# Date 2008-01-16 Time 04:12:47 PST -0800 (1200485567.68 s)
#phil __OFF__

Command line arguments: "../217.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11400
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 217

-------------------------------------------------------------------------------
  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: (68.845, 47.6339, 87.6859, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9291 1.9609
Completeness in resolution range: 0.921705
Completeness with d_max=infinity: 0.918938

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9291
                             d_min =   1.9609

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: (68.845, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9291 1.9609
Completeness in resolution range: 0.921705
Completeness with d_max=infinity: 0.918938

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9295 -  4.1963 [2232/2260]  2005   227  10.2%
  bin  2:  4.1963 -  3.3430 [2140/2163]  1926   214  10.0%
  bin  3:  3.3430 -  2.9240 [2112/2137]  1905   207   9.8%
  bin  4:  2.9240 -  2.6583 [2093/2109]  1884   209  10.0%
  bin  5:  2.6583 -  2.4687 [2078/2122]  1864   214  10.3%
  bin  6:  2.4687 -  2.3237 [2075/2103]  1871   204   9.8%
  bin  7:  2.3237 -  2.2077 [2056/2092]  1858   198   9.6%
  bin  8:  2.2077 -  2.1119 [2068/2110]  1859   209  10.1%
  bin  9:  2.1119 -  2.0308 [2036/2083]  1834   202   9.9%
  bin 10:  2.0308 -  1.9609 [ 699/2074]   624    75  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_217/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:
        1.26 -     1.99: 11
        1.99 -     2.72: 182
        2.72 -     3.44: 4573
        3.44 -     4.17: 9319
        4.17 -     4.90: 14176
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.261 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.458 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.475 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.587 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.651 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28256 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_217/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_217/model_refine_001.geo

CPU time processing inputs: 9.46


============================ 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 = 68.845 47.63395 87.68585 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: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4442   r_free= 0.4388   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.246553                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9295 -  4.6805 0.99   1453  160 0.3384 0.3581      6.4939      6.5267|
|  2:  4.6805 -  3.7342 0.99   1401  155 0.3687 0.3753      6.7221      6.7431|
|  3:  3.7342 -  3.2678 0.99   1360  153 0.4169 0.4002      6.6087      6.5877|
|  4:  3.2678 -  2.9716 0.99   1367  144 0.4338 0.4187      6.4418      6.4466|
|  5:  2.9716 -  2.7601 0.98   1331  154 0.4706 0.4385      6.3247      6.3298|
|  6:  2.7601 -  2.5982 0.99   1350  153 0.4735 0.5277      6.2378      6.1752|
|  7:  2.5982 -  2.4687 0.98   1322  152 0.4739 0.4106      6.1873      6.0931|
|  8:  2.4687 -  2.3617 0.99   1337  141 0.5080 0.4803      6.1589       6.138|
|  9:  2.3617 -  2.2711 0.99   1335  145 0.5054 0.4643      6.1048      6.1419|
| 10:  2.2711 -  2.1930 0.98   1335  146 0.5041 0.4965      6.0805      6.0772|
| 11:  2.1930 -  2.1246 0.97   1291  157 0.5160 0.5108       6.005      6.0018|
| 12:  2.1246 -  2.0640 0.99   1332  146 0.5098 0.5115      5.9317       5.937|
| 13:  2.0640 -  2.0098 0.84   1144  117 0.5053 0.5603      5.8574      5.8491|
| 14:  2.0098 -  1.9609 0.21    272   36 0.4854 0.4884      5.8995      5.7239|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9295 -  4.6805  1453   160  0.72  32.35   0.84     0.74      63516.43|
|  2:  4.6805 -  3.7342  1401   155  0.74  31.65   0.94     0.83      88648.29|
|  3:  3.7342 -  3.2678  1360   153  0.65  39.55   0.91     0.82      92409.53|
|  4:  3.2678 -  2.9716  1367   144  0.57  46.04   0.92     0.76      81219.47|
|  5:  2.9716 -  2.7601  1331   154  0.51  51.18   0.90     0.70      66243.80|
|  6:  2.7601 -  2.5982  1350   153  0.49  52.89   0.91     0.66      58042.45|
|  7:  2.5982 -  2.4687  1322   152  0.48  53.26   0.93     0.66      52896.85|
|  8:  2.4687 -  2.3617  1337   141  0.47  54.15   0.92     0.67      47283.95|
|  9:  2.3617 -  2.2711  1335   145  0.48  53.55   0.91     0.70      43825.11|
| 10:  2.2711 -  2.1930  1335   146  0.47  54.33   0.93     0.67      39941.25|
| 11:  2.1930 -  2.1246  1291   157  0.40  60.13   0.93     0.62      42619.81|
| 12:  2.1246 -  2.0640  1332   146  0.32  65.84   0.94     0.53      42479.82|
| 13:  2.0640 -  2.0098  1144   117  0.30  67.74   0.92     0.49      38537.58|
| 14:  2.0098 -  1.9609   272    36  0.40  59.44   1.00     0.53      28119.01|
|alpha:            min =        0.49 max =            0.83 mean =         0.68|
|beta:             min =    28119.01 max =        92409.53 mean =     58311.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.99 mean =        50.68|
|phase err.(test): min =        0.00 max =           89.98 mean =        50.87|
|-----------------------------------------------------------------------------|

