# Date 2008-01-16 Time 05:58:33 PST -0800 (1200491913.17 s)
#phil __OFF__

Command line arguments: "../955.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5253
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 955

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.8686, 88.1178, 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: 3.24, 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: (70.9525, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 2.0206
Completeness in resolution range: 0.968267
Completeness with d_max=infinity: 0.965213

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1841
                             d_min =   2.0206

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 2.0206
Completeness in resolution range: 0.968267
Completeness with d_max=infinity: 0.965213

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1845 -  4.3229 [2129/2156]  1915   214  10.1%
  bin  2:  4.3229 -  3.4444 [2037/2053]  1834   203  10.0%
  bin  3:  3.4444 -  3.0129 [2025/2044]  1823   202  10.0%
  bin  4:  3.0129 -  2.7392 [1989/2019]  1787   202  10.2%
  bin  5:  2.7392 -  2.5438 [1986/2005]  1789   197   9.9%
  bin  6:  2.5438 -  2.3944 [1977/2002]  1782   195   9.9%
  bin  7:  2.3944 -  2.2749 [1966/1999]  1772   194   9.9%
  bin  8:  2.2749 -  2.1762 [1941/1972]  1743   198  10.2%
  bin  9:  2.1762 -  2.0926 [1946/1988]  1751   195  10.0%
  bin 10:  2.0926 -  2.0206 [1593/1993]  1434   159  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_955/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 13
        2.40 -     3.03: 2038
        3.03 -     3.65: 4521
        3.65 -     4.28: 8836
        4.28 -     4.90: 12233
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.780 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.916 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.043 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.043 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27636 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_955/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_955/model_refine_001.geo

CPU time processing inputs: 9.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.8686 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4591   r_free= 0.4511   ksol= 0.00   Bsol= 0.00   scale= 0.877    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.267228                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1845 -  4.8212 0.99   1383  153 0.3566 0.3530      6.5178      6.4668|
|  2:  4.8212 -  3.8472 0.99   1318  150 0.3932 0.4220      6.8097      6.8722|
|  3:  3.8472 -  3.3670 0.99   1314  144 0.4329 0.3875      6.6795       6.593|
|  4:  3.3670 -  3.0619 0.99   1293  139 0.4452 0.4601      6.5261      6.4575|
|  5:  3.0619 -  2.8439 0.99   1282  143 0.4849 0.4243      6.3661      6.3511|
|  6:  2.8439 -  2.6772 0.99   1277  145 0.4790 0.5008      6.2631      6.2016|
|  7:  2.6772 -  2.5438 0.99   1281  144 0.4972 0.4545      6.2395      6.1641|
|  8:  2.5438 -  2.4335 0.98   1278  139 0.4993 0.4535      6.1746      6.1508|
|  9:  2.4335 -  2.3402 0.98   1248  140 0.5075 0.5140      6.1048      6.1674|
| 10:  2.3402 -  2.2597 0.99   1267  139 0.5161 0.4714       6.112      6.0774|
| 11:  2.2597 -  2.1893 0.99   1265  143 0.5168 0.5267      6.0381      6.0951|
| 12:  2.1893 -  2.1269 0.97   1245  134 0.5175 0.5295      5.9752      6.0221|
| 13:  2.1269 -  2.0710 0.99   1280  143 0.5205 0.5363      5.8958      5.8621|
| 14:  2.0710 -  2.0206 0.72    899  103 0.5053 0.5367      5.8475      5.7697|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1845 -  4.8212  1383   153  0.73  31.77   0.82     0.76      62769.93|
|  2:  4.8212 -  3.8472  1318   150  0.73  32.22   0.89     0.81      92680.31|
|  3:  3.8472 -  3.3670  1314   144  0.65  39.93   0.89     0.79      97608.78|
|  4:  3.3670 -  3.0619  1293   139  0.57  46.50   0.88     0.70      89076.40|
|  5:  3.0619 -  2.8439  1282   143  0.49  53.02   0.88     0.64      69727.04|
|  6:  2.8439 -  2.6772  1277   145  0.46  55.41   0.87     0.59      62847.83|
|  7:  2.6772 -  2.5438  1281   144  0.43  57.31   0.90     0.57      57366.52|
|  8:  2.5438 -  2.4335  1278   139  0.41  59.09   0.88     0.56      55135.54|
|  9:  2.4335 -  2.3402  1248   140  0.38  61.16   0.89     0.55      52339.49|
| 10:  2.3402 -  2.2597  1267   139  0.39  60.63   0.91     0.55      47732.87|
| 11:  2.2597 -  2.1893  1265   143  0.36  63.29   0.90     0.52      45841.11|
| 12:  2.1893 -  2.1269  1245   134  0.33  65.59   0.89     0.48      43356.79|
| 13:  2.1269 -  2.0710  1280   143  0.28  69.06   0.88     0.41      39195.41|
| 14:  2.0710 -  2.0206   899   103  0.27  70.16   0.92     0.35      31829.55|
|alpha:            min =        0.35 max =            0.81 mean =         0.60|
|beta:             min =    31829.55 max =        97608.78 mean =     61403.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.06|
|phase err.(test): min =        0.00 max =           89.64 mean =        54.44|
|-----------------------------------------------------------------------------|

