# Date 2008-01-16 Time 04:44:28 PST -0800 (1200487468.53 s)
#phil __OFF__

Command line arguments: "../443.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27663
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 443

-------------------------------------------------------------------------------
  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: (69.5475, 47.3993, 85.5261, 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: 3.29, per 1000 atoms: 1.17


================================== 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: (69.5475, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98049
Completeness in resolution range: 0.967119
Completeness with d_max=infinity: 0.964073

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8440
                             d_min =   1.9805

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: (69.5475, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98049
Completeness in resolution range: 0.967119
Completeness with d_max=infinity: 0.964073

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8444 -  4.2369 [2122/2150]  1911   211   9.9%
  bin  2:  4.2369 -  3.3759 [2038/2057]  1832   206  10.1%
  bin  3:  3.3759 -  2.9530 [2026/2046]  1824   202  10.0%
  bin  4:  2.9530 -  2.6848 [1988/2013]  1792   196   9.9%
  bin  5:  2.6848 -  2.4933 [1987/2007]  1786   201  10.1%
  bin  6:  2.4933 -  2.3469 [1967/2013]  1774   193   9.8%
  bin  7:  2.3469 -  2.2298 [1962/1994]  1764   198  10.1%
  bin  8:  2.2298 -  2.1330 [1960/1996]  1760   200  10.2%
  bin  9:  2.1330 -  2.0511 [1944/1974]  1753   191   9.8%
  bin 10:  2.0511 -  1.9805 [1595/2005]  1434   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_443/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 28
        2.42 -     3.04: 2203
        3.04 -     3.66: 4726
        3.66 -     4.28: 9053
        4.28 -     4.90: 12421
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.919 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.921 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.010 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  2.053 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28426 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_443/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_443/model_refine_001.geo

CPU time processing inputs: 9.24


============================ 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 = 69.5475 47.3993 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3365   r_free= 0.3311   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| 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:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.064157                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7251 0.99   1380  154 0.2872 0.2979      6.3572      6.3623|
|  2:  4.7251 -  3.7707 0.99   1329  146 0.2668 0.2477      6.4506      6.4229|
|  3:  3.7707 -  3.3000 0.99   1305  147 0.2855 0.2715      6.3456      6.3987|
|  4:  3.3000 -  3.0010 0.99   1293  138 0.3073 0.3060      6.2395      6.1628|
|  5:  3.0010 -  2.7875 0.99   1283  146 0.3359 0.2988      6.1159      6.0478|
|  6:  2.7875 -  2.6241 0.98   1281  142 0.3534 0.3352        6.06      5.9389|
|  7:  2.6241 -  2.4933 0.99   1274  143 0.3597 0.3044      6.0528      5.8652|
|  8:  2.4933 -  2.3852 0.98   1267  140 0.3654 0.4112       5.991      6.1088|
|  9:  2.3852 -  2.2937 0.98   1276  146 0.3878 0.3927      5.9535      5.9848|
| 10:  2.2937 -  2.2148 0.97   1235  132 0.3903 0.4202      5.9566      5.9661|
| 11:  2.2148 -  2.1458 0.99   1273  144 0.3847 0.4179      5.8737      5.9774|
| 12:  2.1458 -  2.0846 0.98   1270  133 0.3948 0.3829      5.8412      5.8626|
| 13:  2.0846 -  2.0299 0.97   1227  139 0.4077 0.3922      5.7819      5.7427|
| 14:  2.0299 -  1.9805 0.73    937  109 0.4068 0.3923      5.7228      5.6173|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8444 -  4.7251  1380   154  0.77  27.92   0.87     0.78      48009.77|
|  2:  4.7251 -  3.7707  1329   146  0.83  22.86   0.98     0.91      47994.89|
|  3:  3.7707 -  3.3000  1305   147  0.81  25.77   0.99     0.96      44262.19|
|  4:  3.3000 -  3.0010  1293   138  0.79  27.57   1.00     0.96      37296.54|
|  5:  3.0010 -  2.7875  1283   146  0.75  30.94   0.99     0.94      30081.19|
|  6:  2.7875 -  2.6241  1281   142  0.74  32.08   1.00     0.94      25734.47|
|  7:  2.6241 -  2.4933  1274   143  0.75  31.38   0.99     0.95      23889.38|
|  8:  2.4933 -  2.3852  1267   140  0.71  35.16   1.01     0.91      25698.75|
|  9:  2.3852 -  2.2937  1276   146  0.65  39.70   1.02     0.87      26389.53|
| 10:  2.2937 -  2.2148  1235   132  0.64  40.90   1.03     0.85      26813.75|
| 11:  2.2148 -  2.1458  1273   144  0.63  41.57   1.04     0.88      24881.45|
| 12:  2.1458 -  2.0846  1270   133  0.64  40.61   1.05     0.91      22346.94|
| 13:  2.0846 -  2.0299  1227   139  0.66  39.65   1.02     0.91      18450.40|
| 14:  2.0299 -  1.9805   937   109  0.68  37.53   1.02     0.90      14035.24|
|alpha:            min =        0.78 max =            0.96 mean =         0.90|
|beta:             min =    14035.24 max =        48009.77 mean =     30244.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           89.98 mean =        33.64|
|phase err.(test): min =        0.00 max =           89.33 mean =        33.43|
|-----------------------------------------------------------------------------|