============================== 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 = 9.554387              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.652   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.574987              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.567   (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 |  1.261 -  1.624:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.624 -  1.988:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.988 -  2.352:       21 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.352 -  2.716:      161 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.716 -  3.080:     2285 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.080 -  3.444:     2288 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.444 -  3.808:     4110 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.808 -  4.172:     5209 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.172 -  4.536:     6349 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.536 -  4.900:     7827 |
|-----------------------------------------------------------------------------|
|-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 |        0.192 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.261 |       0.603 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    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: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4442   r_free= 0.4388   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.246553                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4371   r_free= 0.4292   ksol= 0.31   Bsol= 35.10   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,1.83,1.42,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.239296                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.276602              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.272   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.892941              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.283   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4371      final r-factor (work) = 0.2871          |
| start r-factor (free) = 0.4292      final r-factor (free) = 0.3149          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.0129 = 8.28 * 0.50 * 6.2396 + 1.00 * 0.1917                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.1893 = 8.28 * 0.50 * 6.0589 + 1.00 * 0.1159                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2871      final r-factor (work) = 0.2585          |
| start r-factor (free) = 0.3149      final r-factor (free) = 0.3260          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4163 = 0.89 * 1.00 * 6.0589 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2525 = 0.89 * 1.00 * 5.8593 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.98   18.22    None  None   None       |
|    all(noH): 2823   0      0.00    74.98   18.22    None  None   None       |
|    Sol.    : 438    0      4.04    74.98   39.55    None  None   None       |
|    Mac.    : 2385   0      0.00    66.05   14.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.498:  612   |   5:    37.488 -  44.986:  128        |
|      1:     7.498 -  14.995:  941   |   6:    44.986 -  52.483:  102        |
|      2:    14.995 -  22.493:  508   |   7:    52.483 -  59.981:   61        |
|      3:    22.493 -  29.991:  239   |   8:    59.981 -  67.479:   35        |
|      4:    29.991 -  37.488:  186   |   9:    67.479 -  74.976:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2585 r_free = 0.3260             target_work(ml) = 5.870         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2584 r_free = 0.3262             target_work(ml) = 5.870         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2584   r_free= 0.3262   ksol= 0.31   Bsol= 35.10   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,1.83,1.42,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.870070                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2553   r_free= 0.3235   ksol= 0.33   Bsol= 60.48   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-0.16,-0.14,-0.00,-0.00,-0.00); trace/3= -0.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.864710                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.548356              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.665   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.282146              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.358   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2553      final r-factor (work) = 0.1855          |
| start r-factor (free) = 0.3235      final r-factor (free) = 0.2338          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4491 = 4.55 * 0.50 * 5.8629 + 1.00 * 0.1159                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1468 = 4.55 * 0.50 * 5.7516 + 1.00 * 0.0667                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1855      final r-factor (work) = 0.1701          |
| start r-factor (free) = 0.2338      final r-factor (free) = 0.2143          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6400 = 0.28 * 1.00 * 5.7516 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5707 = 0.28 * 1.00 * 5.5350 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    75.44   17.70    None  None   None       |
|    all(noH): 2823   0      0.81    75.44   17.70    None  None   None       |
|    Sol.    : 438    0      5.86    74.89   39.87    None  None   None       |
|    Mac.    : 2385   0      0.81    75.44   13.63    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:     0.811 -   8.273:  635   |   5:    38.123 -  45.586:  120        |
|      1:     8.273 -  15.736: 1142   |   6:    45.586 -  53.048:   88        |
|      2:    15.736 -  23.198:  455   |   7:    53.048 -  60.511:   61        |
|      3:    23.198 -  30.661:  157   |   8:    60.511 -  67.974:   36        |
|      4:    30.661 -  38.123:  115   |   9:    67.974 -  75.436:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1701 r_free = 0.2143             target_work(ml) = 5.497         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1699 r_free = 0.2139             target_work(ml) = 5.496         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1699   r_free= 0.2139   ksol= 0.33   Bsol= 60.48   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-0.16,-0.14,-0.00,-0.00,-0.00); trace/3= -0.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.495940                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1696   r_free= 0.2136   ksol= 0.33   Bsol= 58.03   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-1.29,-0.67,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.495126                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.007944              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.228  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245665              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.884  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1696      final r-factor (work) = 0.1392          |
| start r-factor (free) = 0.2136      final r-factor (free) = 0.1806          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6271 = 2.01 * 0.50 * 5.5384 + 1.00 * 0.0667                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4837 = 2.01 * 0.50 * 5.4089 + 1.00 * 0.0533                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1392      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.1806      final r-factor (free) = 0.1760          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3378 = 0.25 * 1.00 * 5.4089 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3113 = 0.25 * 1.00 * 5.3024 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.51    81.13   17.50    None  None   None       |
|    all(noH): 2823   0      1.51    81.13   17.50    None  None   None       |
|    Sol.    : 438    0      6.24    74.34   40.35    None  None   None       |
|    Mac.    : 2385   0      1.51    81.13   13.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.508 -   9.470:  849   |   5:    41.319 -  49.281:  107        |
|      1:     9.470 -  17.432: 1171   |   6:    49.281 -  57.243:   84        |
|      2:    17.432 -  25.395:  298   |   7:    57.243 -  65.205:   53        |
|      3:    25.395 -  33.357:  118   |   8:    65.205 -  73.167:   22        |
|      4:    33.357 -  41.319:  117   |   9:    73.167 -  81.129:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1336 r_free = 0.1760             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1334 r_free = 0.1761             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1761   ksol= 0.33   Bsol= 58.03   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-1.29,-0.67,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.287885                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1337   r_free= 0.1764   ksol= 0.33   Bsol= 59.58   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.40,-1.87,-0.98,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.289523                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.870430              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.639  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.123425              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.220  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1337      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1764      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6671 = 2.87 * 0.50 * 5.3050 + 1.00 * 0.0533                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5830 = 2.87 * 0.50 * 5.2355 + 1.00 * 0.0689                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1186      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8903 = 1.12 * 1.00 * 5.2355 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8351 = 1.12 * 1.00 * 5.1853 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.07    85.22   17.51    None  None   None       |
