# Date 2008-01-16 Time 06:04:44 PST -0800 (1200492284.79 s)
#phil __OFF__

Command line arguments: "../995.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8377
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 995

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.2261, 86.39, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 1.9734
Completeness in resolution range: 0.947564
Completeness with d_max=infinity: 0.944777

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   1.9734

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 1.9734
Completeness in resolution range: 0.947564
Completeness with d_max=infinity: 0.944777

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1573 -  4.2238 [2174/2200]  1957   217  10.0%
  bin  2:  4.2238 -  3.3646 [2078/2098]  1872   206   9.9%
  bin  3:  3.3646 -  2.9428 [2068/2087]  1855   213  10.3%
  bin  4:  2.9428 -  2.6754 [2031/2061]  1829   202   9.9%
  bin  5:  2.6754 -  2.4845 [2034/2053]  1838   196   9.6%
  bin  6:  2.4845 -  2.3386 [2011/2036]  1800   211  10.5%
  bin  7:  2.3386 -  2.2218 [2017/2045]  1820   197   9.8%
  bin  8:  2.2218 -  2.1254 [1992/2028]  1796   196   9.8%
  bin  9:  2.1254 -  2.0438 [1991/2033]  1792   199  10.0%
  bin 10:  2.0438 -  1.9734 [1193/2032]  1071   122  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_995/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: 0.15 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: 28
        2.42 -     3.04: 2186
        3.04 -     3.66: 4713
        3.66 -     4.28: 9053
        4.28 -     4.90: 12324
  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 201 " - " O   HOH Z 349 "  2.002 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.151 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28299 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_995/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_995/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.22605 86.39 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 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3818   r_free= 0.3788   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.172133                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7115 0.99   1410  158 0.3190 0.3120      6.4299      6.3902|
|  2:  4.7115 -  3.7585 0.99   1351  151 0.3102 0.2950      6.6266      6.5512|
|  3:  3.7585 -  3.2889 0.99   1331  141 0.3303 0.3027       6.477      6.5267|
|  4:  3.2889 -  2.9907 0.99   1326  154 0.3679 0.4000      6.3874      6.4131|
|  5:  2.9907 -  2.7778 0.99   1318  151 0.4014 0.3623      6.2478       6.234|
|  6:  2.7778 -  2.6149 0.99   1312  139 0.3912 0.4157      6.1514      6.1444|
|  7:  2.6149 -  2.4845 0.99   1303  140 0.4144 0.3969      6.1471       6.113|
|  8:  2.4845 -  2.3768 0.98   1282  143 0.4231 0.4227       6.079      6.0755|
|  9:  2.3768 -  2.2856 0.98   1275  154 0.4121 0.4418      6.0409      6.0663|
| 10:  2.2856 -  2.2070 1.00   1317  146 0.4348 0.4014      6.0226      5.9704|
| 11:  2.2070 -  2.1382 0.98   1288  133 0.4339 0.4723      5.9753      6.0088|
| 12:  2.1382 -  2.0772 0.98   1268  143 0.4517 0.4502      5.9124      5.9643|
| 13:  2.0772 -  2.0226 0.98   1276  137 0.4512 0.4602      5.8253      5.7472|
| 14:  2.0226 -  1.9734 0.44    573   69 0.4719 0.4872      5.8238      5.8359|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1573 -  4.7115  1410   158  0.77  27.69   0.85     0.81      48698.07|
|  2:  4.7115 -  3.7585  1351   151  0.81  25.60   0.95     0.90      61340.47|
|  3:  3.7585 -  3.2889  1331   141  0.73  32.34   0.98     0.91      66914.27|
|  4:  3.2889 -  2.9907  1326   154  0.68  37.62   0.96     0.86      63142.48|
|  5:  2.9907 -  2.7778  1318   151  0.60  43.98   0.94     0.81      54002.56|
|  6:  2.7778 -  2.6149  1312   139  0.60  44.04   0.96     0.80      46295.05|
|  7:  2.6149 -  2.4845  1303   140  0.59  45.09   0.97     0.77      42188.39|
|  8:  2.4845 -  2.3768  1282   143  0.57  46.14   0.96     0.78      38458.00|
|  9:  2.3768 -  2.2856  1275   154  0.58  46.16   0.99     0.77      35498.62|
| 10:  2.2856 -  2.2070  1317   146  0.56  47.12   0.99     0.79      32884.97|
| 11:  2.2070 -  2.1382  1288   133  0.55  48.66   1.01     0.79      33025.97|
| 12:  2.1382 -  2.0772  1268   143  0.51  51.61   0.97     0.74      31232.90|
| 13:  2.0772 -  2.0226  1276   137  0.45  55.83   0.99     0.69      29390.04|
| 14:  2.0226 -  1.9734   573    69  0.45  56.66   0.99     0.61      26231.32|
|alpha:            min =        0.61 max =            0.91 mean =         0.80|
|beta:             min =    26231.32 max =        66914.27 mean =     44455.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           90.00 mean =        42.71|
|phase err.(test): min =        0.00 max =           89.98 mean =        42.72|
|-----------------------------------------------------------------------------|

============================== 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 = 6.956250              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.036   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.329154              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.707   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      195 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1991 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1873 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2840 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4646 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4407 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5618 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6706 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.211 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    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 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3818   r_free= 0.3788   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.172133                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3704   r_free= 0.3699   ksol= 0.34   Bsol= 50.00   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,1.81,-1.82,0.00,-0.00,-0.00); trace/3= -0.05                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.157979                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.166630              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.268   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.644671              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.522   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3704      final r-factor (work) = 0.2250          |
| start r-factor (free) = 0.3699      final r-factor (free) = 0.2562          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1515 = 6.17 * 0.50 * 6.1579 + 1.00 * 0.1647                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3590 = 6.17 * 0.50 * 5.9277 + 1.00 * 0.0819                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2250      final r-factor (work) = 0.2059          |
| start r-factor (free) = 0.2562      final r-factor (free) = 0.2666          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8275 = 0.64 * 1.00 * 5.9277 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6631 = 0.64 * 1.00 * 5.6634 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.28   17.69    None  None   None       |
|    all(noH): 2823   0      0.00    88.28   17.69    None  None   None       |
|    Sol.    : 438    0      4.89    88.28   41.32    None  None   None       |
|    Mac.    : 2385   0      0.00    72.90   13.34    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 -   8.828:  751   |   5:    44.141 -  52.969:  104        |
|      1:     8.828 -  17.657: 1191   |   6:    52.969 -  61.798:   84        |
|      2:    17.657 -  26.485:  362   |   7:    61.798 -  70.626:   27        |
|      3:    26.485 -  35.313:  156   |   8:    70.626 -  79.454:   12        |
