# Date 2008-01-16 Time 06:10:04 PST -0800 (1200492604.10 s)
#phil __OFF__

Command line arguments: "../1029.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7604
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1029

-------------------------------------------------------------------------------
  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: (71.3037, 46.93, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.00158
Completeness in resolution range: 0.968793
Completeness with d_max=infinity: 0.965832

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             d_min =   2.0016

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: (71.3037, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.00158
Completeness in resolution range: 0.968793
Completeness with d_max=infinity: 0.965832

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.2830 [2115/2140]  1905   210   9.9%
  bin  2:  4.2830 -  3.4122 [2042/2062]  1836   206  10.1%
  bin  3:  3.4122 -  2.9846 [2018/2037]  1815   203  10.1%
  bin  4:  2.9846 -  2.7134 [2001/2031]  1808   193   9.6%
  bin  5:  2.7134 -  2.5199 [1983/2002]  1784   199  10.0%
  bin  6:  2.5199 -  2.3719 [1968/1993]  1764   204  10.4%
  bin  7:  2.3719 -  2.2535 [1949/1977]  1753   196  10.1%
  bin  8:  2.2535 -  2.1557 [1976/2012]  1779   197  10.0%
  bin  9:  2.1557 -  2.0729 [1951/1993]  1760   191   9.8%
  bin 10:  2.0729 -  2.0016 [1586/1973]  1426   160  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1029/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 8
        2.42 -     3.04: 2177
        3.04 -     3.66: 4597
        3.66 -     4.28: 8976
        4.28 -     4.90: 12244
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.952 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.346 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27997 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_1029/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1029/model_refine_001.geo

