# Date 2008-01-16 Time 04:42:04 PST -0800 (1200487324.21 s)
#phil __OFF__

Command line arguments: "../420.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29436
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 420

-------------------------------------------------------------------------------
  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, 46.93, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, 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, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.97114
Completeness in resolution range: 0.967597
Completeness with d_max=infinity: 0.964548

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8236
                             d_min =   1.9711

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, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.97114
Completeness in resolution range: 0.967597
Completeness with d_max=infinity: 0.964548

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8240 -  4.2172 [2122/2149]  1910   212  10.0%
  bin  2:  4.2172 -  3.3601 [2035/2051]  1831   204  10.0%
  bin  3:  3.3601 -  2.9391 [2020/2039]  1817   203  10.0%
  bin  4:  2.9391 -  2.6721 [1996/2026]  1798   198   9.9%
  bin  5:  2.6721 -  2.4815 [1978/1997]  1780   198  10.0%
  bin  6:  2.4815 -  2.3358 [1966/2002]  1774   192   9.8%
  bin  7:  2.3358 -  2.2192 [1975/2008]  1771   204  10.3%
  bin  8:  2.2192 -  2.1229 [1951/1985]  1755   196  10.0%
  bin  9:  2.1229 -  2.0414 [1948/1976]  1757   191   9.8%
  bin 10:  2.0414 -  1.9711 [1598/2012]  1437   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_420/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:
        1.69 -     2.33: 26
        2.33 -     2.97: 1798
        2.97 -     3.62: 4637
        3.62 -     4.26: 9269
        4.26 -     4.90: 12905
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.690 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.809 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  2.023 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.033 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28630 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_420/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_420/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.93 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3125   r_free= 0.3118   ksol= 0.00   Bsol= 0.00   scale= 0.987    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.009720                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7033 0.99   1376  155 0.2813 0.2840      6.3457      6.3496|
|  2:  4.7033 -  3.7531 0.99   1335  144 0.2503 0.2354      6.4018      6.3772|
|  3:  3.7531 -  3.2846 0.99   1300  148 0.2634 0.2628      6.2859      6.3973|
|  4:  3.2846 -  2.9869 0.99   1293  143 0.2782 0.2969      6.1616      6.1938|
|  5:  2.9869 -  2.7743 0.99   1285  139 0.3109 0.2854      6.0631      5.9952|
|  6:  2.7743 -  2.6117 0.99   1279  145 0.3284 0.3379      6.0046      5.9742|
|  7:  2.6117 -  2.4815 0.99   1268  141 0.3343 0.2968      5.9945      5.8698|
|  8:  2.4815 -  2.3740 0.98   1277  140 0.3335 0.3159      5.9426      5.9873|
|  9:  2.3740 -  2.2829 0.98   1276  144 0.3550 0.3661      5.9066      5.9448|
| 10:  2.2829 -  2.2044 0.98   1235  133 0.3408 0.3922      5.8745      5.9662|
| 11:  2.2044 -  2.1357 1.00   1273  148 0.3583 0.3772      5.8349      5.9038|
| 12:  2.1357 -  2.0748 0.97   1252  131 0.3560 0.3214      5.7856      5.7723|
| 13:  2.0748 -  2.0203 0.98   1240  142 0.3619 0.3785      5.6863      5.6963|
| 14:  2.0203 -  1.9711 0.73    941  106 0.3860 0.3707      5.6956      5.5606|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7033  1376   155  0.78  26.79   0.87     0.79      44641.79|
|  2:  4.7033 -  3.7531  1335   144  0.84  21.82   0.99     0.93      45147.78|
|  3:  3.7531 -  3.2846  1300   148  0.81  25.05   1.01     0.98      42105.01|
|  4:  3.2846 -  2.9869  1293   143  0.79  27.30   1.02     0.97      36590.22|
|  5:  2.9869 -  2.7743  1285   139  0.75  31.32   1.00     0.95      30047.59|
|  6:  2.7743 -  2.6117  1279   145  0.74  32.04   1.01     0.95      26196.87|
|  7:  2.6117 -  2.4815  1268   141  0.75  31.14   1.00     0.97      23555.46|
|  8:  2.4815 -  2.3740  1277   140  0.73  33.24   1.03     0.95      23325.40|
|  9:  2.3740 -  2.2829  1276   144  0.70  35.99   1.05     0.92      22552.49|
| 10:  2.2829 -  2.2044  1235   133  0.69  36.91   1.06     0.90      22283.85|
| 11:  2.2044 -  2.1357  1273   148  0.68  37.38   1.07     0.93      20482.62|
| 12:  2.1357 -  2.0748  1252   131  0.70  36.08   1.08     0.97      18660.06|
| 13:  2.0748 -  2.0203  1240   142  0.68  37.28   1.06     0.95      16249.22|
| 14:  2.0203 -  1.9711   941   106  0.68  37.65   1.06     0.89      13909.79|
|alpha:            min =        0.79 max =            0.98 mean =         0.93|
|beta:             min =    13909.79 max =        45147.78 mean =     28048.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.74|
|phase err.(work): min =        0.00 max =           90.00 mean =        31.93|