|      4:    35.313 -  44.141:  134   |   9:    79.454 -  88.282:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2059 r_free = 0.2666             target_work(ml) = 5.680         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2057 r_free = 0.2661             target_work(ml) = 5.679         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2057   r_free= 0.2661   ksol= 0.34   Bsol= 50.00   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,1.81,-1.82,0.00,-0.00,-0.00); trace/3= -0.05                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.678995                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2035   r_free= 0.2622   ksol= 0.34   Bsol= 62.52   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.40,-1.66,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.670371                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.112174              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.990   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.174395              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.928  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2035      final r-factor (work) = 0.1545          |
| start r-factor (free) = 0.2622      final r-factor (free) = 0.2037          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0730 = 2.11 * 0.50 * 5.6730 + 1.00 * 0.0819                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9202 = 2.11 * 0.50 * 5.5565 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1545      final r-factor (work) = 0.1461          |
| start r-factor (free) = 0.2037      final r-factor (free) = 0.1897          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9811 = 0.17 * 1.00 * 5.5565 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9493 = 0.17 * 1.00 * 5.3996 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    83.01   17.10    None  None   None       |
|    all(noH): 2823   0      1.67    83.01   17.10    None  None   None       |
|    Sol.    : 438    0      6.58    83.01   39.09    None  None   None       |
|    Mac.    : 2385   0      1.67    73.16   13.07    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:     1.668 -   9.802:  900   |   5:    42.339 -  50.474:  100        |
|      1:     9.802 -  17.937: 1154   |   6:    50.474 -  58.608:   76        |
|      2:    17.937 -  26.071:  285   |   7:    58.608 -  66.742:   29        |
|      3:    26.071 -  34.205:  140   |   8:    66.742 -  74.876:   11        |
|      4:    34.205 -  42.339:  125   |   9:    74.876 -  83.011:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1461 r_free = 0.1897             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1461 r_free = 0.1899             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1461   r_free= 0.1899   ksol= 0.34   Bsol= 62.52   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.40,-1.66,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.367127                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1894   ksol= 0.33   Bsol= 55.33   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.41,-1.48,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.364110                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.626004              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.858   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.050262              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.556  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1459      final r-factor (work) = 0.1263          |
| start r-factor (free) = 0.1894      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4414 = 1.63 * 0.50 * 5.3989 + 1.00 * 0.0521                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3560 = 1.63 * 0.50 * 5.2977 + 1.00 * 0.0490                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1263      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1689      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8692 = 2.05 * 1.00 * 5.2977 + 1.00 * 0.0075                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7069 = 2.05 * 1.00 * 5.2171 + 1.00 * 0.0105                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.42   17.84    None  None   None       |
|    all(noH): 2823   0      0.00    93.42   17.84    None  None   None       |
|    Sol.    : 438    0      5.18    92.60   43.13    None  None   None       |
|    Mac.    : 2385   0      0.00    93.42   13.19    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:     0.000 -   9.342:  867   |   5:    46.710 -  56.052:  104        |
|      1:     9.342 -  18.684: 1229   |   6:    56.052 -  65.394:   75        |
|      2:    18.684 -  28.026:  258   |   7:    65.394 -  74.736:   33        |
|      3:    28.026 -  37.368:  138   |   8:    74.736 -  84.078:   24        |
|      4:    37.368 -  46.710:   90   |   9:    84.078 -  93.420:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1216 r_free = 0.1679             target_work(ml) = 5.213         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1215 r_free = 0.1680             target_work(ml) = 5.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1680   ksol= 0.33   Bsol= 55.33   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.41,-1.48,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.213163                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1678   ksol= 0.32   Bsol= 56.89   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.61,-1.44,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.212377                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.915518              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.108  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.825603              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.281  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1678      final r-factor (free) = 0.1617          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0452 = 1.92 * 0.50 * 5.2166 + 1.00 * 0.0490                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0202 = 1.92 * 0.50 * 5.1850 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2912 = 0.83 * 1.00 * 5.1850 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2709 = 0.83 * 1.00 * 5.1606 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.10   17.60    None  None   None       |
|    all(noH): 2823   0      0.00    97.10   17.60    None  None   None       |
|    Sol.    : 438    0      3.81    94.52   42.34    None  None   None       |
|    Mac.    : 2385   0      0.00    97.10   13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.710:  985   |   5:    48.550 -  58.260:   93        |
|      1:     9.710 -  19.420: 1155   |   6:    58.260 -  67.970:   57        |
|      2:    19.420 -  29.130:  239   |   7:    67.970 -  77.680:   29        |
|      3:    29.130 -  38.840:  134   |   8:    77.680 -  87.390:   15        |
|      4:    38.840 -  48.550:  111   |   9:    87.390 -  97.100:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1602             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1603             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1603   ksol= 0.32   Bsol= 56.89   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.61,-1.44,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.156492                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1601   ksol= 0.32   Bsol= 56.89   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.58,-1.28,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157713                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.887432              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.277  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.635358              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.710  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5061 = 2.89 * 0.50 * 5.1616 + 1.00 * 0.0542                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4845 = 2.89 * 0.50 * 5.1382 + 1.00 * 0.0665                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1086      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2748 = 0.64 * 1.00 * 5.1382 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2692 = 0.64 * 1.00 * 5.1300 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.12   17.25    None  None   None       |
|    all(noH): 2823   0      0.00    99.12   17.25    None  None   None       |
|    Sol.    : 438    0      5.47    96.08   41.10    None  None   None       |
|    Mac.    : 2385   0      0.00    99.12   12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.912: 1059   |   5:    49.560 -  59.472:   90        |
|      1:     9.912 -  19.824: 1116   |   6:    59.472 -  69.384:   46        |
|      2:    19.824 -  29.736:  228   |   7:    69.384 -  79.296:   19        |
|      3:    29.736 -  39.648:  125   |   8:    79.296 -  89.208:   14        |
