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_917/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_917/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_917/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 318.35 
  Macro-tasks:
    bulk solvent and scale       = 38.13  
    individual site refinement   = 126.19 
    weights calculation          = 28.91  
    collect and process          = 6.61   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 199.95 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 100.57 
    alpha_beta                      = 8.23   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 109.01 
    fmodel                         = 6.32   
    r_factors                      = 0.19   
    phase_errors                   = 11.40  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 238.23 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.548 micro seconds
Total CPU time: 5.53 minutes
from_scatterers_fft:    652 calls, 100.21 s
gradients_fft:          597 calls,  95.80 s

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

# Date 2008-01-16 Time 05:58:37 PST -0800 (1200491917.84 s)
Start R-work = 0.2574, R-free = 0.2552 (no bulk solvent and anisotropic scale)
Final R-work = 0.1292, R-free = 0.1742 (no bulk solvent and anisotropic scale)

Start R-work = 0.2423, R-free = 0.2407
Final R-work = 0.1064, R-free = 0.1557