|phase err.(test): min =        0.00 max =           89.23 mean =        31.78|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.474526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.701   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.647126              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.999   (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 |  1.690 -  2.011:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.011 -  2.332:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.332 -  2.653:       63 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.653 -  2.974:     1735 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.974 -  3.295:     1939 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.295 -  3.616:     2698 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.616 -  3.937:     4767 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.937 -  4.258:     4502 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.258 -  4.579:     5888 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.579 -  4.900:     7017 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.690 |       0.286 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3125   r_free= 0.3118   ksol= 0.00   Bsol= 0.00   scale= 0.987    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.009720                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2967   r_free= 0.2930   ksol= 0.31   Bsol= 26.00   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.83,1.22,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.984997                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.162352              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.638   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.328888              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.896   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2967      final r-factor (work) = 0.1875          |
| start r-factor (free) = 0.2930      final r-factor (free) = 0.2066          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6543 = 2.16 * 0.50 * 5.9990 + 1.00 * 0.1682                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2393 = 2.16 * 0.50 * 5.7156 + 1.00 * 0.0596                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1875      final r-factor (work) = 0.1737          |
| start r-factor (free) = 0.2066      final r-factor (free) = 0.2126          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8860 = 0.33 * 1.00 * 5.7156 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8441 = 0.33 * 1.00 * 5.4935 + 1.00 * 0.0373                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.02   16.78    None  None   None       |
|    all(noH): 2823   0      0.00    72.02   16.78    None  None   None       |
|    Sol.    : 438    0      7.59    62.21   37.62    None  None   None       |
|    Mac.    : 2385   0      0.00    72.02   12.95    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 -   7.202:  379   |   5:    36.009 -  43.211:  123        |
|      1:     7.202 -  14.404: 1305   |   6:    43.211 -  50.413:   99        |
|      2:    14.404 -  21.606:  553   |   7:    50.413 -  57.615:   60        |
|      3:    21.606 -  28.808:  160   |   8:    57.615 -  64.817:   13        |
|      4:    28.808 -  36.009:  130   |   9:    64.817 -  72.019:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1737 r_free = 0.2126             target_work(ml) = 5.505         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1733 r_free = 0.2132             target_work(ml) = 5.504         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1733   r_free= 0.2132   ksol= 0.31   Bsol= 26.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.83,1.22,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.503913                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1712   r_free= 0.2112   ksol= 0.31   Bsol= 33.06   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.04,-2.87,-1.16,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.496976                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.699433              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.658   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.259495              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.121   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1712      final r-factor (work) = 0.1267          |
| start r-factor (free) = 0.2112      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4816 = 2.70 * 0.50 * 5.4989 + 1.00 * 0.0596                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2848 = 2.70 * 0.50 * 5.3575 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1267      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1653      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4831 = 0.26 * 1.00 * 5.3575 + 1.00 * 0.0929                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3542 = 0.26 * 1.00 * 5.1898 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.02   16.99    None  None   None       |
|    all(noH): 2823   0      0.00    70.02   16.99    None  None   None       |
|    Sol.    : 438    0      5.41    67.19   38.31    None  None   None       |
|    Mac.    : 2385   0      0.00    70.02   13.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.002:  262   |   5:    35.011 -  42.013:  108        |
|      1:     7.002 -  14.005: 1474   |   6:    42.013 -  49.016:  109        |
|      2:    14.005 -  21.007:  497   |   7:    49.016 -  56.018:   87        |
|      3:    21.007 -  28.009:  136   |   8:    56.018 -  63.020:   28        |