|      4:    39.648 -  49.560:  122   |   9:    89.208 -  99.120:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1082 r_free = 0.1574             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1574             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1574   ksol= 0.32   Bsol= 56.89   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.58,-1.28,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127275                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7115 0.99   1410  158 0.0934 0.1289      5.3409       5.548|
|  2:  4.7115 -  3.7585 0.99   1351  151 0.0815 0.1048      5.4101      5.5862|
|  3:  3.7585 -  3.2889 0.99   1331  141 0.1048 0.1572      5.4576      5.8567|
|  4:  3.2889 -  2.9907 0.99   1326  154 0.1180 0.1714      5.4429      5.6091|
|  5:  2.9907 -  2.7778 0.99   1318  151 0.1295 0.1725      5.3022      5.5608|
|  6:  2.7778 -  2.6149 0.99   1312  139 0.1153 0.1747      5.1771      5.4046|
|  7:  2.6149 -  2.4845 0.99   1303  140 0.1236 0.1633      5.1448      5.3384|
|  8:  2.4845 -  2.3768 0.98   1282  143 0.1112 0.1765      5.0288        5.36|
|  9:  2.3768 -  2.2856 0.98   1275  154 0.1147 0.1760      5.0234      5.3208|
| 10:  2.2856 -  2.2070 1.00   1317  146 0.1062 0.1650      4.9206      5.1598|
| 11:  2.2070 -  2.1382 0.98   1288  133 0.1089 0.1847      4.9292       5.314|
| 12:  2.1382 -  2.0772 0.98   1268  143 0.1088 0.1586      4.8494      5.0964|
| 13:  2.0772 -  2.0226 0.98   1276  137 0.1099 0.1737      4.7736      5.0214|
| 14:  2.0226 -  1.9734 0.44    573   69 0.1020 0.1594       4.655      4.9018|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1573 -  4.7115  1410   158  0.94   8.90   0.97     0.95       6762.99|
|  2:  4.7115 -  3.7585  1351   151  0.95   7.72   1.01     1.01       8855.81|
|  3:  3.7585 -  3.2889  1331   141  0.94  11.19   1.03     1.02      10119.17|
|  4:  3.2889 -  2.9907  1326   154  0.92  13.86   1.01     0.98      10389.48|
|  5:  2.9907 -  2.7778  1318   151  0.90  15.86   0.99     0.98       8102.32|
|  6:  2.7778 -  2.6149  1312   139  0.90  15.63   0.99     0.97       6795.81|
|  7:  2.6149 -  2.4845  1303   140  0.91  15.30   0.99     0.96       6042.40|
|  8:  2.4845 -  2.3768  1282   143  0.91  15.01   0.98     0.95       4971.10|
|  9:  2.3768 -  2.2856  1275   154  0.91  15.32   1.00     0.96       4927.69|
| 10:  2.2856 -  2.2070  1317   146  0.91  15.23   0.99     0.96       4182.66|
| 11:  2.2070 -  2.1382  1288   133  0.90  15.82   0.98     0.94       4291.09|
| 12:  2.1382 -  2.0772  1268   143  0.91  15.52   1.00     1.00       3867.87|
| 13:  2.0772 -  2.0226  1276   137  0.90  16.07   0.99     0.97       3318.52|
| 14:  2.0226 -  1.9734   573    69  0.92  14.39   0.97     0.94       2575.08|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2575.08 max =        10389.48 mean =      6268.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.91|
|phase err.(test): min =        0.00 max =           89.18 mean =        13.43|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1574   ksol= 0.32   Bsol= 56.89   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.46,-1.09,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127393                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1574   ksol= 0.32   Bsol= 56.89   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.46,-1.09,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127393                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7115 0.99   1410  158 0.0935 0.1292      5.3423      5.5495|
|  2:  4.7115 -  3.7585 0.99   1351  151 0.0815 0.1048      5.4104      5.5861|
|  3:  3.7585 -  3.2889 0.99   1331  141 0.1048 0.1572      5.4575      5.8565|
|  4:  3.2889 -  2.9907 0.99   1326  154 0.1180 0.1714       5.443      5.6091|
|  5:  2.9907 -  2.7778 0.99   1318  151 0.1295 0.1726      5.3021      5.5607|
|  6:  2.7778 -  2.6149 0.99   1312  139 0.1153 0.1746       5.177      5.4041|
|  7:  2.6149 -  2.4845 0.99   1303  140 0.1236 0.1633      5.1448      5.3385|
|  8:  2.4845 -  2.3768 0.98   1282  143 0.1113 0.1765      5.0287      5.3599|
|  9:  2.3768 -  2.2856 0.98   1275  154 0.1147 0.1758      5.0235      5.3204|
| 10:  2.2856 -  2.2070 1.00   1317  146 0.1062 0.1653      4.9208      5.1611|
| 11:  2.2070 -  2.1382 0.98   1288  133 0.1089 0.1848      4.9295      5.3142|
| 12:  2.1382 -  2.0772 0.98   1268  143 0.1087 0.1586      4.8495      5.0965|
| 13:  2.0772 -  2.0226 0.98   1276  137 0.1099 0.1737      4.7733       5.021|
| 14:  2.0226 -  1.9734 0.44    573   69 0.1019 0.1591      4.6543      4.9005|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1573 -  4.7115  1410   158  0.94   8.93   0.97     0.95       6785.07|
|  2:  4.7115 -  3.7585  1351   151  0.95   7.73   1.01     1.01       8867.92|
|  3:  3.7585 -  3.2889  1331   141  0.94  11.19   1.03     1.02      10118.47|
|  4:  3.2889 -  2.9907  1326   154  0.92  13.86   1.01     0.99      10390.04|
|  5:  2.9907 -  2.7778  1318   151  0.90  15.86   1.00     0.98       8099.35|
|  6:  2.7778 -  2.6149  1312   139  0.90  15.63   0.99     0.97       6794.44|
|  7:  2.6149 -  2.4845  1303   140  0.91  15.30   1.00     0.97       6041.56|
|  8:  2.4845 -  2.3768  1282   143  0.91  15.01   0.99     0.96       4969.86|
|  9:  2.3768 -  2.2856  1275   154  0.91  15.32   1.00     0.96       4926.05|
| 10:  2.2856 -  2.2070  1317   146  0.91  15.24   1.00     0.97       4185.87|
| 11:  2.2070 -  2.1382  1288   133  0.90  15.83   0.99     0.94       4295.44|
| 12:  2.1382 -  2.0772  1268   143  0.91  15.53   1.01     1.01       3870.47|
| 13:  2.0772 -  2.0226  1276   137  0.90  16.07   1.00     0.98       3316.16|
| 14:  2.0226 -  1.9734   573    69  0.92  14.37   0.98     0.95       2570.31|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2570.31 max =        10390.04 mean =      6271.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.91|
|phase err.(test): min =        0.00 max =           89.19 mean =        13.44|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.900)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.12   17.25    None  None   None       |
|    all(noH): 2823   0      0.00    99.12   17.25    None  None   None       |
|    Sol.    : 438    0      5.47    96.08   41.10    None  None   None       |
|    Mac.    : 2385   0      0.00    99.12   12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.915: 1059   |   5:    49.563 -  59.475:   90        |
|      1:     9.915 -  19.827: 1116   |   6:    59.475 -  69.387:   46        |
|      2:    19.827 -  29.739:  228   |   7:    69.387 -  79.299:   19        |
|      3:    29.739 -  39.651:  125   |   8:    79.299 -  89.211:   14        |
|      4:    39.651 -  49.563:  122   |   9:    89.211 -  99.123:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.515 - 4.656
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 309
   mapped sites are within: 0.735 - 4.656

peak=    6.352 closest distance to " NE2 GLN A  11 " =    1.248
peak=    5.634 closest distance to " NH2 ARG A  56 " =    2.107
peak=    5.373 closest distance to " O   HOH Z 126 " =    2.017
peak=    5.339 closest distance to " CG  PRO A  54 " =    1.223
peak=    5.174 closest distance to " CB  GLN A 223 " =    1.482
peak=    5.069 closest distance to " O   HOH Z 144 " =    1.684
peak=    5.055 closest distance to " O   HOH Z 232 " =    2.274
peak=    4.871 closest distance to " O   HOH Z 369 " =    2.183
peak=    4.849 closest distance to " CB  SER A  63 " =    1.226
peak=    4.821 closest distance to " CB  GLN A 183 " =    1.221
peak=    4.800 closest distance to " C   PRO A 198 " =    1.519
peak=    4.799 closest distance to " O   HOH Z 427 " =    2.744
peak=    4.760 closest distance to " O   HOH Z 298 " =    2.065
peak=    4.702 closest distance to " O   HOH Z 423 " =    1.728
peak=    4.629 closest distance to " CG  PRO A 213 " =    1.241
peak=    4.537 closest distance to " O   HOH Z 287 " =    2.122
peak=    4.474 closest distance to " O   HOH Z  78 " =    1.977
peak=    4.457 closest distance to " CB  ASN A 148 " =    1.386
peak=    4.430 closest distance to " O   HOH Z 133 " =    2.383
peak=    4.425 closest distance to " CB  PRO A  54 " =    0.916
peak=    4.419 closest distance to " O   HOH Z  15 " =    2.165
peak=    4.411 closest distance to " CB  LEU A 228 " =    1.097
peak=    4.391 closest distance to " CB  ARG A 275 " =    0.942
peak=    4.359 closest distance to " O   HOH Z 425 " =    1.354
peak=    4.352 closest distance to " ND2 ASN A 187 " =    1.501