|    all(noH): 2823   0      1.07    85.22   17.51    None  None   None       |
|    Sol.    : 438    0      4.89    77.09   41.12    None  None   None       |
|    Mac.    : 2385   0      1.07    85.22   13.17    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:     1.067 -   9.483:  874   |   5:    43.145 -  51.560:  108        |
|      1:     9.483 -  17.898: 1192   |   6:    51.560 -  59.976:   76        |
|      2:    17.898 -  26.314:  267   |   7:    59.976 -  68.391:   58        |
|      3:    26.314 -  34.729:  124   |   8:    68.391 -  76.807:   16        |
|      4:    34.729 -  43.145:  104   |   9:    76.807 -  85.222:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1630             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1162 r_free = 0.1630             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1630   ksol= 0.33   Bsol= 59.58   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.40,-1.87,-0.98,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185292                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1630   ksol= 0.33   Bsol= 57.94   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,-1.84,-0.86,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185491                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.904012              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.573  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.310723              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.800  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5982 = 2.90 * 0.50 * 5.1854 + 1.00 * 0.0689                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5825 = 2.90 * 0.50 * 5.1744 + 1.00 * 0.0692                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.4898 = 5.31 * 1.00 * 5.1744 + 1.00 * 0.0097                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.4403 = 5.31 * 1.00 * 5.1649 + 1.00 * 0.0108                              |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.89   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    92.89   17.52    None  None   None       |
|    Sol.    : 438    0      0.00    85.66   41.78    None  None   None       |
|    Mac.    : 2385   0      0.00    92.89   13.06    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 -   9.289:  868   |   5:    46.443 -  55.732:   98        |
|      1:     9.289 -  18.577: 1240   |   6:    55.732 -  65.020:   79        |
|      2:    18.577 -  27.866:  247   |   7:    65.020 -  74.309:   38        |
|      3:    27.866 -  37.154:  134   |   8:    74.309 -  83.597:   11        |
|      4:    37.154 -  46.443:  105   |   9:    83.597 -  92.886:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1614             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1613             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1613   ksol= 0.33   Bsol= 57.94   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,-1.84,-0.86,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165857                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9295 -  4.6805 0.99   1453  160 0.0965 0.1296       5.383      5.5722|
|  2:  4.6805 -  3.7342 0.99   1401  155 0.0812 0.1051      5.4029       5.596|
|  3:  3.7342 -  3.2678 0.99   1360  153 0.1057 0.1511      5.4536      5.8206|
|  4:  3.2678 -  2.9716 0.99   1367  144 0.1257 0.1681      5.4546      5.6479|
|  5:  2.9716 -  2.7601 0.98   1331  154 0.1314 0.1674      5.3384      5.5232|
|  6:  2.7601 -  2.5982 0.99   1350  153 0.1249 0.2130      5.2329      5.5301|
|  7:  2.5982 -  2.4687 0.98   1322  152 0.1271 0.1696      5.1864      5.3774|
|  8:  2.4687 -  2.3617 0.99   1337  141 0.1177 0.1715      5.1005       5.293|
|  9:  2.3617 -  2.2711 0.99   1335  145 0.1159 0.1852      5.0319      5.3554|
| 10:  2.2711 -  2.1930 0.98   1335  146 0.1133 0.1862      4.9698       5.223|
| 11:  2.1930 -  2.1246 0.97   1291  157 0.1172 0.1839       4.928      5.2506|
| 12:  2.1246 -  2.0640 0.99   1332  146 0.1137 0.1600      4.8651      5.0726|
| 13:  2.0640 -  2.0098 0.84   1144  117 0.1102 0.2016      4.7888      5.1067|
| 14:  2.0098 -  1.9609 0.21    272   36 0.0992 0.1516      4.7462      4.8697|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9295 -  4.6805  1453   160  0.94   9.45   0.97     0.95       7582.66|
|  2:  4.6805 -  3.7342  1401   155  0.95   7.99   1.01     1.00       8868.09|
|  3:  3.7342 -  3.2678  1360   153  0.93  11.32   1.02     1.02      10137.30|
|  4:  3.2678 -  2.9716  1367   144  0.91  14.64   1.01     1.00      10662.44|
|  5:  2.9716 -  2.7601  1331   154  0.90  16.54   1.00     0.97       8942.26|
|  6:  2.7601 -  2.5982  1350   153  0.89  17.25   0.98     0.95       7655.79|
|  7:  2.5982 -  2.4687  1322   152  0.90  16.33   0.98     0.95       6662.03|
|  8:  2.4687 -  2.3617  1337   141  0.90  16.45   0.99     0.96       5924.59|
|  9:  2.3617 -  2.2711  1335   145  0.90  16.39   0.99     0.94       5192.57|
| 10:  2.2711 -  2.1930  1335   146  0.90  16.46   0.98     0.95       4683.91|
| 11:  2.1930 -  2.1246  1291   157  0.90  16.56   0.98     0.94       4376.41|
| 12:  2.1246 -  2.0640  1332   146  0.90  16.29   0.99     0.99       3971.49|
| 13:  2.0640 -  2.0098  1144   117  0.90  16.98   0.98     0.96       3508.68|
| 14:  2.0098 -  1.9609   272    36  0.91  15.08   0.96     0.91       3038.67|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3038.67 max =        10662.44 mean =      6791.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.73|
|phase err.(test): min =        0.00 max =           89.11 mean =        14.30|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1612   ksol= 0.32   Bsol= 57.94   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-1.65,-0.63,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165971                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1612   ksol= 0.32   Bsol= 57.94   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-1.65,-0.63,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165971                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9295 -  4.6805 0.99   1453  160 0.0965 0.1299       5.383       5.574|
|  2:  4.6805 -  3.7342 0.99   1401  155 0.0813 0.1051      5.4039      5.5964|
|  3:  3.7342 -  3.2678 0.99   1360  153 0.1058 0.1511      5.4539      5.8209|
|  4:  3.2678 -  2.9716 0.99   1367  144 0.1257 0.1681      5.4544      5.6478|
|  5:  2.9716 -  2.7601 0.98   1331  154 0.1314 0.1673      5.3381      5.5226|
|  6:  2.7601 -  2.5982 0.99   1350  153 0.1249 0.2130      5.2327      5.5301|
|  7:  2.5982 -  2.4687 0.98   1322  152 0.1271 0.1697      5.1864      5.3774|
|  8:  2.4687 -  2.3617 0.99   1337  141 0.1178 0.1715      5.1007       5.293|
|  9:  2.3617 -  2.2711 0.99   1335  145 0.1159 0.1853      5.0322      5.3558|
| 10:  2.2711 -  2.1930 0.98   1335  146 0.1133 0.1861      4.9701      5.2231|
| 11:  2.1930 -  2.1246 0.97   1291  157 0.1172 0.1839      4.9282      5.2508|
| 12:  2.1246 -  2.0640 0.99   1332  146 0.1138 0.1600       4.865      5.0724|
| 13:  2.0640 -  2.0098 0.84   1144  117 0.1102 0.2015      4.7887      5.1054|
| 14:  2.0098 -  1.9609 0.21    272   36 0.0991 0.1516      4.7469      4.8703|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9295 -  4.6805  1453   160  0.94   9.46   0.97     0.95       7584.03|
|  2:  4.6805 -  3.7342  1401   155  0.95   8.00   1.02     1.00       8879.14|
|  3:  3.7342 -  3.2678  1360   153  0.93  11.34   1.03     1.02      10149.59|
|  4:  3.2678 -  2.9716  1367   144  0.91  14.65   1.01     1.00      10661.95|
|  5:  2.9716 -  2.7601  1331   154  0.90  16.54   1.00     0.98       8936.40|
|  6:  2.7601 -  2.5982  1350   153  0.89  17.25   0.99     0.96       7651.16|
|  7:  2.5982 -  2.4687  1322   152  0.90  16.33   0.99     0.96       6660.33|
|  8:  2.4687 -  2.3617  1337   141  0.90  16.46   1.00     0.96       5925.15|
|  9:  2.3617 -  2.2711  1335   145  0.90  16.40   1.00     0.95       5194.56|
| 10:  2.2711 -  2.1930  1335   146  0.90  16.47   0.99     0.96       4684.27|
| 11:  2.1930 -  2.1246  1291   157  0.90  16.56   0.99     0.95       4376.12|
| 12:  2.1246 -  2.0640  1332   146  0.90  16.29   1.01     1.00       3971.27|
| 13:  2.0640 -  2.0098  1144   117  0.90  16.99   0.99     0.97       3507.56|
| 14:  2.0098 -  1.9609   272    36  0.91  15.09   0.97     0.92       3037.97|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3037.97 max =        10661.95 mean =      6792.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.73|
|phase err.(test): min =        0.00 max =           89.11 mean =        14.31|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.883)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.89   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    92.89   17.52    None  None   None       |
|    Sol.    : 438    0      0.00    85.66   41.79    None  None   None       |
|    Mac.    : 2385   0      0.00    92.89   13.06    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:     0.003 -   9.292:  868   |   5:    46.446 -  55.735:   98        |
|      1:     9.292 -  18.580: 1240   |   6:    55.735 -  65.023:   79        |
|      2:    18.580 -  27.869:  247   |   7:    65.023 -  74.312:   38        |
|      3:    27.869 -  37.157:  134   |   8:    74.312 -  83.600:   11        |
|      4:    37.157 -  46.446:  105   |   9:    83.600 -  92.889:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.496 - 5.719
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 291 from: 295
   mapped sites are within: 0.711 - 5.719

