# Date 2008-01-16 Time 05:37:36 PST -0800 (1200490656.21 s)
#phil __OFF__

Command line arguments: "../816.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9965
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 816

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.6339, 85.0941, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97137
Completeness in resolution range: 0.940693
Completeness with d_max=infinity: 0.937856

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9858
                             d_min =   1.9714

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97137
Completeness in resolution range: 0.940693
Completeness with d_max=infinity: 0.937856

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9863 -  4.2186 [2192/2221]  1973   219  10.0%
  bin  2:  4.2186 -  3.3608 [2090/2113]  1883   207   9.9%
  bin  3:  3.3608 -  2.9396 [2067/2092]  1854   213  10.3%
  bin  4:  2.9396 -  2.6725 [2066/2082]  1868   198   9.6%
  bin  5:  2.6725 -  2.4819 [2035/2073]  1825   210  10.3%
  bin  6:  2.4819 -  2.3361 [2039/2072]  1838   201   9.9%
  bin  7:  2.3361 -  2.2195 [2006/2043]  1805   201  10.0%
  bin  8:  2.2195 -  2.1232 [2001/2043]  1801   200  10.0%
  bin  9:  2.1232 -  2.0417 [2012/2048]  1809   203  10.1%
  bin 10:  2.0417 -  1.9714 [1081/2037]   974   107   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_816/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 27
        2.42 -     3.04: 2197
        3.04 -     3.66: 4662
        3.66 -     4.28: 9000
        4.28 -     4.90: 12370
  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 206 " - " O   HOH Z 342 "  1.880 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.883 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.886 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.940 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28251 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_816/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_816/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.63395 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3906   r_free= 0.3838   ksol= 0.00   Bsol= 0.00   scale= 0.938    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.179016                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7053 0.99   1418  161 0.3121 0.3253      6.4197      6.4217|
|  2:  4.7053 -  3.7541 0.99   1368  145 0.3127 0.3271      6.6186      6.6142|
|  3:  3.7541 -  3.2852 0.99   1335  154 0.3446 0.3216      6.4983      6.4977|
|  4:  3.2852 -  2.9875 0.99   1338  149 0.3644 0.3518      6.3703      6.3333|
|  5:  2.9875 -  2.7748 0.98   1317  145 0.3883 0.3711      6.2311      6.2229|
|  6:  2.7748 -  2.6121 0.99   1314  143 0.4236 0.3953      6.1922      6.0624|
|  7:  2.6121 -  2.4819 0.99   1313  150 0.4180 0.3694      6.1523      6.0738|
|  8:  2.4819 -  2.3743 0.99   1298  145 0.4419 0.4518      6.0882      6.1562|
|  9:  2.3743 -  2.2832 0.99   1307  146 0.4657 0.4387      6.0795      6.0666|
| 10:  2.2832 -  2.2047 0.98   1301  140 0.4476 0.4998      6.0339      6.0704|
| 11:  2.2047 -  2.1359 0.98   1282  139 0.4598 0.4421      5.9787      6.0109|
| 12:  2.1359 -  2.0750 1.00   1277  148 0.4483 0.4896      5.9034      5.9554|
| 13:  2.0750 -  2.0206 0.96   1277  145 0.4670 0.4157      5.8254      5.7997|
| 14:  2.0206 -  1.9714 0.37    485   49 0.4792 0.4555      5.8111      5.7229|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7053  1418   161  0.76  29.09   0.85     0.77      52940.07|
|  2:  4.7053 -  3.7541  1368   145  0.79  26.87   0.95     0.87      64336.79|
|  3:  3.7541 -  3.2852  1335   154  0.73  32.34   0.96     0.89      65521.57|
|  4:  3.2852 -  2.9875  1338   149  0.69  36.47   0.97     0.87      57993.53|
|  5:  2.9875 -  2.7748  1317   145  0.64  40.61   0.94     0.83      48256.26|
|  6:  2.7748 -  2.6121  1314   143  0.61  43.07   0.96     0.81      42244.39|
|  7:  2.6121 -  2.4819  1313   150  0.61  43.02   0.96     0.79      39038.09|
|  8:  2.4819 -  2.3743  1298   145  0.55  48.21   0.94     0.76      40103.71|
|  9:  2.3743 -  2.2832  1307   146  0.52  50.50   0.96     0.72      39220.14|
| 10:  2.2832 -  2.2047  1301   140  0.49  52.83   1.00     0.70      40003.75|
| 11:  2.2047 -  2.1359  1282   139  0.48  53.92   0.96     0.69      36456.13|
| 12:  2.1359 -  2.0750  1277   148  0.47  54.62   1.00     0.71      34431.18|
| 13:  2.0750 -  2.0206  1277   145  0.47  54.50   0.96     0.70      28516.54|
| 14:  2.0206 -  1.9714   485    49  0.48  53.39   0.97     0.68      23975.65|
|alpha:            min =        0.68 max =            0.89 mean =         0.78|
|beta:             min =    23975.65 max =        65521.57 mean =     44956.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.97 mean =        43.57|
|phase err.(test): min =        0.00 max =           89.74 mean =        43.65|
|-----------------------------------------------------------------------------|