CPU time processing inputs: 9.66


============================ 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 = 71.30375 46.93 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2717   r_free= 0.2658   ksol= 0.00   Bsol= 0.00   scale= 0.981    |
|                                                                             |
| 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:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.895524                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7771 0.99   1383  154 0.2662 0.2447      6.2889      6.1977|
|  2:  4.7771 -  3.8115 0.99   1327  146 0.2123 0.1921      6.2684      6.2072|
|  3:  3.8115 -  3.3355 0.99   1300  143 0.2284 0.2223      6.1457      6.2175|
|  4:  3.3355 -  3.0332 0.99   1285  148 0.2350 0.2432      6.0419      6.0499|
|  5:  3.0332 -  2.8173 0.99   1291  141 0.2789 0.2824      5.9708      6.0585|
|  6:  2.8173 -  2.6521 0.99   1279  141 0.2702 0.2762      5.8803      5.8175|
|  7:  2.6521 -  2.5199 0.99   1283  138 0.2906 0.2764      5.8771      5.9407|
|  8:  2.5199 -  2.4107 0.98   1255  147 0.2929 0.2669      5.8316      5.7783|
|  9:  2.4107 -  2.3182 0.98   1267  138 0.2907 0.2905      5.7645      5.7528|
| 10:  2.3182 -  2.2385 1.00   1264  141 0.2972 0.3055      5.7594      5.7983|
| 11:  2.2385 -  2.1687 0.97   1251  137 0.3141 0.3160      5.7509      5.8063|
| 12:  2.1687 -  2.1068 0.98   1256  142 0.3152 0.3010      5.6794      5.7382|
| 13:  2.1068 -  2.0515 0.99   1281  139 0.3128 0.3343      5.5858        5.54|
| 14:  2.0515 -  2.0016 0.72    908  104 0.3018 0.2834      5.5221      5.4733|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1782 -  4.7771  1383   154  0.82  23.56   0.86     0.83      34833.57|
|  2:  4.7771 -  3.8115  1327   146  0.88  17.99   0.98     0.93      31812.30|
|  3:  3.8115 -  3.3355  1300   143  0.85  21.13   1.00     0.96      29933.83|
|  4:  3.3355 -  3.0332  1285   148  0.84  22.94   1.00     0.95      26705.25|
|  5:  3.0332 -  2.8173  1291   141  0.78  28.36   1.00     0.93      23871.79|
|  6:  2.8173 -  2.6521  1279   141  0.79  27.61   1.02     0.93      19963.61|
|  7:  2.6521 -  2.5199  1283   138  0.78  28.23   1.02     0.93      18313.41|
|  8:  2.5199 -  2.4107  1255   147  0.79  27.93   1.03     0.96      16590.70|
|  9:  2.4107 -  2.3182  1267   138  0.79  28.28   1.04     0.97      15994.56|
| 10:  2.3182 -  2.2385  1264   141  0.76  30.43   1.07     0.96      15671.54|
| 11:  2.2385 -  2.1687  1251   137  0.75  31.80   1.07     0.95      15616.24|
| 12:  2.1687 -  2.1068  1256   142  0.75  31.13   1.05     0.98      14298.18|
| 13:  2.1068 -  2.0515  1281   139  0.76  30.98   1.06     0.99      11674.19|
| 14:  2.0515 -  2.0016   908   104  0.80  27.15   1.06     0.99       8254.26|
|alpha:            min =        0.83 max =            0.99 mean =         0.95|
|beta:             min =     8254.26 max =        34833.57 mean =     20664.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.80|
|phase err.(work): min =        0.00 max =           89.93 mean =        26.89|
|phase err.(test): min =        0.00 max =           89.98 mean =        26.59|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.472585              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.479   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.456123              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.659   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      173 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2004 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1822 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2775 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4626 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4350 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5569 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6675 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.137 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2717   r_free= 0.2658   ksol= 0.00   Bsol= 0.00   scale= 0.981    |
|                                                                             |
| 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:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.895524                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2553   r_free= 0.2521   ksol= 0.31   Bsol= 54.02   scale= 0.976   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.06,-3.09,-1.12,-0.00,-0.00,-0.00); trace/3= -1.38                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.865586                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.260210              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.723   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.260421              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.397   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2553      final r-factor (work) = 0.1655          |
| start r-factor (free) = 0.2521      final r-factor (free) = 0.1834          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8096 = 2.26 * 0.50 * 5.8832 + 1.00 * 0.1609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3851 = 2.26 * 0.50 * 5.6000 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1655      final r-factor (work) = 0.1505          |
| start r-factor (free) = 0.1834      final r-factor (free) = 0.1872          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4645 = 0.26 * 1.00 * 5.6000 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4070 = 0.26 * 1.00 * 5.3714 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    73.89   17.04    None  None   None       |
|    all(noH): 2823   0      0.88    73.89   17.04    None  None   None       |
|    Sol.    : 438    0      5.18    73.89   38.54    None  None   None       |
|    Mac.    : 2385   0      0.88    70.44   13.09    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:     0.880 -   8.181:  520   |   5:    37.384 -  44.685:   95        |
|      1:     8.181 -  15.481: 1350   |   6:    44.685 -  51.986:   93        |
|      2:    15.481 -  22.782:  405   |   7:    51.986 -  59.287:   69        |
|      3:    22.782 -  30.083:  147   |   8:    59.287 -  66.588:   25        |
|      4:    30.083 -  37.384:  110   |   9:    66.588 -  73.888:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1505 r_free = 0.1872             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1500 r_free = 0.1867             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1500   r_free= 0.1867   ksol= 0.31   Bsol= 54.02   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.06,-3.09,-1.12,-0.00,-0.00,-0.00); trace/3= -1.38                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.377095                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1490   r_free= 0.1851   ksol= 0.33   Bsol= 63.59   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-3.00,-1.56,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.372807                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.172605              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.827  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.153867              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.491  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1490      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1851      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5818 = 3.17 * 0.50 * 5.3743 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4232 = 3.17 * 0.50 * 5.2665 + 1.00 * 0.0689                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8185 = 0.15 * 1.00 * 5.2665 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8035 = 0.15 * 1.00 * 5.1763 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.75    72.43   16.79    None  None   None       |
|    all(noH): 2823   0      1.75    72.43   16.79    None  None   None       |
|    Sol.    : 438    0      6.07    72.43   37.43    None  None   None       |
|    Mac.    : 2385   0      1.75    72.42   13.00    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:     1.750 -   8.818:  615   |   5:    37.090 -  44.158:  113        |
|      1:     8.818 -  15.886: 1312   |   6:    44.158 -  51.226:   79        |
|      2:    15.886 -  22.954:  360   |   7:    51.226 -  58.294:   69        |
|      3:    22.954 -  30.022:  136   |   8:    58.294 -  65.361:   15        |
|      4:    30.022 -  37.090:  114   |   9:    65.361 -  72.429:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1159 r_free = 0.1573             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1158 r_free = 0.1572             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1572   ksol= 0.33   Bsol= 63.59   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-3.00,-1.56,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.160089                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1565   ksol= 0.33   Bsol= 63.59   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.83,-1.51,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158740                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.027501              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.346  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.240485              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.930  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3160 = 2.03 * 0.50 * 5.1760 + 1.00 * 0.0689                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2834 = 2.03 * 0.50 * 5.1507 + 1.00 * 0.0619                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2456 = 0.24 * 1.00 * 5.1507 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2447 = 0.24 * 1.00 * 5.1450 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.43    73.40   16.76    None  None   None       |
|    all(noH): 2823   0      1.43    73.40   16.76    None  None   None       |
|    Sol.    : 438    0      5.64    73.18   37.69    None  None   None       |
|    Mac.    : 2385   0      1.43    73.40   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.432 -   8.628:  622   |   5:    37.414 -  44.611:  116        |
|      1:     8.628 -  15.825: 1299   |   6:    44.611 -  51.808:   85        |
|      2:    15.825 -  23.021:  362   |   7:    51.808 -  59.004:   64        |
|      3:    23.021 -  30.218:  142   |   8:    59.004 -  66.201:   15        |