============================== 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 = 3.223212              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.587   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.712406              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.460   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      194 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2009 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1891 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2835 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4636 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4417 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5677 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6744 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.236 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3365   r_free= 0.3311   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| 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:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.064157                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3245   r_free= 0.3171   ksol= 0.30   Bsol= 30.71   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,0.49,-0.42,0.00,-0.00,-0.00); trace/3= -0.73                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.043892                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.934250              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.523   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.392977              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.330   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3245      final r-factor (work) = 0.1934          |
| start r-factor (free) = 0.3171      final r-factor (free) = 0.2100          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0493 = 2.93 * 0.50 * 6.0550 + 1.00 * 0.1658                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5099 = 2.93 * 0.50 * 5.7554 + 1.00 * 0.0660                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1934      final r-factor (work) = 0.1762          |
| start r-factor (free) = 0.2100      final r-factor (free) = 0.2178          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2677 = 0.39 * 1.00 * 5.7554 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1735 = 0.39 * 1.00 * 5.5073 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.92   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    78.92   17.22    None  None   None       |
|    Sol.    : 438    0      7.47    71.86   38.61    None  None   None       |
|    Mac.    : 2385   0      0.00    78.92   13.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.892:  541   |   5:    39.458 -  47.349:  119        |
|      1:     7.892 -  15.783: 1313   |   6:    47.349 -  55.241:   78        |
|      2:    15.783 -  23.675:  410   |   7:    55.241 -  63.133:   59        |
|      3:    23.675 -  31.566:  143   |   8:    63.133 -  71.024:   18        |
|      4:    31.566 -  39.458:  138   |   9:    71.024 -  78.916:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1762 r_free = 0.2178             target_work(ml) = 5.520         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1758 r_free = 0.2181             target_work(ml) = 5.520         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1758   r_free= 0.2181   ksol= 0.30   Bsol= 30.71   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,0.49,-0.42,0.00,-0.00,-0.00); trace/3= -0.73                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.519543                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1749   r_free= 0.2168   ksol= 0.31   Bsol= 41.97   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-1.29,-1.45,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.517707                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.948232              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.015   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.139282              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.425  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1749      final r-factor (work) = 0.1280          |
| start r-factor (free) = 0.2168      final r-factor (free) = 0.1691          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2010 = 2.95 * 0.50 * 5.5185 + 1.00 * 0.0660                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9924 = 2.95 * 0.50 * 5.3825 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1280      final r-factor (work) = 0.1223          |
| start r-factor (free) = 0.1691      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7590 = 0.14 * 1.00 * 5.3825 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7335 = 0.14 * 1.00 * 5.2180 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.22    79.28   16.63    None  None   None       |
|    all(noH): 2823   0      2.22    79.28   16.63    None  None   None       |
|    Sol.    : 438    0      6.07    66.12   37.00    None  None   None       |
|    Mac.    : 2385   0      2.22    79.28   12.88    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:     2.224 -   9.929:  959   |   5:    40.751 -  48.456:  111        |
|      1:     9.929 -  17.635: 1120   |   6:    48.456 -  56.162:   78        |
|      2:    17.635 -  25.340:  264   |   7:    56.162 -  63.867:   27        |
|      3:    25.340 -  33.046:  121   |   8:    63.867 -  71.573:    9        |
|      4:    33.046 -  40.751:  132   |   9:    71.573 -  79.278:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1223 r_free = 0.1603             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1221 r_free = 0.1601             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1601   ksol= 0.31   Bsol= 41.97   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-1.29,-1.45,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.189861                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1588   ksol= 0.32   Bsol= 42.58   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-1.70,-1.47,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.189286                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.084953              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.696  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.449891              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.977  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1224      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1522          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4978 = 2.08 * 0.50 * 5.2181 + 1.00 * 0.0580                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4293 = 2.08 * 0.50 * 5.1519 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1522      final r-factor (free) = 0.1522          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3245 = 0.45 * 1.00 * 5.1519 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3111 = 0.45 * 1.00 * 5.1191 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.40    84.24   16.76    None  None   None       |
|    all(noH): 2823   0      1.40    84.24   16.76    None  None   None       |
|    Sol.    : 438    0      5.57    69.44   38.43    None  None   None       |
|    Mac.    : 2385   0      1.40    84.24   12.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.401 -   9.684:  948   |   5:    42.820 -  51.104:  119        |
|      1:     9.684 -  17.968: 1149   |   6:    51.104 -  59.387:   79        |
|      2:    17.968 -  26.252:  251   |   7:    59.387 -  67.671:   23        |
|      3:    26.252 -  34.536:  126   |   8:    67.671 -  75.955:    7        |
|      4:    34.536 -  42.820:  119   |   9:    75.955 -  84.239:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1099 r_free = 0.1522             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1099 r_free = 0.1522             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1522   ksol= 0.32   Bsol= 42.58   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-1.70,-1.47,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119538                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1522   ksol= 0.32   Bsol= 44.06   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-1.72,-1.38,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119446                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.662110              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.503  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.355372              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.739  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1522      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8723 = 2.66 * 0.50 * 5.1190 + 1.00 * 0.0585                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8610 = 2.66 * 0.50 * 5.1045 + 1.00 * 0.0667                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1061      final r-factor (work) = 0.1054          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9266 = 1.36 * 1.00 * 5.1045 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9191 = 1.36 * 1.00 * 5.0980 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.34    92.97   16.82    None  None   None       |
|    all(noH): 2823   0      0.34    92.97   16.82    None  None   None       |
|    Sol.    : 438    0      5.76    76.50   39.35    None  None   None       |