============================== 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 = 8.290457              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.047   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.304187              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.790   (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 |  1.780 -  2.092:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.092 -  2.404:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.404 -  2.716:      134 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.716 -  3.028:     1904 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.028 -  3.340:     1826 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.340 -  3.652:     2695 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.652 -  3.964:     4588 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.964 -  4.276:     4248 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.276 -  4.588:     5540 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.588 -  4.900:     6693 |
|-----------------------------------------------------------------------------|
|-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 |   4.115    4.900  1.780 |       0.177 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4591   r_free= 0.4511   ksol= 0.00   Bsol= 0.00   scale= 0.877    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.267228                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4508   r_free= 0.4431   ksol= 0.28   Bsol= 55.07   scale= 0.922   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,3.27,2.68,0.00,0.00,0.00); trace/3= 1.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.259980                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.045710              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.659   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.129847              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.437   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4508      final r-factor (work) = 0.3445          |
| start r-factor (free) = 0.4431      final r-factor (free) = 0.3698          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2107 = 7.05 * 0.50 * 6.2578 + 1.00 * 0.1654                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7091 = 7.05 * 0.50 * 6.1283 + 1.00 * 0.1200                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3445      final r-factor (work) = 0.3138          |
| start r-factor (free) = 0.3698      final r-factor (free) = 0.3832          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9300 = 1.13 * 1.00 * 6.1283 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8181 = 1.13 * 1.00 * 6.0167 + 1.00 * 0.0202                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.80  18.66    None  None   None       |
|    all(noH): 2823   0      0.00    117.80  18.66    None  None   None       |
|    Sol.    : 438    0      0.00    117.80  40.05    None  None   None       |
|    Mac.    : 2385   0      0.00    87.42   14.74    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 -  11.780: 1182   |   5:    58.899 -  70.678:   63        |
|      1:    11.780 -  23.560:  910   |   6:    70.678 -  82.458:   26        |
|      2:    23.560 -  35.339:  353   |   7:    82.458 -  94.238:    7        |
|      3:    35.339 -  47.119:  174   |   8:    94.238 - 106.018:    1        |
|      4:    47.119 -  58.899:  106   |   9:   106.018 - 117.797:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3138 r_free = 0.3832             target_work(ml) = 6.024         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3134 r_free = 0.3828             target_work(ml) = 6.024         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3134   r_free= 0.3828   ksol= 0.28   Bsol= 55.07   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,3.27,2.68,0.00,0.00,0.00); trace/3= 1.01                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.023922                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3124   r_free= 0.3816   ksol= 0.31   Bsol= 68.68   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,1.87,1.49,0.00,0.00,0.00); trace/3= 0.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.024547                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.929814             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.080   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.433122              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.386  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3124      final r-factor (work) = 0.2260          |
| start r-factor (free) = 0.3816      final r-factor (free) = 0.2751          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.0036 = 10.93 * 0.50 * 6.0172 + 1.00 * 0.1200                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.4094 = 10.93 * 0.50 * 5.9107 + 1.00 * 0.1082                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2260      final r-factor (work) = 0.2017          |
| start r-factor (free) = 0.2751      final r-factor (free) = 0.2535          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5803 = 0.43 * 1.00 * 5.9107 + 1.00 * 0.0203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5056 = 0.43 * 1.00 * 5.6773 + 1.00 * 0.0467                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.09  17.99    None  None   None       |
|    all(noH): 2823   0      0.00    117.09  17.99    None  None   None       |
|    Sol.    : 438    0      3.10    117.09  41.48    None  None   None       |
|    Mac.    : 2385   0      0.00    86.11   13.67    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 -  11.709: 1338   |   5:    58.547 -  70.256:   56        |
|      1:    11.709 -  23.419:  812   |   6:    70.256 -  81.965:   22        |
|      2:    23.419 -  35.128:  289   |   7:    81.965 -  93.674:    8        |
|      3:    35.128 -  46.837:  187   |   8:    93.674 - 105.384:    1        |
|      4:    46.837 -  58.547:  109   |   9:   105.384 - 117.093:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2017 r_free = 0.2535             target_work(ml) = 5.643         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2012 r_free = 0.2537             target_work(ml) = 5.643         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2012   r_free= 0.2537   ksol= 0.31   Bsol= 68.68   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,1.87,1.49,0.00,0.00,0.00); trace/3= 0.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.642879                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2007   r_free= 0.2531   ksol= 0.33   Bsol= 81.44   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,0.19,0.40,0.00,0.00,0.00); trace/3= -0.30                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.641712                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.639790              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.788  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.610945              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.051   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2007      final r-factor (work) = 0.1629          |
| start r-factor (free) = 0.2531      final r-factor (free) = 0.2062          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4423 = 3.64 * 0.50 * 5.6784 + 1.00 * 0.1082                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1735 = 3.64 * 0.50 * 5.5529 + 1.00 * 0.0678                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1629      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.2062      final r-factor (free) = 0.1978          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.5162 = 2.61 * 1.00 * 5.5529 + 1.00 * 0.0179                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.1294 = 2.61 * 1.00 * 5.4055 + 1.00 * 0.0160                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.22  18.18    None  None   None       |
|    all(noH): 2823   0      0.00    116.22  18.18    None  None   None       |
|    Sol.    : 438    0      4.47    116.22  46.73    None  None   None       |
|    Mac.    : 2385   0      0.00    105.32  12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.622: 1447   |   5:    58.110 -  69.732:   94        |
|      1:    11.622 -  23.244:  786   |   6:    69.732 -  81.354:   58        |
|      2:    23.244 -  34.866:  199   |   7:    81.354 -  92.976:   18        |
|      3:    34.866 -  46.488:  123   |   8:    92.976 - 104.599:    6        |
|      4:    46.488 -  58.110:   88   |   9:   104.599 - 116.221:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1475 r_free = 0.1978             target_work(ml) = 5.385         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1475 r_free = 0.1977             target_work(ml) = 5.384         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1475   r_free= 0.1977   ksol= 0.33   Bsol= 81.44   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,0.19,0.40,0.00,0.00,0.00); trace/3= -0.30                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.384483                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1477   r_free= 0.1980   ksol= 0.34   Bsol= 89.66   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-0.28,0.39,-0.00,0.00,0.00); trace/3= -0.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.385111                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.207437              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.191  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.443901              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.588  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1477      final r-factor (work) = 0.1299          |
| start r-factor (free) = 0.1980      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7378 = 3.21 * 0.50 * 5.4060 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6233 = 3.21 * 0.50 * 5.3297 + 1.00 * 0.0760                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1299      final r-factor (work) = 0.1267          |