|      4:    30.218 -  37.414:  108   |   9:    66.201 -  73.397:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1562             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1125 r_free = 0.1562             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1562   ksol= 0.33   Bsol= 63.59   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.83,-1.51,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145182                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1562   ksol= 0.33   Bsol= 63.59   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.65,-1.38,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145189                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.048993              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.911  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.252699              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.914  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9057 = 3.05 * 0.50 * 5.1452 + 1.00 * 0.0619                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8969 = 3.05 * 0.50 * 5.1295 + 1.00 * 0.0769                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5627 = 2.25 * 1.00 * 5.1295 + 1.00 * 0.0074                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5478 = 2.25 * 1.00 * 5.1219 + 1.00 * 0.0097                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.20    85.47   17.21    None  None   None       |
|    all(noH): 2823   0      0.20    85.47   17.21    None  None   None       |
|    Sol.    : 438    0      6.28    80.83   40.29    None  None   None       |
|    Mac.    : 2385   0      0.20    85.47   12.97    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:     0.199 -   8.726:  726   |   5:    42.834 -  51.361:   90        |
|      1:     8.726 -  17.253: 1312   |   6:    51.361 -  59.888:   86        |
|      2:    17.253 -  25.780:  301   |   7:    59.888 -  68.415:   44        |
|      3:    25.780 -  34.307:  128   |   8:    68.415 -  76.942:   18        |
|      4:    34.307 -  42.834:  113   |   9:    76.942 -  85.468:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1076 r_free = 0.1576             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1076 r_free = 0.1577             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1577   ksol= 0.33   Bsol= 63.59   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.65,-1.38,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.125178                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1575   ksol= 0.33   Bsol= 63.59   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.34,-1.11,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.124988                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.544178              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.272  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.228249              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.693  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1074      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0325 = 1.54 * 0.50 * 5.1232 + 1.00 * 0.0769                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0262 = 1.54 * 0.50 * 5.1426 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1835 = 0.23 * 1.00 * 5.1426 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1847 = 0.23 * 1.00 * 5.1549 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.11    84.06   16.64    None  None   None       |
|    all(noH): 2823   0      1.11    84.06   16.64    None  None   None       |
|    Sol.    : 438    0      6.11    80.21   38.16    None  None   None       |
|    Mac.    : 2385   0      1.11    84.06   12.69    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:     1.109 -   9.404:  926   |   5:    42.586 -  50.881:   93        |
|      1:     9.404 -  17.699: 1155   |   6:    50.881 -  59.177:   76        |
|      2:    17.699 -  25.995:  272   |   7:    59.177 -  67.472:   24        |
|      3:    25.995 -  34.290:  134   |   8:    67.472 -  75.767:   13        |
|      4:    34.290 -  42.586:  126   |   9:    75.767 -  84.063:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1585             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1125 r_free = 0.1586             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1586   ksol= 0.33   Bsol= 63.59   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.34,-1.11,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.152626                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7771 0.99   1383  154 0.1017 0.1304       5.411      5.5372|
|  2:  4.7771 -  3.8115 0.99   1327  146 0.0879 0.1097       5.456      5.6207|
|  3:  3.8115 -  3.3355 0.99   1300  143 0.1045 0.1485      5.4715      5.8646|
|  4:  3.3355 -  3.0332 0.99   1285  148 0.1212 0.1578      5.4592      5.5923|
|  5:  3.0332 -  2.8173 0.99   1291  141 0.1339 0.1780       5.341      5.5847|
|  6:  2.8173 -  2.6521 0.99   1279  141 0.1221 0.1925      5.2298       5.483|
|  7:  2.6521 -  2.5199 0.99   1283  138 0.1291 0.1550      5.1891      5.3532|
|  8:  2.5199 -  2.4107 0.98   1255  147 0.1156 0.1779      5.0625      5.3644|
|  9:  2.4107 -  2.3182 0.98   1267  138 0.1158 0.1657      5.0337       5.249|
| 10:  2.3182 -  2.2385 1.00   1264  141 0.1121 0.1803      4.9595      5.2836|
| 11:  2.2385 -  2.1687 0.97   1251  137 0.1160 0.1718      4.9624      5.2228|
| 12:  2.1687 -  2.1068 0.98   1256  142 0.1118 0.1730      4.8874      5.2097|
| 13:  2.1068 -  2.0515 0.99   1281  139 0.1136 0.1765      4.7987      5.0974|
| 14:  2.0515 -  2.0016 0.72    908  104 0.1088 0.1705       4.685      4.9227|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1782 -  4.7771  1383   154  0.94   9.52   0.97     0.94       7504.02|
|  2:  4.7771 -  3.8115  1327   146  0.95   7.96   1.00     0.99       9200.80|
|  3:  3.8115 -  3.3355  1300   143  0.93  11.15   1.01     1.01      10280.40|
|  4:  3.3355 -  3.0332  1285   148  0.92  13.63   1.00     0.98      10374.09|
|  5:  3.0332 -  2.8173  1291   141  0.90  16.04   0.99     0.96       8528.87|
|  6:  2.8173 -  2.6521  1279   141  0.90  16.06   0.98     0.96       7361.66|
|  7:  2.6521 -  2.5199  1283   138  0.90  15.91   0.98     0.96       6460.88|
|  8:  2.5199 -  2.4107  1255   147  0.91  14.84   0.98     0.96       5170.74|
|  9:  2.4107 -  2.3182  1267   138  0.91  15.08   0.99     0.95       4934.91|
| 10:  2.3182 -  2.2385  1264   141  0.91  15.19   0.99     0.95       4319.66|
| 11:  2.2385 -  2.1687  1251   137  0.89  16.77   0.98     0.95       4546.46|
| 12:  2.1687 -  2.1068  1256   142  0.91  14.96   0.99     0.98       3994.90|
| 13:  2.1068 -  2.0515  1281   139  0.90  15.94   0.98     0.96       3392.24|
| 14:  2.0515 -  2.0016   908   104  0.92  14.60   0.96     0.92       2592.43|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2592.43 max =        10374.09 mean =      6443.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.05|
|phase err.(test): min =        0.00 max =           88.66 mean =        13.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1586   ksol= 0.33   Bsol= 63.55   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.20,-0.97,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.152700                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1586   ksol= 0.33   Bsol= 63.55   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.20,-0.97,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.152700                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7771 0.99   1383  154 0.1017 0.1304      5.4114      5.5375|
|  2:  4.7771 -  3.8115 0.99   1327  146 0.0879 0.1096      5.4559      5.6203|
|  3:  3.8115 -  3.3355 0.99   1300  143 0.1045 0.1485      5.4711      5.8642|
|  4:  3.3355 -  3.0332 0.99   1285  148 0.1211 0.1578      5.4591      5.5923|
|  5:  3.0332 -  2.8173 0.99   1291  141 0.1339 0.1781      5.3412      5.5851|
|  6:  2.8173 -  2.6521 0.99   1279  141 0.1222 0.1924        5.23      5.4828|
|  7:  2.6521 -  2.5199 0.99   1283  138 0.1290 0.1549       5.189      5.3528|
|  8:  2.5199 -  2.4107 0.98   1255  147 0.1155 0.1780      5.0624      5.3647|
|  9:  2.4107 -  2.3182 0.98   1267  138 0.1159 0.1657      5.0339      5.2489|
| 10:  2.3182 -  2.2385 1.00   1264  141 0.1121 0.1803      4.9596      5.2831|
| 11:  2.2385 -  2.1687 0.97   1251  137 0.1160 0.1720      4.9627      5.2233|
| 12:  2.1687 -  2.1068 0.98   1256  142 0.1118 0.1731      4.8877      5.2098|
| 13:  2.1068 -  2.0515 0.99   1281  139 0.1136 0.1766      4.7988      5.0976|
| 14:  2.0515 -  2.0016 0.72    908  104 0.1088 0.1706      4.6852      4.9231|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1782 -  4.7771  1383   154  0.94   9.52   0.97     0.94       7509.92|
|  2:  4.7771 -  3.8115  1327   146  0.95   7.96   1.00     0.99       9199.32|
|  3:  3.8115 -  3.3355  1300   143  0.93  11.14   1.01     1.01      10271.28|
|  4:  3.3355 -  3.0332  1285   148  0.92  13.63   1.00     0.98      10374.03|
|  5:  3.0332 -  2.8173  1291   141  0.90  16.04   0.99     0.96       8529.56|
|  6:  2.8173 -  2.6521  1279   141  0.90  16.06   0.98     0.96       7362.89|
|  7:  2.6521 -  2.5199  1283   138  0.90  15.91   0.99     0.96       6458.74|
|  8:  2.5199 -  2.4107  1255   147  0.91  14.84   0.99     0.97       5170.99|
|  9:  2.4107 -  2.3182  1267   138  0.91  15.08   0.99     0.96       4932.95|
| 10:  2.3182 -  2.2385  1264   141  0.91  15.20   0.99     0.95       4322.32|
| 11:  2.2385 -  2.1687  1251   137  0.89  16.78   0.99     0.95       4547.69|
| 12:  2.1687 -  2.1068  1256   142  0.91  14.97   1.00     0.98       3996.78|
| 13:  2.1068 -  2.0515  1281   139  0.90  15.95   0.98     0.97       3392.83|
| 14:  2.0515 -  2.0016   908   104  0.92  14.60   0.96     0.93       2594.49|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2594.49 max =        10374.03 mean =      6443.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.06|
|phase err.(test): min =        0.00 max =           88.66 mean =        13.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.159)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.07    84.02   16.60    None  None   None       |
|    all(noH): 2823   0      1.07    84.02   16.60    None  None   None       |
|    Sol.    : 438    0      6.07    80.17   38.12    None  None   None       |
|    Mac.    : 2385   0      1.07    84.02   12.65    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:     1.070 -   9.365:  926   |   5:    42.547 -  50.842:   93        |
|      1:     9.365 -  17.661: 1155   |   6:    50.842 -  59.138:   76        |
|      2:    17.661 -  25.956:  272   |   7:    59.138 -  67.433:   24        |
|      3:    25.956 -  34.252:  134   |   8:    67.433 -  75.729:   13        |
|      4:    34.252 -  42.547:  126   |   9:    75.729 -  84.024:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 292         
Filter by distance & map next to the model:
   mapped sites are within: 0.570 - 4.729
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 289 from: 292
   mapped sites are within: 0.703 - 4.729