============================== 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 = 6.769705              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.369   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.293738              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.406   (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:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      187 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2010 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1854 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2808 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4613 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4387 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5649 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6721 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.260 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3906   r_free= 0.3838   ksol= 0.00   Bsol= 0.00   scale= 0.938    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.179016                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3787   r_free= 0.3698   ksol= 0.31   Bsol= 36.23   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,2.94,0.56,0.00,0.00,0.00); trace/3= 0.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.166002                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.869424              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.254   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.633679              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.171   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3787      final r-factor (work) = 0.2384          |
| start r-factor (free) = 0.3698      final r-factor (free) = 0.2671          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2628 = 5.87 * 0.50 * 6.1657 + 1.00 * 0.1682                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5105 = 5.87 * 0.50 * 5.9355 + 1.00 * 0.0915                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2384      final r-factor (work) = 0.2165          |
| start r-factor (free) = 0.2671      final r-factor (free) = 0.2748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7673 = 0.63 * 1.00 * 5.9355 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6306 = 0.63 * 1.00 * 5.7104 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.46   17.48    None  None   None       |
|    all(noH): 2823   0      0.00    82.46   17.48    None  None   None       |
|    Sol.    : 438    0      6.08    82.46   39.93    None  None   None       |
|    Mac.    : 2385   0      0.00    79.62   13.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.246:  731   |   5:    41.228 -  49.474:  106        |
|      1:     8.246 -  16.491: 1115   |   6:    49.474 -  57.720:   78        |
|      2:    16.491 -  24.737:  427   |   7:    57.720 -  65.965:   56        |
|      3:    24.737 -  32.983:  156   |   8:    65.965 -  74.211:   17        |
|      4:    32.983 -  41.228:  129   |   9:    74.211 -  82.456:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2165 r_free = 0.2748             target_work(ml) = 5.721         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2161 r_free = 0.2751             target_work(ml) = 5.720         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2161   r_free= 0.2751   ksol= 0.31   Bsol= 36.23   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,2.94,0.56,0.00,0.00,0.00); trace/3= 0.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.719926                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2137   r_free= 0.2729   ksol= 0.32   Bsol= 54.50   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,0.07,-0.99,0.00,-0.00,-0.00); trace/3= -1.15                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.714842                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.031866              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.518   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.273787              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.629  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2137      final r-factor (work) = 0.1573          |
| start r-factor (free) = 0.2729      final r-factor (free) = 0.1973          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7535 = 3.03 * 0.50 * 5.7139 + 1.00 * 0.0915                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5412 = 3.03 * 0.50 * 5.5964 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1573      final r-factor (work) = 0.1457          |
| start r-factor (free) = 0.1973      final r-factor (free) = 0.1864          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5443 = 0.27 * 1.00 * 5.5964 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4834 = 0.27 * 1.00 * 5.3854 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    83.46   17.14    None  None   None       |
|    all(noH): 2823   0      1.60    83.46   17.14    None  None   None       |
|    Sol.    : 438    0      5.06    81.71   40.06    None  None   None       |
|    Mac.    : 2385   0      1.60    83.46   12.93    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:     1.598 -   9.785: 1020   |   5:    42.530 -  50.717:  108        |
|      1:     9.785 -  17.971: 1045   |   6:    50.717 -  58.903:   82        |
|      2:    17.971 -  26.157:  270   |   7:    58.903 -  67.090:   40        |
|      3:    26.157 -  34.344:  126   |   8:    67.090 -  75.276:   17        |
|      4:    34.344 -  42.530:  110   |   9:    75.276 -  83.462:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1457 r_free = 0.1864             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1455 r_free = 0.1863             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1455   r_free= 0.1863   ksol= 0.32   Bsol= 54.50   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,0.07,-0.99,0.00,-0.00,-0.00); trace/3= -1.15                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.357831                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1456   r_free= 0.1861   ksol= 0.32   Bsol= 54.50   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-0.93,-1.35,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.357356                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.250313              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.403  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.490275              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.191  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1456      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1861      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5035 = 4.25 * 0.50 * 5.3860 + 1.00 * 0.0574                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2671 = 4.25 * 0.50 * 5.2667 + 1.00 * 0.0746                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1243 = 2.49 * 1.00 * 5.2667 + 1.00 * 0.0089                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.8844 = 2.49 * 1.00 * 5.1696 + 1.00 * 0.0106                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.06    98.85   17.28    None  None   None       |
|    all(noH): 2823   0      1.06    98.85   17.28    None  None   None       |
|    Sol.    : 438    0      5.38    84.93   41.71    None  None   None       |
|    Mac.    : 2385   0      1.06    98.85   12.80    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:     1.057 -  10.837: 1282   |   5:    49.955 -  59.735:  103        |
|      1:    10.837 -  20.616:  928   |   6:    59.735 -  69.514:   55        |
|      2:    20.616 -  30.396:  190   |   7:    69.514 -  79.294:   24        |
|      3:    30.396 -  40.175:  125   |   8:    79.294 -  89.074:    6        |
|      4:    40.175 -  49.955:  108   |   9:    89.074 -  98.853:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1609             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1132 r_free = 0.1609             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1609   ksol= 0.32   Bsol= 54.50   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-0.93,-1.35,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164714                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1611   ksol= 0.32   Bsol= 54.50   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-1.22,-1.33,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166532                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.094261              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.863  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.313110              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.262  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0739 = 3.09 * 0.50 * 5.1701 + 1.00 * 0.0750                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0441 = 3.09 * 0.50 * 5.1547 + 1.00 * 0.0691                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6245 = 0.31 * 1.00 * 5.1547 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6203 = 0.31 * 1.00 * 5.1465 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.38    98.51   16.59    None  None   None       |