| start r-factor (free) = 0.1810      final r-factor (free) = 0.1751          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3817 = 0.44 * 1.00 * 5.3297 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3523 = 0.44 * 1.00 * 5.2698 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.10  17.33    None  None   None       |
|    all(noH): 2823   0      0.00    113.10  17.33    None  None   None       |
|    Sol.    : 438    0      4.81    113.10  44.60    None  None   None       |
|    Mac.    : 2385   0      0.00    103.63  12.32    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 -  11.310: 1459   |   5:    56.548 -  67.857:   82        |
|      1:    11.310 -  22.619:  816   |   6:    67.857 -  79.167:   45        |
|      2:    22.619 -  33.929:  178   |   7:    79.167 -  90.477:   21        |
|      3:    33.929 -  45.238:  104   |   8:    90.477 - 101.786:    5        |
|      4:    45.238 -  56.548:  108   |   9:   101.786 - 113.096:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1267 r_free = 0.1751             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1266 r_free = 0.1749             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1749   ksol= 0.34   Bsol= 89.66   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-0.28,0.39,-0.00,0.00,0.00); trace/3= -0.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248734                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1748   ksol= 0.33   Bsol= 80.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.44,0.52,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248364                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.668283              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.866  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.336195              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.591  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1265      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1748      final r-factor (free) = 0.1737          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4716 = 1.67 * 0.50 * 5.2696 + 1.00 * 0.0760                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4387 = 1.67 * 0.50 * 5.2510 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1256          |
| start r-factor (free) = 0.1737      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0293 = 1.34 * 1.00 * 5.2510 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0207 = 1.34 * 1.00 * 5.2439 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.77  17.05    None  None   None       |
|    all(noH): 2823   0      0.00    116.77  17.05    None  None   None       |
|    Sol.    : 438    0      4.70    116.77  44.20    None  None   None       |
|    Mac.    : 2385   0      0.00    107.30  12.07    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:     0.000 -  11.677: 1553   |   5:    58.387 -  70.065:   68        |
|      1:    11.677 -  23.355:  744   |   6:    70.065 -  81.742:   49        |
|      2:    23.355 -  35.032:  169   |   7:    81.742 -  93.419:   13        |
|      3:    35.032 -  46.710:  116   |   8:    93.419 - 105.097:    6        |
|      4:    46.710 -  58.387:  101   |   9:   105.097 - 116.774:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1256 r_free = 0.1750             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1255 r_free = 0.1750             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1750   ksol= 0.33   Bsol= 80.00   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.44,0.52,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.248808                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1845 -  4.8212 0.99   1383  153 0.1049 0.1369      5.4405      5.5806|
|  2:  4.8212 -  3.8472 0.99   1318  150 0.0873 0.1058      5.4592      5.6311|
|  3:  3.8472 -  3.3670 0.99   1314  144 0.1123 0.1578      5.5281      5.8929|
|  4:  3.3670 -  3.0619 0.99   1293  139 0.1333 0.1833      5.5445      5.7149|
|  5:  3.0619 -  2.8439 0.99   1282  143 0.1562 0.1987      5.4767      5.6587|
|  6:  2.8439 -  2.6772 0.99   1277  145 0.1424 0.2287      5.3525      5.6237|
|  7:  2.6772 -  2.5438 0.99   1281  144 0.1463 0.1833      5.2971      5.4479|
|  8:  2.5438 -  2.4335 0.98   1278  139 0.1387 0.1908      5.2178       5.449|
|  9:  2.4335 -  2.3402 0.98   1248  140 0.1349 0.2039      5.1458       5.392|
| 10:  2.3402 -  2.2597 0.99   1267  139 0.1303 0.1852      5.1057      5.3078|
| 11:  2.2597 -  2.1893 0.99   1265  143 0.1343 0.1977      5.0628      5.3325|
| 12:  2.1893 -  2.1269 0.97   1245  134 0.1293 0.1958      4.9942      5.3368|
| 13:  2.1269 -  2.0710 0.99   1280  143 0.1257 0.1853         4.9      5.1221|
| 14:  2.0710 -  2.0206 0.72    899  103 0.1144 0.1993      4.7705      5.0792|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1845 -  4.8212  1383   153  0.93  10.00   0.95     0.93       8235.99|
|  2:  4.8212 -  3.8472  1318   150  0.95   8.36   1.00     0.98       9468.89|
|  3:  3.8472 -  3.3670  1314   144  0.93  11.73   1.01     1.01      11229.57|
|  4:  3.3670 -  3.0619  1293   139  0.91  15.13   1.00     0.98      12244.37|
|  5:  3.0619 -  2.8439  1282   143  0.88  18.64   1.00     0.98      11197.77|
|  6:  2.8439 -  2.6772  1277   145  0.88  18.35   0.98     0.95       9277.03|
|  7:  2.6772 -  2.5438  1281   144  0.88  18.09   0.99     0.96       8048.58|
|  8:  2.5438 -  2.4335  1278   139  0.89  17.59   0.98     0.94       6929.03|
|  9:  2.4335 -  2.3402  1248   140  0.89  17.79   0.99     0.94       6266.74|
| 10:  2.3402 -  2.2597  1267   139  0.88  17.89   0.98     0.92       5665.91|
| 11:  2.2597 -  2.1893  1265   143  0.88  18.29   0.97     0.92       5379.22|
| 12:  2.1893 -  2.1269  1245   134  0.89  17.84   0.99     0.97       5025.73|
| 13:  2.1269 -  2.0710  1280   143  0.89  17.58   0.97     0.94       4135.73|
| 14:  2.0710 -  2.0206   899   103  0.90  16.40   0.94     0.89       3143.01|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     3143.01 max =        12244.37 mean =      7714.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.90|
|phase err.(test): min =        0.00 max =           89.91 mean =        15.28|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1257   r_free= 0.1748   ksol= 0.33   Bsol= 80.00   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,-0.50,0.54,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.247625                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1257   r_free= 0.1748   ksol= 0.33   Bsol= 80.00   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,-0.50,0.54,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.247625                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1845 -  4.8212 0.99   1383  153 0.1052 0.1335      5.4281      5.5537|
|  2:  4.8212 -  3.8472 0.99   1318  150 0.0880 0.1058      5.4571      5.6253|
|  3:  3.8472 -  3.3670 0.99   1314  144 0.1126 0.1570      5.5281      5.8906|
|  4:  3.3670 -  3.0619 0.99   1293  139 0.1333 0.1835      5.5451      5.7169|
|  5:  3.0619 -  2.8439 0.99   1282  143 0.1562 0.1989      5.4772      5.6579|
|  6:  2.8439 -  2.6772 0.99   1277  145 0.1424 0.2281       5.352       5.622|
|  7:  2.6772 -  2.5438 0.99   1281  144 0.1464 0.1835      5.2966      5.4477|
|  8:  2.5438 -  2.4335 0.98   1278  139 0.1387 0.1907      5.2175      5.4486|
|  9:  2.4335 -  2.3402 0.98   1248  140 0.1349 0.2040      5.1457      5.3925|
| 10:  2.3402 -  2.2597 0.99   1267  139 0.1302 0.1855      5.1057      5.3084|
| 11:  2.2597 -  2.1893 0.99   1265  143 0.1342 0.1976      5.0627      5.3322|
| 12:  2.1893 -  2.1269 0.97   1245  134 0.1293 0.1957      4.9942      5.3366|
| 13:  2.1269 -  2.0710 0.99   1280  143 0.1257 0.1854      4.8999      5.1223|
| 14:  2.0710 -  2.0206 0.72    899  103 0.1144 0.1992      4.7701      5.0787|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1845 -  4.8212  1383   153  0.93   9.76   0.95     0.93       7786.03|
|  2:  4.8212 -  3.8472  1318   150  0.95   8.23   1.00     0.98       9206.95|
|  3:  3.8472 -  3.3670  1314   144  0.93  11.66   1.01     1.01      11141.34|
|  4:  3.3670 -  3.0619  1293   139  0.91  15.13   1.00     0.98      12228.32|
|  5:  3.0619 -  2.8439  1282   143  0.88  18.63   1.00     0.98      11188.98|
|  6:  2.8439 -  2.6772  1277   145  0.88  18.34   0.98     0.95       9258.63|
|  7:  2.6772 -  2.5438  1281   144  0.88  18.06   0.99     0.96       8034.63|
|  8:  2.5438 -  2.4335  1278   139  0.89  17.59   0.98     0.94       6925.29|
|  9:  2.4335 -  2.3402  1248   140  0.89  17.79   0.99     0.94       6269.72|
| 10:  2.3402 -  2.2597  1267   139  0.88  17.90   0.98     0.92       5667.66|
| 11:  2.2597 -  2.1893  1265   143  0.88  18.29   0.97     0.92       5380.22|
| 12:  2.1893 -  2.1269  1245   134  0.89  17.84   0.99     0.97       5026.31|
| 13:  2.1269 -  2.0710  1280   143  0.89  17.57   0.97     0.94       4133.82|
| 14:  2.0710 -  2.0206   899   103  0.90  16.39   0.94     0.89       3139.62|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     3139.62 max =        12228.32 mean =      7648.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.86|
|phase err.(test): min =        0.00 max =           89.92 mean =        15.26|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.78  17.06    None  None   None       |
|    all(noH): 2823   0      0.00    116.78  17.06    None  None   None       |
|    Sol.    : 438    0      4.70    116.78  44.20    None  None   None       |
|    Mac.    : 2385   0      0.00    107.30  12.07    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:     0.003 -  11.680: 1553   |   5:    58.390 -  70.067:   68        |
|      1:    11.680 -  23.358:  744   |   6:    70.067 -  81.745:   49        |
|      2:    23.358 -  35.035:  169   |   7:    81.745 -  93.422:   13        |
|      3:    35.035 -  46.713:  116   |   8:    93.422 - 105.100:    6        |
|      4:    46.713 -  58.390:  101   |   9:   105.100 - 116.777:    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)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.512 - 4.832
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 336
   mapped sites are within: 0.724 - 4.832