peak=    5.734 closest distance to " NH2 ARG A  56 " =    2.277
peak=    5.643 closest distance to " CB  GLN A 223 " =    1.410
peak=    5.627 closest distance to " CG  PRO A  54 " =    1.379
peak=    5.160 closest distance to " O   HOH Z 232 " =    2.291
peak=    5.019 closest distance to " O   HOH Z 126 " =    1.886
peak=    4.949 closest distance to " CG  PRO A 213 " =    1.213
peak=    4.890 closest distance to " CB  SER A  63 " =    1.257
peak=    4.877 closest distance to " CB  ARG A 275 " =    0.912
peak=    4.788 closest distance to " CB  PRO A  54 " =    0.951
peak=    4.722 closest distance to " CG  PRO A 198 " =    1.275
peak=    4.662 closest distance to " CB  LEU A 228 " =    1.084
peak=    4.632 closest distance to " O   HOH Z 298 " =    1.990
peak=    4.549 closest distance to " O   HOH Z  78 " =    1.692
peak=    4.519 closest distance to " CB  GLN A 183 " =    1.214
peak=    4.478 closest distance to " O   HOH Z 369 " =    2.109
peak=    4.454 closest distance to " O   HOH Z 236 " =    2.118
peak=    4.451 closest distance to " O   HOH Z  15 " =    2.216
peak=    4.431 closest distance to " CZ  PHE A 218 " =    1.045
peak=    4.416 closest distance to " NE2 GLN A  11 " =    1.093
peak=    4.415 closest distance to " CB  ASN A 148 " =    1.396
peak=    4.408 closest distance to " CB  GLU A 128 " =    1.029
peak=    4.393 closest distance to " CB  ARG A 190 " =    1.617
peak=    4.385 closest distance to " C   PRO A 198 " =    1.512
peak=    4.341 closest distance to " CA  TYR A  30 " =    0.948
peak=    4.329 closest distance to " CB  ASN A 187 " =    1.304
peak=    4.308 closest distance to " CB  ARG A  79 " =    1.335
peak=    4.289 closest distance to " CG  PRO A 243 " =    1.071
peak=    4.277 closest distance to " CB  TYR A 169 " =    0.709
peak=    4.244 closest distance to " O   HOH Z 234 " =    3.830
peak=    4.239 closest distance to " ND2 ASN A 187 " =    1.442
peak=    4.225 closest distance to " O   HOH Z 189 " =    2.645
peak=    4.199 closest distance to " CD1 LEU A 300 " =    1.198
peak=    4.157 closest distance to " CB  ASP A 124 " =    0.781
peak=    4.132 closest distance to " CB  TRP A 266 " =    0.963
peak=    4.116 closest distance to " OD1 ASN A  69 " =    2.593
peak=    4.101 closest distance to " CB  GLU A 152 " =    1.143
peak=    4.089 closest distance to " O   HOH Z 250 " =    1.544
peak=    4.089 closest distance to " O   HOH Z  54 " =    2.435
peak=    4.085 closest distance to " CD  ARG A 269 " =    0.919
peak=    4.074 closest distance to " O   HOH Z 303 " =    2.158
peak=    4.069 closest distance to " CG2 VAL A 257 " =    0.969
peak=    4.058 closest distance to " O   HOH Z 142 " =    1.712
peak=    4.000 closest distance to " O   HOH Z 158 " =    3.063
peak=    3.961 closest distance to " O   HOH Z 261 " =    1.981
peak=    3.951 closest distance to " NH1AARG A 145 " =    1.288
peak=    3.950 closest distance to " CA  THR A 264 " =    0.894
peak=    3.924 closest distance to " CB  VAL A 265 " =    1.252
peak=    3.922 closest distance to " O   HOH Z 368 " =    2.043
peak=    3.913 closest distance to " CA  ASN A 215 " =    1.172
peak=    3.909 closest distance to " NH2 ARG A 156 " =    1.236
peak=    3.908 closest distance to " CB  ASN A  39 " =    0.895
peak=    3.904 closest distance to " O   HOH Z 316 " =    3.129
peak=    3.899 closest distance to " CD  ARG A 159 " =    0.785
peak=    3.882 closest distance to " CB  GLU A  46 " =    0.962
peak=    3.870 closest distance to " CB  VAL A 202 " =    1.588
peak=    3.864 closest distance to " O   HOH Z 193 " =    1.988
peak=    3.848 closest distance to " O   HOH Z 427 " =    3.075
peak=    3.842 closest distance to " CE  LYS A  76 " =    0.841
peak=    3.824 closest distance to " CB  LEU A 143 " =    1.134
peak=    3.813 closest distance to " CB  ASP A 140 " =    0.935
peak=    3.812 closest distance to " CB  MET A  40 " =    0.784
peak=    3.811 closest distance to " O   HOH Z 214 " =    2.043
peak=    3.805 closest distance to " O   HOH Z  21 " =    1.797
peak=    3.805 closest distance to " NZ  LYS A 117 " =    3.230
peak=    3.801 closest distance to " CA  SER A  87 " =    1.033
peak=    3.789 closest distance to " CA  ALA A  51 " =    0.902
peak=    3.785 closest distance to " CB  SER A 216 " =    0.836
peak=    3.777 closest distance to " CA  ASP A 124 " =    0.705
peak=    3.762 closest distance to " CG2 ILE A 120 " =    1.130
peak=    3.757 closest distance to " CB  SER A   3 " =    1.343
peak=    3.748 closest distance to " CA  ARG A  36 " =    1.152
peak=    3.737 closest distance to " CD  ARG A  66 " =    2.344
peak=    3.736 closest distance to " CB  GLU A 277 " =    3.677
peak=    3.735 closest distance to " O   HOH Z  61 " =    1.611
peak=    3.733 closest distance to " CD2 TRP A 179 " =    1.302
peak=    3.727 closest distance to " CB  ALA A 104 " =    0.709
peak=    3.725 closest distance to " CG2 THR A 221 " =    1.040
peak=    3.724 closest distance to " O   HOH Z 133 " =    2.387
peak=    3.721 closest distance to " O   HOH Z   1 " =    2.087
peak=    3.713 closest distance to " O   HOH Z 346 " =    1.641
peak=    3.703 closest distance to " CB  ASN A 142 " =    1.022
peak=    3.683 closest distance to " O   HOH Z 126 " =    2.047
peak=    3.681 closest distance to " O   HOH Z 197 " =    3.128
peak=    3.676 closest distance to " ND2 ASN A 249 " =    1.971
peak=    3.675 closest distance to " O   HOH Z 291 " =    1.576
peak=    3.670 closest distance to " CD  LYS A 166 " =    1.258
peak=    3.665 closest distance to " O   HOH Z  40 " =    1.837
peak=    3.660 closest distance to " CB  SER A 212 " =    1.180
peak=    3.654 closest distance to " CA  ARG A 195 " =    1.222
peak=    3.654 closest distance to " CD ALYS A 290 " =    1.003
peak=    3.652 closest distance to " O   HOH Z 272 " =    1.872
peak=    3.644 closest distance to " O   HOH Z  10 " =    1.866
peak=    3.641 closest distance to " CB  MET A  47 " =    1.024
peak=    3.640 closest distance to " CG1 VAL A 153 " =    0.902
peak=    3.635 closest distance to " O   THR A 251 " =    1.164
peak=    3.634 closest distance to " ND1 HIS A  86 " =    1.737
peak=    3.625 closest distance to " O   HOH Z  68 " =    2.175
peak=    3.623 closest distance to " N   ASN A 127 " =    1.255
peak=    3.622 closest distance to " CD  ARG A  66 " =    2.276
peak=    3.620 closest distance to " O   HOH Z 411 " =    3.809
peak=    3.620 closest distance to " O   HOH Z  53 " =    2.546
peak=    3.619 closest distance to " CB  ALA A  34 " =    0.983
peak=    3.605 closest distance to " O   HOH Z 132 " =    2.674
peak=    3.602 closest distance to " CG  LEU A 167 " =    1.227
peak=    3.599 closest distance to " O   HOH Z 285 " =    2.770
peak=    3.596 closest distance to " O   HOH Z 426 " =    1.696
peak=    3.595 closest distance to " O   TYR A 116 " =    1.272
peak=    3.592 closest distance to " O   HOH Z 313 " =    1.838
peak=    3.585 closest distance to " CG1 ILE A  33 " =    1.286
peak=    3.584 closest distance to " O   HOH Z 193 " =    1.708
peak=    3.581 closest distance to " O   HOH Z 344 " =    3.219
peak=    3.579 closest distance to " CA  TYR A  30 " =    1.064
peak=    3.578 closest distance to " O   HOH Z 203 " =    1.823
peak=    3.577 closest distance to " O   HOH Z 305 " =    3.707
peak=    3.575 closest distance to " O   HOH Z 403 " =    1.682
peak=    3.574 closest distance to " O   HOH Z 423 " =    1.796
peak=    3.570 closest distance to " CG1BVAL A  72 " =    1.727
peak=    3.564 closest distance to " CA  THR A 221 " =    0.963
peak=    3.563 closest distance to " CB  ILE A 120 " =    1.202
peak=    3.562 closest distance to " OD2 ASP A 286 " =    2.885
peak=    3.550 closest distance to " O   SER A  87 " =    2.204
peak=    3.547 closest distance to " O   HOH Z 273 " =    2.792
peak=    3.541 closest distance to " O   HOH Z 180 " =    2.135
peak=    3.541 closest distance to " O   HOH Z   9 " =    2.061
peak=    3.538 closest distance to " CB  TYR A 116 " =    0.818
peak=    3.536 closest distance to " CA  MET A  40 " =    1.150
peak=    3.534 closest distance to " O  BHOH Z 338 " =    2.379
peak=    3.532 closest distance to " CD  ARG A 219 " =    1.088
peak=    3.531 closest distance to " O   HOH Z 213 " =    1.997
peak=    3.528 closest distance to " CZ  PHE A 192 " =    0.934
peak=    3.526 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.523 closest distance to " O   HOH Z 209 " =    2.307
peak=    3.516 closest distance to " O   HOH Z 234 " =    1.767
peak=    3.500 closest distance to " CB  ALA A 291 " =    1.232
peak=    3.496 closest distance to " CB  GLN A  88 " =    1.247
peak=    3.489 closest distance to " N   ASN A  39 " =    1.307
peak=    3.488 closest distance to " O   MET A 105 " =    1.863
peak=    3.486 closest distance to " N   ARG A 156 " =    1.400
peak=    3.475 closest distance to " O   HOH Z 135 " =    1.660
peak=    3.464 closest distance to " O   HOH Z 353 " =    2.692
peak=    3.455 closest distance to " CB  TRP A 179 " =    1.431
peak=    3.454 closest distance to " ND2 ASN A 249 " =    0.870
peak=    3.453 closest distance to " O   HOH Z 371 " =    3.029
peak=    3.448 closest distance to " CB  SER A 210 " =    0.790
peak=    3.442 closest distance to " CD1 LEU A  96 " =    0.766