|    all(noH): 2823   0      1.38    98.51   16.59    None  None   None       |
|    Sol.    : 438    0      5.27    79.58   39.11    None  None   None       |
|    Mac.    : 2385   0      1.38    98.51   12.46    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:     1.379 -  11.093: 1386   |   5:    49.946 -  59.659:   88        |
|      1:    11.093 -  20.806:  852   |   6:    59.659 -  69.372:   33        |
|      2:    20.806 -  30.519:  193   |   7:    69.372 -  79.086:   11        |
|      3:    30.519 -  40.233:  124   |   8:    79.086 -  88.799:    4        |
|      4:    40.233 -  49.946:  130   |   9:    88.799 -  98.512:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1578             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1578             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1578   ksol= 0.32   Bsol= 54.50   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-1.22,-1.33,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141879                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1577   ksol= 0.32   Bsol= 52.26   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.26,-1.20,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.141945                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.864443              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.161  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284698              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.465  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8669 = 1.86 * 0.50 * 5.1466 + 1.00 * 0.0691                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8562 = 1.86 * 0.50 * 5.1488 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4747 = 0.28 * 1.00 * 5.1488 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4748 = 0.28 * 1.00 * 5.1507 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.25    97.60   16.30    None  None   None       |
|    all(noH): 2823   0      1.25    97.60   16.30    None  None   None       |
|    Sol.    : 438    0      5.17    79.54   38.17    None  None   None       |
|    Mac.    : 2385   0      1.25    97.60   12.28    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:     1.247 -  10.882: 1371   |   5:    49.423 -  59.058:   84        |
|      1:    10.882 -  20.517:  865   |   6:    59.058 -  68.694:   30        |
|      2:    20.517 -  30.153:  194   |   7:    68.694 -  78.329:   11        |
|      3:    30.153 -  39.788:  130   |   8:    78.329 -  87.964:    4        |
|      4:    39.788 -  49.423:  132   |   9:    87.964 -  97.600:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1582             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1582             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1582   ksol= 0.32   Bsol= 52.26   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.26,-1.20,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151585                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7053 0.99   1418  161 0.0981 0.1264      5.3694      5.5303|
|  2:  4.7053 -  3.7541 0.99   1368  145 0.0851 0.1092      5.4247      5.6326|
|  3:  3.7541 -  3.2852 0.99   1335  154 0.1029 0.1517      5.4543      5.8329|
|  4:  3.2852 -  2.9875 0.99   1338  149 0.1237 0.1520      5.4585      5.6105|
|  5:  2.9875 -  2.7748 0.98   1317  145 0.1321 0.1821      5.3293      5.5114|
|  6:  2.7748 -  2.6121 0.99   1314  143 0.1228 0.1978      5.2234      5.4611|
|  7:  2.6121 -  2.4819 0.99   1313  150 0.1228 0.1684      5.1546      5.4026|
|  8:  2.4819 -  2.3743 0.99   1298  145 0.1158 0.1757      5.0633      5.2912|
|  9:  2.3743 -  2.2832 0.99   1307  146 0.1159 0.1801      5.0242      5.3078|
| 10:  2.2832 -  2.2047 0.98   1301  140 0.1123 0.1719      4.9725       5.216|
| 11:  2.2047 -  2.1359 0.98   1282  139 0.1135 0.1835      4.9276      5.3021|
| 12:  2.1359 -  2.0750 1.00   1277  148 0.1090 0.1585      4.8624      5.0611|
| 13:  2.0750 -  2.0206 0.96   1277  145 0.1163 0.1782      4.8032      5.0909|
| 14:  2.0206 -  1.9714 0.37    485   49 0.1125 0.1732      4.7098      4.9462|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7053  1418   161  0.94   8.88   0.97     0.95       6952.46|
|  2:  4.7053 -  3.7541  1368   145  0.95   7.84   1.01     0.99       8670.92|
|  3:  3.7541 -  3.2852  1335   154  0.94  11.16   1.02     1.02      10187.67|
|  4:  3.2852 -  2.9875  1338   149  0.92  14.02   1.00     0.98      10446.00|
|  5:  2.9875 -  2.7748  1317   145  0.89  16.44   0.99     0.96       8521.89|
|  6:  2.7748 -  2.6121  1314   143  0.90  16.32   0.98     0.96       7298.74|
|  7:  2.6121 -  2.4819  1313   150  0.91  15.35   0.98     0.95       6101.13|
|  8:  2.4819 -  2.3743  1298   145  0.91  15.65   0.99     0.96       5473.60|
|  9:  2.3743 -  2.2832  1307   146  0.90  15.98   0.99     0.96       4964.62|
| 10:  2.2832 -  2.2047  1301   140  0.91  15.42   0.99     0.95       4519.67|
| 11:  2.2047 -  2.1359  1282   139  0.90  16.43   0.99     0.95       4317.85|
| 12:  2.1359 -  2.0750  1277   148  0.92  14.98   0.99     0.98       3870.53|
| 13:  2.0750 -  2.0206  1277   145  0.89  16.95   0.99     0.99       3499.86|
| 14:  2.0206 -  1.9714   485    49  0.90  16.25   0.97     0.93       2849.23|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2849.23 max =        10446.00 mean =      6462.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.73|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1582   ksol= 0.32   Bsol= 52.17   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.19,-1.07,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151671                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1582   ksol= 0.32   Bsol= 52.17   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.19,-1.07,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151671                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7053 0.99   1418  161 0.0981 0.1264        5.37      5.5309|
|  2:  4.7053 -  3.7541 0.99   1368  145 0.0851 0.1092       5.425      5.6326|
|  3:  3.7541 -  3.2852 0.99   1335  154 0.1030 0.1517      5.4544      5.8331|
|  4:  3.2852 -  2.9875 0.99   1338  149 0.1237 0.1520      5.4585      5.6105|
|  5:  2.9875 -  2.7748 0.98   1317  145 0.1321 0.1821      5.3292      5.5112|
|  6:  2.7748 -  2.6121 0.99   1314  143 0.1227 0.1977      5.2231      5.4606|
|  7:  2.6121 -  2.4819 0.99   1313  150 0.1228 0.1685      5.1546      5.4027|
|  8:  2.4819 -  2.3743 0.99   1298  145 0.1158 0.1757      5.0633      5.2909|
|  9:  2.3743 -  2.2832 0.99   1307  146 0.1159 0.1801      5.0243      5.3083|
| 10:  2.2832 -  2.2047 0.98   1301  140 0.1123 0.1719      4.9727      5.2164|
| 11:  2.2047 -  2.1359 0.98   1282  139 0.1136 0.1834      4.9277       5.302|
| 12:  2.1359 -  2.0750 1.00   1277  148 0.1090 0.1586      4.8625      5.0616|
| 13:  2.0750 -  2.0206 0.96   1277  145 0.1164 0.1783      4.8033      5.0909|
| 14:  2.0206 -  1.9714 0.37    485   49 0.1125 0.1730      4.7097      4.9453|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7053  1418   161  0.94   8.89   0.97     0.95       6959.80|
|  2:  4.7053 -  3.7541  1368   145  0.95   7.85   1.01     0.99       8675.90|
|  3:  3.7541 -  3.2852  1335   154  0.94  11.16   1.02     1.02      10191.00|
|  4:  3.2852 -  2.9875  1338   149  0.92  14.03   1.00     0.98      10446.58|
|  5:  2.9875 -  2.7748  1317   145  0.89  16.43   0.99     0.97       8516.25|
|  6:  2.7748 -  2.6121  1314   143  0.90  16.32   0.99     0.96       7293.64|
|  7:  2.6121 -  2.4819  1313   150  0.91  15.35   0.99     0.96       6098.89|
|  8:  2.4819 -  2.3743  1298   145  0.91  15.66   0.99     0.97       5474.61|
|  9:  2.3743 -  2.2832  1307   146  0.90  15.99   1.00     0.96       4967.47|
| 10:  2.2832 -  2.2047  1301   140  0.91  15.42   0.99     0.95       4522.00|
| 11:  2.2047 -  2.1359  1282   139  0.90  16.44   0.99     0.96       4318.84|
| 12:  2.1359 -  2.0750  1277   148  0.92  14.98   0.99     0.98       3872.88|
| 13:  2.0750 -  2.0206  1277   145  0.89  16.95   1.00     0.99       3499.56|
| 14:  2.0206 -  1.9714   485    49  0.90  16.25   0.98     0.94       2846.80|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2846.80 max =        10446.58 mean =      6462.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.73|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.20    97.56   16.26    None  None   None       |
|    all(noH): 2823   0      1.20    97.56   16.26    None  None   None       |
|    Sol.    : 438    0      5.12    79.49   38.13    None  None   None       |
|    Mac.    : 2385   0      1.20    97.56   12.24    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:     1.203 -  10.838: 1371   |   5:    49.379 -  59.015:   84        |
|      1:    10.838 -  20.474:  865   |   6:    59.015 -  68.650:   30        |
|      2:    20.474 -  30.109:  194   |   7:    68.650 -  78.285:   11        |
|      3:    30.109 -  39.744:  130   |   8:    78.285 -  87.920:    4        |
|      4:    39.744 -  49.379:  132   |   9:    87.920 -  97.556:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.543 - 4.538
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 312
   mapped sites are within: 0.726 - 4.538