peak=    5.974 closest distance to " O   HOH Z 210 " =    1.296
peak=    5.711 closest distance to " CB  GLN A 223 " =    1.420
peak=    5.231 closest distance to " O   HOH Z 113 " =    2.162
peak=    5.035 closest distance to " CG  PRO A  54 " =    1.421
peak=    5.013 closest distance to " O   HOH Z  49 " =    1.338
peak=    4.943 closest distance to " CG  PRO A 198 " =    1.194
peak=    4.862 closest distance to " CZ  PHE A 218 " =    1.129
peak=    4.834 closest distance to " CB  GLN A 183 " =    1.250
peak=    4.741 closest distance to " CB  SER A  63 " =    1.251
peak=    4.496 closest distance to " CB  ARG A 190 " =    1.655
peak=    4.464 closest distance to " CD  ARG A 269 " =    0.996
peak=    4.419 closest distance to " CD  LYS A 166 " =    1.460
peak=    4.408 closest distance to " O   HOH Z 433 " =    1.521
peak=    4.399 closest distance to " O   HOH Z 412 " =    3.662
peak=    4.370 closest distance to " CA  ALA A  51 " =    0.991
peak=    4.352 closest distance to " O   HOH Z 369 " =    2.165
peak=    4.349 closest distance to " CA  TYR A  30 " =    0.959
peak=    4.335 closest distance to " O   HOH Z  43 " =    2.011
peak=    4.332 closest distance to " CZ  PHE A  38 " =    1.246
peak=    4.293 closest distance to " CA  ARG A 195 " =    1.182
peak=    4.281 closest distance to " O   HOH Z 425 " =    1.525
peak=    4.276 closest distance to " CB  VAL A 202 " =    1.541
peak=    4.266 closest distance to " O   HOH Z  54 " =    1.187
peak=    4.262 closest distance to " CB  ARG A 275 " =    0.933
peak=    4.256 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.251 closest distance to " O   HOH Z 189 " =    2.953
peak=    4.243 closest distance to " O   HOH Z 134 " =    1.601
peak=    4.238 closest distance to " CB  GLU A 128 " =    1.084
peak=    4.235 closest distance to " O   PRO A 198 " =    1.534
peak=    4.226 closest distance to " O   HOH Z 234 " =    3.968
peak=    4.212 closest distance to " O   HOH Z 403 " =    1.691
peak=    4.177 closest distance to " CD  ARG A  66 " =    2.524
peak=    4.176 closest distance to " CZ3 TRP A 266 " =    1.171
peak=    4.167 closest distance to " CG2BVAL A  41 " =    0.930
peak=    4.136 closest distance to " CG  PRO A 213 " =    1.220
peak=    4.134 closest distance to " CB  TRP A 266 " =    1.088
peak=    4.122 closest distance to " O   HOH Z 214 " =    1.344
peak=    4.119 closest distance to " O   HOH Z 368 " =    2.259
peak=    4.072 closest distance to " CG  PRO A 243 " =    1.103
peak=    4.047 closest distance to " O   HOH Z 422 " =    0.923
peak=    4.035 closest distance to " CB  TYR A 169 " =    0.785
peak=    4.029 closest distance to " CB  ASN A  39 " =    0.921
peak=    4.009 closest distance to " CD2 TRP A 179 " =    1.331
peak=    4.002 closest distance to " CA  ALA A 160 " =    0.980
peak=    3.997 closest distance to " CB  PRO A  54 " =    0.915
peak=    3.977 closest distance to " O   HOH Z 402 " =    1.541
peak=    3.972 closest distance to " O   TYR A 116 " =    1.379
peak=    3.954 closest distance to " OE1 GLN A  88 " =    0.961
peak=    3.929 closest distance to " O   THR A 220 " =    1.107
peak=    3.929 closest distance to " CB  ARG A  79 " =    1.252
peak=    3.924 closest distance to " CG1 ILE A  33 " =    1.232
peak=    3.921 closest distance to " CB  ASP A 140 " =    0.940
peak=    3.916 closest distance to " O   HOH Z 176 " =    1.685
peak=    3.896 closest distance to " CA  ARG A  36 " =    1.112
peak=    3.894 closest distance to " O   HOH Z 394 " =    1.511
peak=    3.891 closest distance to " O   HOH Z 298 " =    1.988
peak=    3.884 closest distance to " O   ASN A  74 " =    1.532
peak=    3.880 closest distance to " O   HOH Z  48 " =    1.815
peak=    3.857 closest distance to " N   SER A 164 " =    1.025
peak=    3.854 closest distance to " O   ALA A 165 " =    1.438
peak=    3.847 closest distance to " O   HOH Z 248 " =    1.608
peak=    3.835 closest distance to " CA  GLU A 152 " =    0.907
peak=    3.834 closest distance to " CB  SER A  62 " =    0.876
peak=    3.833 closest distance to " CG1 VAL A 153 " =    1.088
peak=    3.830 closest distance to " O   HOH Z  19 " =    1.942
peak=    3.819 closest distance to " CG  ARG A 138 " =    1.265
peak=    3.809 closest distance to " CB  ASP A 124 " =    0.764
peak=    3.807 closest distance to " CB  GLU A 277 " =    3.852
peak=    3.801 closest distance to " CA  SER A  87 " =    1.105
peak=    3.800 closest distance to " CB  TRP A 179 " =    1.388
peak=    3.794 closest distance to " O   HOH Z  44 " =    2.081
peak=    3.782 closest distance to " OE1 GLN A  11 " =    2.138
peak=    3.771 closest distance to " O   HOH Z 406 " =    1.660
peak=    3.770 closest distance to " CD1 LEU A  96 " =    0.794
peak=    3.766 closest distance to " O   HOH Z 133 " =    2.880
peak=    3.755 closest distance to " O   HOH Z  15 " =    2.246
peak=    3.754 closest distance to " O   HOH Z 346 " =    1.625
peak=    3.743 closest distance to " CA  ALA A 100 " =    1.029
peak=    3.743 closest distance to " CG  LEU A 167 " =    1.099
peak=    3.742 closest distance to " CE1 HIS A 115 " =    1.085
peak=    3.732 closest distance to " O   HOH Z 131 " =    2.480
peak=    3.728 closest distance to " CB  GLU A 152 " =    1.175
peak=    3.723 closest distance to " CB  ASN A 148 " =    1.439
peak=    3.713 closest distance to " O   HOH Z  40 " =    1.685
peak=    3.713 closest distance to " ND2 ASN A 187 " =    1.422
peak=    3.712 closest distance to " O   HOH Z 423 " =    1.829
peak=    3.707 closest distance to " CD  ARG A 159 " =    0.835
peak=    3.706 closest distance to " O   HOH Z 285 " =    2.636
peak=    3.702 closest distance to " NE2 GLN A  11 " =    1.134
peak=    3.700 closest distance to " O   HOH Z 261 " =    1.913
peak=    3.694 closest distance to " O   HOH Z 361 " =    3.421
peak=    3.692 closest distance to " CA  ALA A 295 " =    1.105
peak=    3.674 closest distance to " CG  GLN A  11 " =    1.392
peak=    3.674 closest distance to " O   THR A 251 " =    1.158
peak=    3.668 closest distance to " CA  ASP A 162 " =    1.102
peak=    3.667 closest distance to " CB  LEU A 228 " =    1.092
peak=    3.662 closest distance to " O   HOH Z  78 " =    2.366
peak=    3.660 closest distance to " CB  GLU A  37 " =    0.858
peak=    3.660 closest distance to " NH1AARG A 145 " =    1.268
peak=    3.660 closest distance to " O   HOH Z 126 " =    1.616
peak=    3.657 closest distance to " CA  PRO A  54 " =    1.395
peak=    3.656 closest distance to " CG2 THR A 221 " =    1.159
peak=    3.646 closest distance to " O   HOH Z 271 " =    2.583
peak=    3.646 closest distance to " O   HOH Z  21 " =    1.843
peak=    3.642 closest distance to " NH2 ARG A 156 " =    1.126
peak=    3.637 closest distance to " N   HIS A 108 " =    1.887
peak=    3.630 closest distance to " CA  GLU A  46 " =    0.939
peak=    3.628 closest distance to " CD1 LEU A 300 " =    1.136
peak=    3.616 closest distance to " O   HOH Z 193 " =    1.811
peak=    3.615 closest distance to " CA  VAL A 125 " =    1.349
peak=    3.614 closest distance to " CG AARG A 275 " =    1.215
peak=    3.607 closest distance to " O   HOH Z 325 " =    2.273
peak=    3.607 closest distance to " CB  ASN A 285 " =    0.855
peak=    3.605 closest distance to " CZ  PHE A 192 " =    1.010
peak=    3.604 closest distance to " OG  SER A 245 " =    1.643
peak=    3.595 closest distance to " O   HOH Z 287 " =    1.761
peak=    3.580 closest distance to " CA  ALA A 154 " =    1.018
peak=    3.576 closest distance to " O   HOH Z 417 " =    3.002
peak=    3.570 closest distance to " CA  GLY A 196 " =    0.999
peak=    3.570 closest distance to " CB  ASN A 142 " =    0.958
peak=    3.568 closest distance to " O   HOH Z  80 " =    1.984
peak=    3.567 closest distance to " CB  PRO A 243 " =    1.470
peak=    3.564 closest distance to " CB  ALA A 291 " =    1.098
peak=    3.556 closest distance to " O   HOH Z 427 " =    3.160
peak=    3.549 closest distance to " NE2 GLN A  77 " =    3.391
peak=    3.547 closest distance to " CA  ARG A 156 " =    1.123
peak=    3.539 closest distance to " N   ILE A  33 " =    0.928
peak=    3.539 closest distance to " CB  GLN A  89 " =    1.252
peak=    3.536 closest distance to " CB  ALA A  71 " =    1.396
peak=    3.533 closest distance to " CA  ILE A 106 " =    0.864
peak=    3.531 closest distance to " CB  VAL A 265 " =    1.268
peak=    3.518 closest distance to " CG  GLU A  37 " =    0.933
peak=    3.517 closest distance to " O   SER A  87 " =    2.398
peak=    3.511 closest distance to " O   HOH Z 214 " =    2.244
peak=    3.509 closest distance to " O   HOH Z 357 " =    2.147
peak=    3.508 closest distance to " O   HOH Z  78 " =    1.706
peak=    3.502 closest distance to " O   HOH Z 316 " =    3.116
peak=    3.495 closest distance to " N   THR A  52 " =    1.150
peak=    3.492 closest distance to " CB  ALA A 248 " =    1.350
peak=    3.490 closest distance to " CG2 VAL A 257 " =    0.856
peak=    3.489 closest distance to " CA  ASP A 124 " =    0.879
peak=    3.487 closest distance to " N   CYS A 260 " =    0.794
peak=    3.486 closest distance to " O   HOH Z 265 " =    2.107
peak=    3.485 closest distance to " CB  ALA A  43 " =    0.919
peak=    3.484 closest distance to " OG BSER A 164 " =    2.294
peak=    3.481 closest distance to " N   ASN A  39 " =    1.307
peak=    3.480 closest distance to " O   HOH Z 196 " =    1.261
peak=    3.476 closest distance to " CB  LEU A  83 " =    0.862
peak=    3.471 closest distance to " CA  MET A 105 " =    1.171
peak=    3.470 closest distance to " O   HOH Z 303 " =    2.441
peak=    3.467 closest distance to " O   HOH Z 291 " =    1.448
peak=    3.465 closest distance to " O   HOH Z 156 " =    2.697
peak=    3.464 closest distance to " O   ASP A 124 " =    1.186
peak=    3.462 closest distance to " O   HOH Z 251 " =    1.610
peak=    3.461 closest distance to " O   HOH Z 126 " =    2.385
peak=    3.461 closest distance to " CA  ARG A 102 " =    1.177
peak=    3.453 closest distance to " CB  GLN A  88 " =    1.199
peak=    3.452 closest distance to " O   HOH Z 435 " =    2.992
peak=    3.452 closest distance to " CB  MET A  40 " =    0.795
peak=    3.448 closest distance to " O   HOH Z 132 " =    2.870
peak=    3.445 closest distance to " CE  LYS A  76 " =    0.852
peak=    3.443 closest distance to " O   HOH Z 199 " =    1.708
peak=    3.439 closest distance to " CA  ARG A 139 " =    1.391
peak=    3.439 closest distance to " ND2 ASN A 249 " =    0.861
peak=    3.438 closest distance to " O   HOH Z 359 " =    1.638
peak=    3.437 closest distance to " OD1 ASN A 217 " =    1.585
peak=    3.437 closest distance to " O   HOH Z 124 " =    1.970