peak=    5.678 closest distance to " O   HOH Z 113 " =    2.170
peak=    5.183 closest distance to " CB  ARG A 275 " =    0.960
peak=    5.061 closest distance to " CG  PRO A  54 " =    1.307
peak=    4.822 closest distance to " CB  GLN A 223 " =    1.429
peak=    4.757 closest distance to " CB  ARG A 190 " =    1.694
peak=    4.632 closest distance to " O   HOH Z 232 " =    2.290
peak=    4.614 closest distance to " CA  TYR A  30 " =    0.893
peak=    4.567 closest distance to " CA  ARG A  36 " =    1.054
peak=    4.557 closest distance to " O   HOH Z 142 " =    1.527
peak=    4.536 closest distance to " O   HOH Z 369 " =    2.506
peak=    4.506 closest distance to " CB  GLN A 183 " =    1.278
peak=    4.478 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.448 closest distance to " O   HOH Z 234 " =    3.655
peak=    4.433 closest distance to " O   GLY A  23 " =    2.381
peak=    4.407 closest distance to " O   HOH Z 403 " =    1.778
peak=    4.357 closest distance to " CG  PRO A  90 " =    1.139
peak=    4.309 closest distance to " CB  SER A  63 " =    1.078
peak=    4.296 closest distance to " C   PRO A 198 " =    1.523
peak=    4.287 closest distance to " CB  ARG A  79 " =    1.461
peak=    4.286 closest distance to " NZ  LYS A 117 " =    3.120
peak=    4.272 closest distance to " CD2 TRP A 179 " =    1.364
peak=    4.253 closest distance to " O   HOH Z  97 " =    2.048
peak=    4.233 closest distance to " NE2 GLN A  11 " =    1.029
peak=    4.199 closest distance to " CZ  PHE A 218 " =    1.156
peak=    4.182 closest distance to " CB  PRO A  54 " =    1.001
peak=    4.180 closest distance to " O   HOH Z  49 " =    1.122
peak=    4.178 closest distance to " CD  ARG A 269 " =    0.977
peak=    4.156 closest distance to " O   HOH Z  97 " =    2.123
peak=    4.130 closest distance to " O   HOH Z  43 " =    1.548
peak=    4.119 closest distance to " O   HOH Z 298 " =    1.734
peak=    4.117 closest distance to " O   HOH Z  63 " =    1.870
peak=    4.078 closest distance to " CB  GLU A 277 " =    3.664
peak=    4.077 closest distance to " O   HOH Z 368 " =    2.119
peak=    4.075 closest distance to " CB  GLU A 152 " =    1.174
peak=    4.068 closest distance to " O   HOH Z 346 " =    1.631
peak=    4.054 closest distance to " CG  ARG A  66 " =    2.587
peak=    4.047 closest distance to " O   HOH Z 189 " =    2.800
peak=    3.997 closest distance to " O   HOH Z  40 " =    2.000
peak=    3.991 closest distance to " O   HOH Z 109 " =    2.085
peak=    3.990 closest distance to " O   HOH Z 248 " =    1.418
peak=    3.981 closest distance to " O   HOH Z 180 " =    2.224
peak=    3.977 closest distance to " CG2 ILE A 120 " =    1.218
peak=    3.974 closest distance to " O   HOH Z 423 " =    1.938
peak=    3.969 closest distance to " O   HOH Z 272 " =    1.872
peak=    3.965 closest distance to " O   HOH Z 365 " =    2.647
peak=    3.965 closest distance to " O   HOH Z 287 " =    1.843
peak=    3.962 closest distance to " CG  PRO A 198 " =    1.215
peak=    3.958 closest distance to " O   HOH Z 209 " =    2.280
peak=    3.953 closest distance to " O   HOH Z 185 " =    1.874
peak=    3.937 closest distance to " O   SER A  87 " =    2.267
peak=    3.936 closest distance to " CD  LYS A  76 " =    1.831
peak=    3.930 closest distance to " O   HOH Z  85 " =    1.557
peak=    3.927 closest distance to " ND2 ASN A 187 " =    1.530
peak=    3.924 closest distance to " NH2BARG A 145 " =    2.100
peak=    3.923 closest distance to " CA  ALA A  51 " =    0.990
peak=    3.922 closest distance to " O   HOH Z  44 " =    2.198
peak=    3.919 closest distance to " O   HOH Z 389 " =    1.865
peak=    3.910 closest distance to " O   HOH Z 345 " =    1.707
peak=    3.903 closest distance to " CG  PRO A 243 " =    1.053
peak=    3.879 closest distance to " O   HOH Z  59 " =    2.183
peak=    3.876 closest distance to " N   ASN A  39 " =    1.271
peak=    3.874 closest distance to " O   HOH Z 250 " =    1.393
peak=    3.866 closest distance to " CB  THR A  31 " =    1.673
peak=    3.864 closest distance to " O   HOH Z 126 " =    1.830
peak=    3.847 closest distance to " O   HOH Z 417 " =    1.179
peak=    3.844 closest distance to " CD  LYS A 166 " =    1.351
peak=    3.840 closest distance to " CA  ARG A 195 " =    1.254
peak=    3.837 closest distance to " CD2 LEU A 297 " =    0.894
peak=    3.835 closest distance to " O   HOH Z 359 " =    1.650
peak=    3.833 closest distance to " O   HOH Z 361 " =    3.531
peak=    3.832 closest distance to " O   HOH Z 291 " =    1.453
peak=    3.818 closest distance to " O   HOH Z 203 " =    1.800
peak=    3.813 closest distance to " O   HOH Z 327 " =    1.612
peak=    3.800 closest distance to " CG1 ILE A  33 " =    1.153
peak=    3.795 closest distance to " O   HOH Z 193 " =    1.705
peak=    3.776 closest distance to " CA  ALA A 295 " =    1.026
peak=    3.767 closest distance to " CB  SER A  26 " =    1.877
peak=    3.766 closest distance to " CB  TRP A 266 " =    1.104
peak=    3.762 closest distance to " O   HOH Z  15 " =    2.161
peak=    3.761 closest distance to " ND2 ASN A 249 " =    0.936
peak=    3.758 closest distance to " CA  ASN A 176 " =    1.559
peak=    3.755 closest distance to " O   HOH Z  80 " =    1.797
peak=    3.752 closest distance to " CB  ASN A 148 " =    1.449
peak=    3.749 closest distance to " CA  ALA A 160 " =    0.876
peak=    3.745 closest distance to " CB  GLU A 128 " =    1.126
peak=    3.743 closest distance to " NH1AARG A 145 " =    1.361
peak=    3.736 closest distance to " O   HOH Z 126 " =    1.544
peak=    3.736 closest distance to " O   HOH Z 132 " =    2.458
peak=    3.729 closest distance to " O   HOH Z 258 " =    2.123
peak=    3.728 closest distance to " N   CYS A 260 " =    0.923
peak=    3.726 closest distance to " CZ  PHE A  38 " =    1.234
peak=    3.715 closest distance to " O   HOH Z 146 " =    2.341
peak=    3.713 closest distance to " CE  LYS A 119 " =    1.099
peak=    3.711 closest distance to " O   HOH Z 158 " =    3.015
peak=    3.711 closest distance to " O   HOH Z 421 " =    2.010
peak=    3.701 closest distance to " O   HOH Z 316 " =    3.058
peak=    3.700 closest distance to " O   HOH Z 227 " =    1.650
peak=    3.697 closest distance to " O   HOH Z 280 " =    3.003
peak=    3.696 closest distance to " NE2 GLN A  77 " =    3.161
peak=    3.696 closest distance to " O   HOH Z 402 " =    1.409
peak=    3.696 closest distance to " O   HOH Z 427 " =    3.057
peak=    3.681 closest distance to " CB  TRP A 179 " =    1.298
peak=    3.669 closest distance to " CB  ALA A 248 " =    1.333
peak=    3.665 closest distance to " O   HOH Z 412 " =    3.831
peak=    3.662 closest distance to " O   HOH Z 325 " =    2.237
peak=    3.658 closest distance to " CD  ARG A 159 " =    0.797
peak=    3.656 closest distance to " CA  ALA A  84 " =    1.238
peak=    3.654 closest distance to " CE  LYS A  76 " =    0.867
peak=    3.651 closest distance to " O   HOH Z 261 " =    2.206
peak=    3.649 closest distance to " NH2AARG A 275 " =    3.502
peak=    3.643 closest distance to " O   HOH Z 134 " =    1.333
peak=    3.637 closest distance to " O   HOH Z 371 " =    3.153
peak=    3.637 closest distance to " N   HIS A 108 " =    1.819
peak=    3.634 closest distance to " O   HOH Z 303 " =    2.189
peak=    3.632 closest distance to " O   HOH Z 285 " =    2.652
peak=    3.632 closest distance to " CG2 ILE A  20 " =    1.359
peak=    3.627 closest distance to " O   HOH Z 128 " =    1.954
peak=    3.613 closest distance to " CB  VAL A 202 " =    1.497
peak=    3.612 closest distance to " O   HOH Z  21 " =    1.844
peak=    3.611 closest distance to " NZ  LYS A  48 " =    1.174
peak=    3.602 closest distance to " O  BHOH Z 338 " =    2.277
peak=    3.601 closest distance to " O   HOH Z 279 " =    2.166
peak=    3.583 closest distance to " O   HOH Z 245 " =    1.312
peak=    3.572 closest distance to " CD  PRO A  54 " =    1.033
peak=    3.565 closest distance to " O   HOH Z  78 " =    1.740
peak=    3.563 closest distance to " CB  VAL A 265 " =    1.220
peak=    3.561 closest distance to " O   HOH Z 214 " =    2.764
peak=    3.559 closest distance to " CB  ASN A  39 " =    0.761
peak=    3.558 closest distance to " CZ3 TRP A 266 " =    1.076
peak=    3.546 closest distance to " CG1BVAL A  72 " =    1.811
peak=    3.543 closest distance to " OH  TYR A 116 " =    1.151
peak=    3.539 closest distance to " O   HOH Z 173 " =    2.091
peak=    3.526 closest distance to " OG BSER A 164 " =    2.234
peak=    3.521 closest distance to " O   ALA A 165 " =    1.456
peak=    3.519 closest distance to " O   HOH Z 417 " =    3.242
peak=    3.509 closest distance to " O   HOH Z 380 " =    1.997
peak=    3.499 closest distance to " CB  TYR A 169 " =    0.762
peak=    3.493 closest distance to " O   HOH Z 426 " =    1.476
peak=    3.481 closest distance to " O   HOH Z 120 " =    2.628
peak=    3.479 closest distance to " O   HOH Z  88 " =    2.730
peak=    3.475 closest distance to " O   HOH Z 357 " =    2.108
peak=    3.469 closest distance to " O   HOH Z 392 " =    2.492
peak=    3.469 closest distance to " O   HOH Z 361 " =    2.536
peak=    3.469 closest distance to " O   HOH Z  61 " =    1.569
peak=    3.462 closest distance to " OD1 ASN A 301 " =    1.673
peak=    3.462 closest distance to " CD  LYS A 119 " =    1.737