peak=    5.854 closest distance to " NH2 ARG A  56 " =    2.315
peak=    5.769 closest distance to " CG  PRO A  54 " =    1.294
peak=    5.758 closest distance to " CB  GLN A 223 " =    1.400
peak=    5.394 closest distance to " CB  SER A  63 " =    1.211
peak=    5.004 closest distance to " CG  PRO A 213 " =    1.224
peak=    4.989 closest distance to " CB  ARG A 275 " =    0.890
peak=    4.706 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.664 closest distance to " CG  PRO A  90 " =    1.168
peak=    4.651 closest distance to " C   PRO A 198 " =    1.504
peak=    4.650 closest distance to " CB  GLN A 183 " =    1.312
peak=    4.636 closest distance to " CG  PRO A 198 " =    1.265
peak=    4.594 closest distance to " O   HOH Z 403 " =    1.806
peak=    4.575 closest distance to " O   HOH Z 232 " =    2.308
peak=    4.543 closest distance to " CB  PRO A  54 " =    0.866
peak=    4.540 closest distance to " O   HOH Z 234 " =    3.849
peak=    4.451 closest distance to " CB  GLU A 152 " =    1.166
peak=    4.427 closest distance to " O   HOH Z 298 " =    1.887
peak=    4.419 closest distance to " CB  TYR A 169 " =    0.824
peak=    4.411 closest distance to " CG  PRO A 243 " =    1.145
peak=    4.406 closest distance to " O   HOH Z  15 " =    2.087
peak=    4.397 closest distance to " CG  PRO A 280 " =    0.740
peak=    4.388 closest distance to " CB  GLU A 128 " =    1.167
peak=    4.366 closest distance to " OD1 ASN A  69 " =    2.553
peak=    4.339 closest distance to " CA  ALA A  21 " =    1.296
peak=    4.316 closest distance to " O   HOH Z  78 " =    1.824
peak=    4.290 closest distance to " O   HOH Z 193 " =    1.906
peak=    4.286 closest distance to " O   HOH Z 126 " =    1.828
peak=    4.283 closest distance to " O   HOH Z 236 " =    1.882
peak=    4.271 closest distance to " OD2 ASP A 286 " =    2.849
peak=    4.270 closest distance to " CB  SER A   3 " =    1.342
peak=    4.267 closest distance to " O   HOH Z 209 " =    2.246
peak=    4.223 closest distance to " NH2 ARG A 156 " =    1.189
peak=    4.195 closest distance to " CB  ARG A 190 " =    1.701
peak=    4.191 closest distance to " O   HOH Z 368 " =    2.045
peak=    4.167 closest distance to " CG1 ILE A  33 " =    1.283
peak=    4.155 closest distance to " CB  GLU A 277 " =    3.601
peak=    4.145 closest distance to " O   HOH Z 133 " =    2.346
peak=    4.144 closest distance to " CB  ASN A 148 " =    1.429
peak=    4.129 closest distance to " CB  ARG A  79 " =    1.329
peak=    4.128 closest distance to " O   HOH Z  97 " =    1.943
peak=    4.127 closest distance to " CB  LEU A 228 " =    1.118
peak=    4.123 closest distance to " O   HOH Z 272 " =    1.881
peak=    4.085 closest distance to " O   HOH Z 369 " =    2.127
peak=    4.085 closest distance to " O   SER A  87 " =    2.188
peak=    4.070 closest distance to " O   HOH Z 426 " =    1.533
peak=    4.049 closest distance to " O   HOH Z  40 " =    1.869
peak=    4.023 closest distance to " CA  THR A 221 " =    0.923
peak=    4.021 closest distance to " NH2BARG A 145 " =    2.175
peak=    4.013 closest distance to " O   HOH Z 261 " =    2.158
peak=    4.010 closest distance to " NZ  LYS A 117 " =    3.221
peak=    3.987 closest distance to " O   HOH Z 352 " =    1.874
peak=    3.976 closest distance to " O   HOH Z  67 " =    1.940
peak=    3.959 closest distance to " NE2 GLN A  11 " =    1.047
peak=    3.958 closest distance to " O   HOH Z  20 " =    1.664
peak=    3.958 closest distance to " O   HOH Z 316 " =    2.990
peak=    3.950 closest distance to " O   HOH Z 108 " =    2.441
peak=    3.941 closest distance to " O   MET A 105 " =    1.878
peak=    3.925 closest distance to " O   HOH Z 189 " =    2.080
peak=    3.920 closest distance to " CB  TRP A 179 " =    1.317
peak=    3.915 closest distance to " O   HOH Z 132 " =    2.700
peak=    3.914 closest distance to " CG  ARG A  66 " =    2.546
peak=    3.911 closest distance to " O   HOH Z  78 " =    2.369
peak=    3.908 closest distance to " O   HOH Z 147 " =    1.776
peak=    3.906 closest distance to " O   HOH Z  21 " =    1.758
peak=    3.905 closest distance to " CD1 LEU A 300 " =    1.184
peak=    3.905 closest distance to " O   HOH Z 411 " =    3.647
peak=    3.903 closest distance to " O   HOH Z 389 " =    1.916
peak=    3.902 closest distance to " CA  ARG A 195 " =    1.249
peak=    3.894 closest distance to " O   HOH Z 214 " =    2.156
peak=    3.858 closest distance to " CB  VAL A 202 " =    1.532
peak=    3.857 closest distance to " CB  VAL A 265 " =    1.193
peak=    3.854 closest distance to " O   HOH Z 142 " =    1.578
peak=    3.846 closest distance to " ND2 ASN A 187 " =    1.606
peak=    3.835 closest distance to " CD  ARG A 269 " =    0.952
peak=    3.833 closest distance to " CG1BVAL A  72 " =    1.635
peak=    3.832 closest distance to " O   HOH Z 128 " =    2.135
peak=    3.821 closest distance to " O   HOH Z 133 " =    1.612
peak=    3.811 closest distance to " CB  SER A 141 " =    1.012
peak=    3.809 closest distance to " O   HOH Z 406 " =    1.665
peak=    3.797 closest distance to " O   HOH Z  80 " =    1.645
peak=    3.795 closest distance to " CZ  PHE A 218 " =    1.053
peak=    3.771 closest distance to " CG2 THR A 221 " =    1.080
peak=    3.765 closest distance to " O   HOH Z 134 " =    1.405
peak=    3.764 closest distance to " O   HOH Z 158 " =    2.978
peak=    3.760 closest distance to " O   HOH Z 247 " =    1.387
peak=    3.759 closest distance to " O   HOH Z  49 " =    2.271
peak=    3.741 closest distance to " O   HOH Z 423 " =    1.955
peak=    3.739 closest distance to " O   HOH Z 374 " =    2.709
peak=    3.736 closest distance to " O   HOH Z 303 " =    2.036
peak=    3.732 closest distance to " O   HOH Z 265 " =    2.317
peak=    3.721 closest distance to " O   HOH Z  43 " =    2.103
peak=    3.719 closest distance to " CA  ASP A 140 " =    1.147
peak=    3.719 closest distance to " O   HOH Z 346 " =    1.569
peak=    3.716 closest distance to " O   HOH Z 402 " =    1.480
peak=    3.709 closest distance to " O   HOH Z 183 " =    1.561
peak=    3.702 closest distance to " CA  ASN A 176 " =    1.176
peak=    3.694 closest distance to " CA  ARG A  36 " =    1.155
peak=    3.691 closest distance to " O   HOH Z 284 " =    2.954
peak=    3.689 closest distance to " O   HOH Z 427 " =    2.846
peak=    3.682 closest distance to " O   HOH Z 345 " =    3.130
peak=    3.681 closest distance to " O   HOH Z 279 " =    2.185
peak=    3.677 closest distance to " O   HOH Z 344 " =    3.095
peak=    3.677 closest distance to " O   HOH Z  54 " =    1.738
peak=    3.677 closest distance to " CG2 VAL A 257 " =    0.912
peak=    3.675 closest distance to " CB  ILE A 120 " =    1.277
peak=    3.674 closest distance to " CB  TRP A 266 " =    0.891
peak=    3.673 closest distance to " O   HOH Z 250 " =    1.443
peak=    3.672 closest distance to " CB  PRO A 198 " =    1.029
peak=    3.664 closest distance to " CB  ALA A 291 " =    1.280
peak=    3.656 closest distance to " CD  ARG A 159 " =    0.808
peak=    3.651 closest distance to " O   HOH Z 371 " =    3.324
peak=    3.651 closest distance to " O   HOH Z 180 " =    2.267
peak=    3.651 closest distance to " CD  LYS A 166 " =    1.341
peak=    3.641 closest distance to " CA  ASP A 124 " =    0.726
peak=    3.638 closest distance to " CA  ALA A  51 " =    0.930
peak=    3.634 closest distance to " CB  TYR A 169 " =    0.926
peak=    3.629 closest distance to " O   HOH Z   6 " =    2.205
peak=    3.628 closest distance to " CG  GLN A  58 " =    2.665
peak=    3.627 closest distance to " CB  ASN A  39 " =    0.867
peak=    3.623 closest distance to " CG2 VAL A 197 " =    1.104
peak=    3.622 closest distance to " O   HOH Z  44 " =    1.912
peak=    3.620 closest distance to " O   HOH Z 368 " =    3.637
peak=    3.619 closest distance to " OD2 ASP A 298 " =    3.980
peak=    3.609 closest distance to " O   TRP A 274 " =    1.905
peak=    3.609 closest distance to " O   HOH Z 163 " =    1.546
peak=    3.607 closest distance to " O   HOH Z 124 " =    1.365
peak=    3.607 closest distance to " CA  ASP A 191 " =    0.776
peak=    3.592 closest distance to " CD2 LEU A 297 " =    0.883
peak=    3.592 closest distance to " O   HOH Z 245 " =    1.362
peak=    3.592 closest distance to " O   HOH Z  61 " =    1.539
peak=    3.586 closest distance to " OG BSER A 164 " =    2.420
peak=    3.567 closest distance to " O   HOH Z 185 " =    1.734
peak=    3.556 closest distance to " CG2BVAL A  41 " =    0.839
peak=    3.555 closest distance to " O   HOH Z  97 " =    2.577
peak=    3.552 closest distance to " CB  ARG A  79 " =    0.879
peak=    3.551 closest distance to " ND1 HIS A  81 " =    1.670
peak=    3.550 closest distance to " CG2 ILE A 120 " =    1.119
peak=    3.549 closest distance to " CD1 LEU A  96 " =    0.729
peak=    3.544 closest distance to " CB  ARG A 139 " =    0.880
peak=    3.544 closest distance to " O   HOH Z 291 " =    1.480
peak=    3.535 closest distance to " O   HOH Z  59 " =    2.428
peak=    3.535 closest distance to " O   HOH Z 327 " =    2.183
peak=    3.528 closest distance to " O   HOH Z 383 " =    1.995
peak=    3.525 closest distance to " CA  MET A  40 " =    1.079
peak=    3.521 closest distance to " O   HOH Z 214 " =    2.274
peak=    3.519 closest distance to " O   HOH Z 411 " =    1.730
peak=    3.510 closest distance to " O   HOH Z 102 " =    1.286
peak=    3.504 closest distance to " CG2 VAL A  78 " =    0.967
peak=    3.504 closest distance to " ND2 ASN A 110 " =    1.647
peak=    3.500 closest distance to " O   ALA A 165 " =    1.413
peak=    3.490 closest distance to " O   HOH Z 261 " =    2.091
peak=    3.490 closest distance to " NH1AARG A 145 " =    1.145
peak=    3.489 closest distance to " O   HOH Z  66 " =    2.213
peak=    3.489 closest distance to " CA  ASN A 215 " =    1.176
peak=    3.488 closest distance to " O   HOH Z 345 " =    1.646