peak=    3.434 closest distance to " O   HOH Z 383 " =    2.215
peak=    3.423 closest distance to " O   HOH Z 353 " =    2.656
peak=    3.418 closest distance to " O   HOH Z 389 " =    2.010
peak=    3.412 closest distance to " CD  ARG A 195 " =    1.010
peak=    3.410 closest distance to " O   HOH Z 139 " =    4.832
peak=    3.410 closest distance to " O   HOH Z 294 " =    1.567
peak=    3.408 closest distance to " CB  SER A 210 " =    0.923
peak=    3.408 closest distance to " CB  MET A  47 " =    0.901
peak=    3.407 closest distance to " O   HOH Z 171 " =    3.977
peak=    3.404 closest distance to " CD2 LEU A 297 " =    0.974
peak=    3.400 closest distance to " CD2 LEU A 255 " =    1.730
peak=    3.392 closest distance to " O   HOH Z 258 " =    2.042
peak=    3.389 closest distance to " OG1 THR A  82 " =    0.959
peak=    3.389 closest distance to " CB  ASN A 187 " =    1.160
peak=    3.389 closest distance to " CG2 VAL A 197 " =    1.220
peak=    3.388 closest distance to " O   HOH Z  32 " =    1.776
peak=    3.386 closest distance to " CB  PRO A  90 " =    1.241
peak=    3.385 closest distance to " CB  PRO A 198 " =    1.095
peak=    3.383 closest distance to " CE1 TYR A 186 " =    1.320
peak=    3.382 closest distance to " N   ARG A 156 " =    1.545
peak=    3.380 closest distance to " O   HOH Z 193 " =    2.272
peak=    3.380 closest distance to " OD1 ASN A  69 " =    2.482
peak=    3.377 closest distance to " CA  ALA A  21 " =    1.378
peak=    3.376 closest distance to " O   ALA A 158 " =    1.200
peak=    3.375 closest distance to " O   HOH Z 377 " =    1.184
peak=    3.368 closest distance to " O   HOH Z  48 " =    1.332
peak=    3.365 closest distance to " CB  ALA A 114 " =    0.724
peak=    3.361 closest distance to " O   HOH Z 180 " =    2.135
peak=    3.354 closest distance to " O   HOH Z 280 " =    3.023
peak=    3.352 closest distance to " CB  SER A 141 " =    1.077
peak=    3.349 closest distance to " CE1 HIS A 108 " =    1.125
peak=    3.346 closest distance to " O   ASP A 200 " =    1.689
peak=    3.344 closest distance to " O   HOH Z 174 " =    2.291
peak=    3.340 closest distance to " O   HOH Z 128 " =    2.309
peak=    3.339 closest distance to " O   HOH Z  30 " =    1.161
peak=    3.335 closest distance to " N   GLY A 111 " =    1.353
peak=    3.333 closest distance to " CZ3 TRP A  85 " =    0.846
peak=    3.330 closest distance to " NZ  LYS A 117 " =    2.999
peak=    3.326 closest distance to " O   HOH Z  88 " =    1.781
peak=    3.322 closest distance to " CG2AVAL A 121 " =    2.164
peak=    3.319 closest distance to " NH1 ARG A 269 " =    0.734
peak=    3.316 closest distance to " CA  SER A  12 " =    1.539
peak=    3.315 closest distance to " C   GLY A  80 " =    1.060
peak=    3.315 closest distance to " O   HOH Z 298 " =    2.413
peak=    3.313 closest distance to " CA  TYR A 116 " =    1.314
peak=    3.309 closest distance to " CA  ALA A 233 " =    1.646
peak=    3.308 closest distance to " NH2BARG A 145 " =    2.171
peak=    3.306 closest distance to " CA  ASP A 191 " =    0.888
peak=    3.306 closest distance to " CA  ASN A 217 " =    1.327
peak=    3.305 closest distance to " O   HOH Z 279 " =    2.253
peak=    3.302 closest distance to " OG  SER A  28 " =    1.637
peak=    3.300 closest distance to " O   HOH Z 141 " =    1.718
peak=    3.298 closest distance to " CB  SER A   3 " =    1.604
peak=    3.297 closest distance to " CA  MET A 188 " =    1.043
peak=    3.296 closest distance to " O   HOH Z 148 " =    3.474
peak=    3.296 closest distance to " O   ASP A 191 " =    1.447
peak=    3.295 closest distance to " O   HOH Z 361 " =    2.669
peak=    3.294 closest distance to " CG2 THR A 220 " =    0.805
peak=    3.292 closest distance to " O   HOH Z 327 " =    1.796
peak=    3.291 closest distance to " CB  SER A 273 " =    0.897
peak=    3.291 closest distance to " CB  ALA A  34 " =    0.907
peak=    3.290 closest distance to " N   TYR A 247 " =    1.137
peak=    3.290 closest distance to " CB  THR A  52 " =    0.733
peak=    3.289 closest distance to " O   HOH Z 285 " =    2.026
peak=    3.289 closest distance to " O  BHOH Z 338 " =    2.263
peak=    3.285 closest distance to " O   HOH Z 404 " =    1.602
peak=    3.283 closest distance to " O   HOH Z 130 " =    1.115
peak=    3.283 closest distance to " O   HOH Z 203 " =    1.808
peak=    3.281 closest distance to " CG2 ILE A 234 " =    0.814
peak=    3.277 closest distance to " O   THR A 182 " =    1.468
peak=    3.274 closest distance to " CB  ALA A 299 " =    0.750
peak=    3.274 closest distance to " CE3 TRP A  85 " =    1.178
peak=    3.273 closest distance to " CB  ARG A 269 " =    0.878
peak=    3.273 closest distance to " O   HOH Z 301 " =    1.883
peak=    3.272 closest distance to " O   HOH Z 336 " =    1.815
peak=    3.265 closest distance to " OG BSER A 134 " =    2.790
peak=    3.263 closest distance to " O   PRO A 213 " =    1.450
peak=    3.263 closest distance to " CE1 TYR A  30 " =    0.912
peak=    3.262 closest distance to " O   ALA A 242 " =    1.234
peak=    3.261 closest distance to " N   ASN A 252 " =    1.299
peak=    3.261 closest distance to " NE1 TRP A  92 " =    1.838
peak=    3.260 closest distance to " OD2 ASP A 298 " =    3.829
peak=    3.257 closest distance to " O   HOH Z 195 " =    4.079
peak=    3.255 closest distance to " N   GLU A  44 " =    1.122
peak=    3.253 closest distance to " O   HOH Z 371 " =    2.906
peak=    3.252 closest distance to " O   HOH Z  20 " =    1.678
peak=    3.247 closest distance to " O   HOH Z  88 " =    3.364
peak=    3.245 closest distance to " OE2 GLU A  53 " =    1.131
peak=    3.245 closest distance to " O   HOH Z 357 " =    2.377
peak=    3.244 closest distance to " CD  ARG A  66 " =    2.203
peak=    3.243 closest distance to " N   TYR A 116 " =    1.573
peak=    3.242 closest distance to " O   HOH Z 261 " =    1.283
peak=    3.239 closest distance to " O   HOH Z 374 " =    2.909
peak=    3.237 closest distance to " O   HOH Z 130 " =    2.213
peak=    3.235 closest distance to " O   HOH Z 245 " =    1.208
peak=    3.232 closest distance to " OE1 GLN A 223 " =    3.481
peak=    3.232 closest distance to " OH  TYR A 293 " =    1.398
peak=    3.231 closest distance to " CD  PRO A  54 " =    0.986
peak=    3.231 closest distance to " O   PHE A  61 " =    1.351
peak=    3.226 closest distance to " CA  LEU A  83 " =    1.439
peak=    3.225 closest distance to " CA  THR A 246 " =    1.029
peak=    3.223 closest distance to " OD1 ASN A 301 " =    1.164
peak=    3.220 closest distance to " O   HOH Z  44 " =    1.739
peak=    3.219 closest distance to " O   HOH Z 162 " =    1.659
peak=    3.215 closest distance to " CD BLYS A 290 " =    0.962
peak=    3.214 closest distance to " O   HOH Z 125 " =    3.806
peak=    3.208 closest distance to " O   HOH Z 117 " =    1.070
peak=    3.204 closest distance to " O   HOH Z 394 " =    4.025
peak=    3.203 closest distance to " N   ALA A 292 " =    1.119
peak=    3.201 closest distance to " CB  ILE A 199 " =    1.154
peak=    3.199 closest distance to " CG1 VAL A 257 " =    1.111
peak=    3.196 closest distance to " O   HOH Z 106 " =    3.747
peak=    3.186 closest distance to " CA  ASN A 176 " =    1.342
peak=    3.186 closest distance to " N   ASN A 127 " =    1.272
peak=    3.185 closest distance to " O   HOH Z  63 " =    1.910
peak=    3.184 closest distance to " NE2 GLN A  58 " =    3.645
peak=    3.182 closest distance to " CD1 ILE A 199 " =    1.217
peak=    3.180 closest distance to " N   GLY A  98 " =    1.123
peak=    3.176 closest distance to " CA  ASP A 140 " =    1.504
peak=    3.172 closest distance to " CA  GLN A 223 " =    0.898
peak=    3.171 closest distance to " CG2 ILE A 120 " =    1.002
peak=    3.166 closest distance to " NZ  LYS A  48 " =    1.300
peak=    3.165 closest distance to " CG2 THR A  29 " =    1.381
peak=    3.164 closest distance to " CB  SER A  62 " =    0.883
peak=    3.164 closest distance to " N   TYR A  15 " =    0.796
peak=    3.164 closest distance to " O   HOH Z 116 " =    3.124
peak=    3.163 closest distance to " O   HOH Z 142 " =    1.553
peak=    3.162 closest distance to " CH2 TRP A  70 " =    0.890
peak=    3.156 closest distance to " O   HOH Z 344 " =    3.278
peak=    3.151 closest distance to " CG  MET A 185 " =    1.239
peak=    3.151 closest distance to " CB  ILE A 120 " =    1.330
peak=    3.151 closest distance to " N   LYS A 166 " =    0.889
peak=    3.148 closest distance to " CB  LEU A 300 " =    0.910
peak=    3.147 closest distance to " O   HOH Z 287 " =    2.319
peak=    3.146 closest distance to " CG  ARG A 219 " =    1.175
peak=    3.145 closest distance to " C   ALA A 299 " =    1.069
peak=    3.140 closest distance to " O   HOH Z 313 " =    1.929
peak=    3.139 closest distance to " CA  ASP A 191 " =    1.121
peak=    3.139 closest distance to " O   HOH Z 368 " =    4.716
peak=    3.139 closest distance to " OG  SER A 271 " =    1.978
peak=    3.136 closest distance to " CG1 ILE A  20 " =    1.277
peak=    3.132 closest distance to " CB  GLU A  46 " =    1.124
peak=    3.131 closest distance to " NH1 ARG A  14 " =    1.119
peak=    3.130 closest distance to " O   HOH Z 437 " =    1.178
peak=    3.129 closest distance to " NH2AARG A 275 " =    3.551
peak=    3.129 closest distance to " O   THR A 294 " =    1.532
peak=    3.123 closest distance to " O   HOH Z 343 " =    2.309
peak=    3.122 closest distance to " O   HOH Z  68 " =    1.848
peak=    3.119 closest distance to " CB  PHE A  16 " =    1.125
peak=    3.116 closest distance to " N   GLU A 152 " =    1.507
peak=    3.115 closest distance to " O   HOH Z 365 " =    2.821
peak=    3.103 closest distance to " O   HOH Z 213 " =    2.021
peak=    3.101 closest distance to " CD1 LEU A   5 " =    1.245
peak=    3.100 closest distance to " O   HOH Z 128 " =    2.010
peak=    3.099 closest distance to " O   GLY A  91 " =    1.177
peak=    3.099 closest distance to " CG2 VAL A 126 " =    0.931
peak=    3.091 closest distance to " NZ  LYS A 117 " =    1.331
peak=    3.085 closest distance to " NE  ARG A 138 " =    1.230
peak=    3.083 closest distance to " CB  TYR A 247 " =    0.901
peak=    3.081 closest distance to " O   HOH Z 305 " =    3.802
peak=    3.081 closest distance to " N   GLY A 262 " =    1.255
peak=    3.080 closest distance to " O   HOH Z 422 " =    2.480
peak=    3.068 closest distance to " O   HOH Z 201 " =    2.853
peak=    3.064 closest distance to " O   HOH Z 150 " =    1.572
peak=    3.040 closest distance to " O   ASP A 124 " =    1.787
peak=    3.034 closest distance to " CG2 VAL A 268 " =    1.047
peak=    3.007 closest distance to " CB  ASN A 187 " =    1.511