peak=    4.282 closest distance to " CA  TYR A  30 " =    0.976
peak=    4.222 closest distance to " O   HOH Z   1 " =    1.836
peak=    4.209 closest distance to " CB  ARG A  79 " =    1.456
peak=    4.206 closest distance to " O   HOH Z 419 " =    2.074
peak=    4.200 closest distance to " CB  GLU A 128 " =    1.003
peak=    4.145 closest distance to " O   HOH Z  63 " =    1.429
peak=    4.145 closest distance to " O   HOH Z 261 " =    1.716
peak=    4.137 closest distance to " CB  ARG A 190 " =    1.623
peak=    4.133 closest distance to " ND1 HIS A  86 " =    1.719
peak=    4.124 closest distance to " CG  PRO A 198 " =    1.254
peak=    4.122 closest distance to " O   HOH Z 316 " =    3.039
peak=    4.110 closest distance to " CG  TRP A 179 " =    2.228
peak=    4.108 closest distance to " O   HOH Z  61 " =    1.616
peak=    4.107 closest distance to " O   HOH Z 132 " =    2.376
peak=    4.084 closest distance to " O   HOH Z   2 " =    1.487
peak=    4.064 closest distance to " CE  LYS A  76 " =    0.858
peak=    4.059 closest distance to " O   HOH Z 214 " =    2.094
peak=    4.034 closest distance to " CD  ARG A  66 " =    2.163
peak=    4.013 closest distance to " CB  ASN A 187 " =    1.162
peak=    4.011 closest distance to " CB  GLU A 152 " =    1.320
peak=    4.011 closest distance to " CD  ARG A 159 " =    0.770
peak=    3.997 closest distance to " O   HOH Z 217 " =    2.948
peak=    3.985 closest distance to " OD1 ASN A  69 " =    2.684
peak=    3.984 closest distance to " CB  VAL A 265 " =    1.331
peak=    3.984 closest distance to " O   HOH Z 250 " =    1.461
peak=    3.983 closest distance to " O   HOH Z 437 " =    1.633
peak=    3.966 closest distance to " O   HOH Z 158 " =    3.008
peak=    3.940 closest distance to " CG2 VAL A 257 " =    0.929
peak=    3.936 closest distance to " O   HOH Z 180 " =    2.088
peak=    3.915 closest distance to " O   HOH Z 209 " =    2.311
peak=    3.911 closest distance to " O   HOH Z 272 " =    1.833
peak=    3.910 closest distance to " O   HOH Z 193 " =    1.816
peak=    3.882 closest distance to " CB  TRP A 266 " =    1.044
peak=    3.871 closest distance to " O   HOH Z 352 " =    1.824
peak=    3.851 closest distance to " O   HOH Z 368 " =    3.590
peak=    3.848 closest distance to " CG  LEU A 167 " =    1.269
peak=    3.821 closest distance to " O   HOH Z   1 " =    1.785
peak=    3.819 closest distance to " O   HOH Z 193 " =    1.704
peak=    3.812 closest distance to " CB  SER A   3 " =    1.441
peak=    3.810 closest distance to " O   HOH Z 234 " =    3.703
peak=    3.810 closest distance to " CD BLYS A 290 " =    1.026
peak=    3.805 closest distance to " CG1 ILE A  33 " =    1.237
peak=    3.801 closest distance to " O   HOH Z  61 " =    1.497
peak=    3.799 closest distance to " O   HOH Z  40 " =    2.080
peak=    3.796 closest distance to " CG2 THR A 221 " =    0.986
peak=    3.791 closest distance to " CB  SER A 212 " =    1.134
peak=    3.778 closest distance to " O   HOH Z 368 " =    2.015
peak=    3.767 closest distance to " N   PHE A 130 " =    1.241
peak=    3.766 closest distance to " O   HOH Z 213 " =    1.933
peak=    3.762 closest distance to " CB  SER A 216 " =    0.887
peak=    3.756 closest distance to " CA  GLY A 241 " =    3.852
peak=    3.751 closest distance to " O   HOH Z  58 " =    1.588
peak=    3.747 closest distance to " O   HOH Z 371 " =    1.950
peak=    3.746 closest distance to " O   HOH Z 265 " =    2.313
peak=    3.744 closest distance to " O   HOH Z  10 " =    1.823
peak=    3.742 closest distance to " NH1AARG A 145 " =    1.216
peak=    3.739 closest distance to " O   HOH Z 327 " =    1.705
peak=    3.730 closest distance to " O   HOH Z 175 " =    2.134
peak=    3.726 closest distance to " CD2 TRP A 179 " =    1.280
peak=    3.711 closest distance to " O   HOH Z 380 " =    1.602
peak=    3.711 closest distance to " CZ  PHE A 218 " =    1.032
peak=    3.701 closest distance to " CD1 LEU A 300 " =    1.215
peak=    3.699 closest distance to " O   HOH Z 389 " =    1.908
peak=    3.695 closest distance to " O   HOH Z  88 " =    4.001
peak=    3.692 closest distance to " O   HOH Z 289 " =    1.678
peak=    3.679 closest distance to " CB  ARG A 139 " =    1.018
peak=    3.666 closest distance to " N   ALA A   1 " =    2.117
peak=    3.665 closest distance to " CA  ASN A 215 " =    1.213
peak=    3.657 closest distance to " O   HOH Z  21 " =    1.725
peak=    3.654 closest distance to " CB  ALA A  34 " =    1.152
peak=    3.650 closest distance to " O   HOH Z 386 " =    3.137
peak=    3.648 closest distance to " CB  GLU A 277 " =    3.626
peak=    3.647 closest distance to " O   HOH Z 403 " =    1.668
peak=    3.642 closest distance to " CA  THR A 264 " =    0.872
peak=    3.640 closest distance to " O   HOH Z 425 " =    1.953
peak=    3.636 closest distance to " O   HOH Z 417 " =    1.127
peak=    3.636 closest distance to " CB  VAL A 202 " =    1.669
peak=    3.628 closest distance to " O   SER A  87 " =    2.348
peak=    3.627 closest distance to " O   HOH Z 391 " =    2.898
peak=    3.625 closest distance to " OD2 ASP A 286 " =    2.844
peak=    3.625 closest distance to " O   HOH Z 362 " =    2.348
peak=    3.609 closest distance to " O   HOH Z 133 " =    1.668
peak=    3.606 closest distance to " CB  ASP A 124 " =    0.756
peak=    3.602 closest distance to " CG  PRO A  90 " =    1.063
peak=    3.592 closest distance to " CG  PRO A 243 " =    1.095
peak=    3.592 closest distance to " CA  ALA A 233 " =    1.087
peak=    3.589 closest distance to " O   HOH Z 371 " =    2.902
peak=    3.584 closest distance to " CD2 LEU A 255 " =    1.689
peak=    3.575 closest distance to " O   ASN A 209 " =    1.397
peak=    3.563 closest distance to " CA  SER A  87 " =    1.027
peak=    3.562 closest distance to " O   HOH Z 193 " =    2.072
peak=    3.555 closest distance to " O   HOH Z 147 " =    1.740
peak=    3.544 closest distance to " CA  MET A  40 " =    1.169
peak=    3.543 closest distance to " O   HOH Z 135 " =    1.691
peak=    3.542 closest distance to " CB  ASP A 140 " =    0.933
peak=    3.541 closest distance to " O   HOH Z 405 " =    1.290
peak=    3.540 closest distance to " O   HOH Z 365 " =    2.768
peak=    3.537 closest distance to " CB  ASN A 142 " =    0.947
peak=    3.537 closest distance to " NH2AARG A 190 " =    1.873
peak=    3.535 closest distance to " O   HOH Z 258 " =    2.167
peak=    3.534 closest distance to " O   HOH Z 407 " =    2.169
peak=    3.527 closest distance to " CB  ALA A   1 " =    4.656
peak=    3.524 closest distance to " NE2 GLN A  73 " =    3.782
peak=    3.517 closest distance to " O   HOH Z  68 " =    2.100
peak=    3.514 closest distance to " CB  TYR A 169 " =    0.816
peak=    3.510 closest distance to " CA  ILE A 234 " =    1.035
peak=    3.508 closest distance to " O   HOH Z 189 " =    2.442
peak=    3.508 closest distance to " OG  SER A  62 " =    3.017
peak=    3.507 closest distance to " O   HOH Z 128 " =    2.279
peak=    3.502 closest distance to " O   HOH Z   7 " =    1.215
peak=    3.499 closest distance to " O   HOH Z 285 " =    2.661
peak=    3.498 closest distance to " O   HOH Z 236 " =    1.562
peak=    3.496 closest distance to " CB  ASN A  39 " =    0.894
peak=    3.489 closest distance to " CA  ALA A 158 " =    1.138
peak=    3.486 closest distance to " CA  LYS A 290 " =    1.311
peak=    3.483 closest distance to " CB  LYS A 117 " =    1.231
peak=    3.481 closest distance to " O   HOH Z 423 " =    2.229
peak=    3.479 closest distance to " O   HOH Z 116 " =    3.021
peak=    3.477 closest distance to " O   HOH Z 305 " =    3.626
peak=    3.476 closest distance to " CA  TYR A 116 " =    1.332
peak=    3.469 closest distance to " OG BSER A 164 " =    2.331
peak=    3.468 closest distance to " CA  TYR A  30 " =    1.050
peak=    3.466 closest distance to " O   HOH Z 286 " =    2.299
peak=    3.465 closest distance to " O   HOH Z  88 " =    3.227
peak=    3.463 closest distance to " O   MET A 105 " =    1.760
peak=    3.462 closest distance to " NH2BARG A 145 " =    2.099
peak=    3.453 closest distance to " NH2 ARG A 156 " =    1.231
peak=    3.452 closest distance to " O   HOH Z 373 " =    1.481
peak=    3.451 closest distance to " CG1 VAL A 189 " =    1.904
peak=    3.445 closest distance to " O   HOH Z 219 " =    2.112
peak=    3.445 closest distance to " CB  MET A  47 " =    1.102
peak=    3.441 closest distance to " CD  PRO A 243 " =    1.692
peak=    3.441 closest distance to " CG  MET A 113 " =    1.491