peak=    3.486 closest distance to " O   HOH Z 281 " =    4.427
peak=    3.486 closest distance to " O   HOH Z  19 " =    1.896
peak=    3.483 closest distance to " O   HOH Z 193 " =    2.156
peak=    3.479 closest distance to " CE  LYS A  76 " =    0.862
peak=    3.479 closest distance to " CZ  PHE A 192 " =    1.001
peak=    3.477 closest distance to " O   HOH Z 427 " =    3.059
peak=    3.476 closest distance to " N   ASN A  39 " =    1.292
peak=    3.473 closest distance to " O   HOH Z  88 " =    3.368
peak=    3.466 closest distance to " O   HOH Z  63 " =    1.890
peak=    3.465 closest distance to " O   HOH Z  61 " =    1.550
peak=    3.463 closest distance to " CD1 ILE A 106 " =    0.892
peak=    3.460 closest distance to " CD2 TRP A 179 " =    1.352
peak=    3.459 closest distance to " O   HOH Z 126 " =    1.600
peak=    3.455 closest distance to " O   HOH Z 128 " =    2.137
peak=    3.454 closest distance to " O   THR A 251 " =    1.157
peak=    3.452 closest distance to " CB  ASP A 140 " =    0.855
peak=    3.446 closest distance to " O   HOH Z 337 " =    3.772
peak=    3.445 closest distance to " O   HOH Z 295 " =    1.495
peak=    3.439 closest distance to " O   HOH Z 173 " =    2.144
peak=    3.437 closest distance to " O   HOH Z 130 " =    2.226
peak=    3.432 closest distance to " CB  SER A 216 " =    0.786
peak=    3.430 closest distance to " CA  ALA A  84 " =    1.313
peak=    3.429 closest distance to " CA  ALA A 248 " =    1.166
peak=    3.429 closest distance to " CA  GLY A  80 " =    1.055
peak=    3.415 closest distance to " CB  PHE A  16 " =    1.059
peak=    3.412 closest distance to " O   HOH Z 227 " =    1.665
peak=    3.406 closest distance to " CB  ARG A 259 " =    1.881
peak=    3.406 closest distance to " CA  SER A  87 " =    0.968
peak=    3.397 closest distance to " O   HOH Z 135 " =    1.737
peak=    3.390 closest distance to " O   HOH Z 425 " =    2.034
peak=    3.385 closest distance to " O   HOH Z 197 " =    2.695
peak=    3.384 closest distance to " O   SER A  26 " =    1.709
peak=    3.379 closest distance to " CB  SER A  62 " =    0.781
peak=    3.374 closest distance to " CG AARG A 275 " =    1.082
peak=    3.372 closest distance to " CG1 VAL A 153 " =    0.959
peak=    3.366 closest distance to " CB  TRP A 150 " =    1.639
peak=    3.365 closest distance to " NZ ALYS A 290 " =    1.142
peak=    3.364 closest distance to " O   HOH Z 286 " =    2.196
peak=    3.362 closest distance to " CA  LYS A 117 " =    1.228
peak=    3.360 closest distance to " OG1 THR A 294 " =    2.399
peak=    3.359 closest distance to " O   HOH Z 421 " =    2.007
peak=    3.356 closest distance to " O   HOH Z 416 " =    2.790
peak=    3.356 closest distance to " CG1 ILE A 151 " =    0.958
peak=    3.355 closest distance to " O   HOH Z 299 " =    2.420
peak=    3.354 closest distance to " CA  ASP A 162 " =    1.184
peak=    3.354 closest distance to " SD AMET A  47 " =    0.967
peak=    3.350 closest distance to " CG2 THR A 220 " =    0.760
peak=    3.345 closest distance to " O   HOH Z 357 " =    2.022
peak=    3.338 closest distance to " CB  MET A  47 " =    0.957
peak=    3.333 closest distance to " CB  MET A  40 " =    0.936
peak=    3.330 closest distance to " O   HOH Z 313 " =    1.838
peak=    3.329 closest distance to " CG  LYS A  76 " =    1.053
peak=    3.329 closest distance to " C   SER A  32 " =    1.036
peak=    3.318 closest distance to " CD2 LEU A 255 " =    1.265
peak=    3.313 closest distance to " CG  GLU A 277 " =    2.220
peak=    3.312 closest distance to " CG2 ILE A  20 " =    1.350
peak=    3.310 closest distance to " CE1 TYR A 186 " =    1.253
peak=    3.308 closest distance to " O   HOH Z  10 " =    1.794
peak=    3.307 closest distance to " O   HOH Z  89 " =    2.186
peak=    3.305 closest distance to " CG BARG A 102 " =    1.881
peak=    3.305 closest distance to " CA  GLN A 223 " =    0.907
peak=    3.303 closest distance to " CA  ALA A 160 " =    0.883
peak=    3.300 closest distance to " OG  SER A  97 " =    3.540
peak=    3.297 closest distance to " O   HOH Z   4 " =    1.871
peak=    3.292 closest distance to " CA  THR A 264 " =    0.887
peak=    3.286 closest distance to " CB  TYR A 116 " =    0.925
peak=    3.285 closest distance to " CA  GLU A 152 " =    0.877
peak=    3.279 closest distance to " O   ALA A   1 " =    1.464
peak=    3.275 closest distance to " O   HOH Z 365 " =    2.949
peak=    3.269 closest distance to " NZ  LYS A  76 " =    1.185
peak=    3.269 closest distance to " O   GLY A  57 " =    2.627
peak=    3.268 closest distance to " CB  ALA A 242 " =    0.945
peak=    3.264 closest distance to " CG  MET A 185 " =    1.160
peak=    3.263 closest distance to " CA  TYR A 116 " =    1.424
peak=    3.262 closest distance to " O   GLN A 278 " =    1.429
peak=    3.262 closest distance to " CD  LYS A 119 " =    1.616
peak=    3.256 closest distance to " CA  ILE A  33 " =    1.489
peak=    3.253 closest distance to " O   ALA A 158 " =    1.224
peak=    3.252 closest distance to " CB  SER A 212 " =    1.152
peak=    3.252 closest distance to " NZ  LYS A 166 " =    3.089
peak=    3.246 closest distance to " O   HOH Z 250 " =    1.695
peak=    3.236 closest distance to " O   HOH Z 438 " =    2.093
peak=    3.231 closest distance to " O   HOH Z 423 " =    3.349
peak=    3.230 closest distance to " CG2 VAL A 296 " =    0.934
peak=    3.227 closest distance to " OG  SER A 245 " =    1.607
peak=    3.221 closest distance to " O   HOH Z 148 " =    3.168
peak=    3.219 closest distance to " O   HOH Z 292 " =    1.662
peak=    3.217 closest distance to " NH2AARG A 190 " =    1.259
peak=    3.217 closest distance to " CB  ASN A 127 " =    0.944
peak=    3.217 closest distance to " CB  ASN A 215 " =    1.133
peak=    3.215 closest distance to " O   HOH Z 273 " =    2.784
peak=    3.214 closest distance to " N   ARG A 190 " =    1.012
peak=    3.214 closest distance to " CB  ALA A  71 " =    1.211
peak=    3.209 closest distance to " CB  GLN A 103 " =    0.889
peak=    3.209 closest distance to " O   HOH Z 334 " =    1.542
peak=    3.208 closest distance to " O   HOH Z 128 " =    1.567
peak=    3.206 closest distance to " O   HOH Z 387 " =    2.544
peak=    3.206 closest distance to " CG  ARG A 219 " =    1.226
peak=    3.206 closest distance to " N   ARG A 156 " =    1.404
peak=    3.205 closest distance to " O   HOH Z 305 " =    3.735
peak=    3.204 closest distance to " O   HOH Z 234 " =    1.718
peak=    3.202 closest distance to " OG  SER A  62 " =    2.923
peak=    3.199 closest distance to " CB  TYR A  30 " =    1.412
peak=    3.197 closest distance to " O   HOH Z  35 " =    2.465
peak=    3.196 closest distance to " CA  VAL A  41 " =    0.852
peak=    3.194 closest distance to " CD2 HIS A  81 " =    1.253
peak=    3.193 closest distance to " CA  LEU A 282 " =    1.130
peak=    3.190 closest distance to " O   HOH Z 437 " =    1.495
peak=    3.188 closest distance to " CB  LEU A 143 " =    1.087
peak=    3.187 closest distance to " CG1 ILE A 120 " =    1.043
peak=    3.186 closest distance to " O   HOH Z 358 " =    2.080
peak=    3.183 closest distance to " OH  TYR A  30 " =    1.146
peak=    3.181 closest distance to " CG  GLN A  11 " =    1.254
peak=    3.181 closest distance to " CD  PRO A  54 " =    1.143
peak=    3.177 closest distance to " O   HOH Z 368 " =    2.537
peak=    3.177 closest distance to " O   HOH Z 329 " =    3.643
peak=    3.176 closest distance to " O   HOH Z 419 " =    2.910
peak=    3.156 closest distance to " CB  ALA A 100 " =    1.246
peak=    3.153 closest distance to " CA  ALA A 291 " =    0.904
peak=    3.149 closest distance to " CG BARG A 275 " =    1.410
peak=    3.148 closest distance to " CZ2 TRP A 179 " =    1.736
peak=    3.144 closest distance to " NZ  LYS A 117 " =    1.691
peak=    3.142 closest distance to " OH  TYR A 116 " =    1.086
peak=    3.140 closest distance to " NZ  LYS A 119 " =    1.412
peak=    3.136 closest distance to " O   HOH Z 417 " =    3.111
peak=    3.133 closest distance to " O   HOH Z 144 " =    1.807
peak=    3.132 closest distance to " CB  SER A 273 " =    0.798
peak=    3.132 closest distance to " O   HOH Z   1 " =    2.380
peak=    3.129 closest distance to " ND2 ASN A 209 " =    1.637
peak=    3.129 closest distance to " O   HOH Z 267 " =    2.063
peak=    3.127 closest distance to " O   HOH Z 109 " =    2.683
peak=    3.126 closest distance to " O   HOH Z 409 " =    3.361
peak=    3.123 closest distance to " O   HOH Z  85 " =    1.997
peak=    3.118 closest distance to " O   HOH Z 341 " =    1.741
peak=    3.116 closest distance to " NE2 HIS A 115 " =    0.989
peak=    3.113 closest distance to " CD1 LEU A 222 " =    0.746
peak=    3.102 closest distance to " O   HOH Z 409 " =    3.051
peak=    3.101 closest distance to " CG1 VAL A 202 " =    2.127
peak=    3.098 closest distance to " O   HOH Z 197 " =    1.983
peak=    3.097 closest distance to " N   VAL A 126 " =    1.433
peak=    3.093 closest distance to " CB  GLN A 278 " =    0.883
peak=    3.092 closest distance to " O   HOH Z 425 " =    1.278
peak=    3.092 closest distance to " O   HOH Z 166 " =    3.532
peak=    3.090 closest distance to " CA  MET A 105 " =    1.083
peak=    3.087 closest distance to " O   HOH Z 353 " =    2.775
peak=    3.085 closest distance to " O   HOH Z 359 " =    1.460
peak=    3.079 closest distance to " CG  MET A 113 " =    1.408
peak=    3.078 closest distance to " O   HOH Z 227 " =    1.614
peak=    3.071 closest distance to " O   HOH Z  20 " =    2.095
peak=    3.070 closest distance to " CA  ALA A 158 " =    1.100
peak=    3.058 closest distance to " NE2 GLN A  58 " =    4.538
peak=    3.049 closest distance to " CD1AILE A 234 " =    0.916
peak=    3.040 closest distance to " O   HOH Z 271 " =    2.165
peak=    3.029 closest distance to " O   ALA A 100 " =    1.290