peak=    3.440 closest distance to " CD2 LEU A 297 " =    0.848
peak=    3.439 closest distance to " CB  ASN A 110 " =    1.144
peak=    3.435 closest distance to " O   HOH Z 128 " =    2.194
peak=    3.433 closest distance to " CZ  PHE A 208 " =    1.101
peak=    3.433 closest distance to " ND2 ASN A 110 " =    1.670
peak=    3.431 closest distance to " CB  LEU A  83 " =    0.807
peak=    3.431 closest distance to " O   HOH Z 147 " =    1.787
peak=    3.430 closest distance to " O   HOH Z 280 " =    3.026
peak=    3.427 closest distance to " CD1 ILE A 106 " =    0.818
peak=    3.415 closest distance to " CB  HIS A 108 " =    0.795
peak=    3.413 closest distance to " O   HOH Z 294 " =    1.520
peak=    3.410 closest distance to " NE2 HIS A 207 " =    1.304
peak=    3.409 closest distance to " CB  SER A 141 " =    0.997
peak=    3.408 closest distance to " O   HOH Z 245 " =    1.286
peak=    3.405 closest distance to " O   HOH Z 419 " =    1.967
peak=    3.402 closest distance to " O   HOH Z 185 " =    1.870
peak=    3.401 closest distance to " O   HOH Z 227 " =    1.712
peak=    3.400 closest distance to " O   HOH Z 172 " =    3.402
peak=    3.395 closest distance to " CA  ALA A  21 " =    1.194
peak=    3.386 closest distance to " CA  ALA A 154 " =    0.965
peak=    3.381 closest distance to " CB  ALA A 242 " =    0.836
peak=    3.380 closest distance to " CA  ALA A 233 " =    1.380
peak=    3.375 closest distance to " OE1 GLU A 236 " =    1.115
peak=    3.375 closest distance to " N   GLY A  98 " =    1.106
peak=    3.371 closest distance to " OD1BASN A 224 " =    2.348
peak=    3.371 closest distance to " NH2BARG A 145 " =    2.193
peak=    3.369 closest distance to " O   HOH Z 425 " =    1.937
peak=    3.363 closest distance to " CB  ALA A 248 " =    1.229
peak=    3.359 closest distance to " O   HOH Z 219 " =    1.824
peak=    3.359 closest distance to " CA  ALA A 158 " =    1.217
peak=    3.356 closest distance to " O   HOH Z 108 " =    2.707
peak=    3.344 closest distance to " CA  MET A 105 " =    0.985
peak=    3.336 closest distance to " O   HOH Z 166 " =    3.800
peak=    3.332 closest distance to " O   HOH Z  66 " =    2.120
peak=    3.323 closest distance to " O   THR A 220 " =    1.228
peak=    3.320 closest distance to " CB  ALA A 248 " =    1.022
peak=    3.316 closest distance to " O   HOH Z 402 " =    1.424
peak=    3.315 closest distance to " O   HOH Z 128 " =    2.352
peak=    3.304 closest distance to " O   HOH Z 329 " =    3.853
peak=    3.298 closest distance to " OG  SER A  22 " =    2.804
peak=    3.295 closest distance to " CB  ARG A 139 " =    0.901
peak=    3.295 closest distance to " O   ASN A 209 " =    1.321
peak=    3.284 closest distance to " N   VAL A 126 " =    1.423
peak=    3.283 closest distance to " CA  ASN A 217 " =    1.297
peak=    3.281 closest distance to " O   HOH Z 411 " =    1.751
peak=    3.281 closest distance to " CZ2 TRP A 179 " =    1.768
peak=    3.281 closest distance to " CB  ALA A   1 " =    4.729
peak=    3.281 closest distance to " O   HOH Z 133 " =    1.674
peak=    3.280 closest distance to " O   HOH Z 133 " =    3.260
peak=    3.277 closest distance to " CB  LYS A 193 " =    0.977
peak=    3.276 closest distance to " CD2 LEU A 255 " =    1.583
peak=    3.275 closest distance to " O   HOH Z  62 " =    1.973
peak=    3.271 closest distance to " C   TYR A 214 " =    1.542
peak=    3.270 closest distance to " O   HOH Z  43 " =    1.779
peak=    3.265 closest distance to " CA  GLY A 267 " =    1.127
peak=    3.262 closest distance to " CG  ARG A 159 " =    0.919
peak=    3.262 closest distance to " CB  TYR A 169 " =    1.231
peak=    3.261 closest distance to " CE1 TYR A 186 " =    1.384
peak=    3.260 closest distance to " N   PHE A 130 " =    1.193
peak=    3.259 closest distance to " O   HOH Z 295 " =    1.506
peak=    3.258 closest distance to " CZ  PHE A  38 " =    1.272
peak=    3.253 closest distance to " CG  GLN A  11 " =    1.501
peak=    3.250 closest distance to " O   HOH Z  97 " =    2.737
peak=    3.249 closest distance to " OG BSER A 164 " =    2.394
peak=    3.249 closest distance to " CB  ALA A 291 " =    0.829
peak=    3.249 closest distance to " CB  PRO A 198 " =    0.991
peak=    3.248 closest distance to " CB  GLN A 103 " =    0.855
peak=    3.248 closest distance to " O   HOH Z 171 " =    2.230
peak=    3.246 closest distance to " O   HOH Z 383 " =    1.902
peak=    3.244 closest distance to " O   HOH Z 188 " =    2.131
peak=    3.243 closest distance to " CB  ALA A   9 " =    1.571
peak=    3.242 closest distance to " CA  ASP A 191 " =    0.788
peak=    3.241 closest distance to " O   HOH Z  88 " =    3.570
peak=    3.239 closest distance to " CB  GLN A  89 " =    1.228
peak=    3.239 closest distance to " O   HOH Z 148 " =    3.347
peak=    3.235 closest distance to " ND1 HIS A  81 " =    1.651
peak=    3.234 closest distance to " CB  ALA A 114 " =    1.039
peak=    3.231 closest distance to " O   TRP A 274 " =    1.822
peak=    3.228 closest distance to " CG  MET A 185 " =    1.200
peak=    3.226 closest distance to " CB  THR A 235 " =    1.111
peak=    3.219 closest distance to " O   HOH Z  20 " =    1.665
peak=    3.217 closest distance to " O   HOH Z  96 " =    1.957
peak=    3.215 closest distance to " N   GLN A 278 " =    1.006
peak=    3.214 closest distance to " CG1 ILE A 151 " =    1.025
peak=    3.213 closest distance to " O   HOH Z 171 " =    3.966
peak=    3.210 closest distance to " CA  GLN A 223 " =    0.934
peak=    3.201 closest distance to " CG2BVAL A  41 " =    0.806
peak=    3.196 closest distance to " O   ALA A 158 " =    1.265
peak=    3.195 closest distance to " CG  MET A 113 " =    1.337
peak=    3.190 closest distance to " O   HOH Z 326 " =    2.466
peak=    3.188 closest distance to " OG1 THR A 294 " =    2.437
peak=    3.185 closest distance to " CB  TRP A 150 " =    1.377
peak=    3.185 closest distance to " O   HOH Z 216 " =    2.976
peak=    3.183 closest distance to " O   HOH Z 403 " =    1.352
peak=    3.182 closest distance to " OD1 ASP A 171 " =    1.250
peak=    3.182 closest distance to " OG BSER A 134 " =    2.951
peak=    3.182 closest distance to " O   HOH Z  49 " =    2.899
peak=    3.181 closest distance to " CB  THR A 157 " =    1.111
peak=    3.177 closest distance to " O   HOH Z  88 " =    2.091
peak=    3.171 closest distance to " O   HOH Z 409 " =    2.926
peak=    3.167 closest distance to " CD1 ILE A 263 " =    1.318
peak=    3.164 closest distance to " NZ  LYS A  48 " =    1.350
peak=    3.164 closest distance to " OH  TYR A 186 " =    1.029
peak=    3.163 closest distance to " N   TYR A  15 " =    0.708
peak=    3.163 closest distance to " O   HOH Z  40 " =    1.944
peak=    3.160 closest distance to " O   HOH Z 391 " =    2.894
peak=    3.160 closest distance to " CA  GLY A 241 " =    0.703
peak=    3.158 closest distance to " N   ASN A 252 " =    1.409
peak=    3.157 closest distance to " O   HOH Z  88 " =    2.971
peak=    3.156 closest distance to " CA  ALA A 291 " =    0.864
peak=    3.153 closest distance to " O   HOH Z 152 " =    2.225
peak=    3.150 closest distance to " OG  SER A  97 " =    3.677
peak=    3.148 closest distance to " CB  ASN A 215 " =    1.129
peak=    3.147 closest distance to " N   SER A 146 " =    1.687
peak=    3.145 closest distance to " OG  SER A 206 " =    1.208
peak=    3.143 closest distance to " CB  LYS A 117 " =    1.198
peak=    3.143 closest distance to " O   HOH Z  59 " =    2.009
peak=    3.140 closest distance to " OD1 ASN A 217 " =    1.658
peak=    3.137 closest distance to " N   SER A 135 " =    1.362
peak=    3.136 closest distance to " CB  ALA A 137 " =    1.033
peak=    3.130 closest distance to " CA  TYR A 116 " =    1.398
peak=    3.125 closest distance to " CB  ASP A 171 " =    0.714
peak=    3.125 closest distance to " O   HOH Z 359 " =    1.432
peak=    3.123 closest distance to " CA  ILE A 234 " =    0.908
peak=    3.122 closest distance to " NE2 GLN A  58 " =    3.730
peak=    3.121 closest distance to " CA  ILE A 106 " =    0.832
peak=    3.120 closest distance to " CG2 ILE A 151 " =    0.807
peak=    3.116 closest distance to " O   HOH Z 406 " =    1.602
peak=    3.112 closest distance to " CA  VAL A 125 " =    1.066
peak=    3.106 closest distance to " O   HOH Z 437 " =    1.287
peak=    3.104 closest distance to " CB  ASN A 224 " =    1.033
peak=    3.101 closest distance to " CG BARG A 102 " =    1.882
peak=    3.094 closest distance to " NZ  LYS A  76 " =    1.561
peak=    3.091 closest distance to " CA  ASP A 140 " =    1.248
peak=    3.086 closest distance to " O   HOH Z 302 " =    1.976
peak=    3.086 closest distance to " CB  ARG A 138 " =    1.009
peak=    3.078 closest distance to " OH  TYR A 214 " =    1.176
peak=    3.077 closest distance to " CA  GLN A  88 " =    1.465
peak=    3.074 closest distance to " CA  GLU A  46 " =    0.757
peak=    3.074 closest distance to " CG  LYS A  76 " =    0.946
peak=    3.069 closest distance to " O   HOH Z 407 " =    2.419
peak=    3.059 closest distance to " O   HOH Z 271 " =    2.283
peak=    3.035 closest distance to " NH1BARG A 145 " =    0.985
peak=    3.026 closest distance to " O   GLN A 278 " =    1.545