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.780 - 5.927
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 203
   mapped sites are within: 0.780 - 5.927

peak=   -4.479 closest distance to " O   HOH Z  10 " =    1.668
peak=   -4.461 closest distance to " O   HOH Z 411 " =    5.540
peak=   -4.444 closest distance to " CD  GLN A 223 " =    1.408
peak=   -4.319 closest distance to " CG1 VAL A 250 " =    2.721
peak=   -4.307 closest distance to " CB  PRO A 243 " =    2.783
peak=   -4.227 closest distance to " CD  GLN A  88 " =    0.912
peak=   -4.222 closest distance to " CG1 VAL A 112 " =    2.617
peak=   -4.222 closest distance to " CG  ARG A 269 " =    2.360
peak=   -4.217 closest distance to " CD2 TYR A 293 " =    1.826
peak=   -4.181 closest distance to " O   PRO A 198 " =    1.318
peak=   -4.143 closest distance to " O   HOH Z 166 " =    1.518
peak=   -4.093 closest distance to " OXT GLY A 302 " =    3.069
peak=   -4.082 closest distance to " CD  ARG A 156 " =    2.130
peak=   -4.077 closest distance to " CA  ASP A 298 " =    1.084
peak=   -4.055 closest distance to " CD  GLN A  58 " =    0.867
peak=   -4.016 closest distance to " CE2 PHE A  61 " =    2.676
peak=   -3.978 closest distance to " O   GLY A 136 " =    2.374
peak=   -3.972 closest distance to " O   HOH Z 166 " =    2.437
peak=   -3.965 closest distance to " CB  ALA A 291 " =    2.482
peak=   -3.928 closest distance to " CD  ARG A  14 " =    3.413
peak=   -3.908 closest distance to " CG  MET A 105 " =    0.929
peak=   -3.892 closest distance to " O   HOH Z 128 " =    2.712
peak=   -3.887 closest distance to " CB  ALA A  10 " =    2.182
peak=   -3.870 closest distance to " CD1 PHE A  59 " =    2.035
peak=   -3.867 closest distance to " N   ALA A  43 " =    2.673
peak=   -3.847 closest distance to " CD1 LEU A 101 " =    2.464
peak=   -3.841 closest distance to " O   HOH Z 368 " =    1.920
peak=   -3.831 closest distance to " O   HOH Z 185 " =    2.482
peak=   -3.824 closest distance to " OD1 ASN A 148 " =    1.376
peak=   -3.813 closest distance to " C   ASN A 285 " =    2.397
peak=   -3.806 closest distance to " O   VAL A  67 " =    2.736
peak=   -3.803 closest distance to " CE3 TRP A 150 " =    2.102
peak=   -3.800 closest distance to " CG2 ILE A  49 " =    2.823
peak=   -3.793 closest distance to " O   HOH Z 283 " =    2.195
peak=   -3.787 closest distance to " O   HOH Z 418 " =    1.185
peak=   -3.773 closest distance to " NE  ARG A  79 " =    1.265
peak=   -3.773 closest distance to " C   SER A 206 " =    1.387
peak=   -3.766 closest distance to " O   HOH Z 394 " =    1.659
peak=   -3.737 closest distance to " O   HOH Z 407 " =    0.955
peak=   -3.725 closest distance to " O   HOH Z 149 " =    2.012
peak=   -3.706 closest distance to " CA  GLY A 241 " =    3.286
peak=   -3.703 closest distance to " O   ALA A  34 " =    2.551
peak=   -3.701 closest distance to " O   HOH Z   6 " =    1.329
peak=   -3.700 closest distance to " O   HOH Z 211 " =    1.170
peak=   -3.696 closest distance to " O   HOH Z 377 " =    2.122
peak=   -3.680 closest distance to " CG  GLN A  11 " =    1.392
peak=   -3.675 closest distance to " CG  GLN A 103 " =    2.510
peak=   -3.661 closest distance to " NE2 GLN A 194 " =    2.073
peak=   -3.648 closest distance to " O   HOH Z  37 " =    1.919
peak=   -3.648 closest distance to " CG  GLN A  58 " =    1.273
peak=   -3.637 closest distance to " O   SER A 210 " =    1.920
peak=   -3.630 closest distance to " O   HOH Z 348 " =    2.294
peak=   -3.629 closest distance to " ND2 ASN A  45 " =    1.996
peak=   -3.624 closest distance to " CB  GLU A 277 " =    1.285
peak=   -3.624 closest distance to " C   HIS A 108 " =    1.043
peak=   -3.622 closest distance to " CE2 TYR A  30 " =    2.725
peak=   -3.591 closest distance to " CD2 PHE A  61 " =    2.116
peak=   -3.591 closest distance to " CH2 TRP A 179 " =    1.207
peak=   -3.590 closest distance to " O   GLY A  17 " =    1.215
peak=   -3.577 closest distance to " O   HOH Z 150 " =    1.189
peak=   -3.571 closest distance to " O   HOH Z 154 " =    1.363
peak=   -3.555 closest distance to " O   HOH Z  19 " =    2.089
peak=   -3.552 closest distance to " O   HOH Z 114 " =    1.064
peak=   -3.547 closest distance to " CA  VAL A  67 " =    3.066
peak=   -3.542 closest distance to " CG  PRO A 243 " =    1.740
peak=   -3.532 closest distance to " NE2 GLN A 223 " =    1.258
peak=   -3.526 closest distance to " O   HOH Z 275 " =    1.617
peak=   -3.521 closest distance to " O   HOH Z 377 " =    1.135
peak=   -3.518 closest distance to " CA  GLY A 241 " =    2.319
peak=   -3.499 closest distance to " CA  GLY A 203 " =    2.451
peak=   -3.497 closest distance to " CZ  PHE A  38 " =    2.593
peak=   -3.497 closest distance to " CD1 TRP A  70 " =    1.114
peak=   -3.495 closest distance to " O   HOH Z  52 " =    1.611
peak=   -3.490 closest distance to " OG  SER A  97 " =    2.284
peak=   -3.484 closest distance to " CG  GLU A  53 " =    1.426
peak=   -3.480 closest distance to " NE2 HIS A  86 " =    1.089
peak=   -3.469 closest distance to " OG1 THR A  82 " =    1.265
peak=   -3.466 closest distance to " CG2 VAL A 189 " =    2.234
peak=   -3.463 closest distance to " CB  ALA A 161 " =    2.685
peak=   -3.462 closest distance to " O   HOH Z 111 " =    1.728
peak=   -3.434 closest distance to " N   ILE A 120 " =    1.003
peak=   -3.430 closest distance to " O   HOH Z 191 " =    5.927
peak=   -3.429 closest distance to " OD1 ASP A 191 " =    1.392
peak=   -3.427 closest distance to " CG  PRO A 198 " =    2.036
peak=   -3.418 closest distance to " O   HOH Z 252 " =    3.632
peak=   -3.417 closest distance to " O   HOH Z 201 " =    2.066
peak=   -3.415 closest distance to " O   ALA A  10 " =    1.686
peak=   -3.415 closest distance to " CE  MET A  93 " =    1.866
peak=   -3.410 closest distance to " O   VAL A 189 " =    2.535
peak=   -3.404 closest distance to " N   SER A 134 " =    1.147
peak=   -3.400 closest distance to " O   HOH Z 234 " =    4.572
peak=   -3.399 closest distance to " OD2 ASP A 171 " =    1.838
peak=   -3.391 closest distance to " O   HOH Z  78 " =    1.923
peak=   -3.388 closest distance to " O   HOH Z 407 " =    3.748
peak=   -3.383 closest distance to " CA  VAL A 197 " =    1.044
peak=   -3.383 closest distance to " O   HOH Z  90 " =    3.711
peak=   -3.380 closest distance to " CH2 TRP A 150 " =    1.223
peak=   -3.380 closest distance to " CE3 TRP A  70 " =    1.900
peak=   -3.379 closest distance to " OE1 GLN A  88 " =    1.066
peak=   -3.378 closest distance to " NH2 ARG A 159 " =    2.323