|    Mac.    : 2385   0      0.34    92.97   12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.344 -   9.607:  994   |   5:    46.658 -  55.920:   94        |
|      1:     9.607 -  18.870: 1156   |   6:    55.920 -  65.183:   68        |
|      2:    18.870 -  28.132:  226   |   7:    65.183 -  74.446:   14        |
|      3:    28.132 -  37.395:  137   |   8:    74.446 -  83.709:    5        |
|      4:    37.395 -  46.658:  124   |   9:    83.709 -  92.971:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1054 r_free = 0.1535             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1054 r_free = 0.1535             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1535   ksol= 0.32   Bsol= 44.06   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-1.72,-1.38,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104887                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1535   ksol= 0.32   Bsol= 45.96   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-1.53,-1.13,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104837                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.109920              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.035  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.997788              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.698  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1052      final r-factor (work) = 0.1043          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9957 = 3.11 * 0.50 * 5.0992 + 1.00 * 0.0667                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0005 = 3.11 * 0.50 * 5.1008 + 1.00 * 0.0689                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1043      final r-factor (work) = 0.1043          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1996 = 2.00 * 1.00 * 5.1008 + 1.00 * 0.0093                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2012 = 2.00 * 1.00 * 5.1014 + 1.00 * 0.0097                              |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.19   16.66    None  None   None       |
|    all(noH): 2823   0      0.00    94.19   16.66    None  None   None       |
|    Sol.    : 438    0      5.49    77.96   39.34    None  None   None       |
|    Mac.    : 2385   0      0.00    94.19   12.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.419: 1017   |   5:    47.097 -  56.516:   98        |
|      1:     9.419 -  18.839: 1144   |   6:    56.516 -  65.935:   63        |
|      2:    18.839 -  28.258:  219   |   7:    65.935 -  75.354:   14        |
|      3:    28.258 -  37.677:  134   |   8:    75.354 -  84.774:    4        |
|      4:    37.677 -  47.097:  125   |   9:    84.774 -  94.193:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1043 r_free = 0.1549             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1043 r_free = 0.1549             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1043   r_free= 0.1549   ksol= 0.32   Bsol= 45.96   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-1.53,-1.13,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.103890                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7251 0.99   1380  154 0.0943 0.1243      5.3496      5.5052|
|  2:  4.7251 -  3.7707 0.99   1329  146 0.0801 0.1083      5.3935        5.59|
|  3:  3.7707 -  3.3000 0.99   1305  147 0.0977 0.1481       5.422      5.8542|
|  4:  3.3000 -  3.0010 0.99   1293  138 0.1133 0.1558      5.4125      5.6005|
|  5:  3.0010 -  2.7875 0.99   1283  146 0.1201 0.1673      5.2795      5.4939|
|  6:  2.7875 -  2.6241 0.98   1281  142 0.1172 0.1811      5.1912      5.4253|
|  7:  2.6241 -  2.4933 0.99   1274  143 0.1124 0.1625      5.0981       5.329|
|  8:  2.4933 -  2.3852 0.98   1267  140 0.1072 0.1693      5.0359      5.3319|
|  9:  2.3852 -  2.2937 0.98   1276  146 0.1099 0.1770      4.9817      5.3135|
| 10:  2.2937 -  2.2148 0.97   1235  132 0.1045 0.1763      4.9472      5.1741|
| 11:  2.2148 -  2.1458 0.99   1273  144 0.1062 0.1730      4.9039      5.2643|
| 12:  2.1458 -  2.0846 0.98   1270  133 0.1029 0.1683      4.8389        5.17|
| 13:  2.0846 -  2.0299 0.97   1227  139 0.1054 0.1616       4.762      4.9814|
| 14:  2.0299 -  1.9805 0.73    937  109 0.0986 0.1790      4.6536      4.9583|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8444 -  4.7251  1380   154  0.94   9.02   0.98     0.95       6915.49|
|  2:  4.7251 -  3.7707  1329   146  0.95   7.67   1.02     1.00       8530.71|
|  3:  3.7707 -  3.3000  1305   147  0.94  10.70   1.03     1.02       9708.59|
|  4:  3.3000 -  3.0010  1293   138  0.92  13.03   1.01     1.00       9855.39|
|  5:  3.0010 -  2.7875  1283   146  0.90  15.28   1.00     0.97       7920.12|
|  6:  2.7875 -  2.6241  1281   142  0.90  15.71   0.98     0.95       6894.92|
|  7:  2.6241 -  2.4933  1274   143  0.91  14.74   0.98     0.96       5634.77|
|  8:  2.4933 -  2.3852  1267   140  0.91  14.56   0.99     0.97       5177.40|
|  9:  2.3852 -  2.2937  1276   146  0.91  15.17   0.99     0.96       4628.09|
| 10:  2.2937 -  2.2148  1235   132  0.90  15.38   0.99     0.96       4449.33|
| 11:  2.2148 -  2.1458  1273   144  0.90  15.69   0.99     0.96       4217.62|
| 12:  2.1458 -  2.0846  1270   133  0.92  14.53   1.00     0.98       3741.48|
| 13:  2.0846 -  2.0299  1227   139  0.91  15.24   0.99     0.98       3243.02|
| 14:  2.0299 -  1.9805   937   109  0.91  14.99   0.97     0.93       2591.29|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2591.29 max =         9855.39 mean =      6066.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.61|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.19|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1042   r_free= 0.1549   ksol= 0.32   Bsol= 46.49   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-1.32,-0.90,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1042   r_free= 0.1549   ksol= 0.32   Bsol= 46.49   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-1.32,-0.90,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104014                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7251 0.99   1380  154 0.0944 0.1247      5.3513      5.5071|
|  2:  4.7251 -  3.7707 0.99   1329  146 0.0802 0.1083      5.3944      5.5901|
|  3:  3.7707 -  3.3000 0.99   1305  147 0.0978 0.1482      5.4222      5.8545|
|  4:  3.3000 -  3.0010 0.99   1293  138 0.1133 0.1558      5.4124      5.6005|
|  5:  3.0010 -  2.7875 0.99   1283  146 0.1201 0.1673      5.2791      5.4935|
|  6:  2.7875 -  2.6241 0.98   1281  142 0.1172 0.1810      5.1909      5.4247|
|  7:  2.6241 -  2.4933 0.99   1274  143 0.1124 0.1625      5.0979       5.329|
|  8:  2.4933 -  2.3852 0.98   1267  140 0.1072 0.1692      5.0358      5.3315|
|  9:  2.3852 -  2.2937 0.98   1276  146 0.1099 0.1771      4.9817      5.3138|
| 10:  2.2937 -  2.2148 0.97   1235  132 0.1045 0.1764      4.9473      5.1743|
| 11:  2.2148 -  2.1458 0.99   1273  144 0.1062 0.1730      4.9039      5.2643|
| 12:  2.1458 -  2.0846 0.98   1270  133 0.1028 0.1683      4.8388      5.1699|
| 13:  2.0846 -  2.0299 0.97   1227  139 0.1054 0.1615      4.7619      4.9812|
| 14:  2.0299 -  1.9805 0.73    937  109 0.0986 0.1789      4.6536       4.958|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8444 -  4.7251  1380   154  0.94   9.04   0.98     0.95       6943.01|
|  2:  4.7251 -  3.7707  1329   146  0.95   7.68   1.02     1.00       8547.03|
|  3:  3.7707 -  3.3000  1305   147  0.94  10.70   1.03     1.03       9711.50|
|  4:  3.3000 -  3.0010  1293   138  0.92  13.03   1.02     1.01       9852.55|
|  5:  3.0010 -  2.7875  1283   146  0.90  15.28   1.00     0.98       7914.40|
|  6:  2.7875 -  2.6241  1281   142  0.90  15.71   0.99     0.96       6889.52|
|  7:  2.6241 -  2.4933  1274   143  0.91  14.74   0.99     0.97       5631.23|
|  8:  2.4933 -  2.3852  1267   140  0.91  14.56   1.00     0.98       5175.97|
|  9:  2.3852 -  2.2937  1276   146  0.91  15.17   1.00     0.97       4628.51|
| 10:  2.2937 -  2.2148  1235   132  0.90  15.38   1.00     0.97       4449.60|
| 11:  2.2148 -  2.1458  1273   144  0.90  15.69   1.01     0.97       4217.50|
| 12:  2.1458 -  2.0846  1270   133  0.92  14.52   1.01     0.99       3740.12|
| 13:  2.0846 -  2.0299  1227   139  0.91  15.24   1.01     0.99       3241.41|
| 14:  2.0299 -  1.9805   937   109  0.91  14.99   0.99     0.95       2590.14|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2590.14 max =         9852.55 mean =      6068.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.61|
|phase err.(test): min =        0.00 max =           89.82 mean =        13.19|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.20   16.66    None  None   None       |
|    all(noH): 2823   0      0.00    94.20   16.66    None  None   None       |
|    Sol.    : 438    0      5.49    77.96   39.34    None  None   None       |
|    Mac.    : 2385   0      0.00    94.20   12.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.422: 1017   |   5:    47.100 -  56.519:   98        |
|      1:     9.422 -  18.842: 1144   |   6:    56.519 -  65.938:   63        |
|      2:    18.842 -  28.261:  219   |   7:    65.938 -  75.357:   14        |
|      3:    28.261 -  37.680:  134   |   8:    75.357 -  84.777:    4        |
|      4:    37.680 -  47.100:  125   |   9:    84.777 -  94.196:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 278         
Filter by distance & map next to the model:
   mapped sites are within: 0.665 - 4.599
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 277 from: 278
   mapped sites are within: 0.701 - 4.599