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.706 - 5.475
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 200
   mapped sites are within: 0.706 - 5.475

peak=   -4.479 closest distance to " CD  ARG A 156 " =    2.054
peak=   -4.442 closest distance to " CB  PRO A 243 " =    2.652
peak=   -4.262 closest distance to " O   HOH Z 266 " =    5.276
peak=   -4.257 closest distance to " CZ3 TRP A 179 " =    1.138
peak=   -4.195 closest distance to " O   VAL A  67 " =    2.661
peak=   -4.179 closest distance to " CG  GLN A 223 " =    1.988
peak=   -4.156 closest distance to " CD  ARG A  14 " =    3.455
peak=   -4.128 closest distance to " O   HOH Z 231 " =    2.250
peak=   -4.088 closest distance to " CD  GLN A  58 " =    0.972
peak=   -4.029 closest distance to " CE2 TYR A  30 " =    2.792
peak=   -4.023 closest distance to " O   PRO A 198 " =    1.262
peak=   -4.011 closest distance to " O   HOH Z 389 " =    1.943
peak=   -3.997 closest distance to " O   HOH Z 377 " =    1.950
peak=   -3.986 closest distance to " CG1 VAL A 112 " =    2.655
peak=   -3.966 closest distance to " O   HOH Z 290 " =    1.170
peak=   -3.965 closest distance to " O   HOH Z  10 " =    1.552
peak=   -3.907 closest distance to " O   ILE A 109 " =    2.598
peak=   -3.899 closest distance to " N   ALA A  43 " =    2.618
peak=   -3.872 closest distance to " O   HOH Z  73 " =    2.155
peak=   -3.848 closest distance to " O   HOH Z 435 " =    2.833
peak=   -3.847 closest distance to " C   HIS A 108 " =    1.079
peak=   -3.838 closest distance to " O   HOH Z 372 " =    2.392
peak=   -3.835 closest distance to " O   HOH Z 198 " =    2.150
peak=   -3.827 closest distance to " O   HOH Z  38 " =    1.307
peak=   -3.823 closest distance to " OG BSER A 134 " =    1.209
peak=   -3.789 closest distance to " O   HOH Z 114 " =    3.310
peak=   -3.788 closest distance to " ND2 ASN A  45 " =    1.792
peak=   -3.782 closest distance to " NH2AARG A 275 " =    5.475
peak=   -3.765 closest distance to " CB  ALA A  43 " =    2.614
peak=   -3.742 closest distance to " CG  MET A 105 " =    0.957
peak=   -3.742 closest distance to " OG  SER A  97 " =    2.229
peak=   -3.729 closest distance to " CA  GLY A 241 " =    3.171
peak=   -3.728 closest distance to " CG1 VAL A 112 " =    2.940
peak=   -3.727 closest distance to " O   GLY A 211 " =    1.407
peak=   -3.720 closest distance to " CD2 TYR A 293 " =    2.021
peak=   -3.708 closest distance to " CD1 PHE A  59 " =    1.890
peak=   -3.701 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.700 closest distance to " O   HOH Z 394 " =    1.424
peak=   -3.699 closest distance to " O   HOH Z 353 " =    2.123
peak=   -3.697 closest distance to " CB  ALA A 291 " =    2.265
peak=   -3.694 closest distance to " CG1 VAL A 250 " =    2.677
peak=   -3.671 closest distance to " OD1 ASN A 148 " =    1.498
peak=   -3.663 closest distance to " CD2 PHE A 192 " =    2.040
peak=   -3.659 closest distance to " O   HOH Z  52 " =    1.317
peak=   -3.652 closest distance to " O   HOH Z 196 " =    2.048
peak=   -3.645 closest distance to " CG  ARG A 269 " =    2.417
peak=   -3.638 closest distance to " CG1 VAL A 265 " =    2.384
peak=   -3.637 closest distance to " CE  MET A 105 " =    2.360
peak=   -3.635 closest distance to " CB  ASN A  39 " =    2.292
peak=   -3.633 closest distance to " ND2 ASN A  45 " =    1.117
peak=   -3.622 closest distance to " O   HOH Z 185 " =    2.331
peak=   -3.618 closest distance to " CB  PRO A 163 " =    2.535
peak=   -3.606 closest distance to " O   HOH Z 407 " =    3.350
peak=   -3.606 closest distance to " O   HOH Z 126 " =    1.889
peak=   -3.567 closest distance to " O   HOH Z 313 " =    1.978
peak=   -3.558 closest distance to " C   ASN A 285 " =    2.477
peak=   -3.551 closest distance to " C   ALA A 158 " =    1.449
peak=   -3.549 closest distance to " CD2 LEU A 237 " =    2.882
peak=   -3.545 closest distance to " N   THR A 157 " =    1.579
peak=   -3.537 closest distance to " O   VAL A 189 " =    2.601
peak=   -3.532 closest distance to " O   HOH Z  60 " =    2.443
peak=   -3.531 closest distance to " CG  ASP A 231 " =    0.779
peak=   -3.531 closest distance to " O   HOH Z  11 " =    1.763
peak=   -3.525 closest distance to " O   HOH Z  43 " =    1.595
peak=   -3.522 closest distance to " CG  PHE A 283 " =    2.767
peak=   -3.516 closest distance to " O   HOH Z 211 " =    1.605
peak=   -3.516 closest distance to " OXT GLY A 302 " =    2.899
peak=   -3.511 closest distance to " CA  GLY A 241 " =    2.305
peak=   -3.505 closest distance to " O   HOH Z 198 " =    1.327
peak=   -3.505 closest distance to " CD  ARG A 139 " =    1.589
peak=   -3.505 closest distance to " O   HOH Z 426 " =    1.633
peak=   -3.504 closest distance to " CD1 LEU A 101 " =    2.400
peak=   -3.487 closest distance to " O   HOH Z 298 " =    2.528
peak=   -3.481 closest distance to " NH2 ARG A  79 " =    1.542
peak=   -3.467 closest distance to " C   GLY A  17 " =    1.296
peak=   -3.463 closest distance to " CZ  TYR A 169 " =    1.740
peak=   -3.456 closest distance to " CB  ALA A 291 " =    2.164
peak=   -3.448 closest distance to " OE1 GLN A  88 " =    1.167
peak=   -3.444 closest distance to " CG1 VAL A 197 " =    2.327
peak=   -3.437 closest distance to " O   PRO A 163 " =    2.074
peak=   -3.434 closest distance to " O   HOH Z  44 " =    2.248
peak=   -3.426 closest distance to " OD2 ASP A 171 " =    1.876
peak=   -3.421 closest distance to " ND2 ASN A 249 " =    2.185
peak=   -3.419 closest distance to " CD1 LEU A 228 " =    2.393
peak=   -3.418 closest distance to " CG  TRP A 266 " =    1.820
peak=   -3.418 closest distance to " O   HOH Z 311 " =    3.746
peak=   -3.409 closest distance to " CA  GLY A 203 " =    2.428
peak=   -3.405 closest distance to " CD2 PHE A  61 " =    2.586
peak=   -3.405 closest distance to " NE2 GLN A 278 " =    1.729
peak=   -3.401 closest distance to " O   HOH Z 377 " =    0.759
peak=   -3.398 closest distance to " CB  PRO A  54 " =    2.538
peak=   -3.394 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.390 closest distance to " CB  ASP A 132 " =    2.317
peak=   -3.382 closest distance to " CA  GLY A 241 " =    2.846
peak=   -3.376 closest distance to " CG  GLU A 277 " =    1.176
peak=   -3.371 closest distance to " OD1 ASP A 171 " =    1.582
peak=   -3.370 closest distance to " C   LEU A 222 " =    0.798
peak=   -3.366 closest distance to " CD  ARG A 195 " =    5.138