peak=    3.439 closest distance to " O   HOH Z 409 " =    2.377
peak=    3.435 closest distance to " O   HOH Z 207 " =    2.176
peak=    3.430 closest distance to " CB  LEU A 143 " =    1.116
peak=    3.427 closest distance to " O   HOH Z 344 " =    3.173
peak=    3.425 closest distance to " O   HOH Z 426 " =    1.853
peak=    3.423 closest distance to " OD1BASN A 224 " =    2.331
peak=    3.420 closest distance to " O   HOH Z   3 " =    1.856
peak=    3.419 closest distance to " O   TYR A 116 " =    1.331
peak=    3.417 closest distance to " O   HOH Z 207 " =    1.734
peak=    3.415 closest distance to " CD  LYS A 166 " =    1.306
peak=    3.413 closest distance to " CB  THR A 157 " =    1.134
peak=    3.411 closest distance to " CB  TRP A 179 " =    1.490
peak=    3.409 closest distance to " CB  ILE A 120 " =    1.398
peak=    3.408 closest distance to " CA  ALA A 291 " =    0.866
peak=    3.406 closest distance to " CB  MET A  40 " =    0.800
peak=    3.406 closest distance to " CA  ALA A  21 " =    1.185
peak=    3.401 closest distance to " CA  ARG A 195 " =    1.250
peak=    3.398 closest distance to " CB  GLN A  88 " =    1.268
peak=    3.392 closest distance to " O   HOH Z 109 " =    2.576
peak=    3.390 closest distance to " N   CYS A 260 " =    0.842
peak=    3.381 closest distance to " O   HOH Z  44 " =    2.846
peak=    3.377 closest distance to " O   HOH Z 280 " =    3.141
peak=    3.372 closest distance to " CB  ASN A 110 " =    1.125
peak=    3.366 closest distance to " O  BHOH Z 338 " =    2.378
peak=    3.366 closest distance to " N   GLN A 278 " =    1.234
peak=    3.365 closest distance to " CB  GLU A 152 " =    0.961
peak=    3.363 closest distance to " CB  TYR A 116 " =    0.868
peak=    3.362 closest distance to " CD2 LEU A 297 " =    0.956
peak=    3.349 closest distance to " O   HOH Z 108 " =    2.258
peak=    3.349 closest distance to " CB  SER A  62 " =    1.171
peak=    3.344 closest distance to " O   HOH Z  53 " =    2.523
peak=    3.342 closest distance to " O   HOH Z 130 " =    3.813
peak=    3.335 closest distance to " O   HOH Z  44 " =    1.590
peak=    3.334 closest distance to " O   HOH Z 115 " =    1.775
peak=    3.332 closest distance to " N   SER A 146 " =    1.709
peak=    3.330 closest distance to " O   HOH Z  20 " =    1.662
peak=    3.329 closest distance to " O   HOH Z 188 " =    1.950
peak=    3.328 closest distance to " O   HOH Z 345 " =    3.473
peak=    3.326 closest distance to " CB  THR A  82 " =    1.404
peak=    3.323 closest distance to " OG  SER A  62 " =    3.043
peak=    3.319 closest distance to " OG  SER A  22 " =    2.886
peak=    3.318 closest distance to " NE2 HIS A 207 " =    1.380
peak=    3.315 closest distance to " CB  SER A 276 " =    1.095
peak=    3.311 closest distance to " O   HOH Z 172 " =    3.047
peak=    3.311 closest distance to " CB  GLU A  46 " =    0.957
peak=    3.308 closest distance to " O   HOH Z 126 " =    1.438
peak=    3.307 closest distance to " CB  TYR A 169 " =    0.864
peak=    3.306 closest distance to " CA  GLY A 267 " =    1.224
peak=    3.305 closest distance to " CB  ALA A 114 " =    1.451
peak=    3.302 closest distance to " CG2 VAL A 197 " =    1.064
peak=    3.301 closest distance to " CB  GLN A  89 " =    1.430
peak=    3.301 closest distance to " CZ  ARG A  14 " =    2.075
peak=    3.300 closest distance to " CD  ARG A 269 " =    0.951
peak=    3.297 closest distance to " OE2 GLU A  53 " =    2.139
peak=    3.297 closest distance to " CB  TRP A 150 " =    1.252
peak=    3.295 closest distance to " O   HOH Z 128 " =    1.967
peak=    3.295 closest distance to " N   TYR A  15 " =    0.766
peak=    3.295 closest distance to " O   HOH Z  64 " =    2.207
peak=    3.291 closest distance to " O   HOH Z 145 " =    2.297
peak=    3.290 closest distance to " N   SER A 134 " =    1.371
peak=    3.272 closest distance to " O   HOH Z 345 " =    1.659
peak=    3.271 closest distance to " O   HOH Z 227 " =    1.721
peak=    3.270 closest distance to " CA  ARG A 102 " =    1.161
peak=    3.269 closest distance to " CB  ALA A 104 " =    0.735
peak=    3.262 closest distance to " O   HOH Z 271 " =    2.508
peak=    3.262 closest distance to " ND2 ASN A 249 " =    0.837
peak=    3.260 closest distance to " NH2 ARG A 219 " =    1.841
peak=    3.260 closest distance to " O   HOH Z  59 " =    1.920
peak=    3.257 closest distance to " O   HOH Z  30 " =    1.628
peak=    3.255 closest distance to " O   ASN A  74 " =    1.585
peak=    3.254 closest distance to " O   HOH Z 119 " =    1.605
peak=    3.252 closest distance to " O   HOH Z 211 " =    2.730
peak=    3.250 closest distance to " CG  GLN A  88 " =    1.067
peak=    3.244 closest distance to " CZ3 TRP A 266 " =    1.144
peak=    3.239 closest distance to " CB  THR A  31 " =    1.756
peak=    3.236 closest distance to " O   HOH Z 132 " =    3.563
peak=    3.235 closest distance to " O   HOH Z 356 " =    2.773
peak=    3.232 closest distance to " CB  HIS A 108 " =    0.791
peak=    3.231 closest distance to " N   ASN A 127 " =    1.318
peak=    3.231 closest distance to " CB  VAL A 265 " =    2.101
peak=    3.230 closest distance to " CB  LEU A 237 " =    0.771
peak=    3.229 closest distance to " O   HOH Z 213 " =    2.895
peak=    3.228 closest distance to " CG1 ILE A 151 " =    1.031
peak=    3.227 closest distance to " O   HOH Z  64 " =    2.098
peak=    3.227 closest distance to " O   THR A 220 " =    1.378
peak=    3.227 closest distance to " CB  GLU A 236 " =    1.204
peak=    3.225 closest distance to " OG BSER A  99 " =    2.209
peak=    3.225 closest distance to " NE AARG A 275 " =    1.327
peak=    3.224 closest distance to " O   HOH Z 402 " =    1.432
peak=    3.222 closest distance to " O   HOH Z 149 " =    2.117
peak=    3.222 closest distance to " CA  ALA A 154 " =    0.997
peak=    3.220 closest distance to " CD1 ILE A  33 " =    1.617
peak=    3.216 closest distance to " ND1 HIS A  81 " =    1.605
peak=    3.216 closest distance to " O   HOH Z 422 " =    2.667
peak=    3.212 closest distance to " CG BARG A 275 " =    1.460
peak=    3.205 closest distance to " O   HOH Z 154 " =    1.983
peak=    3.204 closest distance to " O   HOH Z  97 " =    2.103
peak=    3.202 closest distance to " O   HOH Z 217 " =    1.512
peak=    3.202 closest distance to " O   HOH Z 128 " =    2.040
peak=    3.200 closest distance to " CA  LEU A 101 " =    1.570
peak=    3.199 closest distance to " CA  MET A 105 " =    0.939
peak=    3.199 closest distance to " O   HOH Z  66 " =    2.117
peak=    3.197 closest distance to " O   HOH Z 153 " =    1.618
peak=    3.196 closest distance to " CG1BVAL A  72 " =    1.548
peak=    3.195 closest distance to " CG  GLN A  77 " =    2.359
peak=    3.189 closest distance to " NE2 GLN A  58 " =    3.620
peak=    3.189 closest distance to " O   HOH Z  59 " =    1.629
peak=    3.189 closest distance to " CA  ALA A 160 " =    0.897
peak=    3.188 closest distance to " O   HOH Z 302 " =    1.746
peak=    3.187 closest distance to " CD  GLN A 240 " =    1.666
peak=    3.183 closest distance to " O   HOH Z 325 " =    3.862
peak=    3.174 closest distance to " O   HOH Z  43 " =    2.155
peak=    3.169 closest distance to " CD1 ILE A 263 " =    1.305
peak=    3.167 closest distance to " CD  ARG A 219 " =    1.137
peak=    3.166 closest distance to " N   ASN A  39 " =    1.361
peak=    3.166 closest distance to " O   HOH Z 386 " =    2.776
peak=    3.163 closest distance to " CG  ARG A 159 " =    0.808
peak=    3.161 closest distance to " CA  TYR A 186 " =    1.582
peak=    3.154 closest distance to " O   HOH Z 148 " =    3.381
peak=    3.150 closest distance to " CG  GLU A 277 " =    2.027
peak=    3.149 closest distance to " CB  SER A 212 " =    1.205
peak=    3.145 closest distance to " O   HOH Z  85 " =    2.119
peak=    3.144 closest distance to " CD1 ILE A 106 " =    0.770
peak=    3.144 closest distance to " O   HOH Z 281 " =    1.757
peak=    3.140 closest distance to " O   HOH Z 286 " =    2.241
peak=    3.137 closest distance to " CB  ARG A 138 " =    0.942
peak=    3.131 closest distance to " O   HOH Z 273 " =    2.889
peak=    3.131 closest distance to " CA  ALA A 299 " =    0.897
peak=    3.127 closest distance to " O   HOH Z 238 " =    3.661
peak=    3.125 closest distance to " CB  VAL A 250 " =    1.042
peak=    3.123 closest distance to " O   ALA A 158 " =    1.370
peak=    3.123 closest distance to " CA  GLU A  46 " =    0.890
peak=    3.123 closest distance to " N   ARG A 156 " =    1.319