peak=    5.456 closest distance to " CB  ARG A 275 " =    0.957
peak=    5.417 closest distance to " NH2 ARG A  56 " =    2.298
peak=    5.269 closest distance to " CG  PRO A  54 " =    1.199
peak=    5.243 closest distance to " CB  GLN A 223 " =    1.408
peak=    5.073 closest distance to " CB  SER A  63 " =    1.118
peak=    4.993 closest distance to " CB  GLN A 183 " =    1.325
peak=    4.987 closest distance to " O   HOH Z 142 " =    1.636
peak=    4.795 closest distance to " O   HOH Z 126 " =    1.817
peak=    4.755 closest distance to " O   HOH Z 232 " =    2.363
peak=    4.709 closest distance to " NE2 GLN A  11 " =    1.006
peak=    4.659 closest distance to " O   HOH Z 298 " =    1.844
peak=    4.648 closest distance to " CB  ARG A  79 " =    1.348
peak=    4.581 closest distance to " CB  GLU A 152 " =    1.152
peak=    4.557 closest distance to " CA  TYR A  30 " =    0.936
peak=    4.537 closest distance to " CG  PRO A 213 " =    1.171
peak=    4.494 closest distance to " C   PRO A 198 " =    1.454
peak=    4.476 closest distance to " O   HOH Z 236 " =    2.005
peak=    4.462 closest distance to " CB  TYR A 169 " =    0.868
peak=    4.444 closest distance to " NZ  LYS A 117 " =    3.255
peak=    4.435 closest distance to " O   HOH Z 234 " =    3.667
peak=    4.400 closest distance to " O   HOH Z 193 " =    1.781
peak=    4.390 closest distance to " O   HOH Z 403 " =    1.713
peak=    4.372 closest distance to " O   HOH Z  44 " =    2.003
peak=    4.278 closest distance to " O   HOH Z  15 " =    2.102
peak=    4.275 closest distance to " O   HOH Z  78 " =    1.648
peak=    4.250 closest distance to " O   HOH Z 272 " =    1.825
peak=    4.211 closest distance to " CB  ASN A 148 " =    1.766
peak=    4.177 closest distance to " CA  ALA A  21 " =    1.227
peak=    4.169 closest distance to " O   HOH Z 203 " =    1.776
peak=    4.144 closest distance to " O   HOH Z 144 " =    2.221
peak=    4.139 closest distance to " O   HOH Z 427 " =    2.913
peak=    4.139 closest distance to " O   HOH Z 369 " =    2.171
peak=    4.137 closest distance to " O   HOH Z 316 " =    2.965
peak=    4.122 closest distance to " CB  ARG A 190 " =    1.668
peak=    4.093 closest distance to " OD1 ASN A  69 " =    2.537
peak=    4.076 closest distance to " OG BSER A 164 " =    2.295
peak=    4.073 closest distance to " NH2BARG A 145 " =    2.150
peak=    4.073 closest distance to " ND2 ASN A 187 " =    1.456
peak=    4.068 closest distance to " O   HOH Z 402 " =    1.463
peak=    4.049 closest distance to " CB  GLU A 277 " =    3.531
peak=    4.037 closest distance to " O   HOH Z 303 " =    2.144
peak=    4.030 closest distance to " CD2 TRP A 179 " =    1.405
peak=    4.029 closest distance to " O   HOH Z 284 " =    2.977
peak=    4.018 closest distance to " CA  ASN A 176 " =    1.190
peak=    4.017 closest distance to " O   SER A  87 " =    2.211
peak=    4.000 closest distance to " CB  PRO A  54 " =    0.871
peak=    3.992 closest distance to " O   HOH Z 147 " =    1.780
peak=    3.991 closest distance to " O   HOH Z 327 " =    1.669
peak=    3.990 closest distance to " O   HOH Z 158 " =    2.979
peak=    3.984 closest distance to " CG  ARG A  66 " =    2.584
peak=    3.981 closest distance to " CB  SER A   3 " =    1.288
peak=    3.977 closest distance to " O   HOH Z 346 " =    1.704
peak=    3.974 closest distance to " CD2 LEU A 297 " =    0.862
peak=    3.967 closest distance to " OD2 ASP A 286 " =    2.827
peak=    3.965 closest distance to " CB  VAL A 265 " =    1.269
peak=    3.950 closest distance to " O   HOH Z  54 " =    1.753
peak=    3.947 closest distance to " O   HOH Z 368 " =    2.018
peak=    3.944 closest distance to " O   HOH Z 250 " =    1.470
peak=    3.937 closest distance to " O   HOH Z 371 " =    3.358
peak=    3.937 closest distance to " O   HOH Z  97 " =    1.893
peak=    3.930 closest distance to " CG  PRO A  90 " =    1.115
peak=    3.925 closest distance to " O   HOH Z 245 " =    1.316
peak=    3.924 closest distance to " OD2 ASP A 298 " =    3.893
peak=    3.909 closest distance to " O   HOH Z 180 " =    2.228
peak=    3.905 closest distance to " O   HOH Z 132 " =    2.610
peak=    3.897 closest distance to " O   HOH Z 183 " =    1.511
peak=    3.894 closest distance to " O   MET A 105 " =    1.896
peak=    3.888 closest distance to " CA  ASN A 215 " =    1.174
peak=    3.887 closest distance to " O   HOH Z  97 " =    2.546
peak=    3.860 closest distance to " O   HOH Z  19 " =    1.981
peak=    3.858 closest distance to " O   HOH Z  40 " =    1.828
peak=    3.852 closest distance to " CG1 ILE A  33 " =    1.173
peak=    3.846 closest distance to " CG2 ILE A  20 " =    1.364
peak=    3.826 closest distance to " O   HOH Z  43 " =    1.972
peak=    3.818 closest distance to " O   HOH Z  61 " =    1.567
peak=    3.791 closest distance to " CB  TRP A 266 " =    0.970
peak=    3.788 closest distance to " CB  TRP A 179 " =    1.223
peak=    3.778 closest distance to " CE  LYS A  76 " =    0.919
peak=    3.774 closest distance to " CB  ARG A 139 " =    0.940
peak=    3.772 closest distance to " O   HOH Z 389 " =    1.861
peak=    3.771 closest distance to " CB  ASP A 140 " =    0.986
peak=    3.769 closest distance to " O   HOH Z 426 " =    1.502
peak=    3.768 closest distance to " CB  GLU A 128 " =    1.136
peak=    3.750 closest distance to " CG1BVAL A  72 " =    1.595
peak=    3.745 closest distance to " CA  ARG A  36 " =    1.088
peak=    3.743 closest distance to " O   HOH Z 128 " =    1.920
peak=    3.724 closest distance to " CB  LEU A 228 " =    1.084
peak=    3.723 closest distance to " CG  PRO A 198 " =    1.232
peak=    3.722 closest distance to " O   HOH Z 132 " =    2.548
peak=    3.720 closest distance to " CG2 ILE A 120 " =    1.144
peak=    3.719 closest distance to " CB  SER A  26 " =    1.640
peak=    3.715 closest distance to " O   HOH Z 197 " =    2.855
peak=    3.714 closest distance to " CA  ALA A 291 " =    0.844
peak=    3.709 closest distance to " OE1 GLU A   2 " =    2.218
peak=    3.707 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.705 closest distance to " CG  PRO A 243 " =    1.133
peak=    3.695 closest distance to " O   HOH Z 411 " =    3.839
peak=    3.695 closest distance to " CG  GLN A  58 " =    2.564
peak=    3.688 closest distance to " CZ  PHE A 218 " =    1.091
peak=    3.686 closest distance to " O   HOH Z 416 " =    2.803
peak=    3.674 closest distance to " N   ASN A  39 " =    1.351
peak=    3.674 closest distance to " O   HOH Z 344 " =    3.089
peak=    3.671 closest distance to " O   HOH Z 189 " =    2.145
peak=    3.663 closest distance to " CA  LYS A 117 " =    1.248
peak=    3.661 closest distance to " O   HOH Z 291 " =    1.521
peak=    3.661 closest distance to " CB  ALA A 291 " =    1.352
peak=    3.656 closest distance to " CA  ASP A 140 " =    1.125
peak=    3.653 closest distance to " O   HOH Z  59 " =    2.316
peak=    3.646 closest distance to " O   HOH Z  63 " =    1.986
peak=    3.639 closest distance to " CB  ASN A  39 " =    0.844
peak=    3.633 closest distance to " O   HOH Z 423 " =    2.001
peak=    3.623 closest distance to " O   HOH Z 108 " =    2.482
peak=    3.622 closest distance to " CA  THR A 221 " =    0.938
peak=    3.618 closest distance to " O   HOH Z 279 " =    2.116
peak=    3.612 closest distance to " O   HOH Z 345 " =    3.034
peak=    3.608 closest distance to " O   HOH Z 193 " =    2.148
peak=    3.602 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.600 closest distance to " O   HOH Z 185 " =    1.725
peak=    3.598 closest distance to " CD1 LEU A 300 " =    1.239
peak=    3.598 closest distance to " CG  LYS A  76 " =    1.019
peak=    3.586 closest distance to " CA  ARG A 195 " =    1.235
peak=    3.578 closest distance to " O   HOH Z 357 " =    1.881
peak=    3.562 closest distance to " O   HOH Z  35 " =    2.416
peak=    3.562 closest distance to " O   HOH Z 128 " =    2.234
peak=    3.553 closest distance to " O   HOH Z 406 " =    1.548
peak=    3.538 closest distance to " O   HOH Z 417 " =    3.019
peak=    3.537 closest distance to " O   HOH Z 374 " =    2.603
peak=    3.534 closest distance to " O   HOH Z  68 " =    1.720
peak=    3.530 closest distance to " O   HOH Z 337 " =    3.693
peak=    3.529 closest distance to " O   HOH Z 425 " =    2.061
peak=    3.520 closest distance to " CZ2 TRP A 179 " =    1.659
peak=    3.508 closest distance to " O   HOH Z 126 " =    1.567
peak=    3.508 closest distance to " O   HOH Z 265 " =    2.312
peak=    3.508 closest distance to " ND2 ASN A 110 " =    1.648
peak=    3.504 closest distance to " O   HOH Z 325 " =    2.430
peak=    3.503 closest distance to " O   HOH Z 305 " =    3.628
peak=    3.502 closest distance to " O   HOH Z 361 " =    3.471
peak=    3.501 closest distance to " CD1 ILE A 106 " =    0.915
peak=    3.499 closest distance to " CB  TYR A 169 " =    0.936