peak=   -3.365 closest distance to " OH  TYR A 247 " =    2.104
peak=   -3.362 closest distance to " O   GLY A 203 " =    2.427
peak=   -3.362 closest distance to " O   HOH Z 253 " =    4.077
peak=   -3.354 closest distance to " O   HOH Z 114 " =    1.547
peak=   -3.351 closest distance to " CB  PHE A 225 " =    2.233
peak=   -3.348 closest distance to " N   SER A 212 " =    1.899
peak=   -3.337 closest distance to " O   HOH Z 166 " =    1.887
peak=   -3.336 closest distance to " CA  VAL A  67 " =    2.773
peak=   -3.332 closest distance to " O   ALA A  10 " =    1.637
peak=   -3.332 closest distance to " O   GLN A 240 " =    2.190
peak=   -3.326 closest distance to " O   HOH Z 243 " =    2.029
peak=   -3.324 closest distance to " CE3 TRP A 150 " =    2.122
peak=   -3.324 closest distance to " CB  TYR A  15 " =    2.212
peak=   -3.319 closest distance to " CB  PHE A 208 " =    2.284
peak=   -3.316 closest distance to " CE BMET A  47 " =    1.816
peak=   -3.314 closest distance to " CA  GLY A  98 " =    1.976
peak=   -3.312 closest distance to " CZ  PHE A  59 " =    1.614
peak=   -3.310 closest distance to " O   HOH Z  51 " =    1.535
peak=   -3.310 closest distance to " CD  GLU A 236 " =    1.071
peak=   -3.305 closest distance to " CB  TRP A  85 " =    2.425
peak=   -3.304 closest distance to " O   LEU A 101 " =    2.648
peak=   -3.303 closest distance to " O   PHE A 218 " =    1.526
peak=   -3.301 closest distance to " CG1 VAL A 125 " =    1.885
peak=   -3.293 closest distance to " O   HOH Z 176 " =    0.808
peak=   -3.292 closest distance to " O   HOH Z 275 " =    1.527
peak=   -3.285 closest distance to " C   ASP A 231 " =    2.674
peak=   -3.283 closest distance to " CD  GLN A 223 " =    0.706
peak=   -3.278 closest distance to " CD1 ILE A 239 " =    2.108
peak=   -3.277 closest distance to " NE2 GLN A 194 " =    1.800
peak=   -3.276 closest distance to " CB  ALA A 248 " =    2.045
peak=   -3.275 closest distance to " CD1 LEU A 297 " =    2.479
peak=   -3.274 closest distance to " NE2 GLN A  88 " =    1.868
peak=   -3.268 closest distance to " C   PHE A  59 " =    1.335
peak=   -3.265 closest distance to " O   HOH Z 102 " =    1.653
peak=   -3.263 closest distance to " O   HOH Z 111 " =    1.915
peak=   -3.256 closest distance to " NH2 ARG A 159 " =    2.371
peak=   -3.255 closest distance to " O   HOH Z  13 " =    1.481
peak=   -3.252 closest distance to " NH2 ARG A  79 " =    2.026
peak=   -3.250 closest distance to " O   HOH Z 359 " =    3.211
peak=   -3.250 closest distance to " ND2 ASN A  60 " =    1.350
peak=   -3.246 closest distance to " C   LEU A 143 " =    1.203
peak=   -3.242 closest distance to " CB  ALA A 248 " =    2.519
peak=   -3.241 closest distance to " O   GLY A 196 " =    1.182
peak=   -3.237 closest distance to " O   HOH Z 241 " =    1.333
peak=   -3.228 closest distance to " O   SER A  62 " =    2.199
peak=   -3.228 closest distance to " O   ALA A  34 " =    2.664
peak=   -3.228 closest distance to " O   ALA A 180 " =    1.413
peak=   -3.227 closest distance to " OG BSER A 134 " =    1.803
peak=   -3.225 closest distance to " O   HOH Z  51 " =    1.297
peak=   -3.221 closest distance to " CB  ALA A   9 " =    2.586
peak=   -3.218 closest distance to " CD2 LEU A 222 " =    2.147
peak=   -3.218 closest distance to " CD1 ILE A 151 " =    2.414
peak=   -3.214 closest distance to " SD  MET A 188 " =    2.311
peak=   -3.214 closest distance to " O   HOH Z 298 " =    1.232
peak=   -3.204 closest distance to " CE2 PHE A 218 " =    2.428
peak=   -3.198 closest distance to " O   HOH Z 128 " =    2.563
peak=   -3.197 closest distance to " C   MET A 188 " =    1.375
peak=   -3.197 closest distance to " O   HOH Z 322 " =    1.505
peak=   -3.195 closest distance to " NE2 GLN A 103 " =    1.726
peak=   -3.190 closest distance to " CD  GLN A  88 " =    0.880
peak=   -3.190 closest distance to " O   HOH Z 393 " =    1.429
peak=   -3.188 closest distance to " CG  ARG A  66 " =    2.234
peak=   -3.185 closest distance to " N   ALA A 248 " =    1.668
peak=   -3.184 closest distance to " CD2 TYR A 247 " =    2.466
peak=   -3.180 closest distance to " CD  ARG A  79 " =    1.127
peak=   -3.179 closest distance to " O   HOH Z   6 " =    1.441
peak=   -3.178 closest distance to " N   GLN A  58 " =    1.685
peak=   -3.176 closest distance to " OG  SER A  62 " =    1.708
peak=   -3.175 closest distance to " CE3 TRP A 274 " =    2.515
peak=   -3.173 closest distance to " CB  CYS A 254 " =    2.294
peak=   -3.172 closest distance to " O   HOH Z  90 " =    1.600
peak=   -3.172 closest distance to " O   HOH Z 103 " =    1.919
peak=   -3.168 closest distance to " OD2 ASP A  50 " =    1.824
peak=   -3.167 closest distance to " OG  SER A 206 " =    1.851
peak=   -3.162 closest distance to " CG  LEU A  83 " =    1.914
peak=   -3.157 closest distance to " C   GLY A  13 " =    0.950
peak=   -3.155 closest distance to " N   SER A 276 " =    1.268
peak=   -3.155 closest distance to " CB  ASP A 286 " =    2.068
peak=   -3.155 closest distance to " O   HOH Z 222 " =    1.177
peak=   -3.149 closest distance to " OD1 ASP A 191 " =    1.581
peak=   -3.145 closest distance to " O   HOH Z 377 " =    0.900
peak=   -3.142 closest distance to " CD2 PHE A  61 " =    2.030
peak=   -3.142 closest distance to " O   HOH Z 281 " =    2.646
peak=   -3.141 closest distance to " O   SER A 135 " =    1.429
peak=   -3.139 closest distance to " OD1 ASN A 187 " =    1.478
peak=   -3.133 closest distance to " CE  LYS A  76 " =    2.656
peak=   -3.132 closest distance to " CZ BARG A 275 " =    1.883
peak=   -3.126 closest distance to " C   SER A 206 " =    1.567
peak=   -3.123 closest distance to " O   TRP A  70 " =    1.470
peak=   -3.108 closest distance to " CG2 VAL A 189 " =    2.083
peak=   -3.107 closest distance to " O   HOH Z 184 " =    1.745
peak=   -3.103 closest distance to " CG  GLU A 152 " =    0.854
peak=   -3.100 closest distance to " NE1 TRP A  70 " =    1.117
peak=   -3.098 closest distance to " SG ACYS A 201 " =    2.077
peak=   -3.087 closest distance to " OD1AASN A 224 " =    1.718
peak=   -3.085 closest distance to " O   HOH Z 421 " =    3.071
peak=   -3.083 closest distance to " CB  ASP A 132 " =    2.367
peak=   -3.077 closest distance to " O   HOH Z 123 " =    2.513
peak=   -3.070 closest distance to " CG2 THR A 221 " =    2.253
peak=   -3.069 closest distance to " CA  SER A 135 " =    1.284
peak=   -3.060 closest distance to " CG2 ILE A  20 " =    2.810