peak=    3.461 closest distance to " CB  SER A  62 " =    0.901
peak=    3.456 closest distance to " CG  MET A 185 " =    1.165
peak=    3.452 closest distance to " CB  SER A   3 " =    1.239
peak=    3.450 closest distance to " O   HOH Z 299 " =    4.258
peak=    3.447 closest distance to " O   HOH Z  35 " =    2.400
peak=    3.446 closest distance to " O   HOH Z 271 " =    2.786
peak=    3.443 closest distance to " O   TYR A 116 " =    1.437
peak=    3.442 closest distance to " O   HOH Z 265 " =    1.994
peak=    3.441 closest distance to " CD1 LEU A  96 " =    0.761
peak=    3.441 closest distance to " N   TYR A 116 " =    1.612
peak=    3.438 closest distance to " CG2BVAL A  41 " =    0.830
peak=    3.433 closest distance to " CA  MET A 105 " =    1.058
peak=    3.430 closest distance to " O   HOH Z 141 " =    1.732
peak=    3.427 closest distance to " O   HOH Z 406 " =    1.475
peak=    3.423 closest distance to " CB  SER A 141 " =    1.075
peak=    3.411 closest distance to " CG2 VAL A 257 " =    0.748
peak=    3.410 closest distance to " O   THR A 220 " =    1.177
peak=    3.406 closest distance to " CA  SER A  87 " =    1.033
peak=    3.401 closest distance to " CG  LEU A 167 " =    1.161
peak=    3.399 closest distance to " O   HOH Z 250 " =    1.594
peak=    3.397 closest distance to " CA  TYR A 116 " =    1.328
peak=    3.395 closest distance to " O   HOH Z  63 " =    2.255
peak=    3.392 closest distance to " CB  PRO A  90 " =    1.127
peak=    3.384 closest distance to " O   HOH Z 147 " =    1.924
peak=    3.383 closest distance to " O   HOH Z 148 " =    3.351
peak=    3.382 closest distance to " CB  MET A  47 " =    1.058
peak=    3.382 closest distance to " O   HOH Z 353 " =    2.786
peak=    3.381 closest distance to " CB  ASN A 285 " =    0.987
peak=    3.376 closest distance to " O   HOH Z 251 " =    1.570
peak=    3.375 closest distance to " O   HOH Z 247 " =    1.353
peak=    3.371 closest distance to " OE1 GLU A   2 " =    2.137
peak=    3.369 closest distance to " O   HOH Z  78 " =    2.072
peak=    3.367 closest distance to " CG2 THR A 221 " =    1.078
peak=    3.366 closest distance to " O   HOH Z 366 " =    2.472
peak=    3.361 closest distance to " CB  THR A  52 " =    0.711
peak=    3.359 closest distance to " O   HOH Z 345 " =    2.862
peak=    3.356 closest distance to " O   HOH Z 313 " =    1.976
peak=    3.354 closest distance to " O   HOH Z 298 " =    2.306
peak=    3.354 closest distance to " O   HOH Z 282 " =    1.924
peak=    3.354 closest distance to " O   HOH Z 146 " =    2.296
peak=    3.352 closest distance to " CA  ALA A 248 " =    1.225
peak=    3.350 closest distance to " CG  GLN A  11 " =    1.569
peak=    3.346 closest distance to " O   HOH Z 422 " =    2.638
peak=    3.346 closest distance to " CB  ASN A 215 " =    1.194
peak=    3.343 closest distance to " O   HOH Z   1 " =    2.306
peak=    3.343 closest distance to " O   HOH Z 404 " =    2.298
peak=    3.343 closest distance to " O   HOH Z 411 " =    1.681
peak=    3.340 closest distance to " O   HOH Z 391 " =    2.991
peak=    3.338 closest distance to " O   HOH Z 313 " =    1.476
peak=    3.337 closest distance to " OD2 ASP A 298 " =    3.864
peak=    3.336 closest distance to " CG  GLU A  37 " =    0.901
peak=    3.330 closest distance to " O   THR A 182 " =    1.458
peak=    3.329 closest distance to " O   HOH Z 210 " =    0.885
peak=    3.328 closest distance to " CB  PHE A 204 " =    0.744
peak=    3.328 closest distance to " CA  THR A  42 " =    1.003
peak=    3.323 closest distance to " O   ASP A 124 " =    1.678
peak=    3.320 closest distance to " O   HOH Z 421 " =    2.564
peak=    3.318 closest distance to " O   HOH Z 336 " =    1.882
peak=    3.305 closest distance to " O   HOH Z 383 " =    2.160
peak=    3.297 closest distance to " O   HOH Z 344 " =    3.066
peak=    3.295 closest distance to " O   HOH Z 337 " =    3.685
peak=    3.290 closest distance to " O   HOH Z 102 " =    1.265
peak=    3.290 closest distance to " CB  GLU A  46 " =    1.051
peak=    3.289 closest distance to " CB  ALA A 114 " =    0.856
peak=    3.285 closest distance to " O   HOH Z 130 " =    2.286
peak=    3.281 closest distance to " O   HOH Z  85 " =    1.741
peak=    3.279 closest distance to " CB  LEU A 228 " =    1.123
peak=    3.277 closest distance to " O   HOH Z 298 " =    4.191
peak=    3.276 closest distance to " OG1 THR A 294 " =    1.619
peak=    3.273 closest distance to " CB  HIS A 108 " =    0.822
peak=    3.273 closest distance to " O   HOH Z 375 " =    2.095
peak=    3.271 closest distance to " O   HOH Z 214 " =    2.098
peak=    3.271 closest distance to " CB  ASP A 191 " =    1.230
peak=    3.271 closest distance to " O   HOH Z 425 " =    2.000
peak=    3.265 closest distance to " NH2BARG A 190 " =    1.768
peak=    3.264 closest distance to " N   ARG A 156 " =    1.428
peak=    3.260 closest distance to " CE1 TYR A 186 " =    1.246
peak=    3.258 closest distance to " CA  ASN A 215 " =    1.060
peak=    3.256 closest distance to " O   HOH Z 416 " =    2.984
peak=    3.252 closest distance to " CA  VAL A 125 " =    1.219
peak=    3.251 closest distance to " CB  TYR A 169 " =    0.989
peak=    3.250 closest distance to " O   HOH Z 186 " =    1.013
peak=    3.248 closest distance to " O   HOH Z  88 " =    3.229
peak=    3.246 closest distance to " CB  ALA A   9 " =    1.639
peak=    3.240 closest distance to " O   HOH Z  19 " =    1.354
peak=    3.236 closest distance to " CB  ASP A 140 " =    1.144
peak=    3.236 closest distance to " CD1AILE A 234 " =    0.808
peak=    3.233 closest distance to " CA  SER A  32 " =    1.641
peak=    3.221 closest distance to " CB  ASN A 110 " =    1.075
peak=    3.215 closest distance to " O   GLU A   2 " =    1.724
peak=    3.209 closest distance to " CG1 VAL A 153 " =    1.043
peak=    3.194 closest distance to " CB  GLN A  88 " =    1.130
peak=    3.192 closest distance to " CD  GLN A 194 " =    1.537
peak=    3.188 closest distance to " CA  SER A 146 " =    1.980
peak=    3.186 closest distance to " CB  ASP A 298 " =    1.192
peak=    3.184 closest distance to " N   ASP A 162 " =    1.185
peak=    3.183 closest distance to " CB  ASN A 142 " =    1.193
peak=    3.178 closest distance to " CA  ASP A 140 " =    1.179
peak=    3.177 closest distance to " CA  ASP A 162 " =    1.127
peak=    3.173 closest distance to " CB  LEU A  83 " =    0.818
peak=    3.172 closest distance to " OE1 GLN A  73 " =    2.509
peak=    3.171 closest distance to " CA  ALA A 291 " =    0.749
peak=    3.169 closest distance to " O   HOH Z 368 " =    4.340
peak=    3.168 closest distance to " O   HOH Z 199 " =    1.580
peak=    3.166 closest distance to " CG2 VAL A 197 " =    1.151
peak=    3.165 closest distance to " O   HOH Z 403 " =    1.486
peak=    3.158 closest distance to " O   HOH Z 394 " =    1.557
peak=    3.158 closest distance to " NE  ARG A  24 " =    0.912
peak=    3.156 closest distance to " CA  LYS A 117 " =    1.230
peak=    3.153 closest distance to " CA  GLY A 241 " =    0.946
peak=    3.150 closest distance to " CA  ALA A 100 " =    0.993
peak=    3.147 closest distance to " OD2 ASP A 286 " =    3.157
peak=    3.142 closest distance to " O   HOH Z 163 " =    1.456
peak=    3.140 closest distance to " O   HOH Z  88 " =    3.156
peak=    3.135 closest distance to " OG  SER A 245 " =    1.503
peak=    3.126 closest distance to " O   HOH Z 425 " =    1.225
peak=    3.126 closest distance to " CZ2 TRP A 179 " =    1.719
peak=    3.126 closest distance to " CA  ILE A 234 " =    0.979
peak=    3.125 closest distance to " CB  PRO A 243 " =    1.244
peak=    3.119 closest distance to " CB  PHE A 204 " =    0.721
peak=    3.117 closest distance to " O   HOH Z 182 " =    2.026
peak=    3.110 closest distance to " O   HOH Z 305 " =    3.616
peak=    3.104 closest distance to " O   HOH Z 420 " =    5.719
peak=    3.101 closest distance to " CB  LYS A 289 " =    1.052
peak=    3.096 closest distance to " CD2 LEU A 143 " =    1.275
peak=    3.095 closest distance to " CG1AVAL A 121 " =    0.809
peak=    3.094 closest distance to " O   HOH Z  10 " =    1.748
peak=    3.092 closest distance to " N   VAL A 265 " =    1.309
peak=    3.091 closest distance to " CD1 LEU A 300 " =    1.113
peak=    3.091 closest distance to " O   HOH Z  48 " =    1.633
peak=    3.091 closest distance to " CA  LEU A  83 " =    1.314
peak=    3.082 closest distance to " O   TRP A 274 " =    1.797
peak=    3.081 closest distance to " OG  SER A  22 " =    2.692
peak=    3.079 closest distance to " N   PHE A 130 " =    1.360
peak=    3.075 closest distance to " O   HOH Z 130 " =    2.398
peak=    3.069 closest distance to " CD  ARG A  66 " =    2.737
peak=    3.066 closest distance to " O   HOH Z 132 " =    0.906
peak=    3.064 closest distance to " CD1 LEU A 228 " =    1.612
peak=    3.059 closest distance to " O   HOH Z 233 " =    1.873
peak=    3.055 closest distance to " O   HOH Z 303 " =    1.878
peak=    3.051 closest distance to " O   HOH Z  85 " =    2.058
peak=    3.047 closest distance to " O   HOH Z 162 " =    1.606
peak=    3.042 closest distance to " O   HOH Z 358 " =    2.194
peak=    3.023 closest distance to " OG  SER A  62 " =    2.793
peak=    3.014 closest distance to " O   HOH Z  47 " =    2.069