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.863 - 5.381
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 192
   mapped sites are within: 0.863 - 5.381

peak=   -4.647 closest distance to " O   HOH Z 266 " =    4.394
peak=   -4.414 closest distance to " CD  ARG A 156 " =    2.030
peak=   -4.299 closest distance to " CB  PRO A 243 " =    2.642
peak=   -4.122 closest distance to " O   VAL A  67 " =    2.743
peak=   -4.097 closest distance to " O   PRO A 163 " =    2.113
peak=   -4.095 closest distance to " O   HOH Z 290 " =    1.042
peak=   -4.092 closest distance to " CB  ALA A 161 " =    2.656
peak=   -4.049 closest distance to " OG  SER A  97 " =    2.231
peak=   -4.024 closest distance to " O   HOH Z 372 " =    2.388
peak=   -4.010 closest distance to " C   HIS A 108 " =    1.104
peak=   -3.982 closest distance to " OXT GLY A 302 " =    2.818
peak=   -3.979 closest distance to " N   ALA A  43 " =    2.545
peak=   -3.960 closest distance to " O   HOH Z  10 " =    1.639
peak=   -3.944 closest distance to " CE2 TYR A  30 " =    2.742
peak=   -3.938 closest distance to " OG  SER A  62 " =    1.455
peak=   -3.929 closest distance to " OE1 GLN A 223 " =    1.927
peak=   -3.922 closest distance to " O   HOH Z 196 " =    2.058
peak=   -3.910 closest distance to " CD1 LEU A 101 " =    2.512
peak=   -3.909 closest distance to " ND2 ASN A  45 " =    1.195
peak=   -3.904 closest distance to " O   HOH Z  52 " =    1.603
peak=   -3.902 closest distance to " O   PRO A 198 " =    1.278
peak=   -3.868 closest distance to " O   HOH Z 407 " =    3.358
peak=   -3.862 closest distance to " CG  ASP A 231 " =    0.863
peak=   -3.855 closest distance to " O   HOH Z 292 " =    4.529
peak=   -3.855 closest distance to " O   HOH Z 353 " =    2.232
peak=   -3.837 closest distance to " CH2 TRP A 179 " =    1.241
peak=   -3.836 closest distance to " O   HOH Z 118 " =    3.135
peak=   -3.835 closest distance to " CD1 PHE A 130 " =    2.309
peak=   -3.827 closest distance to " CD2 LEU A 237 " =    2.665
peak=   -3.825 closest distance to " SG  CYS A 254 " =    3.358
peak=   -3.814 closest distance to " N   SER A 212 " =    1.948
peak=   -3.808 closest distance to " O   HOH Z 377 " =    1.998
peak=   -3.779 closest distance to " CD  GLN A 223 " =    1.419
peak=   -3.773 closest distance to " CD1 PHE A  59 " =    1.886
peak=   -3.769 closest distance to " O   HOH Z  13 " =    1.646
peak=   -3.756 closest distance to " O   HOH Z 165 " =    1.934
peak=   -3.749 closest distance to " O   HOH Z 394 " =    1.539
peak=   -3.738 closest distance to " CD1 LEU A  25 " =    2.475
peak=   -3.727 closest distance to " CB  ALA A 291 " =    2.285
peak=   -3.713 closest distance to " N   GLN A  58 " =    1.646
peak=   -3.707 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.705 closest distance to " CD1 LEU A 228 " =    2.316
peak=   -3.690 closest distance to " O   HOH Z  43 " =    1.498
peak=   -3.672 closest distance to " CD2 LEU A 300 " =    2.861
peak=   -3.667 closest distance to " O   HOH Z 283 " =    2.017
peak=   -3.663 closest distance to " O   HOH Z 198 " =    2.281
peak=   -3.645 closest distance to " OD1 ASN A 148 " =    1.599
peak=   -3.630 closest distance to " OG BSER A 134 " =    1.216
peak=   -3.630 closest distance to " ND2 ASN A 187 " =    1.607
peak=   -3.615 closest distance to " CD  ARG A 139 " =    1.636
peak=   -3.614 closest distance to " OG BSER A 134 " =    1.803
peak=   -3.610 closest distance to " O   HOH Z 377 " =    1.345
peak=   -3.591 closest distance to " O   HOH Z  17 " =    1.467
peak=   -3.588 closest distance to " O   HOH Z 166 " =    1.738
peak=   -3.586 closest distance to " C   ASN A 285 " =    2.473
peak=   -3.575 closest distance to " O   HOH Z 234 " =    4.269
peak=   -3.566 closest distance to " N   MET A 188 " =    1.944
peak=   -3.561 closest distance to " CG  ASP A 132 " =    2.349
peak=   -3.561 closest distance to " CG  GLU A  53 " =    1.444
peak=   -3.560 closest distance to " NH2AARG A 275 " =    5.335
peak=   -3.549 closest distance to " O   HOH Z  11 " =    1.976
peak=   -3.548 closest distance to " NH2 ARG A  66 " =    1.857
peak=   -3.548 closest distance to " O   HOH Z 185 " =    2.433
peak=   -3.517 closest distance to " CE  MET A 105 " =    2.094
peak=   -3.514 closest distance to " OG  SER A   3 " =    1.751
peak=   -3.502 closest distance to " N   SER A 276 " =    1.423
peak=   -3.501 closest distance to " O   HOH Z 311 " =    3.582
peak=   -3.495 closest distance to " O   ALA A  34 " =    2.390
peak=   -3.494 closest distance to " CZ  TYR A 169 " =    1.800
peak=   -3.491 closest distance to " O   GLY A 196 " =    1.065
peak=   -3.490 closest distance to " C   SER A 206 " =    1.551
peak=   -3.488 closest distance to " NH2 ARG A  79 " =    1.952
peak=   -3.484 closest distance to " OG BSER A 210 " =    2.210
peak=   -3.482 closest distance to " CG2 ILE A 263 " =    2.326
peak=   -3.479 closest distance to " CB  ASN A  39 " =    2.230
peak=   -3.477 closest distance to " O   HOH Z 351 " =    1.462
peak=   -3.473 closest distance to " N   ALA A 248 " =    1.951
peak=   -3.469 closest distance to " CA  VAL A  67 " =    2.714
peak=   -3.463 closest distance to " C   ILE A 234 " =    1.305
peak=   -3.462 closest distance to " NH1 ARG A 195 " =    2.577
peak=   -3.461 closest distance to " CZ  PHE A  59 " =    1.761
peak=   -3.456 closest distance to " CG1 VAL A 112 " =    2.569
peak=   -3.455 closest distance to " OG ASER A 134 " =    1.320
peak=   -3.455 closest distance to " CG  ASP A  50 " =    2.338
peak=   -3.455 closest distance to " CB  PRO A 163 " =    2.623
peak=   -3.453 closest distance to " C   ALA A 158 " =    1.295
peak=   -3.452 closest distance to " CB  TYR A  15 " =    2.264
peak=   -3.436 closest distance to " OD1 ASP A 191 " =    1.649
peak=   -3.432 closest distance to " O   ALA A 160 " =    1.487
peak=   -3.432 closest distance to " CD  GLN A  58 " =    1.193
peak=   -3.424 closest distance to " N   MET A 105 " =    2.960
peak=   -3.404 closest distance to " O   HOH Z 252 " =    4.172
peak=   -3.402 closest distance to " C   LEU A 143 " =    1.128
peak=   -3.395 closest distance to " N   ALA A 226 " =    2.056