peak=    3.495 closest distance to " O   HOH Z 359 " =    1.415
peak=    3.476 closest distance to " CA  ALA A  84 " =    1.297
peak=    3.474 closest distance to " CD  ARG A 159 " =    0.745
peak=    3.467 closest distance to " O   HOH Z 421 " =    1.558
peak=    3.461 closest distance to " O   HOH Z 214 " =    2.282
peak=    3.460 closest distance to " O   HOH Z 148 " =    3.174
peak=    3.459 closest distance to " O   HOH Z  21 " =    1.763
peak=    3.458 closest distance to " O   HOH Z 227 " =    1.429
peak=    3.455 closest distance to " O   HOH Z 380 " =    1.979
peak=    3.452 closest distance to " O   HOH Z 173 " =    1.972
peak=    3.451 closest distance to " CG2 THR A 221 " =    1.148
peak=    3.450 closest distance to " CB  ILE A 120 " =    1.310
peak=    3.450 closest distance to " NH1AARG A 145 " =    1.225
peak=    3.435 closest distance to " O   HOH Z 214 " =    2.370
peak=    3.425 closest distance to " CB  GLN A  89 " =    1.328
peak=    3.411 closest distance to " O   HOH Z  10 " =    1.794
peak=    3.406 closest distance to " OG1 THR A 294 " =    2.362
peak=    3.400 closest distance to " O   HOH Z 368 " =    2.662
peak=    3.399 closest distance to " O   HOH Z  89 " =    2.140
peak=    3.399 closest distance to " O   HOH Z  88 " =    3.168
peak=    3.397 closest distance to " ND1 HIS A  81 " =    1.588
peak=    3.397 closest distance to " CG2 VAL A 257 " =    0.853
peak=    3.397 closest distance to " O   HOH Z 299 " =    4.386
peak=    3.391 closest distance to " CD  LYS A 166 " =    1.310
peak=    3.387 closest distance to " CD BLYS A 290 " =    1.213
peak=    3.375 closest distance to " O   HOH Z 163 " =    1.924
peak=    3.371 closest distance to " O   HOH Z 281 " =    4.599
peak=    3.369 closest distance to " O   HOH Z  66 " =    2.119
peak=    3.361 closest distance to " NH2 ARG A 156 " =    1.141
peak=    3.349 closest distance to " O   HOH Z 383 " =    2.087
peak=    3.345 closest distance to " O   HOH Z 250 " =    1.568
peak=    3.338 closest distance to " O   HOH Z  49 " =    2.082
peak=    3.334 closest distance to " O   HOH Z 313 " =    1.684
peak=    3.334 closest distance to " CA  ALA A  51 " =    0.952
peak=    3.323 closest distance to " CB  SER A 141 " =    0.988
peak=    3.323 closest distance to " CB  VAL A 202 " =    1.500
peak=    3.322 closest distance to " O   HOH Z 423 " =    3.357
peak=    3.318 closest distance to " O   HOH Z  66 " =    2.087
peak=    3.313 closest distance to " CG2 VAL A 197 " =    1.134
peak=    3.311 closest distance to " CD2 HIS A  81 " =    1.163
peak=    3.311 closest distance to " O   HOH Z  85 " =    2.271
peak=    3.308 closest distance to " CB  SER A  62 " =    0.844
peak=    3.301 closest distance to " O   HOH Z 341 " =    1.885
peak=    3.296 closest distance to " O   HOH Z 433 " =    1.843
peak=    3.290 closest distance to " O   HOH Z  80 " =    1.598
peak=    3.290 closest distance to " O   HOH Z 123 " =    2.337
peak=    3.285 closest distance to " O   HOH Z 365 " =    2.951
peak=    3.284 closest distance to " O   HOH Z 209 " =    2.270
peak=    3.283 closest distance to " O   HOH Z 258 " =    2.286
peak=    3.282 closest distance to " NH2 ARG A 219 " =    1.890
peak=    3.281 closest distance to " O   HOH Z 175 " =    2.073
peak=    3.281 closest distance to " CG AARG A 275 " =    1.052
peak=    3.277 closest distance to " CB  MET A  47 " =    0.894
peak=    3.277 closest distance to " CA  ASP A 162 " =    1.127
peak=    3.272 closest distance to " NZ  LYS A 166 " =    3.068
peak=    3.270 closest distance to " CB  THR A  31 " =    1.780
peak=    3.265 closest distance to " O   HOH Z 286 " =    2.140
peak=    3.265 closest distance to " CB  TYR A 116 " =    0.793
peak=    3.262 closest distance to " O   ALA A 165 " =    1.432
peak=    3.260 closest distance to " CB  SER A 212 " =    1.012
peak=    3.257 closest distance to " OG  SER A  62 " =    2.823
peak=    3.257 closest distance to " O   HOH Z 336 " =    1.744
peak=    3.254 closest distance to " CG2BVAL A  41 " =    0.794
peak=    3.253 closest distance to " O   HOH Z 435 " =    1.789
peak=    3.249 closest distance to " CD1 LEU A 228 " =    1.645
peak=    3.248 closest distance to " CB  SER A 216 " =    0.834
peak=    3.245 closest distance to " CG2 VAL A 202 " =    1.163
peak=    3.245 closest distance to " CG1 ILE A 151 " =    0.958
peak=    3.242 closest distance to " CA  ALA A 160 " =    0.853
peak=    3.238 closest distance to " O   HOH Z 193 " =    1.555
peak=    3.234 closest distance to " N   ARG A 156 " =    1.323
peak=    3.233 closest distance to " O   HOH Z 124 " =    2.073
peak=    3.232 closest distance to " O   HOH Z 189 " =    2.620
peak=    3.230 closest distance to " O   HOH Z 163 " =    1.379
peak=    3.230 closest distance to " CA  MET A 105 " =    1.035
peak=    3.227 closest distance to " CE  LYS A  48 " =    1.065
peak=    3.226 closest distance to " O   HOH Z 134 " =    1.236
peak=    3.223 closest distance to " NE2 GLN A  77 " =    3.180
peak=    3.219 closest distance to " CB  ALA A 248 " =    1.340
peak=    3.215 closest distance to " CG  GLN A  77 " =    2.120
peak=    3.213 closest distance to " CG BARG A 275 " =    1.320
peak=    3.212 closest distance to " OG  SER A  22 " =    2.621
peak=    3.206 closest distance to " CE  LYS A 119 " =    1.143
peak=    3.205 closest distance to " CG  ARG A  66 " =    0.906
peak=    3.202 closest distance to " O   TRP A 274 " =    1.942
peak=    3.200 closest distance to " O   HOH Z 171 " =    1.832
peak=    3.199 closest distance to " CB  ALA A 242 " =    1.042
peak=    3.198 closest distance to " CB  GLN A  88 " =    1.148
peak=    3.198 closest distance to " O   HOH Z 273 " =    2.734
peak=    3.193 closest distance to " CB  ALA A 295 " =    1.209
peak=    3.189 closest distance to " O   HOH Z 391 " =    2.970
peak=    3.187 closest distance to " O   HOH Z 292 " =    1.542
peak=    3.186 closest distance to " CB  ASN A 215 " =    1.153
peak=    3.184 closest distance to " CD2 LEU A 255 " =    1.429
peak=    3.181 closest distance to " O   HOH Z 326 " =    1.501
peak=    3.181 closest distance to " CB  ARG A 269 " =    0.701
peak=    3.178 closest distance to " CB  ALA A   9 " =    1.611
peak=    3.175 closest distance to " CA  TYR A 116 " =    1.358
peak=    3.174 closest distance to " O   HOH Z 403 " =    1.285
peak=    3.164 closest distance to " N   HIS A  86 " =    1.902
peak=    3.163 closest distance to " NE2 GLN A  58 " =    2.786
peak=    3.163 closest distance to " CD1AILE A 234 " =    0.934
peak=    3.161 closest distance to " O   GLY A  57 " =    2.644
peak=    3.160 closest distance to " CD2 TYR A  30 " =    1.046
peak=    3.157 closest distance to " O   HOH Z 299 " =    2.450
peak=    3.157 closest distance to " O   HOH Z  46 " =    1.465
peak=    3.152 closest distance to " O   HOH Z 261 " =    1.500
peak=    3.150 closest distance to " CA  GLY A  80 " =    0.872
peak=    3.150 closest distance to " O   HOH Z 256 " =    2.470
peak=    3.149 closest distance to " CA  ASN A 217 " =    1.228
peak=    3.145 closest distance to " CA  LEU A  83 " =    1.360
peak=    3.144 closest distance to " O   HOH Z 438 " =    1.752
peak=    3.140 closest distance to " O   HOH Z 267 " =    2.013
peak=    3.136 closest distance to " CB  GLN A 278 " =    0.901
peak=    3.135 closest distance to " O   HOH Z 411 " =    1.689
peak=    3.130 closest distance to " CE1 HIS A 115 " =    3.719
peak=    3.127 closest distance to " O   HOH Z 234 " =    1.815
peak=    3.127 closest distance to " CA  ILE A  33 " =    1.421
peak=    3.125 closest distance to " CB  ASN A 127 " =    0.807
peak=    3.120 closest distance to " O   SER A  26 " =    1.694
peak=    3.120 closest distance to " O   HOH Z 135 " =    1.585
peak=    3.119 closest distance to " CA  THR A 264 " =    0.898
peak=    3.118 closest distance to " CD  LYS A 119 " =    1.300
peak=    3.117 closest distance to " O   HOH Z 261 " =    2.184
peak=    3.116 closest distance to " O   HOH Z  44 " =    3.379
peak=    3.108 closest distance to " CD1 LEU A  96 " =    0.707
peak=    3.107 closest distance to " O   HOH Z 203 " =    1.193
peak=    3.107 closest distance to " CG  GLU A 277 " =    2.101
peak=    3.102 closest distance to " O   HOH Z 417 " =    2.234
peak=    3.098 closest distance to " CA  ALA A 233 " =    1.060
peak=    3.096 closest distance to " CA  ALA A 158 " =    1.207
peak=    3.094 closest distance to " O   HOH Z 367 " =    3.581
peak=    3.092 closest distance to " O   HOH Z  88 " =    2.579
peak=    3.087 closest distance to " O   HOH Z  49 " =    2.607
peak=    3.080 closest distance to " CB  ARG A 138 " =    0.873
peak=    3.072 closest distance to " O   HOH Z 353 " =    2.785
peak=    3.066 closest distance to " CA  ARG A 102 " =    1.101
peak=    3.047 closest distance to " OE2 GLU A  53 " =    2.131