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.906 - 5.980
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 220
   mapped sites are within: 0.906 - 5.980

peak=   -4.573 closest distance to " CD  ARG A  14 " =    3.474
peak=   -4.398 closest distance to " O   HOH Z 266 " =    5.297
peak=   -4.373 closest distance to " C   HIS A 108 " =    1.096
peak=   -4.364 closest distance to " CD1 LEU A 101 " =    2.447
peak=   -4.310 closest distance to " OXT GLY A 302 " =    3.008
peak=   -4.280 closest distance to " CG2 ILE A  49 " =    2.744
peak=   -4.268 closest distance to " CD  GLN A  58 " =    1.033
peak=   -4.256 closest distance to " O   HOH Z 377 " =    2.147
peak=   -4.109 closest distance to " CD  ARG A 156 " =    2.119
peak=   -4.079 closest distance to " CB  PRO A 243 " =    2.716
peak=   -4.036 closest distance to " O   VAL A  67 " =    2.726
peak=   -4.003 closest distance to " CZ3 TRP A 179 " =    1.305
peak=   -3.986 closest distance to " O   HOH Z 210 " =    1.059
peak=   -3.970 closest distance to " OG BSER A 134 " =    1.387
peak=   -3.929 closest distance to " CG1 VAL A 250 " =    2.704
peak=   -3.919 closest distance to " O   HOH Z 166 " =    1.738
peak=   -3.918 closest distance to " O   HOH Z  13 " =    1.764
peak=   -3.895 closest distance to " CD2 TYR A 293 " =    1.845
peak=   -3.885 closest distance to " CG1AVAL A  41 " =    2.609
peak=   -3.880 closest distance to " CA  VAL A  67 " =    2.992
peak=   -3.876 closest distance to " O   HOH Z 348 " =    2.194
peak=   -3.872 closest distance to " O   PHE A 218 " =    1.516
peak=   -3.868 closest distance to " CE2 TYR A  30 " =    2.729
peak=   -3.866 closest distance to " O   HOH Z 198 " =    1.578
peak=   -3.864 closest distance to " O   PRO A 198 " =    1.326
peak=   -3.863 closest distance to " CG  ASP A 132 " =    2.360
peak=   -3.844 closest distance to " CD1 LEU A  25 " =    2.540
peak=   -3.832 closest distance to " O   HOH Z  10 " =    1.603
peak=   -3.825 closest distance to " CZ  TYR A 169 " =    1.879
peak=   -3.820 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.818 closest distance to " CB  ALA A 161 " =    2.575
peak=   -3.817 closest distance to " CD2 HIS A 207 " =    2.325
peak=   -3.778 closest distance to " CE3 TRP A 150 " =    2.220
peak=   -3.776 closest distance to " CB  ALA A 184 " =    2.357
peak=   -3.757 closest distance to " O   PRO A 163 " =    2.126
peak=   -3.751 closest distance to " O   ALA A  34 " =    2.260
peak=   -3.741 closest distance to " OG  SER A  97 " =    2.187
peak=   -3.723 closest distance to " CA  GLY A 241 " =    3.102
peak=   -3.714 closest distance to " O   HOH Z 165 " =    1.859
peak=   -3.703 closest distance to " ND2BASN A 224 " =    1.759
peak=   -3.703 closest distance to " OE1 GLN A 223 " =    2.210
peak=   -3.700 closest distance to " NE2 GLN A  88 " =    1.789
peak=   -3.694 closest distance to " CB  PHE A 192 " =    2.065
peak=   -3.692 closest distance to " O   HOH Z  71 " =    2.218
peak=   -3.691 closest distance to " CG  GLU A  53 " =    1.475
peak=   -3.683 closest distance to " CD  GLN A 223 " =    1.338
peak=   -3.681 closest distance to " O   HOH Z 196 " =    1.958
peak=   -3.656 closest distance to " O   HOH Z 394 " =    1.615
peak=   -3.656 closest distance to " CB  ALA A 291 " =    2.414
peak=   -3.645 closest distance to " CG  PRO A 243 " =    1.717
peak=   -3.641 closest distance to " O   GLY A 241 " =    2.404
peak=   -3.621 closest distance to " CD2 TYR A 247 " =    2.389
peak=   -3.616 closest distance to " O   HOH Z 193 " =    1.357
peak=   -3.604 closest distance to " CG1 VAL A 112 " =    2.649
peak=   -3.595 closest distance to " O   HOH Z 171 " =    2.391
peak=   -3.583 closest distance to " O   HOH Z 113 " =    1.997
peak=   -3.565 closest distance to " O   HOH Z 374 " =    1.951
peak=   -3.562 closest distance to " C   THR A 279 " =    1.146
peak=   -3.555 closest distance to " O   HOH Z 150 " =    2.312
peak=   -3.554 closest distance to " OD1 ASP A 171 " =    1.507
peak=   -3.554 closest distance to " CB  TRP A  85 " =    2.473
peak=   -3.546 closest distance to " N   THR A  52 " =    1.736
peak=   -3.538 closest distance to " CG1 VAL A  78 " =    2.774
peak=   -3.538 closest distance to " O   HOH Z 102 " =    1.618
peak=   -3.531 closest distance to " CD1 PHE A  59 " =    2.049
peak=   -3.531 closest distance to " O   HOH Z 435 " =    2.366
peak=   -3.528 closest distance to " CG2 VAL A 189 " =    2.217
peak=   -3.528 closest distance to " CB  ALA A  43 " =    2.506
peak=   -3.521 closest distance to " ND2 ASN A  45 " =    1.248
peak=   -3.516 closest distance to " O   HOH Z 351 " =    1.433
peak=   -3.512 closest distance to " O   HOH Z 208 " =    1.920
peak=   -3.509 closest distance to " CE  MET A 105 " =    2.594
peak=   -3.504 closest distance to " O   SER A 210 " =    1.781
peak=   -3.503 closest distance to " OD2 ASP A 191 " =    1.502
peak=   -3.499 closest distance to " CB  ALA A 248 " =    2.267
peak=   -3.499 closest distance to " ND2 ASN A 249 " =    2.258
peak=   -3.494 closest distance to " CD  ARG A 139 " =    1.554
peak=   -3.491 closest distance to " O   HOH Z 283 " =    2.324
peak=   -3.489 closest distance to " O   HOH Z 357 " =    2.168
peak=   -3.485 closest distance to " O   TRP A  92 " =    1.950
peak=   -3.469 closest distance to " ND2 ASN A 187 " =    1.576
peak=   -3.467 closest distance to " NE2 GLN A  88 " =    1.129
peak=   -3.465 closest distance to " CD1 ILE A 106 " =    2.215
peak=   -3.458 closest distance to " CE BMET A  47 " =    1.646
peak=   -3.455 closest distance to " CA  GLY A 133 " =    2.360
peak=   -3.453 closest distance to " O   GLY A  80 " =    2.548
peak=   -3.442 closest distance to " OD1 ASN A 148 " =    1.514
peak=   -3.441 closest distance to " O   HOH Z 174 " =    2.423
peak=   -3.437 closest distance to " CB  ALA A  10 " =    2.278
peak=   -3.435 closest distance to " O   HOH Z  88 " =    4.601
peak=   -3.420 closest distance to " N   ALA A 248 " =    1.769
peak=   -3.417 closest distance to " O   HOH Z  38 " =    1.625
peak=   -3.406 closest distance to " NE  ARG A  66 " =    4.400
peak=   -3.405 closest distance to " O   HOH Z 111 " =    3.749
peak=   -3.404 closest distance to " CE2 PHE A  61 " =    2.642
peak=   -3.401 closest distance to " O   HOH Z   6 " =    1.704
peak=   -3.397 closest distance to " OE1 GLN A 183 " =    1.466
peak=   -3.396 closest distance to " O   VAL A 174 " =    2.204
peak=   -3.394 closest distance to " O   HOH Z   6 " =    2.144
peak=   -3.391 closest distance to " NH2 ARG A  66 " =    1.036
peak=   -3.391 closest distance to " O   HOH Z 211 " =    1.565
peak=   -3.387 closest distance to " CH2 TRP A 150 " =    1.156
peak=   -3.382 closest distance to " O   HOH Z 366 " =    1.603
peak=   -3.381 closest distance to " CG2 ILE A 263 " =    2.244
peak=   -3.380 closest distance to " O   HOH Z  15 " =    1.551
peak=   -3.378 closest distance to " O   HOH Z 264 " =    1.733
peak=   -3.378 closest distance to " O   ALA A  10 " =    1.845
peak=   -3.377 closest distance to " O   HOH Z 185 " =    2.410