peak=   -3.394 closest distance to " CD  ARG A 195 " =    5.108
peak=   -3.393 closest distance to " O   VAL A 125 " =    2.276
peak=   -3.392 closest distance to " O   LEU A 167 " =    1.533
peak=   -3.389 closest distance to " O   HOH Z 102 " =    1.619
peak=   -3.385 closest distance to " NH2 ARG A  66 " =    5.381
peak=   -3.376 closest distance to " NE2 GLN A  88 " =    1.790
peak=   -3.374 closest distance to " OE2 GLU A   2 " =    1.527
peak=   -3.370 closest distance to " O   HOH Z  93 " =    1.524
peak=   -3.368 closest distance to " O   HOH Z 166 " =    1.569
peak=   -3.362 closest distance to " CD  LYS A 289 " =    2.475
peak=   -3.360 closest distance to " O   HOH Z  38 " =    1.524
peak=   -3.356 closest distance to " O   GLY A  80 " =    2.518
peak=   -3.355 closest distance to " CD1 ILE A 239 " =    2.011
peak=   -3.354 closest distance to " O   HOH Z  15 " =    1.548
peak=   -3.353 closest distance to " O   HOH Z  71 " =    1.578
peak=   -3.353 closest distance to " CB  PHE A 192 " =    2.031
peak=   -3.348 closest distance to " O   HOH Z  19 " =    2.125
peak=   -3.347 closest distance to " CD2 TYR A 293 " =    2.035
peak=   -3.342 closest distance to " CB  CYS A 254 " =    2.446
peak=   -3.330 closest distance to " NE2 GLN A 103 " =    1.698
peak=   -3.327 closest distance to " C   THR A 279 " =    1.159
peak=   -3.325 closest distance to " O   HOH Z   6 " =    1.676
peak=   -3.324 closest distance to " CG  PHE A 283 " =    2.746
peak=   -3.324 closest distance to " NH2 ARG A 159 " =    2.267
peak=   -3.320 closest distance to " CE  MET A  93 " =    1.194
peak=   -3.315 closest distance to " O   VAL A 189 " =    2.578
peak=   -3.314 closest distance to " CG  ARG A 269 " =    2.408
peak=   -3.310 closest distance to " OH  TYR A 169 " =    1.062
peak=   -3.309 closest distance to " CB  PHE A 208 " =    2.255
peak=   -3.306 closest distance to " O   TRP A  92 " =    1.878
peak=   -3.304 closest distance to " CA  GLY A 203 " =    2.212
peak=   -3.294 closest distance to " CB  ALA A  10 " =    2.201
peak=   -3.294 closest distance to " ND2 ASN A 249 " =    2.298
peak=   -3.292 closest distance to " O   HOH Z 211 " =    1.619
peak=   -3.290 closest distance to " CG  GLU A 277 " =    1.077
peak=   -3.282 closest distance to " C   MET A 188 " =    1.674
peak=   -3.280 closest distance to " O   HOH Z 252 " =    3.674
peak=   -3.280 closest distance to " SG ACYS A 201 " =    2.070
peak=   -3.270 closest distance to " NE2 GLN A  58 " =    1.088
peak=   -3.269 closest distance to " O   HOH Z  11 " =    1.854
peak=   -3.262 closest distance to " O   HOH Z 313 " =    1.064
peak=   -3.262 closest distance to " O   HOH Z 389 " =    1.716
peak=   -3.258 closest distance to " CB  SER A 245 " =    2.361
peak=   -3.255 closest distance to " O   HOH Z 393 " =    1.545
peak=   -3.252 closest distance to " OD2 ASP A 171 " =    1.838
peak=   -3.250 closest distance to " CE3 TRP A 150 " =    2.064
peak=   -3.248 closest distance to " O   HOH Z 417 " =    2.525
peak=   -3.241 closest distance to " CB  ALA A 248 " =    1.989
peak=   -3.240 closest distance to " O   HOH Z  61 " =    1.583
peak=   -3.231 closest distance to " O   SER A 135 " =    1.581
peak=   -3.230 closest distance to " O   GLY A 211 " =    1.487
peak=   -3.226 closest distance to " N   GLN A 122 " =    1.561
peak=   -3.224 closest distance to " CG  PRO A 163 " =    2.553
peak=   -3.219 closest distance to " CB  ALA A 291 " =    2.287
peak=   -3.214 closest distance to " O   HOH Z  76 " =    1.956
peak=   -3.213 closest distance to " O   ASN A 187 " =    1.531
peak=   -3.213 closest distance to " O   HOH Z 262 " =    2.701
peak=   -3.206 closest distance to " O   HOH Z 388 " =    2.073
peak=   -3.201 closest distance to " CG1 VAL A 112 " =    2.931
peak=   -3.200 closest distance to " CG  TRP A 266 " =    1.869
peak=   -3.189 closest distance to " OG1 THR A 178 " =    1.359
peak=   -3.189 closest distance to " O   ALA A  10 " =    1.780
peak=   -3.181 closest distance to " CD1 PHE A  16 " =    2.673
peak=   -3.180 closest distance to " OD2 ASP A 171 " =    2.287
peak=   -3.177 closest distance to " NE  ARG A 259 " =    1.058
peak=   -3.175 closest distance to " CD2 PHE A  59 " =    2.521
peak=   -3.170 closest distance to " O   HOH Z  37 " =    1.830
peak=   -3.165 closest distance to " O   HOH Z 426 " =    1.619
peak=   -3.164 closest distance to " CD  PRO A 198 " =    1.345
peak=   -3.158 closest distance to " O   PHE A 218 " =    1.556
peak=   -3.157 closest distance to " CA  VAL A 197 " =    0.994
peak=   -3.151 closest distance to " CG2 THR A 221 " =    2.295
peak=   -3.142 closest distance to " O   HOH Z 111 " =    1.462
peak=   -3.136 closest distance to " O   HOH Z 414 " =    1.545
peak=   -3.136 closest distance to " O   HOH Z 298 " =    2.734
peak=   -3.133 closest distance to " CB  ASP A 162 " =    2.768
peak=   -3.132 closest distance to " O   HOH Z 128 " =    2.499
peak=   -3.130 closest distance to " CG1 VAL A 112 " =    2.812
peak=   -3.129 closest distance to " CB  TRP A  85 " =    2.403
peak=   -3.127 closest distance to " OD1 ASP A 171 " =    1.548
peak=   -3.126 closest distance to " O   HOH Z 241 " =    1.362
peak=   -3.126 closest distance to " O   HOH Z 418 " =    1.419
peak=   -3.116 closest distance to " CD  GLN A  88 " =    0.998
peak=   -3.113 closest distance to " O   HOH Z 423 " =    2.347
peak=   -3.110 closest distance to " C   ALA A   8 " =    1.583
peak=   -3.105 closest distance to " CD2 PHE A  61 " =    2.448
peak=   -3.102 closest distance to " O   HOH Z 324 " =    2.284
peak=   -3.101 closest distance to " O   GLY A  80 " =    2.517
peak=   -3.099 closest distance to " CD2 LEU A 237 " =    2.685
peak=   -3.089 closest distance to " O   PRO A 198 " =    2.341
peak=   -3.088 closest distance to " N   LEU A 281 " =    1.716
peak=   -3.078 closest distance to " O   ASN A 301 " =    1.391
peak=   -3.077 closest distance to " O   HOH Z 422 " =    1.530
peak=   -3.043 closest distance to " OD2 ASP A  65 " =    1.785
peak=   -3.042 closest distance to " CD2 TYR A 247 " =    2.398
peak=   -3.034 closest distance to " O   HOH Z 385 " =    3.780
peak=   -3.030 closest distance to " O   HOH Z 193 " =    1.860