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.850 - 5.721
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 210
   mapped sites are within: 0.850 - 5.721

peak=   -5.032 closest distance to " O   HOH Z 266 " =    4.673
peak=   -4.598 closest distance to " SG  CYS A 254 " =    3.408
peak=   -4.445 closest distance to " CB  PRO A 243 " =    2.637
peak=   -4.406 closest distance to " C   HIS A 108 " =    1.107
peak=   -4.337 closest distance to " O   HOH Z 377 " =    2.108
peak=   -4.310 closest distance to " O   VAL A  67 " =    2.712
peak=   -4.240 closest distance to " OG BSER A 134 " =    1.296
peak=   -4.179 closest distance to " CD  ARG A 156 " =    2.075
peak=   -4.157 closest distance to " OXT GLY A 302 " =    2.774
peak=   -4.109 closest distance to " O   HOH Z 196 " =    1.955
peak=   -4.095 closest distance to " O   HOH Z  13 " =    1.672
peak=   -4.080 closest distance to " CG  GLN A 223 " =    1.980
peak=   -4.052 closest distance to " O   HOH Z 372 " =    2.344
peak=   -4.031 closest distance to " CB  ALA A 161 " =    2.595
peak=   -3.997 closest distance to " O   SER A 210 " =    1.845
peak=   -3.990 closest distance to " OG  SER A  97 " =    2.158
peak=   -3.988 closest distance to " CE2 TYR A  30 " =    2.756
peak=   -3.977 closest distance to " CD1 PHE A  59 " =    1.904
peak=   -3.973 closest distance to " CG  ASP A 132 " =    2.333
peak=   -3.958 closest distance to " O   HOH Z 198 " =    2.090
peak=   -3.954 closest distance to " O   HOH Z  10 " =    1.541
peak=   -3.944 closest distance to " CD  GLN A  58 " =    1.150
peak=   -3.923 closest distance to " O   HOH Z 353 " =    2.269
peak=   -3.894 closest distance to " N   GLN A  58 " =    1.475
peak=   -3.894 closest distance to " N   ALA A  43 " =    2.701
peak=   -3.884 closest distance to " CD1 LEU A  25 " =    2.497
peak=   -3.879 closest distance to " CD1 PHE A 130 " =    2.357
peak=   -3.861 closest distance to " O   VAL A  67 " =    2.790
peak=   -3.843 closest distance to " O   HOH Z 389 " =    1.778
peak=   -3.841 closest distance to " CZ  TYR A 169 " =    1.803
peak=   -3.839 closest distance to " CZ3 TRP A 179 " =    1.250
peak=   -3.839 closest distance to " O   PRO A 163 " =    2.091
peak=   -3.837 closest distance to " O   HOH Z 165 " =    2.015
peak=   -3.820 closest distance to " CG1 VAL A 112 " =    2.777
peak=   -3.815 closest distance to " CD1 LEU A 228 " =    2.154
peak=   -3.813 closest distance to " O   HOH Z 114 " =    3.312
peak=   -3.811 closest distance to " O   HOH Z 292 " =    4.498
peak=   -3.806 closest distance to " CA  ASP A 298 " =    1.036
peak=   -3.805 closest distance to " O   HOH Z 126 " =    1.922
peak=   -3.770 closest distance to " O   HOH Z 166 " =    1.568
peak=   -3.764 closest distance to " ND2 ASN A 187 " =    1.470
peak=   -3.747 closest distance to " O   HOH Z 290 " =    1.150
peak=   -3.738 closest distance to " CD1 LEU A 101 " =    2.414
peak=   -3.722 closest distance to " CZ  PHE A  59 " =    1.636
peak=   -3.721 closest distance to " O   HOH Z 407 " =    2.881
peak=   -3.720 closest distance to " N   ALA A 248 " =    1.726
peak=   -3.695 closest distance to " O   HOH Z 234 " =    4.106
peak=   -3.694 closest distance to " OG BSER A 134 " =    1.728
peak=   -3.686 closest distance to " CB  TYR A  15 " =    2.217
peak=   -3.685 closest distance to " O   MET A  40 " =    2.634
peak=   -3.680 closest distance to " CB  ALA A 291 " =    2.354
peak=   -3.667 closest distance to " CD  ARG A 139 " =    1.576
peak=   -3.664 closest distance to " CG2 ILE A 263 " =    2.243
peak=   -3.660 closest distance to " NE2 GLN A  88 " =    1.857
peak=   -3.643 closest distance to " O   HOH Z  11 " =    2.128
peak=   -3.635 closest distance to " CB  ALA A 291 " =    2.291
peak=   -3.628 closest distance to " O   HOH Z 166 " =    1.791
peak=   -3.621 closest distance to " C   LEU A 143 " =    1.039
peak=   -3.617 closest distance to " O   HOH Z 185 " =    2.265
peak=   -3.613 closest distance to " ND2 ASN A  45 " =    1.044
peak=   -3.612 closest distance to " OG  SER A   3 " =    1.750
peak=   -3.607 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.606 closest distance to " CG  ASP A 231 " =    0.850
peak=   -3.592 closest distance to " CB  PHE A 192 " =    1.964
peak=   -3.578 closest distance to " O   PHE A 218 " =    1.608
peak=   -3.575 closest distance to " CB  ASN A  39 " =    2.326
peak=   -3.565 closest distance to " OD1 ASP A 171 " =    1.608
peak=   -3.562 closest distance to " NH1 ARG A 195 " =    2.588
peak=   -3.551 closest distance to " O   HOH Z 311 " =    3.634
peak=   -3.549 closest distance to " O   HOH Z  52 " =    1.377
peak=   -3.549 closest distance to " CB  ALA A 248 " =    2.252
peak=   -3.548 closest distance to " CB  PHE A 208 " =    2.199
peak=   -3.534 closest distance to " ND2 ASN A  45 " =    1.493
peak=   -3.531 closest distance to " SG ACYS A 201 " =    2.008
peak=   -3.514 closest distance to " OD2 ASP A 171 " =    2.375
peak=   -3.511 closest distance to " O   HOH Z 361 " =    3.461
peak=   -3.505 closest distance to " OE2 GLU A   2 " =    1.854
peak=   -3.502 closest distance to " CB  ALA A  43 " =    2.444
peak=   -3.502 closest distance to " OD1 ASN A 148 " =    1.575
peak=   -3.493 closest distance to " CB  TRP A  85 " =    2.567
peak=   -3.486 closest distance to " CD2 LEU A 300 " =    2.965
peak=   -3.486 closest distance to " NH2AARG A 275 " =    5.125
peak=   -3.476 closest distance to " O   HOH Z 252 " =    3.697
peak=   -3.474 closest distance to " CG1 VAL A 250 " =    2.596
peak=   -3.468 closest distance to " O   VAL A 174 " =    2.139
peak=   -3.468 closest distance to " O   HOH Z 394 " =    1.531
peak=   -3.465 closest distance to " CB  ASP A 286 " =    1.910
peak=   -3.464 closest distance to " C   ILE A 234 " =    1.395
peak=   -3.457 closest distance to " OG  SER A  62 " =    1.629
peak=   -3.456 closest distance to " O   HOH Z 243 " =    2.029
peak=   -3.445 closest distance to " O   HOH Z  38 " =    1.581
peak=   -3.441 closest distance to " O   LEU A 167 " =    1.492
peak=   -3.441 closest distance to " CG2 THR A 178 " =    2.205
peak=   -3.439 closest distance to " O   HOH Z 395 " =    5.176
peak=   -3.438 closest distance to " O   HOH Z 211 " =    1.646
peak=   -3.415 closest distance to " O   HOH Z 435 " =    2.645
peak=   -3.412 closest distance to " NH2 ARG A  79 " =    2.005
peak=   -3.398 closest distance to " CA  GLY A 203 " =    2.335
peak=   -3.392 closest distance to " O   HOH Z 298 " =    1.281
peak=   -3.386 closest distance to " OG  SER A  26 " =    1.297
peak=   -3.373 closest distance to " O   HOH Z 385 " =    1.961
peak=   -3.370 closest distance to " OG BSER A 210 " =    2.008
peak=   -3.364 closest distance to " OD1 ASP A 191 " =    1.772