peak=   -3.375 closest distance to " CG  PHE A 283 " =    2.498
peak=   -3.374 closest distance to " O   GLN A  11 " =    1.306
peak=   -3.372 closest distance to " CG  GLU A 277 " =    1.284
peak=   -3.372 closest distance to " CG1 VAL A 112 " =    2.595
peak=   -3.371 closest distance to " CG1 VAL A  78 " =    2.809
peak=   -3.369 closest distance to " O   HOH Z 252 " =    3.660
peak=   -3.365 closest distance to " CG1 VAL A  67 " =    3.059
peak=   -3.359 closest distance to " NE2 GLN A  11 " =    1.702
peak=   -3.354 closest distance to " O   ALA A   1 " =    1.998
peak=   -3.349 closest distance to " O   HOH Z 126 " =    1.923
peak=   -3.341 closest distance to " OD1 ASP A 191 " =    1.403
peak=   -3.334 closest distance to " ND2 ASN A  69 " =    1.826
peak=   -3.324 closest distance to " CA  GLY A 241 " =    2.899
peak=   -3.322 closest distance to " O   HOH Z 395 " =    5.093
peak=   -3.319 closest distance to " O   HOH Z 240 " =    4.000
peak=   -3.318 closest distance to " CA  GLY A 133 " =    2.085
peak=   -3.314 closest distance to " O   HOH Z 377 " =    1.649
peak=   -3.310 closest distance to " CD2 PHE A  61 " =    2.173
peak=   -3.304 closest distance to " O   HOH Z 285 " =    1.284
peak=   -3.302 closest distance to " CD1 ILE A 151 " =    2.389
peak=   -3.301 closest distance to " CB  ALA A   9 " =    2.440
peak=   -3.298 closest distance to " O   HOH Z 372 " =    2.271
peak=   -3.295 closest distance to " NH2AARG A 275 " =    5.083
peak=   -3.295 closest distance to " CB  ALA A 291 " =    2.302
peak=   -3.292 closest distance to " OD2 ASP A 171 " =    2.449
peak=   -3.292 closest distance to " CG  LEU A  83 " =    2.134
peak=   -3.292 closest distance to " O   GLU A 152 " =    1.436
peak=   -3.290 closest distance to " NH2 ARG A  66 " =    5.980
peak=   -3.287 closest distance to " OH  TYR A 172 " =    1.837
peak=   -3.286 closest distance to " CD  ARG A  79 " =    1.237
peak=   -3.280 closest distance to " O   HOH Z 252 " =    4.075
peak=   -3.279 closest distance to " N   SER A 276 " =    1.376
peak=   -3.274 closest distance to " O   SER A   3 " =    1.027
peak=   -3.274 closest distance to " O   HOH Z 154 " =    1.771
peak=   -3.268 closest distance to " O   HOH Z 313 " =    2.071
peak=   -3.259 closest distance to " O   HOH Z  37 " =    1.858
peak=   -3.254 closest distance to " OD1 ASN A 301 " =    1.940
peak=   -3.251 closest distance to " O   HOH Z 174 " =    3.696
peak=   -3.250 closest distance to " O   HOH Z 256 " =    2.358
peak=   -3.249 closest distance to " OE2 GLU A   2 " =    1.951
peak=   -3.248 closest distance to " CG  MET A 105 " =    0.980
peak=   -3.246 closest distance to " O   HOH Z 183 " =    1.680
peak=   -3.239 closest distance to " O   HOH Z  78 " =    1.803
peak=   -3.239 closest distance to " NE2 GLN A 223 " =    1.343
peak=   -3.237 closest distance to " O   HOH Z  43 " =    1.428
peak=   -3.233 closest distance to " O   VAL A 189 " =    1.896
peak=   -3.232 closest distance to " CG  HIS A  86 " =    1.127
peak=   -3.229 closest distance to " OG  SER A  22 " =    5.133
peak=   -3.228 closest distance to " CD  PRO A 243 " =    2.047
peak=   -3.224 closest distance to " CG1 VAL A 125 " =    2.020
peak=   -3.222 closest distance to " O   VAL A 189 " =    2.685
peak=   -3.219 closest distance to " NH2 ARG A  79 " =    1.569
peak=   -3.219 closest distance to " O   HOH Z 290 " =    1.064
peak=   -3.217 closest distance to " CG1BVAL A  72 " =    2.423
peak=   -3.216 closest distance to " CD  LYS A 289 " =    2.356
peak=   -3.214 closest distance to " O   HOH Z 116 " =    1.367
peak=   -3.213 closest distance to " C   GLY A  17 " =    0.906
peak=   -3.211 closest distance to " O   HOH Z 139 " =    3.168
peak=   -3.209 closest distance to " O   ASN A 252 " =    1.423
peak=   -3.208 closest distance to " O   PRO A 198 " =    1.311
peak=   -3.206 closest distance to " O   HOH Z 364 " =    5.266
peak=   -3.205 closest distance to " OG BSER A 134 " =    1.911
peak=   -3.205 closest distance to " O   HOH Z 114 " =    3.355
peak=   -3.203 closest distance to " O   HOH Z 111 " =    1.972
peak=   -3.197 closest distance to " O   HOH Z 426 " =    1.711
peak=   -3.195 closest distance to " O   HOH Z 110 " =    1.310
peak=   -3.192 closest distance to " O   SER A 276 " =    1.658
peak=   -3.190 closest distance to " OG BSER A 210 " =    1.436
peak=   -3.187 closest distance to " O   HOH Z 340 " =    1.865
peak=   -3.181 closest distance to " ND2 ASN A  39 " =    1.145
peak=   -3.178 closest distance to " CA  GLY A 203 " =    2.301
peak=   -3.171 closest distance to " O   SER A  26 " =    1.417
peak=   -3.167 closest distance to " O   HOH Z 123 " =    2.499
peak=   -3.165 closest distance to " C   GLN A 144 " =    0.955
peak=   -3.165 closest distance to " CB  ALA A 248 " =    2.075
peak=   -3.164 closest distance to " CZ  PHE A  38 " =    2.285
peak=   -3.158 closest distance to " CZ3 TRP A 274 " =    2.371
peak=   -3.157 closest distance to " O   HOH Z 389 " =    1.875
peak=   -3.151 closest distance to " CD2 LEU A 282 " =    2.165
peak=   -3.150 closest distance to " CG2 THR A  18 " =    2.855
peak=   -3.148 closest distance to " OG  SER A  26 " =    1.264
peak=   -3.147 closest distance to " OD1 ASN A 249 " =    2.487
peak=   -3.147 closest distance to " CG  ARG A 219 " =    2.400
peak=   -3.144 closest distance to " ND2 ASN A  45 " =    1.928
peak=   -3.140 closest distance to " OD1 ASN A  39 " =    2.246
peak=   -3.140 closest distance to " O   HOH Z 265 " =    2.451
peak=   -3.140 closest distance to " CG  ASP A 286 " =    1.453
peak=   -3.136 closest distance to " N   PHE A  59 " =    1.901
peak=   -3.135 closest distance to " O   HOH Z 422 " =    1.479
peak=   -3.133 closest distance to " O   GLY A  80 " =    2.526
peak=   -3.133 closest distance to " O   HOH Z 106 " =    1.929
peak=   -3.129 closest distance to " CG1 VAL A 265 " =    2.555
peak=   -3.123 closest distance to " O   HOH Z 156 " =    3.481
peak=   -3.122 closest distance to " C   SER A 206 " =    1.518
peak=   -3.118 closest distance to " O   HOH Z 234 " =    3.989
peak=   -3.115 closest distance to " O   HOH Z 135 " =    1.650
peak=   -3.114 closest distance to " C   LEU A 143 " =    1.085
peak=   -3.110 closest distance to " O   HOH Z 145 " =    2.973
peak=   -3.107 closest distance to " O   HOH Z 109 " =    2.522
peak=   -3.102 closest distance to " N   THR A 220 " =    2.312
peak=   -3.087 closest distance to " O   ILE A 263 " =    2.207
peak=   -3.084 closest distance to " O   HOH Z 198 " =    1.656
peak=   -3.075 closest distance to " CB  ASP A 286 " =    1.826
peak=   -3.060 closest distance to " O   PRO A 198 " =    1.657
peak=   -3.055 closest distance to " CB  PHE A  16 " =    2.424
peak=   -3.051 closest distance to " O   HOH Z 196 " =    1.912
peak=   -3.048 closest distance to " CZ  PHE A  38 " =    1.993
peak=   -3.035 closest distance to " O   ARG A  24 " =    2.033
peak=   -3.033 closest distance to " O   HOH Z  11 " =    1.759
peak=   -3.031 closest distance to " O   HOH Z 236 " =    1.628