peak=    3.121 closest distance to " O   HOH Z 406 " =    1.633
peak=    3.120 closest distance to " OG BSER A 134 " =    3.223
peak=    3.119 closest distance to " CA  ASN A 217 " =    1.140
peak=    3.115 closest distance to " CB  GLU A 152 " =    1.369
peak=    3.112 closest distance to " O   ALA A 291 " =    1.467
peak=    3.104 closest distance to " O   HOH Z 183 " =    1.391
peak=    3.101 closest distance to " O   HOH Z 329 " =    3.857
peak=    3.101 closest distance to " O   HOH Z 227 " =    1.975
peak=    3.090 closest distance to " NH1BARG A 145 " =    1.251
peak=    3.081 closest distance to " CG BARG A 102 " =    1.881
peak=    3.057 closest distance to " CD2 TYR A 186 " =    1.024
peak=    3.052 closest distance to " O   HOH Z 303 " =    1.873
peak=    3.038 closest distance to " CG  LYS A  76 " =    0.995
peak=    3.031 closest distance to " OD1 ASN A 217 " =    1.549
peak=    3.002 closest distance to " O   HOH Z  88 " =    2.333

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.705 - 5.846
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 215
   mapped sites are within: 0.705 - 5.846

peak=   -4.745 closest distance to " CB  PRO A 243 " =    2.565
peak=   -4.722 closest distance to " O   HOH Z 377 " =    1.940
peak=   -4.593 closest distance to " CD  ARG A 156 " =    2.072
peak=   -4.417 closest distance to " O   HOH Z 266 " =    5.002
peak=   -4.388 closest distance to " CD  ARG A  14 " =    3.436
peak=   -4.242 closest distance to " CG  GLN A 223 " =    2.025
peak=   -4.187 closest distance to " O   HOH Z 231 " =    2.076
peak=   -4.143 closest distance to " O   PRO A 198 " =    1.307
peak=   -4.122 closest distance to " O   HOH Z 389 " =    1.934
peak=   -4.042 closest distance to " O   HOH Z 435 " =    2.976
peak=   -4.012 closest distance to " O   HOH Z  38 " =    1.470
peak=   -4.001 closest distance to " O   VAL A  67 " =    2.649
peak=   -3.997 closest distance to " OG BSER A 134 " =    1.270
peak=   -3.977 closest distance to " O   HOH Z 407 " =    3.254
peak=   -3.950 closest distance to " CG1 VAL A 112 " =    2.848
peak=   -3.910 closest distance to " CZ3 TRP A 179 " =    1.181
peak=   -3.907 closest distance to " O   HOH Z 185 " =    2.072
peak=   -3.899 closest distance to " CB  ALA A  43 " =    2.478
peak=   -3.896 closest distance to " O   HOH Z 152 " =    5.130
peak=   -3.890 closest distance to " ND2 ASN A  45 " =    1.925
peak=   -3.844 closest distance to " O   HOH Z 290 " =    1.255
peak=   -3.844 closest distance to " N   ALA A  43 " =    2.531
peak=   -3.843 closest distance to " CB  TRP A  85 " =    2.442
peak=   -3.826 closest distance to " O   HOH Z 351 " =    1.597
peak=   -3.785 closest distance to " CB  ASP A  27 " =    2.462
peak=   -3.784 closest distance to " O   HOH Z 313 " =    1.784
peak=   -3.776 closest distance to " CE2 PHE A 218 " =    2.454
peak=   -3.763 closest distance to " O   HOH Z 316 " =    1.906
peak=   -3.760 closest distance to " CA  GLY A  98 " =    1.876
peak=   -3.743 closest distance to " O   HOH Z  52 " =    1.226
peak=   -3.740 closest distance to " C   HIS A 108 " =    1.185
peak=   -3.730 closest distance to " O   HOH Z 372 " =    2.479
peak=   -3.698 closest distance to " O   SER A 135 " =    1.433
peak=   -3.695 closest distance to " O   HOH Z 198 " =    2.035
peak=   -3.689 closest distance to " ND2 ASN A  45 " =    1.198
peak=   -3.668 closest distance to " CD2 LEU A 143 " =    2.602
peak=   -3.656 closest distance to " CA  GLY A 203 " =    2.271
peak=   -3.654 closest distance to " C   ALA A 158 " =    1.526
peak=   -3.647 closest distance to " CB  CYS A 254 " =    2.163
peak=   -3.645 closest distance to " O   PRO A 163 " =    1.970
peak=   -3.636 closest distance to " ND2 ASN A 249 " =    2.082
peak=   -3.628 closest distance to " CD1 LEU A 101 " =    2.290
peak=   -3.621 closest distance to " CB  PRO A  54 " =    2.424
peak=   -3.617 closest distance to " O   PRO A 198 " =    1.346
peak=   -3.617 closest distance to " CZ  PHE A  59 " =    1.568
peak=   -3.606 closest distance to " CG  PHE A 283 " =    2.639
peak=   -3.604 closest distance to " NE  ARG A  36 " =    1.964
peak=   -3.602 closest distance to " O   VAL A 189 " =    2.484
peak=   -3.600 closest distance to " CG  MET A 105 " =    0.965
peak=   -3.595 closest distance to " CE2 TYR A  30 " =    2.693
peak=   -3.592 closest distance to " CB  ALA A 291 " =    2.174
peak=   -3.586 closest distance to " CE  MET A 105 " =    2.335
peak=   -3.579 closest distance to " O   PRO A 243 " =    2.401
peak=   -3.572 closest distance to " N   ASP A 171 " =    2.395
peak=   -3.569 closest distance to " O   PHE A 218 " =    1.485
peak=   -3.568 closest distance to " OD1 ASP A 171 " =    1.588
peak=   -3.562 closest distance to " CZ BARG A 275 " =    1.683
peak=   -3.550 closest distance to " OD1 ASN A 148 " =    1.580
peak=   -3.542 closest distance to " CD1 PHE A  59 " =    1.937
peak=   -3.529 closest distance to " OG  SER A  87 " =    1.330
peak=   -3.526 closest distance to " C   LEU A 222 " =    0.709
peak=   -3.510 closest distance to " CG2 THR A  18 " =    2.832
peak=   -3.508 closest distance to " CG1 VAL A 197 " =    2.223
peak=   -3.506 closest distance to " N   THR A 157 " =    1.523
peak=   -3.496 closest distance to " CG  PRO A 163 " =    2.459
peak=   -3.491 closest distance to " NH2AARG A 275 " =    5.482
peak=   -3.490 closest distance to " CB  ASN A  39 " =    2.274
peak=   -3.489 closest distance to " C   ASN A 285 " =    2.438
peak=   -3.484 closest distance to " O   ILE A 109 " =    2.558
peak=   -3.481 closest distance to " CD2 LEU A 237 " =    2.876
peak=   -3.477 closest distance to " O   HOH Z 359 " =    3.326
peak=   -3.477 closest distance to " CG2 THR A 178 " =    2.236
peak=   -3.475 closest distance to " CA  GLY A 241 " =    2.228
peak=   -3.474 closest distance to " OG BSER A 134 " =    1.619
peak=   -3.474 closest distance to " CB  PHE A 192 " =    1.862
peak=   -3.467 closest distance to " C   ASN A 187 " =    1.820
peak=   -3.463 closest distance to " O   HOH Z 111 " =    1.940
peak=   -3.461 closest distance to " OD1 ASP A 191 " =    1.608
peak=   -3.460 closest distance to " O   HOH Z 409 " =    5.846
peak=   -3.448 closest distance to " O   HOH Z 351 " =    1.694
peak=   -3.445 closest distance to " O   HOH Z 198 " =    1.633
peak=   -3.441 closest distance to " CG  ARG A 269 " =    2.622
peak=   -3.435 closest distance to " O   HOH Z 102 " =    1.635
peak=   -3.429 closest distance to " O   HOH Z  13 " =    1.783
peak=   -3.426 closest distance to " O   HOH Z 292 " =    1.585
peak=   -3.426 closest distance to " O   HOH Z 253 " =    3.956
peak=   -3.422 closest distance to " O   HOH Z 281 " =    2.653
peak=   -3.413 closest distance to " O   GLY A 211 " =    1.323
peak=   -3.411 closest distance to " CB  ALA A 248 " =    2.375
peak=   -3.406 closest distance to " OD1 ASN A 187 " =    1.597
peak=   -3.405 closest distance to " CB  ALA A 131 " =    1.998
peak=   -3.402 closest distance to " CB  ALA A   9 " =    2.424
peak=   -3.397 closest distance to " NH1AARG A 275 " =    1.827
peak=   -3.389 closest distance to " NH2 ARG A  79 " =    1.938
peak=   -3.386 closest distance to " CB  ALA A 248 " =    2.031
peak=   -3.381 closest distance to " O   HOH Z  43 " =    1.679
peak=   -3.379 closest distance to " O   HOH Z 348 " =    1.824
peak=   -3.378 closest distance to " CB  ALA A 291 " =    2.031
peak=   -3.375 closest distance to " O   HOH Z 211 " =    1.494
peak=   -3.374 closest distance to " O   HOH Z 140 " =    1.562
peak=   -3.373 closest distance to " O   HOH Z 298 " =    2.451
peak=   -3.372 closest distance to " CD  LYS A 289 " =    2.334
peak=   -3.372 closest distance to " O   HOH Z 114 " =    3.235
peak=   -3.371 closest distance to " O   HOH Z  73 " =    2.039
peak=   -3.363 closest distance to " CD2 PHE A 225 " =    1.132
peak=   -3.361 closest distance to " O   HOH Z 131 " =    4.164
peak=   -3.358 closest distance to " O   ARG A 145 " =    1.509
peak=   -3.358 closest distance to " C   GLY A  13 " =    1.024
peak=   -3.356 closest distance to " O   HOH Z  11 " =    1.937
peak=   -3.354 closest distance to " O   HOH Z  65 " =    1.267
peak=   -3.349 closest distance to " CB  PRO A 163 " =    2.465
peak=   -3.344 closest distance to " O   GLY A  17 " =    1.192
peak=   -3.342 closest distance to " O   HOH Z 191 " =    5.480
peak=   -3.331 closest distance to " CG1 VAL A 250 " =    2.622
peak=   -3.331 closest distance to " CZ  TYR A 169 " =    1.569
peak=   -3.326 closest distance to " CB  TYR A  15 " =    2.190