|      4:    28.009 -  35.011:  111   |   9:    63.020 -  70.022:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1593             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1182 r_free = 0.1592             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1592   ksol= 0.31   Bsol= 33.06   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.04,-2.87,-1.16,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167340                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1585   ksol= 0.31   Bsol= 35.67   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.52,-1.56,-0.00,-0.00,-0.00); trace/3= -2.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.166593                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.051095              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.043  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.622354              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.668  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1185      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3767 = 2.05 * 0.50 * 5.1903 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3214 = 2.05 * 0.50 * 5.1342 + 1.00 * 0.0561                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2027 = 0.62 * 1.00 * 5.1342 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1869 = 0.62 * 1.00 * 5.1073 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.63   17.09    None  None   None       |
|    all(noH): 2823   0      0.00    83.63   17.09    None  None   None       |
|    Sol.    : 438    0      3.69    72.82   39.18    None  None   None       |
|    Mac.    : 2385   0      0.00    83.63   13.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.363:  587   |   5:    41.813 -  50.176:  120        |
|      1:     8.363 -  16.725: 1399   |   6:    50.176 -  58.539:   81        |
|      2:    16.725 -  25.088:  337   |   7:    58.539 -  66.901:   34        |
|      3:    25.088 -  33.451:  127   |   8:    66.901 -  75.264:   12        |
|      4:    33.451 -  41.813:  121   |   9:    75.264 -  83.627:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1080 r_free = 0.1525             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1079 r_free = 0.1524             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1524   ksol= 0.31   Bsol= 35.67   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.52,-1.56,-0.00,-0.00,-0.00); trace/3= -2.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110117                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1524   ksol= 0.32   Bsol= 37.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.30,-1.57,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109802                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.678323              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.774  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.118549              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.445  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1079      final r-factor (work) = 0.1074          |
| start r-factor (free) = 0.1524      final r-factor (free) = 0.1522          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3416 = 1.68 * 0.50 * 5.1073 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3386 = 1.68 * 0.50 * 5.1087 + 1.00 * 0.0516                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1074      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1522      final r-factor (free) = 0.1515          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6140 = 0.12 * 1.00 * 5.1087 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6130 = 0.12 * 1.00 * 5.1170 + 1.00 * 0.0064                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.07    79.15   16.39    None  None   None       |
|    all(noH): 2823   0      2.07    79.15   16.39    None  None   None       |
|    Sol.    : 438    0      5.22    71.27   36.16    None  None   None       |
|    Mac.    : 2385   0      2.07    79.15   12.76    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:     2.070 -   9.779:  930   |   5:    40.611 -  48.319:  106        |
|      1:     9.779 -  17.487: 1150   |   6:    48.319 -  56.027:   63        |
|      2:    17.487 -  25.195:  265   |   7:    56.027 -  63.735:   19        |
|      3:    25.195 -  32.903:  134   |   8:    63.735 -  71.444:    6        |
|      4:    32.903 -  40.611:  145   |   9:    71.444 -  79.152:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1515             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1515             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1515   ksol= 0.32   Bsol= 37.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.30,-1.57,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113950                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1516   ksol= 0.32   Bsol= 37.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.19,-1.52,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114204                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.246137              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.614  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.365871              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.810  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1045          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3570 = 3.25 * 0.50 * 5.1171 + 1.00 * 0.0516                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3390 = 3.25 * 0.50 * 5.0944 + 1.00 * 0.0703                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1045      final r-factor (work) = 0.1035          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8703 = 0.37 * 1.00 * 5.0944 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8682 = 0.37 * 1.00 * 5.0859 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    80.72   16.46    None  None   None       |
|    all(noH): 2823   0      1.36    80.72   16.46    None  None   None       |
|    Sol.    : 438    0      6.02    71.14   37.15    None  None   None       |