================= 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    :  0.3906 0.3838   6.179016e+00   6.168515e+00
   1_bss:  0.3787 0.3698   6.166002e+00   6.145810e+00
   1_xyz:  0.2384 0.2671   5.772894e+00   5.866623e+00
   1_adp:  0.2165 0.2748   5.721056e+00   5.891073e+00
   1_occ:  0.2161 0.2751   5.719926e+00   5.890288e+00
   2_bss:  0.2137 0.2729   5.714842e+00   5.885375e+00
   2_xyz:  0.1573 0.1973   5.418661e+00   5.614462e+00
   2_adp:  0.1457 0.1864   5.358487e+00   5.554139e+00
   2_occ:  0.1455 0.1863   5.357831e+00   5.553347e+00
   3_bss:  0.1456 0.1861   5.357356e+00   5.551498e+00
   3_xyz:  0.1187 0.1620   5.190961e+00   5.422324e+00
   3_adp:  0.1132 0.1609   5.164751e+00   5.410644e+00
   3_occ:  0.1132 0.1609   5.164714e+00   5.410773e+00
   4_bss:  0.1136 0.1611   5.166532e+00   5.411792e+00
   4_xyz:  0.1098 0.1592   5.147189e+00   5.400001e+00
   4_adp:  0.1096 0.1578   5.141834e+00   5.392299e+00
   4_occ:  0.1095 0.1578   5.141879e+00   5.392704e+00
   5_bss:  0.1095 0.1577   5.141945e+00   5.392744e+00
   5_xyz:  0.1110 0.1581   5.150572e+00   5.395434e+00
   5_adp:  0.1112 0.1582   5.151483e+00   5.395670e+00
   5_occ:  0.1112 0.1582   5.151585e+00   5.396017e+00
   5_bss:  0.1112 0.1582   5.151671e+00   5.396096e+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:  0.306  36.227  -2.852   2.939   0.561   0.000   0.000   0.000
   1_xyz:  0.306  36.227  -2.852   2.939   0.561   0.000   0.000   0.000
   1_adp:  0.306  36.227  -2.852   2.939   0.561   0.000   0.000   0.000
   1_occ:  0.306  36.227  -2.852   2.939   0.561   0.000   0.000   0.000
   2_bss:  0.319  54.496  -2.527   0.073  -0.993   0.000  -0.000  -0.000
   2_xyz:  0.319  54.496  -2.527   0.073  -0.993   0.000  -0.000  -0.000
   2_adp:  0.319  54.496  -2.527   0.073  -0.993   0.000  -0.000  -0.000
   2_occ:  0.319  54.496  -2.527   0.073  -0.993   0.000  -0.000  -0.000
   3_bss:  0.321  54.496  -2.378  -0.926  -1.351  -0.000  -0.000  -0.000
   3_xyz:  0.321  54.496  -2.378  -0.926  -1.351  -0.000  -0.000  -0.000
   3_adp:  0.321  54.496  -2.378  -0.926  -1.351  -0.000  -0.000  -0.000
   3_occ:  0.321  54.496  -2.378  -0.926  -1.351  -0.000  -0.000  -0.000
   4_bss:  0.321  54.496  -2.164  -1.221  -1.329  -0.000  -0.000  -0.000
   4_xyz:  0.321  54.496  -2.164  -1.221  -1.329  -0.000  -0.000  -0.000
   4_adp:  0.321  54.496  -2.164  -1.221  -1.329  -0.000  -0.000  -0.000
   4_occ:  0.321  54.496  -2.164  -1.221  -1.329  -0.000  -0.000  -0.000
   5_bss:  0.321  52.263  -2.010  -1.256  -1.204  -0.000  -0.000  -0.000
   5_xyz:  0.321  52.263  -2.010  -1.256  -1.204  -0.000  -0.000  -0.000
   5_adp:  0.321  52.263  -2.010  -1.256  -1.204  -0.000  -0.000  -0.000
   5_occ:  0.321  52.263  -2.010  -1.256  -1.204  -0.000  -0.000  -0.000
   5_bss:  0.321  52.172  -1.879  -1.191  -1.065  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.581 0.6010  0.7777    44957.344
   1_bss:  42.186 0.6158  0.8015    40992.036
   1_xyz:  27.024 0.7910  0.9724    18691.104
   1_adp:  28.116 0.7782  0.9512    19872.201
   1_occ:  28.101 0.7783  0.9510    19836.790
   2_bss:  27.719 0.7825  0.9142    19518.068
   2_xyz:  19.224 0.8683  0.9782    10054.297
   2_adp:  17.609 0.8841  0.9823     8906.286
   2_occ:  17.601 0.8842  0.9823     8895.073
   3_bss:  17.539 0.8848  0.9693     8861.495
   3_xyz:  14.902 0.9071  0.9809     6783.235
   3_adp:  14.620 0.9097  0.9757     6641.858
   3_occ:  14.621 0.9097  0.9757     6643.810
   4_bss:  14.653 0.9095  0.9749     6692.399
   4_xyz:  14.333 0.9123  0.9752     6478.551
   4_adp:  14.146 0.9139  0.9703     6414.341
   4_occ:  14.152 0.9139  0.9701     6418.365
   5_bss:  14.153 0.9139  0.9731     6417.882
   5_xyz:  14.185 0.9137  0.9729     6439.620
   5_adp:  14.193 0.9136  0.9681     6458.811
   5_occ:  14.196 0.9136  0.9680     6462.464
   5_bss:  14.199 0.9136  0.9704     6463.382
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6821e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6821e-01
   1_xyz:   1.336  0.010  0.081 15.380  0.004  4.116   9.1511e-02
   1_adp:   1.336  0.010  0.081 15.380  0.004  4.116   9.1511e-02
   1_occ:   1.336  0.010  0.081 15.380  0.004  4.116   9.1511e-02
   2_bss:   1.336  0.010  0.081 15.380  0.004  4.116   9.1511e-02
   2_xyz:   1.005  0.007  0.069 14.343  0.004  4.127   5.7396e-02
   2_adp:   1.005  0.007  0.069 14.343  0.004  4.127   5.7396e-02
   2_occ:   1.005  0.007  0.069 14.343  0.004  4.127   5.7396e-02
   3_bss:   1.005  0.007  0.069 14.343  0.004  4.127   5.7396e-02
   3_xyz:   1.142  0.010  0.081 14.838  0.004  4.133   7.4647e-02
   3_adp:   1.142  0.010  0.081 14.838  0.004  4.133   7.4647e-02
   3_occ:   1.142  0.010  0.081 14.838  0.004  4.133   7.4647e-02
   4_bss:   1.142  0.010  0.081 14.838  0.004  4.133   7.4647e-02
   4_xyz:   1.087  0.009  0.079 14.715  0.004  4.119   6.9129e-02
   4_adp:   1.087  0.009  0.079 14.715  0.004  4.119   6.9129e-02
   4_occ:   1.087  0.009  0.079 14.715  0.004  4.119   6.9129e-02
   5_bss:   1.087  0.009  0.079 14.715  0.004  4.119   6.9129e-02
   5_xyz:   0.981  0.007  0.073 14.362  0.004  4.118   5.6390e-02
   5_adp:   0.981  0.007  0.073 14.362  0.004  4.118   5.6390e-02
   5_occ:   0.981  0.007  0.073 14.362  0.004  4.118   5.6390e-02
   5_bss:   0.981  0.007  0.073 14.362  0.004  4.118   5.6390e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4147e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4147e-01
   1_xyz:   8.131  0.066  0.391 88.301  0.022  2.249   1.2218e-01
   1_adp:   8.131  0.066  0.391 88.301  0.022  2.249   1.2218e-01
   1_occ:   8.131  0.066  0.391 88.301  0.022  2.249   1.2218e-01
   2_bss:   8.131  0.066  0.391 88.301  0.022  2.249   1.2218e-01
   2_xyz:   7.383  0.045  0.228 85.249  0.043  2.321   4.6845e-02
   2_adp:   7.383  0.045  0.228 85.249  0.043  2.321   4.6845e-02
   2_occ:   7.383  0.045  0.228 85.249  0.043  2.321   4.6845e-02
   3_bss:   7.383  0.045  0.228 85.249  0.043  2.321   4.6845e-02
   3_xyz:   7.914  0.059  0.251 82.915  0.035  2.285   5.8976e-02
   3_adp:   7.914  0.059  0.251 82.915  0.035  2.285   5.8976e-02
   3_occ:   7.914  0.059  0.251 82.915  0.035  2.285   5.8976e-02
   4_bss:   7.914  0.059  0.251 82.915  0.035  2.285   5.8976e-02
   4_xyz:   7.750  0.045  0.256 80.591  0.038  2.324   6.2689e-02
   4_adp:   7.750  0.045  0.256 80.591  0.038  2.324   6.2689e-02
   4_occ:   7.750  0.045  0.256 80.591  0.038  2.324   6.2689e-02
   5_bss:   7.750  0.045  0.256 80.591  0.038  2.324   6.2689e-02
   5_xyz:   7.104  0.039  0.233 82.213  0.034  2.367   3.7928e-02
   5_adp:   7.104  0.039  0.233 82.213  0.034  2.367   3.7928e-02
   5_occ:   7.104  0.039  0.233 82.213  0.034  2.367   3.7928e-02
   5_bss:   7.104  0.039  0.233 82.213  0.034  2.367   3.7928e-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:  82.46   0.00  17.48  79.62   0.00  13.35  82.46   6.08  39.93
   1_occ:  82.46   0.00  17.48  79.62   0.00  13.35  82.46   6.08  39.93
   2_bss:  82.46   0.00  17.48  79.62   0.00  13.35  82.46   6.08  39.93
   2_xyz:  82.46   0.00  17.48  79.62   0.00  13.35  82.46   6.08  39.93
   2_adp:  83.46   1.60  17.14  83.46   1.60  12.93  81.71   5.06  40.06
   2_occ:  83.46   1.60  17.14  83.46   1.60  12.93  81.71   5.06  40.06
   3_bss:  83.46   1.60  17.14  83.46   1.60  12.93  81.71   5.06  40.06
   3_xyz:  83.46   1.60  17.14  83.46   1.60  12.93  81.71   5.06  40.06
   3_adp:  98.85   1.06  17.28  98.85   1.06  12.80  84.93   5.38  41.71
   3_occ:  98.85   1.06  17.28  98.85   1.06  12.80  84.93   5.38  41.71
   4_bss:  98.85   1.06  17.28  98.85   1.06  12.80  84.93   5.38  41.71
   4_xyz:  98.85   1.06  17.28  98.85   1.06  12.80  84.93   5.38  41.71
   4_adp:  98.51   1.38  16.59  98.51   1.38  12.46  79.58   5.27  39.11
   4_occ:  98.51   1.38  16.59  98.51   1.38  12.46  79.58   5.27  39.11
   5_bss:  98.51   1.38  16.59  98.51   1.38  12.46  79.58   5.27  39.11
   5_xyz:  98.51   1.38  16.59  98.51   1.38  12.46  79.58   5.27  39.11
   5_adp:  97.60   1.25  16.30  97.60   1.25  12.28  79.54   5.17  38.17
   5_occ:  97.60   1.25  16.30  97.60   1.25  12.28  79.54   5.17  38.17
   5_bss:  97.56   1.20  16.26  97.56   1.20  12.24  79.49   5.12  38.13
------------------------------------------------------------------------
 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:    1.745    0.030    0.392
   1_adp:    1.745    0.030    0.392
   1_occ:    1.745    0.030    0.392
   2_bss:    1.745    0.030    0.392
   2_xyz:    1.072    0.032    0.475
   2_adp:    1.072    0.032    0.475
   2_occ:    1.072    0.032    0.475
   3_bss:    1.072    0.032    0.475
   3_xyz:    1.057    0.048    0.555
   3_adp:    1.057    0.048    0.555
   3_occ:    1.057    0.048    0.555
   4_bss:    1.057    0.048    0.555
   4_xyz:    1.129    0.062    0.571
   4_adp:    1.129    0.062    0.571
   4_occ:    1.129    0.062    0.571
   5_bss:    1.129    0.062    0.571
   5_xyz:    1.213    0.039    0.579
   5_adp:    1.213    0.039    0.579
   5_occ:    1.213    0.039    0.579
   5_bss:    1.213    0.039    0.579
------------------------------------------------------------------------

CPU time actual refinement: 330.75


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_816/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_816/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_816/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_816/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_816/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.58 
  Macro-tasks:
    bulk solvent and scale       = 37.75  
    individual site refinement   = 137.15 
    weights calculation          = 30.12  
    collect and process          = 6.70   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 211.85 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 105.62 
    alpha_beta                      = 8.34   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 114.45 
    fmodel                         = 6.50   
    r_factors                      = 0.19   
    phase_errors                   = 11.09  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 249.48 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.691 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    638 calls, 105.30 s
gradients_fft:          583 calls, 100.84 s

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

# Date 2008-01-16 Time 05:43:19 PST -0800 (1200490999.78 s)
Start R-work = 0.3906, R-free = 0.3838 (no bulk solvent and anisotropic scale)
Final R-work = 0.1321, R-free = 0.1759 (no bulk solvent and anisotropic scale)

Start R-work = 0.3787, R-free = 0.3698
Final R-work = 0.1112, R-free = 0.1582