peak=   -3.323 closest distance to " OXT GLY A 302 " =    3.075
peak=   -3.323 closest distance to " O   SER A  22 " =    2.570
peak=   -3.322 closest distance to " O   HOH Z 298 " =    1.218
peak=   -3.317 closest distance to " C   LEU A 143 " =    1.394
peak=   -3.316 closest distance to " CG  TRP A 266 " =    1.703
peak=   -3.315 closest distance to " OH  TYR A 247 " =    1.756
peak=   -3.309 closest distance to " O   ALA A  10 " =    1.647
peak=   -3.304 closest distance to " O   HOH Z   1 " =    1.551
peak=   -3.304 closest distance to " O   HOH Z  90 " =    2.718
peak=   -3.296 closest distance to " OG  SER A  97 " =    2.156
peak=   -3.296 closest distance to " O   HOH Z 337 " =    1.502
peak=   -3.294 closest distance to " O   HOH Z 345 " =    2.215
peak=   -3.294 closest distance to " CD1 LEU A 228 " =    2.294
peak=   -3.292 closest distance to " O   VAL A  67 " =    2.803
peak=   -3.291 closest distance to " O   HOH Z  10 " =    1.454
peak=   -3.290 closest distance to " O   HOH Z  51 " =    1.160
peak=   -3.289 closest distance to " O   HOH Z 218 " =    3.538
peak=   -3.285 closest distance to " CD  ARG A 139 " =    1.543
peak=   -3.282 closest distance to " O   HOH Z 353 " =    2.122
peak=   -3.281 closest distance to " O   HOH Z 266 " =    4.761
peak=   -3.276 closest distance to " O   ALA A 180 " =    1.238
peak=   -3.275 closest distance to " O   HOH Z 384 " =    2.734
peak=   -3.273 closest distance to " O   HOH Z 426 " =    1.647
peak=   -3.272 closest distance to " N   SER A 276 " =    1.241
peak=   -3.271 closest distance to " CG  GLN A  88 " =    0.853
peak=   -3.270 closest distance to " CE1 TYR A 169 " =    2.536
peak=   -3.262 closest distance to " OG  SER A 245 " =    1.315
peak=   -3.262 closest distance to " O   SER A 210 " =    1.950
peak=   -3.260 closest distance to " CD2 PHE A  61 " =    1.987
peak=   -3.259 closest distance to " O   HOH Z 174 " =    2.630
peak=   -3.258 closest distance to " O   HOH Z 111 " =    1.220
peak=   -3.257 closest distance to " CG  ASN A  39 " =    1.697
peak=   -3.256 closest distance to " CE3 TRP A 123 " =    1.328
peak=   -3.256 closest distance to " CG  ASP A 231 " =    0.749
peak=   -3.251 closest distance to " O   HOH Z 168 " =    1.820
peak=   -3.250 closest distance to " O   HOH Z 231 " =    1.234
peak=   -3.249 closest distance to " OE1 GLN A  58 " =    3.086
peak=   -3.249 closest distance to " CD2 TYR A 293 " =    1.982
peak=   -3.247 closest distance to " ND2 ASN A 187 " =    1.494
peak=   -3.240 closest distance to " CE2 PHE A  61 " =    2.654
peak=   -3.239 closest distance to " CE3 TRP A 274 " =    2.414
peak=   -3.235 closest distance to " O   HOH Z 357 " =    1.995
peak=   -3.233 closest distance to " ND2BASN A 224 " =    1.686
peak=   -3.231 closest distance to " CA  GLY A 133 " =    2.047
peak=   -3.218 closest distance to " O   SER A  62 " =    2.208
peak=   -3.215 closest distance to " OD2 ASP A 171 " =    2.084
peak=   -3.213 closest distance to " CG2 VAL A 189 " =    1.903
peak=   -3.210 closest distance to " O   HOH Z 166 " =    1.263
peak=   -3.207 closest distance to " C   ILE A 234 " =    1.368
peak=   -3.204 closest distance to " O   VAL A 197 " =    1.555
peak=   -3.201 closest distance to " O   HOH Z 352 " =    2.158
peak=   -3.201 closest distance to " ND2 ASN A 285 " =    2.091
peak=   -3.201 closest distance to " O   LEU A 101 " =    2.455
peak=   -3.199 closest distance to " O   HOH Z 275 " =    1.778
peak=   -3.197 closest distance to " N   GLN A  58 " =    1.683
peak=   -3.195 closest distance to " OD2 ASP A 171 " =    1.749
peak=   -3.186 closest distance to " OXT GLY A 302 " =    3.359
peak=   -3.185 closest distance to " N   ALA A 248 " =    1.514
peak=   -3.182 closest distance to " O   HOH Z 309 " =    2.445
peak=   -3.176 closest distance to " O   HOH Z 114 " =    0.705
peak=   -3.176 closest distance to " CD  GLN A  58 " =    1.037
peak=   -3.172 closest distance to " CE  MET A  93 " =    1.192
peak=   -3.168 closest distance to " O   ASN A 301 " =    1.436
peak=   -3.165 closest distance to " O   ALA A 161 " =    1.624
peak=   -3.165 closest distance to " CB  ASP A 132 " =    2.363
peak=   -3.163 closest distance to " CA  GLY A 241 " =    3.103
peak=   -3.157 closest distance to " CD1 LEU A 297 " =    2.574
peak=   -3.155 closest distance to " OE1 GLN A  88 " =    1.238
peak=   -3.155 closest distance to " O   HOH Z  98 " =    2.287
peak=   -3.149 closest distance to " O   HOH Z 394 " =    1.421
peak=   -3.138 closest distance to " ND2 ASN A  60 " =    1.399
peak=   -3.137 closest distance to " NH1 ARG A 195 " =    2.736
peak=   -3.130 closest distance to " SD BMET A  47 " =    0.959
peak=   -3.127 closest distance to " O   HOH Z  90 " =    1.755
peak=   -3.120 closest distance to " CB  PHE A 208 " =    2.237
peak=   -3.113 closest distance to " O   ILE A  49 " =    1.715
peak=   -3.109 closest distance to " ND2BASN A 224 " =    1.716
peak=   -3.105 closest distance to " O   VAL A 174 " =    2.243
peak=   -3.103 closest distance to " CE  LYS A  76 " =    2.814
peak=   -3.103 closest distance to " O   HOH Z 165 " =    2.198
peak=   -3.102 closest distance to " O   HOH Z 252 " =    4.240
peak=   -3.102 closest distance to " SD  MET A 188 " =    2.279
peak=   -3.098 closest distance to " NE2 GLN A 278 " =    1.757
peak=   -3.095 closest distance to " O   VAL A 125 " =    2.291
peak=   -3.092 closest distance to " O   HOH Z 174 " =    2.903
peak=   -3.090 closest distance to " CG  GLU A 277 " =    1.304
peak=   -3.082 closest distance to " O   HOH Z 318 " =    1.846
peak=   -3.077 closest distance to " CD2 PHE A 192 " =    2.284
peak=   -3.075 closest distance to " CD  PRO A 198 " =    1.802
peak=   -3.071 closest distance to " C   LYS A  76 " =    1.618
peak=   -3.067 closest distance to " O   ASP A 162 " =    2.238
peak=   -3.066 closest distance to " O   HOH Z 324 " =    2.167
peak=   -3.058 closest distance to " C   ALA A 114 " =    2.328
peak=   -3.057 closest distance to " CG2 ILE A  20 " =    2.847
peak=   -3.055 closest distance to " O   GLY A  80 " =    2.405
peak=   -3.031 closest distance to " O   HOH Z 263 " =    5.167
peak=   -3.030 closest distance to " O   HOH Z 119 " =    4.325
peak=   -3.024 closest distance to " O   HOH Z 377 " =    0.946
peak=   -3.020 closest distance to " O   HOH Z 350 " =    1.897

================= 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    :  0.3818 0.3788   6.172133e+00   6.163753e+00
   1_bss:  0.3704 0.3699   6.157979e+00   6.147190e+00
   1_xyz:  0.2250 0.2562   5.728569e+00   5.812948e+00
   1_adp:  0.2059 0.2666   5.680312e+00   5.853214e+00
   1_occ:  0.2057 0.2661   5.678995e+00   5.852106e+00
   2_bss:  0.2035 0.2622   5.670371e+00   5.840280e+00
   2_xyz:  0.1545 0.2037   5.421123e+00   5.629231e+00
   2_adp:  0.1461 0.1897   5.367275e+00   5.566669e+00
   2_occ:  0.1461 0.1899   5.367127e+00   5.567064e+00
   3_bss:  0.1459 0.1894   5.364110e+00   5.563826e+00
   3_xyz:  0.1263 0.1689   5.237112e+00   5.450515e+00
   3_adp:  0.1216 0.1679   5.213028e+00   5.440746e+00
   3_occ:  0.1215 0.1680   5.213163e+00   5.441226e+00
   4_bss:  0.1215 0.1678   5.212377e+00   5.440724e+00
   4_xyz:  0.1143 0.1617   5.164249e+00   5.407997e+00
   4_adp:  0.1134 0.1602   5.156554e+00   5.400422e+00
   4_occ:  0.1133 0.1603   5.156492e+00   5.400532e+00
   5_bss:  0.1137 0.1601   5.157713e+00   5.399899e+00
   5_xyz:  0.1086 0.1586   5.131793e+00   5.390256e+00
   5_adp:  0.1082 0.1574   5.127188e+00   5.384587e+00
   5_occ:  0.1081 0.1574   5.127275e+00   5.384847e+00
   5_bss:  0.1081 0.1574   5.127393e+00   5.384911e+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:  0.341  50.001  -0.146   1.811  -1.823   0.000  -0.000  -0.000
   1_xyz:  0.341  50.001  -0.146   1.811  -1.823   0.000  -0.000  -0.000
   1_adp:  0.341  50.001  -0.146   1.811  -1.823   0.000  -0.000  -0.000
   1_occ:  0.341  50.001  -0.146   1.811  -1.823   0.000  -0.000  -0.000
   2_bss:  0.342  62.521  -1.733  -1.400  -1.656  -0.000  -0.000  -0.000
   2_xyz:  0.342  62.521  -1.733  -1.400  -1.656  -0.000  -0.000  -0.000
   2_adp:  0.342  62.521  -1.733  -1.400  -1.656  -0.000  -0.000  -0.000
   2_occ:  0.342  62.521  -1.733  -1.400  -1.656  -0.000  -0.000  -0.000
   3_bss:  0.330  55.326  -2.208  -2.408  -1.483  -0.000  -0.000  -0.000
   3_xyz:  0.330  55.326  -2.208  -2.408  -1.483  -0.000  -0.000  -0.000
   3_adp:  0.330  55.326  -2.208  -2.408  -1.483  -0.000  -0.000  -0.000