peak=   -3.363 closest distance to " OG ASER A 134 " =    1.146
peak=   -3.361 closest distance to " O   HOH Z 414 " =    1.600
peak=   -3.361 closest distance to " O   HOH Z 351 " =    1.460
peak=   -3.355 closest distance to " O   HOH Z  43 " =    1.576
peak=   -3.351 closest distance to " NH2 ARG A 159 " =    2.361
peak=   -3.348 closest distance to " O   HOH Z 283 " =    2.029
peak=   -3.347 closest distance to " O   HOH Z   6 " =    1.674
peak=   -3.346 closest distance to " O   ALA A 161 " =    1.690
peak=   -3.341 closest distance to " O   SER A 135 " =    1.564
peak=   -3.340 closest distance to " CG1 VAL A 125 " =    2.302
peak=   -3.328 closest distance to " OD2 ASP A 191 " =    1.518
peak=   -3.318 closest distance to " N   VAL A 189 " =    1.657
peak=   -3.316 closest distance to " O   GLY A  80 " =    2.602
peak=   -3.306 closest distance to " CG1 VAL A  78 " =    2.957
peak=   -3.303 closest distance to " O   HOH Z  11 " =    1.722
peak=   -3.303 closest distance to " CA  PRO A 243 " =    2.331
peak=   -3.302 closest distance to " CE2 PHE A 218 " =    2.417
peak=   -3.302 closest distance to " O   HOH Z   9 " =    2.071
peak=   -3.295 closest distance to " O   ALA A 160 " =    1.462
peak=   -3.294 closest distance to " O   GLY A  75 " =    1.820
peak=   -3.291 closest distance to " CE  MET A  93 " =    1.250
peak=   -3.291 closest distance to " NH2 ARG A  66 " =    5.339
peak=   -3.287 closest distance to " CG  PRO A 163 " =    2.661
peak=   -3.281 closest distance to " CD2 TYR A 247 " =    2.438
peak=   -3.270 closest distance to " O   HOH Z 377 " =    1.699
peak=   -3.267 closest distance to " CA  GLY A 133 " =    2.316
peak=   -3.267 closest distance to " O   HOH Z 191 " =    5.721
peak=   -3.266 closest distance to " O   VAL A 189 " =    2.595
peak=   -3.264 closest distance to " O   HOH Z  88 " =    2.319
peak=   -3.262 closest distance to " O   PRO A 198 " =    1.305
peak=   -3.262 closest distance to " N   ALA A 226 " =    1.998
peak=   -3.260 closest distance to " O   ASN A 187 " =    1.485
peak=   -3.258 closest distance to " O   HOH Z 369 " =    2.244
peak=   -3.258 closest distance to " C   GLY A  80 " =    2.412
peak=   -3.257 closest distance to " O   HOH Z  90 " =    2.816
peak=   -3.257 closest distance to " CZ2 TRP A 274 " =    1.120
peak=   -3.255 closest distance to " O   HOH Z 102 " =    1.573
peak=   -3.253 closest distance to " OE1 GLN A 223 " =    1.934
peak=   -3.251 closest distance to " O   GLY A 196 " =    1.001
peak=   -3.250 closest distance to " CD2 LEU A 237 " =    2.529
peak=   -3.250 closest distance to " O   HOH Z 377 " =    1.811
peak=   -3.248 closest distance to " CB  ALA A 248 " =    1.988
peak=   -3.246 closest distance to " O   HOH Z 233 " =    2.395
peak=   -3.245 closest distance to " O   HOH Z 193 " =    1.792
peak=   -3.242 closest distance to " N   GLN A 122 " =    1.456
peak=   -3.239 closest distance to " O   ALA A  10 " =    1.800
peak=   -3.235 closest distance to " O   PRO A  90 " =    1.797
peak=   -3.234 closest distance to " O   ALA A  34 " =    2.281
peak=   -3.233 closest distance to " CG2 VAL A 189 " =    2.237
peak=   -3.229 closest distance to " OE2 GLU A   2 " =    1.436
peak=   -3.228 closest distance to " O   HOH Z 263 " =    2.985
peak=   -3.227 closest distance to " O   HOH Z 123 " =    2.284
peak=   -3.225 closest distance to " CB  GLN A  11 " =    1.871
peak=   -3.219 closest distance to " O   LYS A 117 " =    1.660
peak=   -3.218 closest distance to " C   ALA A 158 " =    1.263
peak=   -3.216 closest distance to " O   HOH Z 171 " =    1.992
peak=   -3.211 closest distance to " NH2 ARG A  66 " =    4.999
peak=   -3.209 closest distance to " CG  PRO A 280 " =    2.298
peak=   -3.208 closest distance to " CE  MET A 105 " =    2.174
peak=   -3.203 closest distance to " CD1 LEU A  83 " =    2.371
peak=   -3.202 closest distance to " N   SER A 276 " =    1.418
peak=   -3.201 closest distance to " O   HOH Z  71 " =    1.829
peak=   -3.200 closest distance to " O   HOH Z  37 " =    1.798
peak=   -3.195 closest distance to " O   HOH Z 111 " =    1.841
peak=   -3.194 closest distance to " O   HOH Z 427 " =    1.380
peak=   -3.193 closest distance to " O   ASP A 171 " =    2.025
peak=   -3.191 closest distance to " O   ILE A 106 " =    1.837
peak=   -3.190 closest distance to " CE3 TRP A 150 " =    2.236
peak=   -3.182 closest distance to " ND2 ASN A  69 " =    1.530
peak=   -3.181 closest distance to " O   HOH Z 213 " =    1.520
peak=   -3.179 closest distance to " CA  GLY A 133 " =    1.943
peak=   -3.178 closest distance to " CD  ARG A  36 " =    1.963
peak=   -3.174 closest distance to " N   ALA A 248 " =    2.472
peak=   -3.172 closest distance to " NH2 ARG A  79 " =    1.563
peak=   -3.169 closest distance to " OD2 ASP A 171 " =    1.769
peak=   -3.165 closest distance to " O   TRP A  92 " =    1.752
peak=   -3.164 closest distance to " O   HOH Z 148 " =    3.829
peak=   -3.159 closest distance to " CE2 PHE A 192 " =    2.041
peak=   -3.153 closest distance to " O   ILE A 234 " =    1.300
peak=   -3.152 closest distance to " OG1 THR A 178 " =    1.286
peak=   -3.145 closest distance to " CG  LYS A 119 " =    2.854
peak=   -3.141 closest distance to " O   HOH Z 388 " =    2.001
peak=   -3.139 closest distance to " O   HOH Z  44 " =    3.700
peak=   -3.137 closest distance to " O   HOH Z 322 " =    1.694
peak=   -3.136 closest distance to " O   HOH Z 250 " =    1.413
peak=   -3.135 closest distance to " O   HOH Z 111 " =    2.305
peak=   -3.135 closest distance to " O   HOH Z 353 " =    2.194
peak=   -3.134 closest distance to " CG  GLU A 277 " =    1.209
peak=   -3.133 closest distance to " C   PRO A  90 " =    1.500
peak=   -3.132 closest distance to " CB  ASP A 132 " =    2.389
peak=   -3.131 closest distance to " O   HOH Z 422 " =    1.563
peak=   -3.126 closest distance to " CD2 PHE A 225 " =    1.283
peak=   -3.121 closest distance to " CA  GLY A 241 " =    3.100
peak=   -3.095 closest distance to " O   ALA A  51 " =    1.331
peak=   -3.094 closest distance to " O   HOH Z 351 " =    1.397
peak=   -3.094 closest distance to " O   PRO A 198 " =    1.640
peak=   -3.090 closest distance to " NE2 GLN A  58 " =    1.237
peak=   -3.088 closest distance to " CG  GLU A 152 " =    1.288
peak=   -3.081 closest distance to " O   ASN A 301 " =    1.350
peak=   -3.078 closest distance to " CG  ASN A 301 " =    2.002
peak=   -3.054 closest distance to " CG1AVAL A  41 " =    2.817
peak=   -3.047 closest distance to " OG1 THR A  82 " =    1.525
peak=   -3.043 closest distance to " OD2 ASP A 171 " =    2.375
peak=   -3.039 closest distance to " CD2 LEU A 237 " =    2.157
peak=   -3.005 closest distance to " O   HOH Z  15 " =    1.755