================= 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    :  0.2717 0.2658   5.895524e+00   5.895835e+00
   1_bss:  0.2553 0.2521   5.865586e+00   5.863357e+00
   1_xyz:  0.1655 0.1834   5.441768e+00   5.530463e+00
   1_adp:  0.1505 0.1872   5.379493e+00   5.553953e+00
   1_occ:  0.1500 0.1867   5.377095e+00   5.552464e+00
   2_bss:  0.1490 0.1851   5.372807e+00   5.547760e+00
   2_xyz:  0.1189 0.1624   5.188534e+00   5.415835e+00
   2_adp:  0.1159 0.1573   5.160438e+00   5.389287e+00
   2_occ:  0.1158 0.1572   5.160089e+00   5.389222e+00
   3_bss:  0.1158 0.1565   5.158740e+00   5.385028e+00
   3_xyz:  0.1134 0.1564   5.149774e+00   5.383874e+00
   3_adp:  0.1125 0.1562   5.145152e+00   5.383099e+00
   3_occ:  0.1125 0.1562   5.145182e+00   5.383365e+00
   4_bss:  0.1124 0.1562   5.145189e+00   5.383245e+00
   4_xyz:  0.1087 0.1566   5.128507e+00   5.382234e+00
   4_adp:  0.1076 0.1576   5.124958e+00   5.384223e+00
   4_occ:  0.1076 0.1577   5.125178e+00   5.384631e+00
   5_bss:  0.1074 0.1575   5.124988e+00   5.384487e+00
   5_xyz:  0.1118 0.1596   5.152330e+00   5.400295e+00
   5_adp:  0.1125 0.1585   5.152533e+00   5.396693e+00
   5_occ:  0.1125 0.1586   5.152626e+00   5.396956e+00
   5_bss:  0.1125 0.1586   5.152700e+00   5.396972e+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:  0.315  54.017   0.061  -3.085  -1.120  -0.000  -0.000  -0.000
   1_xyz:  0.315  54.017   0.061  -3.085  -1.120  -0.000  -0.000  -0.000
   1_adp:  0.315  54.017   0.061  -3.085  -1.120  -0.000  -0.000  -0.000
   1_occ:  0.315  54.017   0.061  -3.085  -1.120  -0.000  -0.000  -0.000
   2_bss:  0.333  63.588  -1.819  -3.004  -1.558  -0.000  -0.000  -0.000
   2_xyz:  0.333  63.588  -1.819  -3.004  -1.558  -0.000  -0.000  -0.000
   2_adp:  0.333  63.588  -1.819  -3.004  -1.558  -0.000  -0.000  -0.000
   2_occ:  0.333  63.588  -1.819  -3.004  -1.558  -0.000  -0.000  -0.000
   3_bss:  0.333  63.588  -2.341  -2.834  -1.514  -0.000  -0.000  -0.000
   3_xyz:  0.333  63.588  -2.341  -2.834  -1.514  -0.000  -0.000  -0.000
   3_adp:  0.333  63.588  -2.341  -2.834  -1.514  -0.000  -0.000  -0.000
   3_occ:  0.333  63.588  -2.341  -2.834  -1.514  -0.000  -0.000  -0.000
   4_bss:  0.333  63.588  -2.382  -2.650  -1.381  -0.000  -0.000  -0.000
   4_xyz:  0.333  63.588  -2.382  -2.650  -1.381  -0.000  -0.000  -0.000
   4_adp:  0.333  63.588  -2.382  -2.650  -1.381  -0.000  -0.000  -0.000
   4_occ:  0.333  63.588  -2.382  -2.650  -1.381  -0.000  -0.000  -0.000
   5_bss:  0.325  63.588  -2.133  -2.344  -1.109  -0.000  -0.000  -0.000
   5_xyz:  0.325  63.588  -2.133  -2.344  -1.109  -0.000  -0.000  -0.000
   5_adp:  0.325  63.588  -2.133  -2.344  -1.109  -0.000  -0.000  -0.000
   5_occ:  0.325  63.588  -2.133  -2.344  -1.109  -0.000  -0.000  -0.000
   5_bss:  0.326  63.549  -2.062  -2.201  -0.968  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  26.862 0.7959  0.9458    20662.812
   1_bss:  25.774 0.8058  0.9164    18258.373
   1_xyz:  16.721 0.8935  0.9866     8547.737
   1_adp:  17.302 0.8878  0.9873     8851.506
   1_occ:  17.255 0.8881  0.9870     8800.174
   2_bss:  17.140 0.8892  0.9619     8728.439
   2_xyz:  14.572 0.9102  0.9737     6709.678
   2_adp:  13.962 0.9154  0.9727     6392.337
   2_occ:  13.958 0.9154  0.9725     6386.611
   3_bss:  13.902 0.9158  0.9684     6304.893
   3_xyz:  13.769 0.9172  0.9683     6278.434
   3_adp:  13.739 0.9175  0.9639     6263.140
   3_occ:  13.745 0.9174  0.9638     6265.456
   4_bss:  13.745 0.9174  0.9669     6263.228
   4_xyz:  13.752 0.9172  0.9670     6285.342
   4_adp:  13.822 0.9166  0.9602     6274.519
   4_occ:  13.828 0.9166  0.9600     6278.181
   5_bss:  13.825 0.9166  0.9694     6272.811
   5_xyz:  14.079 0.9148  0.9675     6465.231
   5_adp:  13.993 0.9155  0.9620     6443.574
   5_occ:  14.001 0.9154  0.9619     6443.559
   5_bss:  14.002 0.9154  0.9646     6443.658
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6095e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6095e-01
   1_xyz:   0.961  0.007  0.066 15.177  0.004  4.113   5.6525e-02
   1_adp:   0.961  0.007  0.066 15.177  0.004  4.113   5.6525e-02
   1_occ:   0.961  0.007  0.066 15.177  0.004  4.113   5.6525e-02
   2_bss:   0.961  0.007  0.066 15.177  0.004  4.113   5.6525e-02
   2_xyz:   1.061  0.009  0.081 14.940  0.004  4.127   6.8913e-02
   2_adp:   1.061  0.009  0.081 14.940  0.004  4.127   6.8913e-02
   2_occ:   1.061  0.009  0.081 14.940  0.004  4.127   6.8913e-02
   3_bss:   1.061  0.009  0.081 14.940  0.004  4.127   6.8913e-02
   3_xyz:   0.992  0.008  0.077 14.828  0.004  4.115   6.1882e-02
   3_adp:   0.992  0.008  0.077 14.828  0.004  4.115   6.1882e-02
   3_occ:   0.992  0.008  0.077 14.828  0.004  4.115   6.1882e-02
   4_bss:   0.992  0.008  0.077 14.828  0.004  4.115   6.1882e-02
   4_xyz:   1.111  0.011  0.085 15.020  0.004  4.117   7.6911e-02
   4_adp:   1.111  0.011  0.085 15.020  0.004  4.117   7.6911e-02
   4_occ:   1.111  0.011  0.085 15.020  0.004  4.117   7.6911e-02
   5_bss:   1.111  0.011  0.085 15.020  0.004  4.117   7.6911e-02
   5_xyz:   0.945  0.007  0.073 14.731  0.003  4.116   5.5601e-02
   5_adp:   0.945  0.007  0.073 14.731  0.003  4.116   5.5601e-02
   5_occ:   0.945  0.007  0.073 14.731  0.003  4.116   5.5601e-02
   5_bss:   0.945  0.007  0.073 14.731  0.003  4.116   5.5601e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4289e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4289e-01
   1_xyz:   8.641  0.043  0.239 84.023  0.034  2.370   5.6849e-02
   1_adp:   8.641  0.043  0.239 84.023  0.034  2.370   5.6849e-02
   1_occ:   8.641  0.043  0.239 84.023  0.034  2.370   5.6849e-02
   2_bss:   8.641  0.043  0.239 84.023  0.034  2.370   5.6849e-02
   2_xyz:   7.153  0.050  0.252 83.053  0.037  2.327   6.7377e-02
   2_adp:   7.153  0.050  0.252 83.053  0.037  2.327   6.7377e-02
   2_occ:   7.153  0.050  0.252 83.053  0.037  2.327   6.7377e-02
   3_bss:   7.153  0.050  0.252 83.053  0.037  2.327   6.7377e-02
   3_xyz:   7.614  0.042  0.242 83.752  0.034  2.351   4.1941e-02
   3_adp:   7.614  0.042  0.242 83.752  0.034  2.351   4.1941e-02
   3_occ:   7.614  0.042  0.242 83.752  0.034  2.351   4.1941e-02
   4_bss:   7.614  0.042  0.242 83.752  0.034  2.351   4.1941e-02
   4_xyz:   7.297  0.049  0.279 83.648  0.036  2.289   5.7941e-02
   4_adp:   7.297  0.049  0.279 83.648  0.036  2.289   5.7941e-02
   4_occ:   7.297  0.049  0.279 83.648  0.036  2.289   5.7941e-02
   5_bss:   7.297  0.049  0.279 83.648  0.036  2.289   5.7941e-02
   5_xyz:   7.598  0.041  0.227 83.187  0.035  2.390   3.3612e-02
   5_adp:   7.598  0.041  0.227 83.187  0.035  2.390   3.3612e-02
   5_occ:   7.598  0.041  0.227 83.187  0.035  2.390   3.3612e-02
   5_bss:   7.598  0.041  0.227 83.187  0.035  2.390   3.3612e-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:  73.89   0.88  17.04  70.44   0.88  13.09  73.89   5.18  38.54
   1_occ:  73.89   0.88  17.04  70.44   0.88  13.09  73.89   5.18  38.54
   2_bss:  73.89   0.88  17.04  70.44   0.88  13.09  73.89   5.18  38.54
   2_xyz:  73.89   0.88  17.04  70.44   0.88  13.09  73.89   5.18  38.54
   2_adp:  72.43   1.75  16.79  72.42   1.75  13.00  72.43   6.07  37.43
   2_occ:  72.43   1.75  16.79  72.42   1.75  13.00  72.43   6.07  37.43
   3_bss:  72.43   1.75  16.79  72.42   1.75  13.00  72.43   6.07  37.43
   3_xyz:  72.43   1.75  16.79  72.42   1.75  13.00  72.43   6.07  37.43
   3_adp:  73.40   1.43  16.76  73.40   1.43  12.91  73.18   5.64  37.69
   3_occ:  73.40   1.43  16.76  73.40   1.43  12.91  73.18   5.64  37.69
   4_bss:  73.40   1.43  16.76  73.40   1.43  12.91  73.18   5.64  37.69
   4_xyz:  73.40   1.43  16.76  73.40   1.43  12.91  73.18   5.64  37.69
   4_adp:  85.47   0.20  17.21  85.47   0.20  12.97  80.83   6.28  40.29
   4_occ:  85.47   0.20  17.21  85.47   0.20  12.97  80.83   6.28  40.29
   5_bss:  85.47   0.20  17.21  85.47   0.20  12.97  80.83   6.28  40.29
   5_xyz:  85.47   0.20  17.21  85.47   0.20  12.97  80.83   6.28  40.29
   5_adp:  84.06   1.11  16.64  84.06   1.11  12.69  80.21   6.11  38.16
   5_occ:  84.06   1.11  16.64  84.06   1.11  12.69  80.21   6.11  38.16
   5_bss:  84.02   1.07  16.60  84.02   1.07  12.65  80.17   6.07  38.12
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.003    0.005    0.213
   1_adp:    1.003    0.005    0.213
   1_occ:    1.003    0.005    0.213
   2_bss:    1.003    0.005    0.213
   2_xyz:    0.708    0.010    0.277
   2_adp:    0.708    0.010    0.277
   2_occ:    0.708    0.010    0.277
   3_bss:    0.708    0.010    0.277
   3_xyz:    0.847    0.017    0.288
   3_adp:    0.847    0.017    0.288
   3_occ:    0.847    0.017    0.288
   4_bss:    0.847    0.017    0.288
   4_xyz:    0.921    0.023    0.298
   4_adp:    0.921    0.023    0.298
   4_occ:    0.921    0.023    0.298
   5_bss:    0.921    0.023    0.298
   5_xyz:    1.000    0.015    0.300
   5_adp:    1.000    0.015    0.300
   5_occ:    1.000    0.015    0.300
   5_bss:    1.000    0.015    0.300
------------------------------------------------------------------------

CPU time actual refinement: 316.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1029/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_1029/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1029/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1029/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1029/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.71 
  Macro-tasks:
    bulk solvent and scale       = 36.94  
    individual site refinement   = 129.91 
    weights calculation          = 28.83  
    collect and process          = 6.54   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 202.32 
  Micro-tasks:
    mask                            = 1.18   
    f_calc                          = 99.49  
    alpha_beta                      = 8.29   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 108.94 
    fmodel                         = 6.49   
    r_factors                      = 0.15   
    phase_errors                   = 10.98  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 236.98 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.517 micro seconds
Total CPU time: 5.51 minutes
from_scatterers_fft:    640 calls, 99.08 s
gradients_fft:          585 calls, 95.31 s

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

# Date 2008-01-16 Time 06:15:32 PST -0800 (1200492932.98 s)
Start R-work = 0.2717, R-free = 0.2658 (no bulk solvent and anisotropic scale)
Final R-work = 0.1351, R-free = 0.1773 (no bulk solvent and anisotropic scale)

Start R-work = 0.2553, R-free = 0.2521
Final R-work = 0.1125, R-free = 0.1586