================= 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    :  0.4442 0.4388   6.246553e+00   6.234928e+00
   1_bss:  0.4371 0.4292   6.239296e+00   6.225189e+00
   1_xyz:  0.2871 0.3149   5.921976e+00   5.999695e+00
   1_adp:  0.2585 0.3260   5.870184e+00   6.024686e+00
   1_occ:  0.2584 0.3262   5.870070e+00   6.025471e+00
   2_bss:  0.2553 0.3235   5.864710e+00   6.020556e+00
   2_xyz:  0.1855 0.2338   5.573633e+00   5.762729e+00
   2_adp:  0.1701 0.2143   5.496921e+00   5.687545e+00
   2_occ:  0.1699 0.2139   5.495940e+00   5.686444e+00
   3_bss:  0.1696 0.2136   5.495126e+00   5.684747e+00
   3_xyz:  0.1392 0.1806   5.322189e+00   5.526283e+00
   3_adp:  0.1336 0.1760   5.288219e+00   5.495019e+00
   3_occ:  0.1334 0.1761   5.287885e+00   5.494703e+00
   4_bss:  0.1337 0.1764   5.289523e+00   5.494546e+00
   4_xyz:  0.1186 0.1632   5.195341e+00   5.420952e+00
   4_adp:  0.1163 0.1630   5.185226e+00   5.418892e+00
   4_occ:  0.1162 0.1630   5.185292e+00   5.419043e+00
   5_bss:  0.1162 0.1630   5.185491e+00   5.419257e+00
   5_xyz:  0.1127 0.1614   5.168771e+00   5.410176e+00
   5_adp:  0.1120 0.1614   5.166399e+00   5.410926e+00
   5_occ:  0.1119 0.1613   5.165857e+00   5.410913e+00
   5_bss:  0.1118 0.1612   5.165971e+00   5.411006e+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:  0.305  35.105  -0.975   1.832   1.422   0.000   0.000   0.000
   1_xyz:  0.305  35.105  -0.975   1.832   1.422   0.000   0.000   0.000
   1_adp:  0.305  35.105  -0.975   1.832   1.422   0.000   0.000   0.000
   1_occ:  0.305  35.105  -0.975   1.832   1.422   0.000   0.000   0.000
   2_bss:  0.329  60.483  -2.231  -0.161  -0.144  -0.000  -0.000  -0.000
   2_xyz:  0.329  60.483  -2.231  -0.161  -0.144  -0.000  -0.000  -0.000
   2_adp:  0.329  60.483  -2.231  -0.161  -0.144  -0.000  -0.000  -0.000
   2_occ:  0.329  60.483  -2.231  -0.161  -0.144  -0.000  -0.000  -0.000
   3_bss:  0.327  58.028  -3.074  -1.294  -0.670  -0.000  -0.000  -0.000
   3_xyz:  0.327  58.028  -3.074  -1.294  -0.670  -0.000  -0.000  -0.000
   3_adp:  0.327  58.028  -3.074  -1.294  -0.670  -0.000  -0.000  -0.000
   3_occ:  0.327  58.028  -3.074  -1.294  -0.670  -0.000  -0.000  -0.000
   4_bss:  0.328  59.580  -3.397  -1.869  -0.981  -0.000  -0.000  -0.000
   4_xyz:  0.328  59.580  -3.397  -1.869  -0.981  -0.000  -0.000  -0.000
   4_adp:  0.328  59.580  -3.397  -1.869  -0.981  -0.000  -0.000  -0.000
   4_occ:  0.328  59.580  -3.397  -1.869  -0.981  -0.000  -0.000  -0.000
   5_bss:  0.326  57.935  -3.211  -1.839  -0.855  -0.000  -0.000  -0.000
   5_xyz:  0.326  57.935  -3.211  -1.839  -0.855  -0.000  -0.000  -0.000
   5_adp:  0.326  57.935  -3.211  -1.839  -0.855  -0.000  -0.000  -0.000
   5_occ:  0.326  57.935  -3.211  -1.839  -0.855  -0.000  -0.000  -0.000
   5_bss:  0.323  57.938  -2.970  -1.651  -0.632  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.695 0.5126  0.6816    58306.285
   1_bss:  49.903 0.5208  0.7144    55514.989
   1_xyz:  32.780 0.7275  0.9472    26800.023
   1_adp:  34.062 0.7121  0.9353    28569.984
   1_occ:  34.110 0.7116  0.9341    28629.100
   2_bss:  33.779 0.7151  0.8887    28046.080
   2_xyz:  23.475 0.8260  0.9822    14126.002
   2_adp:  21.039 0.8516  0.9931    12076.192
   2_occ:  21.006 0.8519  0.9934    12042.213
   3_bss:  20.912 0.8527  0.9644    11928.927
   3_xyz:  17.112 0.8880  0.9843     8379.474
   3_adp:  16.385 0.8949  0.9835     7971.551
   3_occ:  16.379 0.8949  0.9835     7968.741
   4_bss:  16.391 0.8948  0.9699     7996.563
   4_xyz:  14.963 0.9069  0.9744     6905.267
   4_adp:  14.894 0.9076  0.9679     6892.537
   4_occ:  14.902 0.9076  0.9677     6893.016
   5_bss:  14.906 0.9075  0.9717     6896.426
   5_xyz:  14.687 0.9095  0.9734     6799.389
   5_adp:  14.690 0.9095  0.9662     6795.299
   5_occ:  14.686 0.9096  0.9661     6791.041
   5_bss:  14.692 0.9095  0.9735     6792.116
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.9166e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.9166e-01
   1_xyz:   1.455  0.011  0.090 15.443  0.005  4.105   1.1590e-01
   1_adp:   1.455  0.011  0.090 15.443  0.005  4.105   1.1590e-01
   1_occ:   1.455  0.011  0.090 15.443  0.005  4.105   1.1590e-01
   2_bss:   1.455  0.011  0.090 15.443  0.005  4.105   1.1590e-01
   2_xyz:   1.113  0.008  0.075 14.562  0.004  4.111   6.6728e-02
   2_adp:   1.113  0.008  0.075 14.562  0.004  4.111   6.6728e-02
   2_occ:   1.113  0.008  0.075 14.562  0.004  4.111   6.6728e-02
   3_bss:   1.113  0.008  0.075 14.562  0.004  4.111   6.6728e-02
   3_xyz:   0.944  0.006  0.067 14.457  0.004  4.118   5.3310e-02
   3_adp:   0.944  0.006  0.067 14.457  0.004  4.118   5.3310e-02
   3_occ:   0.944  0.006  0.067 14.457  0.004  4.118   5.3310e-02
   4_bss:   0.944  0.006  0.067 14.457  0.004  4.118   5.3310e-02
   4_xyz:   1.098  0.009  0.081 14.710  0.004  4.127   6.8924e-02
   4_adp:   1.098  0.009  0.081 14.710  0.004  4.127   6.8924e-02
   4_occ:   1.098  0.009  0.081 14.710  0.004  4.127   6.8924e-02
   5_bss:   1.098  0.009  0.081 14.710  0.004  4.127   6.8924e-02
   5_xyz:   1.092  0.009  0.081 14.674  0.004  4.113   6.9153e-02
   5_adp:   1.092  0.009  0.081 14.674  0.004  4.113   6.9153e-02
   5_occ:   1.092  0.009  0.081 14.674  0.004  4.113   6.9153e-02
   5_bss:   1.092  0.009  0.081 14.674  0.004  4.113   6.9153e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.261   2.4291e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.261   2.4291e-01
   1_xyz:   9.289  0.074  0.304 84.924  0.024  2.009   1.1729e-01
   1_adp:   9.289  0.074  0.304 84.924  0.024  2.009   1.1729e-01
   1_occ:   9.289  0.074  0.304 84.924  0.024  2.009   1.1729e-01
   2_bss:   9.289  0.074  0.304 84.924  0.024  2.009   1.1729e-01
   2_xyz:   7.051  0.039  0.249 80.540  0.042  2.254   5.9456e-02
   2_adp:   7.051  0.039  0.249 80.540  0.042  2.254   5.9456e-02
   2_occ:   7.051  0.039  0.249 80.540  0.042  2.254   5.9456e-02
   3_bss:   7.051  0.039  0.249 80.540  0.042  2.254   5.9456e-02
   3_xyz:   6.903  0.044  0.203 79.438  0.040  2.313   3.6352e-02
   3_adp:   6.903  0.044  0.203 79.438  0.040  2.313   3.6352e-02
   3_occ:   6.903  0.044  0.203 79.438  0.040  2.313   3.6352e-02
   4_bss:   6.903  0.044  0.203 79.438  0.040  2.313   3.6352e-02
   4_xyz:   8.004  0.046  0.276 83.486  0.037  2.283   5.2336e-02
   4_adp:   8.004  0.046  0.276 83.486  0.037  2.283   5.2336e-02
   4_occ:   8.004  0.046  0.276 83.486  0.037  2.283   5.2336e-02
   5_bss:   8.004  0.046  0.276 83.486  0.037  2.283   5.2336e-02
   5_xyz:   7.905  0.050  0.279 81.606  0.039  2.360   4.9184e-02
   5_adp:   7.905  0.050  0.279 81.606  0.039  2.360   4.9184e-02
   5_occ:   7.905  0.050  0.279 81.606  0.039  2.360   4.9184e-02
   5_bss:   7.905  0.050  0.279 81.606  0.039  2.360   4.9184e-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:  74.98   0.00  18.22  66.05   0.00  14.31  74.98   4.04  39.55
   1_occ:  74.98   0.00  18.22  66.05   0.00  14.31  74.98   4.04  39.55
   2_bss:  74.98   0.00  18.22  66.05   0.00  14.31  74.98   4.04  39.55
   2_xyz:  74.98   0.00  18.22  66.05   0.00  14.31  74.98   4.04  39.55
   2_adp:  75.44   0.81  17.70  75.44   0.81  13.63  74.89   5.86  39.87
   2_occ:  75.44   0.81  17.70  75.44   0.81  13.63  74.89   5.86  39.87
   3_bss:  75.44   0.81  17.70  75.44   0.81  13.63  74.89   5.86  39.87
   3_xyz:  75.44   0.81  17.70  75.44   0.81  13.63  74.89   5.86  39.87
   3_adp:  81.13   1.51  17.50  81.13   1.51  13.30  74.34   6.24  40.35
   3_occ:  81.13   1.51  17.50  81.13   1.51  13.30  74.34   6.24  40.35
   4_bss:  81.13   1.51  17.50  81.13   1.51  13.30  74.34   6.24  40.35
   4_xyz:  81.13   1.51  17.50  81.13   1.51  13.30  74.34   6.24  40.35
   4_adp:  85.22   1.07  17.51  85.22   1.07  13.17  77.09   4.89  41.12
   4_occ:  85.22   1.07  17.51  85.22   1.07  13.17  77.09   4.89  41.12
   5_bss:  85.22   1.07  17.51  85.22   1.07  13.17  77.09   4.89  41.12
   5_xyz:  85.22   1.07  17.51  85.22   1.07  13.17  77.09   4.89  41.12
   5_adp:  92.89   0.00  17.52  92.89   0.00  13.06  85.66   0.00  41.78
   5_occ:  92.89   0.00  17.52  92.89   0.00  13.06  85.66   0.00  41.78
   5_bss:  92.89   0.00  17.52  92.89   0.00  13.06  85.66   0.00  41.79
------------------------------------------------------------------------
 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:    2.457    0.020    0.436
   1_adp:    2.457    0.020    0.436
   1_occ:    2.457    0.020    0.436
   2_bss:    2.457    0.020    0.436
   2_xyz:    2.265    0.022    0.543
   2_adp:    2.265    0.022    0.543
   2_occ:    2.265    0.022    0.543
   3_bss:    2.265    0.022    0.543
   3_xyz:    2.196    0.065    0.625
   3_adp:    2.196    0.065    0.625
   3_occ:    2.196    0.065    0.625
   4_bss:    2.196    0.065    0.625
   4_xyz:    2.078    0.057    0.662
   4_adp:    2.078    0.057    0.662
   4_occ:    2.078    0.057    0.662
   5_bss:    2.078    0.057    0.662
   5_xyz:    2.115    0.078    0.676
   5_adp:    2.115    0.078    0.676
   5_occ:    2.115    0.078    0.676
   5_bss:    2.115    0.078    0.676
------------------------------------------------------------------------

CPU time actual refinement: 332.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_217/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_217/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_217/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_217/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_217/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.10 
  Macro-tasks:
    bulk solvent and scale       = 38.46  
    individual site refinement   = 137.51 
    weights calculation          = 29.74  
    collect and process          = 6.58   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 212.41 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 106.23 
    alpha_beta                      = 8.33   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 114.45 
    fmodel                         = 6.51   
    r_factors                      = 0.14   
    phase_errors                   = 10.59  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 249.52 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.740 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    639 calls, 105.96 s
gradients_fft:          584 calls, 101.38 s

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

# Date 2008-01-16 Time 04:18:31 PST -0800 (1200485911.93 s)
Start R-work = 0.4442, R-free = 0.4388 (no bulk solvent and anisotropic scale)
Final R-work = 0.1357, R-free = 0.1791 (no bulk solvent and anisotropic scale)

Start R-work = 0.4371, R-free = 0.4292
Final R-work = 0.1118, R-free = 0.1612