================= 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    :  0.3365 0.3311   6.064157e+00   6.044486e+00
   1_bss:  0.3245 0.3171   6.043892e+00   6.012072e+00
   1_xyz:  0.1934 0.2100   5.575662e+00   5.654759e+00
   1_adp:  0.1762 0.2178   5.520146e+00   5.687761e+00
   1_occ:  0.1758 0.2181   5.519543e+00   5.687866e+00
   2_bss:  0.1749 0.2168   5.517707e+00   5.683946e+00
   2_xyz:  0.1280 0.1691   5.240350e+00   5.446971e+00
   2_adp:  0.1223 0.1603   5.190935e+00   5.394486e+00
   2_occ:  0.1221 0.1601   5.189861e+00   5.393567e+00
   3_bss:  0.1224 0.1588   5.189286e+00   5.390373e+00
   3_xyz:  0.1123 0.1522   5.131090e+00   5.354422e+00
   3_adp:  0.1099 0.1522   5.119746e+00   5.353294e+00
   3_occ:  0.1099 0.1522   5.119538e+00   5.353244e+00
   4_bss:  0.1098 0.1522   5.119446e+00   5.353203e+00
   4_xyz:  0.1061 0.1523   5.102600e+00   5.351496e+00
   4_adp:  0.1054 0.1535   5.104780e+00   5.359918e+00
   4_occ:  0.1054 0.1535   5.104887e+00   5.360282e+00
   5_bss:  0.1052 0.1535   5.104837e+00   5.360205e+00
   5_xyz:  0.1043 0.1545   5.103131e+00   5.364928e+00
   5_adp:  0.1043 0.1549   5.103821e+00   5.367659e+00
   5_occ:  0.1043 0.1549   5.103890e+00   5.367879e+00
   5_bss:  0.1042 0.1549   5.104014e+00   5.367973e+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:  0.304  30.712  -2.267   0.492  -0.422   0.000  -0.000  -0.000
   1_xyz:  0.304  30.712  -2.267   0.492  -0.422   0.000  -0.000  -0.000
   1_adp:  0.304  30.712  -2.267   0.492  -0.422   0.000  -0.000  -0.000
   1_occ:  0.304  30.712  -2.267   0.492  -0.422   0.000  -0.000  -0.000
   2_bss:  0.313  41.970  -3.031  -1.289  -1.454  -0.000  -0.000  -0.000
   2_xyz:  0.313  41.970  -3.031  -1.289  -1.454  -0.000  -0.000  -0.000
   2_adp:  0.313  41.970  -3.031  -1.289  -1.454  -0.000  -0.000  -0.000
   2_occ:  0.313  41.970  -3.031  -1.289  -1.454  -0.000  -0.000  -0.000
   3_bss:  0.318  42.585  -2.879  -1.699  -1.475  -0.000  -0.000  -0.000
   3_xyz:  0.318  42.585  -2.879  -1.699  -1.475  -0.000  -0.000  -0.000
   3_adp:  0.318  42.585  -2.879  -1.699  -1.475  -0.000  -0.000  -0.000
   3_occ:  0.318  42.585  -2.879  -1.699  -1.475  -0.000  -0.000  -0.000
   4_bss:  0.321  44.057  -2.726  -1.723  -1.379  -0.000  -0.000  -0.000
   4_xyz:  0.321  44.057  -2.726  -1.723  -1.379  -0.000  -0.000  -0.000
   4_adp:  0.321  44.057  -2.726  -1.723  -1.379  -0.000  -0.000  -0.000
   4_occ:  0.321  44.057  -2.726  -1.723  -1.379  -0.000  -0.000  -0.000
   5_bss:  0.322  45.956  -2.459  -1.530  -1.133  -0.000  -0.000  -0.000
   5_xyz:  0.322  45.956  -2.459  -1.530  -1.133  -0.000  -0.000  -0.000
   5_adp:  0.322  45.956  -2.459  -1.530  -1.133  -0.000  -0.000  -0.000
   5_occ:  0.322  45.956  -2.459  -1.530  -1.133  -0.000  -0.000  -0.000
   5_bss:  0.323  46.490  -2.213  -1.315  -0.895  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.615 0.7205  0.9040    30239.893
   1_bss:  32.336 0.7331  0.8955    26704.912
   1_xyz:  19.828 0.8646  1.0022    11062.387
   1_adp:  20.896 0.8534  0.9917    11884.492
   1_occ:  20.917 0.8532  0.9913    11900.789
   2_bss:  20.755 0.8547  0.9524    11756.817
   2_xyz:  15.506 0.9019  0.9812     7109.930
   2_adp:  14.297 0.9124  0.9816     6451.925
   2_occ:  14.286 0.9125  0.9814     6433.361
   3_bss:  14.210 0.9130  0.9785     6357.492
   3_xyz:  13.408 0.9196  0.9820     5925.427
   3_adp:  13.360 0.9202  0.9768     5913.755
   3_occ:  13.356 0.9202  0.9767     5909.453
   4_bss:  13.353 0.9202  0.9797     5912.295
   4_xyz:  13.298 0.9206  0.9789     5883.572
   4_adp:  13.455 0.9195  0.9707     5968.255
   4_occ:  13.459 0.9194  0.9706     5971.186
   5_bss:  13.459 0.9194  0.9791     5971.242
   5_xyz:  13.519 0.9190  0.9796     6041.716
   5_adp:  13.566 0.9186  0.9721     6064.410
   5_occ:  13.568 0.9186  0.9720     6065.597
   5_bss:  13.570 0.9186  0.9804     6067.589
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6580e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6580e-01
   1_xyz:   1.090  0.008  0.067 15.161  0.004  4.110   6.5985e-02
   1_adp:   1.090  0.008  0.067 15.161  0.004  4.110   6.5985e-02
   1_occ:   1.090  0.008  0.067 15.161  0.004  4.110   6.5985e-02
   2_bss:   1.090  0.008  0.067 15.161  0.004  4.110   6.5985e-02
   2_xyz:   1.011  0.006  0.071 14.614  0.004  4.117   5.8005e-02
   2_adp:   1.011  0.006  0.071 14.614  0.004  4.117   5.8005e-02
   2_occ:   1.011  0.006  0.071 14.614  0.004  4.117   5.8005e-02
   3_bss:   1.011  0.006  0.071 14.614  0.004  4.117   5.8005e-02
   3_xyz:   0.995  0.007  0.073 14.717  0.004  4.119   5.8591e-02
   3_adp:   0.995  0.007  0.073 14.717  0.004  4.119   5.8591e-02
   3_occ:   0.995  0.007  0.073 14.717  0.004  4.119   5.8591e-02
   4_bss:   0.995  0.007  0.073 14.717  0.004  4.119   5.8591e-02
   4_xyz:   1.071  0.008  0.080 14.855  0.004  4.113   6.6674e-02
   4_adp:   1.071  0.008  0.080 14.855  0.004  4.113   6.6674e-02
   4_occ:   1.071  0.008  0.080 14.855  0.004  4.113   6.6674e-02
   5_bss:   1.071  0.008  0.080 14.855  0.004  4.113   6.6674e-02
   5_xyz:   1.082  0.009  0.081 14.857  0.005  4.113   6.8918e-02
   5_adp:   1.082  0.009  0.081 14.857  0.005  4.113   6.8918e-02
   5_occ:   1.082  0.009  0.081 14.857  0.005  4.113   6.8918e-02
   5_bss:   1.082  0.009  0.081 14.857  0.005  4.113   6.8918e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4019e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4019e-01
   1_xyz:   8.017  0.039  0.274 85.628  0.033  2.279   7.1386e-02
   1_adp:   8.017  0.039  0.274 85.628  0.033  2.279   7.1386e-02
   1_occ:   8.017  0.039  0.274 85.628  0.033  2.279   7.1386e-02
   2_bss:   8.017  0.039  0.274 85.628  0.033  2.279   7.1386e-02
   2_xyz:   6.864  0.045  0.221 81.909  0.039  2.324   4.5611e-02
   2_adp:   6.864  0.045  0.221 81.909  0.039  2.324   4.5611e-02
   2_occ:   6.864  0.045  0.221 81.909  0.039  2.324   4.5611e-02
   3_bss:   6.864  0.045  0.221 81.909  0.039  2.324   4.5611e-02
   3_xyz:   7.510  0.043  0.236 83.339  0.040  2.362   5.3423e-02
   3_adp:   7.510  0.043  0.236 83.339  0.040  2.362   5.3423e-02
   3_occ:   7.510  0.043  0.236 83.339  0.040  2.362   5.3423e-02
   4_bss:   7.510  0.043  0.236 83.339  0.040  2.362   5.3423e-02
   4_xyz:   7.633  0.047  0.261 81.948  0.040  2.277   5.0980e-02
   4_adp:   7.633  0.047  0.261 81.948  0.040  2.277   5.0980e-02
   4_occ:   7.633  0.047  0.261 81.948  0.040  2.277   5.0980e-02
   5_bss:   7.633  0.047  0.261 81.948  0.040  2.277   5.0980e-02
   5_xyz:   7.554  0.052  0.266 82.614  0.039  2.292   5.6710e-02
   5_adp:   7.554  0.052  0.266 82.614  0.039  2.292   5.6710e-02
   5_occ:   7.554  0.052  0.266 82.614  0.039  2.292   5.6710e-02
   5_bss:   7.554  0.052  0.266 82.614  0.039  2.292   5.6710e-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:  78.92   0.00  17.22  78.92   0.00  13.29  71.86   7.47  38.61
   1_occ:  78.92   0.00  17.22  78.92   0.00  13.29  71.86   7.47  38.61
   2_bss:  78.92   0.00  17.22  78.92   0.00  13.29  71.86   7.47  38.61
   2_xyz:  78.92   0.00  17.22  78.92   0.00  13.29  71.86   7.47  38.61
   2_adp:  79.28   2.22  16.63  79.28   2.22  12.88  66.12   6.07  37.00
   2_occ:  79.28   2.22  16.63  79.28   2.22  12.88  66.12   6.07  37.00
   3_bss:  79.28   2.22  16.63  79.28   2.22  12.88  66.12   6.07  37.00
   3_xyz:  79.28   2.22  16.63  79.28   2.22  12.88  66.12   6.07  37.00
   3_adp:  84.24   1.40  16.76  84.24   1.40  12.78  69.44   5.57  38.43
   3_occ:  84.24   1.40  16.76  84.24   1.40  12.78  69.44   5.57  38.43
   4_bss:  84.24   1.40  16.76  84.24   1.40  12.78  69.44   5.57  38.43
   4_xyz:  84.24   1.40  16.76  84.24   1.40  12.78  69.44   5.57  38.43
   4_adp:  92.97   0.34  16.82  92.97   0.34  12.69  76.50   5.76  39.35
   4_occ:  92.97   0.34  16.82  92.97   0.34  12.69  76.50   5.76  39.35
   5_bss:  92.97   0.34  16.82  92.97   0.34  12.69  76.50   5.76  39.35
   5_xyz:  92.97   0.34  16.82  92.97   0.34  12.69  76.50   5.76  39.35
   5_adp:  94.19   0.00  16.66  94.19   0.00  12.49  77.96   5.49  39.34
   5_occ:  94.19   0.00  16.66  94.19   0.00  12.49  77.96   5.49  39.34
   5_bss:  94.20   0.00  16.66  94.20   0.00  12.49  77.96   5.49  39.34
------------------------------------------------------------------------
 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:    1.522    0.010    0.291
   1_adp:    1.522    0.010    0.291
   1_occ:    1.522    0.010    0.291
   2_bss:    1.522    0.010    0.291
   2_xyz:    0.864    0.038    0.378
   2_adp:    0.864    0.038    0.378
   2_occ:    0.864    0.038    0.378
   3_bss:    0.864    0.038    0.378
   3_xyz:    1.051    0.038    0.412
   3_adp:    1.051    0.038    0.412
   3_occ:    1.051    0.038    0.412
   4_bss:    1.051    0.038    0.412
   4_xyz:    1.073    0.021    0.427
   4_adp:    1.073    0.021    0.427
   4_occ:    1.073    0.021    0.427
   5_bss:    1.073    0.021    0.427
   5_xyz:    1.256    0.046    0.434
   5_adp:    1.256    0.046    0.434
   5_occ:    1.256    0.046    0.434
   5_bss:    1.256    0.046    0.434
------------------------------------------------------------------------

CPU time actual refinement: 323.50


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_443/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_443/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_443/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_443/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_443/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.34 
  Macro-tasks:
    bulk solvent and scale       = 37.99  
    individual site refinement   = 131.42 
    weights calculation          = 30.19  
    collect and process          = 6.69   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 206.39 
  Micro-tasks:
    mask                            = 1.24   
    f_calc                          = 102.46 
    alpha_beta                      = 8.11   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 110.75 
    fmodel                         = 6.40   
    r_factors                      = 0.20   
    phase_errors                   = 10.85  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 241.34 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.624 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    636 calls, 102.11 s
gradients_fft:          581 calls,  97.61 s

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

# Date 2008-01-16 Time 04:50:05 PST -0800 (1200487805.04 s)
Start R-work = 0.3365, R-free = 0.3311 (no bulk solvent and anisotropic scale)
Final R-work = 0.1271, R-free = 0.1729 (no bulk solvent and anisotropic scale)

Start R-work = 0.3245, R-free = 0.3171
Final R-work = 0.1042, R-free = 0.1549