   3_occ:  0.330  55.326  -2.208  -2.408  -1.483  -0.000  -0.000  -0.000
   4_bss:  0.321  56.887  -2.232  -2.614  -1.438  -0.000  -0.000  -0.000
   4_xyz:  0.321  56.887  -2.232  -2.614  -1.438  -0.000  -0.000  -0.000
   4_adp:  0.321  56.887  -2.232  -2.614  -1.438  -0.000  -0.000  -0.000
   4_occ:  0.321  56.887  -2.232  -2.614  -1.438  -0.000  -0.000  -0.000
   5_bss:  0.321  56.887  -2.123  -2.579  -1.278  -0.000  -0.000  -0.000
   5_xyz:  0.321  56.887  -2.123  -2.579  -1.278  -0.000  -0.000  -0.000
   5_adp:  0.321  56.887  -2.123  -2.579  -1.278  -0.000  -0.000  -0.000
   5_occ:  0.321  56.887  -2.123  -2.579  -1.278  -0.000  -0.000  -0.000
   5_bss:  0.322  56.890  -1.959  -2.462  -1.086  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.709 0.6118  0.7951    44455.123
   1_bss:  41.911 0.6199  0.8070    42035.319
   1_xyz:  24.699 0.8163  0.9940    16589.356
   1_adp:  26.311 0.7981  0.9798    18027.381
   1_occ:  26.297 0.7982  0.9794    17967.274
   2_bss:  25.759 0.8038  0.9343    17393.189
   2_xyz:  19.503 0.8660  0.9784    10433.475
   2_adp:  17.762 0.8833  0.9858     9264.758
   2_occ:  17.781 0.8831  0.9855     9272.226
   3_bss:  17.697 0.8837  0.9703     9182.109
   3_xyz:  15.337 0.9039  0.9801     7240.222
   3_adp:  15.105 0.9061  0.9755     7080.265
   3_occ:  15.114 0.9060  0.9754     7087.463
   4_bss:  15.092 0.9062  0.9734     7077.382
   4_xyz:  14.340 0.9123  0.9765     6544.950
   4_adp:  14.146 0.9140  0.9720     6444.520
   4_occ:  14.147 0.9140  0.9719     6443.327
   5_bss:  14.160 0.9138  0.9755     6443.463
   5_xyz:  13.973 0.9153  0.9763     6334.215
   5_adp:  13.858 0.9163  0.9710     6268.073
   5_occ:  13.861 0.9162  0.9709     6268.928
   5_bss:  13.866 0.9162  0.9765     6271.436
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6465e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6465e-01
   1_xyz:   1.171  0.009  0.083 15.337  0.006  4.111   8.1898e-02
   1_adp:   1.171  0.009  0.083 15.337  0.006  4.111   8.1898e-02
   1_occ:   1.171  0.009  0.083 15.337  0.006  4.111   8.1898e-02
   2_bss:   1.171  0.009  0.083 15.337  0.006  4.111   8.1898e-02
   2_xyz:   0.944  0.006  0.068 13.907  0.004  4.120   5.2080e-02
   2_adp:   0.944  0.006  0.068 13.907  0.004  4.120   5.2080e-02
   2_occ:   0.944  0.006  0.068 13.907  0.004  4.120   5.2080e-02
   3_bss:   0.944  0.006  0.068 13.907  0.004  4.120   5.2080e-02
   3_xyz:   0.899  0.006  0.067 14.164  0.003  4.111   4.8954e-02
   3_adp:   0.899  0.006  0.067 14.164  0.003  4.111   4.8954e-02
   3_occ:   0.899  0.006  0.067 14.164  0.003  4.111   4.8954e-02
   4_bss:   0.899  0.006  0.067 14.164  0.003  4.111   4.8954e-02
   4_xyz:   0.955  0.007  0.072 14.245  0.004  4.113   5.4209e-02
   4_adp:   0.955  0.007  0.072 14.245  0.004  4.113   5.4209e-02
   4_occ:   0.955  0.007  0.072 14.245  0.004  4.113   5.4209e-02
   5_bss:   0.955  0.007  0.072 14.245  0.004  4.113   5.4209e-02
   5_xyz:   1.048  0.009  0.079 14.634  0.004  4.116   6.6495e-02
   5_adp:   1.048  0.009  0.079 14.634  0.004  4.116   6.6495e-02
   5_occ:   1.048  0.009  0.079 14.634  0.004  4.116   6.6495e-02
   5_bss:   1.048  0.009  0.079 14.634  0.004  4.116   6.6495e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4088e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4088e-01
   1_xyz:   8.578  0.072  0.324 86.559  0.050  2.185   1.1127e-01
   1_adp:   8.578  0.072  0.324 86.559  0.050  2.185   1.1127e-01
   1_occ:   8.578  0.072  0.324 86.559  0.050  2.185   1.1127e-01
   2_bss:   8.578  0.072  0.324 86.559  0.050  2.185   1.1127e-01
   2_xyz:   8.199  0.056  0.237 83.250  0.027  2.397   8.3714e-02
   2_adp:   8.199  0.056  0.237 83.250  0.027  2.397   8.3714e-02
   2_occ:   8.199  0.056  0.237 83.250  0.027  2.397   8.3714e-02
   3_bss:   8.199  0.056  0.237 83.250  0.027  2.397   8.3714e-02
   3_xyz:   7.543  0.032  0.213 85.848  0.027  2.360   3.4156e-02
   3_adp:   7.543  0.032  0.213 85.848  0.027  2.360   3.4156e-02
   3_occ:   7.543  0.032  0.213 85.848  0.027  2.360   3.4156e-02
   4_bss:   7.543  0.032  0.213 85.848  0.027  2.360   3.4156e-02
   4_xyz:   7.947  0.046  0.216 83.322  0.030  2.321   4.0035e-02
   4_adp:   7.947  0.046  0.216 83.322  0.030  2.321   4.0035e-02
   4_occ:   7.947  0.046  0.216 83.322  0.030  2.321   4.0035e-02
   5_bss:   7.947  0.046  0.216 83.322  0.030  2.321   4.0035e-02
   5_xyz:   7.981  0.043  0.261 84.980  0.029  2.291   5.5760e-02
   5_adp:   7.981  0.043  0.261 84.980  0.029  2.291   5.5760e-02
   5_occ:   7.981  0.043  0.261 84.980  0.029  2.291   5.5760e-02
   5_bss:   7.981  0.043  0.261 84.980  0.029  2.291   5.5760e-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:  88.28   0.00  17.69  72.90   0.00  13.34  88.28   4.89  41.32
   1_occ:  88.28   0.00  17.69  72.90   0.00  13.34  88.28   4.89  41.32
   2_bss:  88.28   0.00  17.69  72.90   0.00  13.34  88.28   4.89  41.32
   2_xyz:  88.28   0.00  17.69  72.90   0.00  13.34  88.28   4.89  41.32
   2_adp:  83.01   1.67  17.10  73.16   1.67  13.07  83.01   6.58  39.09
   2_occ:  83.01   1.67  17.10  73.16   1.67  13.07  83.01   6.58  39.09
   3_bss:  83.01   1.67  17.10  73.16   1.67  13.07  83.01   6.58  39.09
   3_xyz:  83.01   1.67  17.10  73.16   1.67  13.07  83.01   6.58  39.09
   3_adp:  93.42   0.00  17.84  93.42   0.00  13.19  92.60   5.18  43.13
   3_occ:  93.42   0.00  17.84  93.42   0.00  13.19  92.60   5.18  43.13
   4_bss:  93.42   0.00  17.84  93.42   0.00  13.19  92.60   5.18  43.13
   4_xyz:  93.42   0.00  17.84  93.42   0.00  13.19  92.60   5.18  43.13
   4_adp:  97.10   0.00  17.60  97.10   0.00  13.06  94.52   3.81  42.34
   4_occ:  97.10   0.00  17.60  97.10   0.00  13.06  94.52   3.81  42.34
   5_bss:  97.10   0.00  17.60  97.10   0.00  13.06  94.52   3.81  42.34
   5_xyz:  97.10   0.00  17.60  97.10   0.00  13.06  94.52   3.81  42.34
   5_adp:  99.12   0.00  17.25  99.12   0.00  12.87  96.08   5.47  41.10
   5_occ:  99.12   0.00  17.25  99.12   0.00  12.87  96.08   5.47  41.10
   5_bss:  99.12   0.00  17.25  99.12   0.00  12.87  96.08   5.47  41.10
------------------------------------------------------------------------
 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:    1.392    0.038    0.387
   1_adp:    1.392    0.038    0.387
   1_occ:    1.392    0.038    0.387
   2_bss:    1.392    0.038    0.387
   2_xyz:    1.134    0.023    0.449
   2_adp:    1.134    0.023    0.449
   2_occ:    1.134    0.023    0.449
   3_bss:    1.134    0.023    0.449
   3_xyz:    1.037    0.037    0.506
   3_adp:    1.037    0.037    0.506
   3_occ:    1.037    0.037    0.506
   4_bss:    1.037    0.037    0.506
   4_xyz:    1.077    0.034    0.525
   4_adp:    1.077    0.034    0.525
   4_occ:    1.077    0.034    0.525
   5_bss:    1.077    0.034    0.525
   5_xyz:    1.201    0.040    0.543
   5_adp:    1.201    0.040    0.543
   5_occ:    1.201    0.040    0.543
   5_bss:    1.201    0.040    0.543
------------------------------------------------------------------------

CPU time actual refinement: 351.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_995/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_995/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_995/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_995/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_995/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.44 
  Macro-tasks:
    bulk solvent and scale       = 36.07  
    individual site refinement   = 158.58 
    weights calculation          = 29.95  
    collect and process          = 6.69   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 231.40 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 115.25 
    alpha_beta                      = 8.40   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 126.39 
    fmodel                         = 6.64   
    r_factors                      = 0.16   
    phase_errors                   = 11.03  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 271.18 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.836 micro seconds
Total CPU time: 6.08 minutes
from_scatterers_fft:    663 calls, 114.89 s
gradients_fft:          608 calls, 111.48 s

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

# Date 2008-01-16 Time 06:10:49 PST -0800 (1200492649.17 s)
Start R-work = 0.3818, R-free = 0.3788 (no bulk solvent and anisotropic scale)
Final R-work = 0.1316, R-free = 0.1764 (no bulk solvent and anisotropic scale)

Start R-work = 0.3704, R-free = 0.3699
Final R-work = 0.1081, R-free = 0.1574