peak=   -3.366 closest distance to " O   HOH Z  60 " =    1.857
peak=   -3.361 closest distance to " O   SER A 276 " =    1.918
peak=   -3.356 closest distance to " O   PRO A 163 " =    2.102
peak=   -3.345 closest distance to " O   HOH Z 109 " =    3.748
peak=   -3.341 closest distance to " CG  ARG A  66 " =    2.397
peak=   -3.340 closest distance to " O   HOH Z 371 " =    1.322
peak=   -3.337 closest distance to " CB  HIS A  86 " =    1.137
peak=   -3.335 closest distance to " CB  PHE A 192 " =    1.965
peak=   -3.329 closest distance to " O   HOH Z 366 " =    1.769
peak=   -3.325 closest distance to " O   TYR A 186 " =    1.933
peak=   -3.324 closest distance to " CZ  PHE A 155 " =    1.221
peak=   -3.320 closest distance to " CG2 THR A 221 " =    2.326
peak=   -3.318 closest distance to " OH  TYR A 247 " =    2.325
peak=   -3.317 closest distance to " CB  PHE A  16 " =    2.479
peak=   -3.316 closest distance to " NH2 ARG A  79 " =    1.593
peak=   -3.312 closest distance to " O   HOH Z 216 " =    1.081
peak=   -3.302 closest distance to " O   HOH Z 196 " =    1.914
peak=   -3.299 closest distance to " CG  LEU A 281 " =    1.850
peak=   -3.283 closest distance to " O   HOH Z 183 " =    1.749
peak=   -3.282 closest distance to " CG1AVAL A 121 " =    1.413
peak=   -3.282 closest distance to " O   GLY A  98 " =    2.082
peak=   -3.279 closest distance to " CD1 ILE A 151 " =    2.425
peak=   -3.277 closest distance to " CA  SER A  62 " =    2.562
peak=   -3.277 closest distance to " O   HOH Z 350 " =    2.551
peak=   -3.276 closest distance to " SD  MET A  40 " =    1.950
peak=   -3.272 closest distance to " O   HOH Z  64 " =    1.527
peak=   -3.266 closest distance to " CG  LEU A  83 " =    2.138
peak=   -3.265 closest distance to " ND2 ASN A  69 " =    1.695
peak=   -3.264 closest distance to " O   HOH Z 198 " =    1.700
peak=   -3.263 closest distance to " SG  CYS A 168 " =    1.244
peak=   -3.261 closest distance to " O   HOH Z 331 " =    1.198
peak=   -3.260 closest distance to " CB  TRP A  85 " =    2.408
peak=   -3.254 closest distance to " O   GLN A  11 " =    1.307
peak=   -3.253 closest distance to " O   HOH Z 150 " =    1.970
peak=   -3.247 closest distance to " O   HOH Z  60 " =    1.905
peak=   -3.239 closest distance to " CZ  TYR A 169 " =    1.817
peak=   -3.238 closest distance to " CD1 LEU A   5 " =    2.571
peak=   -3.237 closest distance to " O   ASP A 171 " =    1.076
peak=   -3.234 closest distance to " O   HOH Z 171 " =    2.300
peak=   -3.233 closest distance to " O   HOH Z 120 " =    4.416
peak=   -3.233 closest distance to " CA  ALA A   8 " =    1.503
peak=   -3.232 closest distance to " O   HOH Z 251 " =    1.784
peak=   -3.230 closest distance to " CG2BVAL A  41 " =    1.529
peak=   -3.228 closest distance to " NE  ARG A  66 " =    4.400
peak=   -3.224 closest distance to " OD2 ASP A 270 " =    1.124
peak=   -3.220 closest distance to " NH1 ARG A 195 " =    0.974
peak=   -3.218 closest distance to " O   HOH Z  58 " =    1.202
peak=   -3.216 closest distance to " O   HOH Z 340 " =    1.600
peak=   -3.214 closest distance to " N   SER A 276 " =    1.464
peak=   -3.214 closest distance to " OD1 ASP A 171 " =    1.471
peak=   -3.212 closest distance to " CA  GLY A 241 " =    2.886
peak=   -3.210 closest distance to " CD  LYS A 289 " =    2.333
peak=   -3.207 closest distance to " NH2 ARG A  66 " =    2.033
peak=   -3.207 closest distance to " O   HOH Z 351 " =    1.699
peak=   -3.206 closest distance to " O   HOH Z  38 " =    1.095
peak=   -3.206 closest distance to " O   HOH Z 156 " =    3.654
peak=   -3.205 closest distance to " O   SER A 271 " =    2.147
peak=   -3.205 closest distance to " O   HOH Z 290 " =    1.105
peak=   -3.202 closest distance to " CD1 ILE A 109 " =    2.909
peak=   -3.193 closest distance to " CG  TYR A 169 " =    2.126
peak=   -3.193 closest distance to " O   HOH Z 399 " =    2.404
peak=   -3.188 closest distance to " O   HOH Z 197 " =    2.064
peak=   -3.185 closest distance to " SD  MET A 105 " =    2.593
peak=   -3.181 closest distance to " O   HOH Z 298 " =    2.637
peak=   -3.177 closest distance to " CA  GLY A 133 " =    2.454
peak=   -3.175 closest distance to " O   GLN A 240 " =    2.809
peak=   -3.171 closest distance to " CD1 ILE A 263 " =    2.003
peak=   -3.171 closest distance to " CG1 VAL A 125 " =    1.949
peak=   -3.167 closest distance to " O   HOH Z 105 " =    1.994
peak=   -3.163 closest distance to " C   LEU A 143 " =    1.205
peak=   -3.163 closest distance to " O   HOH Z 259 " =    2.261
peak=   -3.162 closest distance to " CB  ALA A 131 " =    2.426
peak=   -3.161 closest distance to " CB  ASP A 132 " =    2.382
peak=   -3.159 closest distance to " O   HOH Z 200 " =    1.203
peak=   -3.149 closest distance to " O   HOH Z 396 " =    1.749
peak=   -3.144 closest distance to " CG1BVAL A  72 " =    2.469
peak=   -3.142 closest distance to " CG1AVAL A  41 " =    2.657
peak=   -3.140 closest distance to " O   HOH Z 278 " =    1.359
peak=   -3.132 closest distance to " O   HOH Z 189 " =    1.936
peak=   -3.132 closest distance to " CB  ALA A  43 " =    2.740
peak=   -3.130 closest distance to " O   HOH Z 114 " =    3.896
peak=   -3.129 closest distance to " N   ALA A 242 " =    1.829
peak=   -3.125 closest distance to " O   HOH Z 165 " =    1.869
peak=   -3.122 closest distance to " O   HOH Z 264 " =    1.898
peak=   -3.121 closest distance to " OG BSER A 210 " =    2.235
peak=   -3.119 closest distance to " O   HOH Z 210 " =    1.682
peak=   -3.117 closest distance to " O   HOH Z 236 " =    1.561
peak=   -3.115 closest distance to " O   HOH Z 174 " =    3.528
peak=   -3.114 closest distance to " OG BSER A 134 " =    1.405
peak=   -3.105 closest distance to " N   ALA A 226 " =    2.076
peak=   -3.094 closest distance to " O   GLY A  80 " =    1.767
peak=   -3.089 closest distance to " CG1 VAL A  78 " =    2.667
peak=   -3.088 closest distance to " O   TYR A 247 " =    2.909
peak=   -3.075 closest distance to " O   HOH Z 174 " =    2.173
peak=   -3.075 closest distance to " O   HOH Z 231 " =    2.041
peak=   -3.071 closest distance to " ND2 ASN A  45 " =    1.123
peak=   -3.068 closest distance to " O   GLU A 152 " =    1.342
peak=   -3.067 closest distance to " OD1 ASP A 253 " =    0.780
peak=   -3.062 closest distance to " O   HOH Z 246 " =    1.561
peak=   -3.035 closest distance to " CA  GLY A 136 " =    1.697
peak=   -3.028 closest distance to " C   ARG A  79 " =    2.628
peak=   -3.026 closest distance to " O   HOH Z  82 " =    2.196
peak=   -3.021 closest distance to " O   HOH Z  88 " =    2.354

================= 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    :  0.4591 0.4511   6.267228e+00   6.246338e+00
   1_bss:  0.4508 0.4431   6.259980e+00   6.237784e+00
   1_xyz:  0.3445 0.3698   6.072472e+00   6.121247e+00
   1_adp:  0.3138 0.3832   6.024487e+00   6.137765e+00
   1_occ:  0.3134 0.3828   6.023922e+00   6.137758e+00
   2_bss:  0.3124 0.3816   6.024547e+00   6.138014e+00
   2_xyz:  0.2260 0.2751   5.730623e+00   5.888525e+00
   2_adp:  0.2017 0.2535   5.643350e+00   5.820621e+00
   2_occ:  0.2012 0.2537   5.642879e+00   5.821405e+00
   3_bss:  0.2007 0.2531   5.641712e+00   5.819349e+00
   3_xyz:  0.1629 0.2062   5.453581e+00   5.646419e+00
   3_adp:  0.1475 0.1978   5.384933e+00   5.602547e+00
   3_occ:  0.1475 0.1977   5.384483e+00   5.602001e+00
   4_bss:  0.1477 0.1980   5.385111e+00   5.602205e+00
   4_xyz:  0.1299 0.1810   5.280038e+00   5.515200e+00
   4_adp:  0.1267 0.1751   5.249358e+00   5.479783e+00
   4_occ:  0.1266 0.1749   5.248734e+00   5.479166e+00
   5_bss:  0.1265 0.1748   5.248364e+00   5.478886e+00
   5_xyz:  0.1264 0.1737   5.248808e+00   5.473967e+00
   5_adp:  0.1256 0.1750   5.248840e+00   5.479210e+00
   5_occ:  0.1255 0.1750   5.248808e+00   5.479298e+00
   5_bss:  0.1257 0.1748   5.247625e+00   5.476526e+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:  0.284  55.069  -2.897   3.265   2.676   0.000   0.000   0.000
   1_xyz:  0.284  55.069  -2.897   3.265   2.676   0.000   0.000   0.000
   1_adp:  0.284  55.069  -2.897   3.265   2.676   0.000   0.000   0.000
   1_occ:  0.284  55.069  -2.897   3.265   2.676   0.000   0.000   0.000
   2_bss:  0.310  68.675  -1.367   1.866   1.489   0.000   0.000   0.000
   2_xyz:  0.310  68.675  -1.367   1.866   1.489   0.000   0.000   0.000
   2_adp:  0.310  68.675  -1.367   1.866   1.489   0.000   0.000   0.000
   2_occ:  0.310  68.675  -1.367   1.866   1.489   0.000   0.000   0.000
   3_bss:  0.331  81.437  -1.505   0.195   0.401   0.000   0.000   0.000
   3_xyz:  0.331  81.437  -1.505   0.195   0.401   0.000   0.000   0.000
   3_adp:  0.331  81.437  -1.505   0.195   0.401   0.000   0.000   0.000
   3_occ:  0.331  81.437  -1.505   0.195   0.401   0.000   0.000   0.000
   4_bss:  0.339  89.664  -1.453  -0.276   0.393  -0.000   0.000   0.000
   4_xyz:  0.339  89.664  -1.453  -0.276   0.393  -0.000   0.000   0.000
   4_adp:  0.339  89.664  -1.453  -0.276   0.393  -0.000   0.000   0.000
   4_occ:  0.339  89.664  -1.453  -0.276   0.393  -0.000   0.000   0.000
   5_bss:  0.329  80.001  -1.253  -0.444   0.520  -0.000   0.000   0.000
   5_xyz:  0.329  80.001  -1.253  -0.444   0.520  -0.000   0.000   0.000
   5_adp:  0.329  80.001  -1.253  -0.444   0.520  -0.000   0.000   0.000
   5_occ:  0.329  80.001  -1.253  -0.444   0.520  -0.000   0.000   0.000
   5_bss:  0.329  80.004  -1.211  -0.495   0.539  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.094 0.4690  0.5982    61397.035
   1_bss:  52.997 0.4818  0.6400    58934.790
   1_xyz:  41.197 0.6282  0.8141    39001.177
   1_adp:  42.431 0.6127  0.7890    41158.920
   1_occ:  42.440 0.6126  0.7885    41167.218
   2_bss:  42.180 0.6159  0.7864    41028.492
   2_xyz:  28.443 0.7737  0.9507    19655.183
   2_adp:  25.371 0.8076  0.9659    16496.955
   2_occ:  25.389 0.8074  0.9651    16509.121
   3_bss:  25.262 0.8087  0.9351    16380.675
   3_xyz:  19.973 0.8620  0.9685    10879.198
   3_adp:  18.742 0.8738  0.9591     9959.387
   3_occ:  18.725 0.8739  0.9593     9948.243
   4_bss:  18.729 0.8739  0.9549     9963.327
   4_xyz:  16.848 0.8908  0.9660     8290.761
   4_adp:  15.958 0.8988  0.9604     7764.036
   4_occ:  15.943 0.8989  0.9605     7754.057
   5_bss:  15.938 0.8989  0.9626     7747.391
   5_xyz:  15.744 0.9009  0.9629     7622.727
   5_adp:  15.838 0.9002  0.9518     7717.180
   5_occ:  15.836 0.9002  0.9517     7713.372
   5_bss:  15.799 0.9004  0.9520     7647.598
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6539e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6539e-01
   1_xyz:   1.537  0.011  0.094 15.458  0.007  4.116   1.2003e-01
   1_adp:   1.537  0.011  0.094 15.458  0.007  4.116   1.2003e-01
   1_occ:   1.537  0.011  0.094 15.458  0.007  4.116   1.2003e-01
   2_bss:   1.537  0.011  0.094 15.458  0.007  4.116   1.2003e-01
   2_xyz:   1.421  0.012  0.096 15.457  0.006  4.121   1.0819e-01
   2_adp:   1.421  0.012  0.096 15.457  0.006  4.121   1.0819e-01
   2_occ:   1.421  0.012  0.096 15.457  0.006  4.121   1.0819e-01
   3_bss:   1.421  0.012  0.096 15.457  0.006  4.121   1.0819e-01
   3_xyz:   1.051  0.009  0.072 15.023  0.004  4.138   6.7782e-02
   3_adp:   1.051  0.009  0.072 15.023  0.004  4.138   6.7782e-02
   3_occ:   1.051  0.009  0.072 15.023  0.004  4.138   6.7782e-02
   4_bss:   1.051  0.009  0.072 15.023  0.004  4.138   6.7782e-02
   4_xyz:   1.136  0.011  0.082 14.966  0.004  4.137   7.5979e-02
   4_adp:   1.136  0.011  0.082 14.966  0.004  4.137   7.5979e-02
   4_occ:   1.136  0.011  0.082 14.966  0.004  4.137   7.5979e-02
   5_bss:   1.136  0.011  0.082 14.966  0.004  4.137   7.5979e-02
   5_xyz:   0.980  0.008  0.073 14.694  0.003  4.137   5.8622e-02
   5_adp:   0.980  0.008  0.073 14.694  0.003  4.137   5.8622e-02
   5_occ:   0.980  0.008  0.073 14.694  0.003  4.137   5.8622e-02
   5_bss:   0.980  0.008  0.073 14.694  0.003  4.137   5.8622e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.780   2.4548e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.780   2.4548e-01
   1_xyz:  10.062  0.065  0.370 83.851  0.049  2.024   9.8136e-02
   1_adp:  10.062  0.065  0.370 83.851  0.049  2.024   9.8136e-02
   1_occ:  10.062  0.065  0.370 83.851  0.049  2.024   9.8136e-02
   2_bss:  10.062  0.065  0.370 83.851  0.049  2.024   9.8136e-02
   2_xyz:   9.625  0.064  0.300 88.111  0.037  2.154   8.8368e-02
   2_adp:   9.625  0.064  0.300 88.111  0.037  2.154   8.8368e-02
   2_occ:   9.625  0.064  0.300 88.111  0.037  2.154   8.8368e-02
   3_bss:   9.625  0.064  0.300 88.111  0.037  2.154   8.8368e-02
   3_xyz:   7.653  0.054  0.218 81.821  0.045  2.238   5.2765e-02
   3_adp:   7.653  0.054  0.218 81.821  0.045  2.238   5.2765e-02
   3_occ:   7.653  0.054  0.218 81.821  0.045  2.238   5.2765e-02
   4_bss:   7.653  0.054  0.218 81.821  0.045  2.238   5.2765e-02
   4_xyz:   7.824  0.060  0.288 82.843  0.048  2.320   5.4904e-02
   4_adp:   7.824  0.060  0.288 82.843  0.048  2.320   5.4904e-02
   4_occ:   7.824  0.060  0.288 82.843  0.048  2.320   5.4904e-02
   5_bss:   7.824  0.060  0.288 82.843  0.048  2.320   5.4904e-02
   5_xyz:   7.650  0.045  0.235 81.155  0.041  2.434   3.7095e-02
   5_adp:   7.650  0.045  0.235 81.155  0.041  2.434   3.7095e-02
   5_occ:   7.650  0.045  0.235 81.155  0.041  2.434   3.7095e-02
   5_bss:   7.650  0.045  0.235 81.155  0.041  2.434   3.7095e-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: 117.80   0.00  18.66  87.42   0.00  14.74 117.80   0.00  40.05
   1_occ: 117.80   0.00  18.66  87.42   0.00  14.74 117.80   0.00  40.05
   2_bss: 117.80   0.00  18.66  87.42   0.00  14.74 117.80   0.00  40.05
   2_xyz: 117.80   0.00  18.66  87.42   0.00  14.74 117.80   0.00  40.05
   2_adp: 117.09   0.00  17.99  86.11   0.00  13.67 117.09   3.10  41.48
   2_occ: 117.09   0.00  17.99  86.11   0.00  13.67 117.09   3.10  41.48
   3_bss: 117.09   0.00  17.99  86.11   0.00  13.67 117.09   3.10  41.48
   3_xyz: 117.09   0.00  17.99  86.11   0.00  13.67 117.09   3.10  41.48
   3_adp: 116.22   0.00  18.18 105.32   0.00  12.93 116.22   4.47  46.73
   3_occ: 116.22   0.00  18.18 105.32   0.00  12.93 116.22   4.47  46.73
   4_bss: 116.22   0.00  18.18 105.32   0.00  12.93 116.22   4.47  46.73
   4_xyz: 116.22   0.00  18.18 105.32   0.00  12.93 116.22   4.47  46.73
   4_adp: 113.10   0.00  17.33 103.63   0.00  12.32 113.10   4.81  44.60
   4_occ: 113.10   0.00  17.33 103.63   0.00  12.32 113.10   4.81  44.60
   5_bss: 113.10   0.00  17.33 103.63   0.00  12.32 113.10   4.81  44.60
   5_xyz: 113.10   0.00  17.33 103.63   0.00  12.32 113.10   4.81  44.60
   5_adp: 116.77   0.00  17.05 107.30   0.00  12.07 116.77   4.70  44.20
   5_occ: 116.77   0.00  17.05 107.30   0.00  12.07 116.77   4.70  44.20
   5_bss: 116.78   0.00  17.06 107.30   0.00  12.07 116.78   4.70  44.20
------------------------------------------------------------------------
 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:    1.828    0.015    0.364
   1_adp:    1.828    0.015    0.364
   1_occ:    1.828    0.015    0.364
   2_bss:    1.828    0.015    0.364
   2_xyz:    1.387    0.031    0.613
   2_adp:    1.387    0.031    0.613
   2_occ:    1.387    0.031    0.613
   3_bss:    1.387    0.031    0.613
   3_xyz:    1.314    0.102    0.697
   3_adp:    1.314    0.102    0.697
   3_occ:    1.314    0.102    0.697
   4_bss:    1.314    0.102    0.697
   4_xyz:    1.369    0.110    0.747
   4_adp:    1.369    0.110    0.747
   4_occ:    1.369    0.110    0.747
   5_bss:    1.369    0.110    0.747
   5_xyz:    1.360    0.066    0.756
   5_adp:    1.360    0.066    0.756
   5_occ:    1.360    0.066    0.756
   5_bss:    1.360    0.066    0.756
------------------------------------------------------------------------

CPU time actual refinement: 352.22


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_955/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_955/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_955/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_955/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_955/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 352.07 
  Macro-tasks:
    bulk solvent and scale       = 55.12  
    individual site refinement   = 144.83 
    weights calculation          = 30.20  
    collect and process          = 6.71   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 236.99 
  Micro-tasks:
    mask                            = 2.31   
    f_calc                          = 105.46 
    alpha_beta                      = 8.53   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 116.57 
    fmodel                         = 9.19   
    r_factors                      = 0.29   
    phase_errors                   = 10.79  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 254.69 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.851 micro seconds
Total CPU time: 6.09 minutes
from_scatterers_fft:    657 calls, 105.12 s
gradients_fft:          602 calls, 102.24 s

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

# Date 2008-01-16 Time 06:04:37 PST -0800 (1200492277.94 s)
Start R-work = 0.4591, R-free = 0.4511 (no bulk solvent and anisotropic scale)
Final R-work = 0.1416, R-free = 0.1890 (no bulk solvent and anisotropic scale)

Start R-work = 0.4508, R-free = 0.4431
Final R-work = 0.1257, R-free = 0.1748