|    Mac.    : 2385   0      1.36    80.72   12.66    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:     1.359 -   9.295:  869   |   5:    41.040 -  48.976:  112        |
|      1:     9.295 -  17.231: 1188   |   6:    48.976 -  56.913:   73        |
|      2:    17.231 -  25.168:  283   |   7:    56.913 -  64.849:   23        |
|      3:    25.168 -  33.104:  124   |   8:    64.849 -  72.785:    6        |
|      4:    33.104 -  41.040:  140   |   9:    72.785 -  80.722:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1035 r_free = 0.1523             target_work(ml) = 5.090         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1035 r_free = 0.1522             target_work(ml) = 5.089         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1035   r_free= 0.1522   ksol= 0.32   Bsol= 37.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.19,-1.52,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.089476                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7033 0.99   1376  155 0.0982 0.1234      5.3673      5.5192|
|  2:  4.7033 -  3.7531 0.99   1335  144 0.0818 0.1108      5.4039      5.6045|
|  3:  3.7531 -  3.2846 0.99   1300  148 0.0986 0.1492      5.4236      5.8386|
|  4:  3.2846 -  2.9869 0.99   1293  143 0.1134 0.1478      5.4064      5.5603|
|  5:  2.9869 -  2.7743 0.99   1285  139 0.1168 0.1649      5.2511      5.4938|
|  6:  2.7743 -  2.6117 0.99   1279  145 0.1118 0.1756      5.1557      5.3946|
|  7:  2.6117 -  2.4815 0.99   1268  141 0.1125 0.1564      5.0879       5.318|
|  8:  2.4815 -  2.3740 0.98   1277  140 0.1061 0.1708      5.0203      5.3271|
|  9:  2.3740 -  2.2829 0.98   1276  144 0.1085 0.1736      4.9709      5.2809|
| 10:  2.2829 -  2.2044 0.98   1235  133 0.1023 0.1731      4.9181      5.1524|
| 11:  2.2044 -  2.1357 1.00   1273  148 0.1037 0.1685      4.8821      5.2346|
| 12:  2.1357 -  2.0748 0.97   1252  131 0.1003 0.1606      4.8109      5.1211|
| 13:  2.0748 -  2.0203 0.98   1240  142 0.1023 0.1574      4.7334      4.9824|
| 14:  2.0203 -  1.9711 0.73    941  106 0.0975 0.1694      4.6312      4.9236|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7033  1376   155  0.94   8.91   0.99     0.96       6759.96|
|  2:  4.7033 -  3.7531  1335   144  0.95   7.67   1.02     1.01       8562.55|
|  3:  3.7531 -  3.2846  1300   148  0.94  10.70   1.03     1.02       9645.05|
|  4:  3.2846 -  2.9869  1293   143  0.93  12.85   1.01     1.00       9696.63|
|  5:  2.9869 -  2.7743  1285   139  0.91  14.70   0.99     0.97       7369.17|
|  6:  2.7743 -  2.6117  1279   145  0.91  15.04   0.98     0.95       6399.95|
|  7:  2.6117 -  2.4815  1268   141  0.91  14.55   0.99     0.96       5478.58|
|  8:  2.4815 -  2.3740  1277   140  0.92  14.20   1.00     0.98       4978.48|
|  9:  2.3740 -  2.2829  1276   144  0.91  14.64   1.00     0.97       4511.58|
| 10:  2.2829 -  2.2044  1235   133  0.91  14.71   1.00     0.97       4150.36|
| 11:  2.2044 -  2.1357  1273   148  0.90  15.50   1.00     0.97       4036.75|
| 12:  2.1357 -  2.0748  1252   131  0.92  14.00   1.01     0.99       3535.15|
| 13:  2.0748 -  2.0203  1240   142  0.91  14.86   1.01     1.00       3059.48|
| 14:  2.0203 -  1.9711   941   106  0.92  14.30   0.99     0.95       2435.81|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2435.81 max =         9696.63 mean =      5859.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.26|
|phase err.(test): min =        0.00 max =           89.99 mean =        12.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1034   r_free= 0.1522   ksol= 0.32   Bsol= 39.16   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.99,-1.33,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.089262                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1034   r_free= 0.1522   ksol= 0.32   Bsol= 39.16   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.99,-1.33,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.089262                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7033 0.99   1376  155 0.0983 0.1238      5.3691      5.5219|
|  2:  4.7033 -  3.7531 0.99   1335  144 0.0820 0.1108      5.4058      5.6053|
|  3:  3.7531 -  3.2846 0.99   1300  148 0.0987 0.1491      5.4243      5.8391|
|  4:  3.2846 -  2.9869 0.99   1293  143 0.1134 0.1477       5.406      5.5596|
|  5:  2.9869 -  2.7743 0.99   1285  139 0.1167 0.1646        5.25      5.4926|
|  6:  2.7743 -  2.6117 0.99   1279  145 0.1116 0.1754      5.1546      5.3931|
|  7:  2.6117 -  2.4815 0.99   1268  141 0.1124 0.1561      5.0867      5.3168|
|  8:  2.4815 -  2.3740 0.98   1277  140 0.1060 0.1706      5.0195      5.3257|
|  9:  2.3740 -  2.2829 0.98   1276  144 0.1084 0.1737      4.9704      5.2818|
| 10:  2.2829 -  2.2044 0.98   1235  133 0.1022 0.1730      4.9178      5.1514|
| 11:  2.2044 -  2.1357 1.00   1273  148 0.1036 0.1684      4.8816      5.2341|
| 12:  2.1357 -  2.0748 0.97   1252  131 0.1002 0.1606      4.8104      5.1208|
| 13:  2.0748 -  2.0203 0.98   1240  142 0.1023 0.1574      4.7329       4.982|
| 14:  2.0203 -  1.9711 0.73    941  106 0.0975 0.1692      4.6306      4.9229|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7033  1376   155  0.94   8.94   0.99     0.96       6800.22|
|  2:  4.7033 -  3.7531  1335   144  0.95   7.68   1.03     1.02       8593.46|
|  3:  3.7531 -  3.2846  1300   148  0.94  10.71   1.03     1.02       9655.20|
|  4:  3.2846 -  2.9869  1293   143  0.93  12.84   1.01     1.00       9686.26|
|  5:  2.9869 -  2.7743  1285   139  0.91  14.68   1.00     0.97       7353.61|
|  6:  2.7743 -  2.6117  1279   145  0.91  15.03   0.99     0.96       6384.09|
|  7:  2.6117 -  2.4815  1268   141  0.91  14.53   0.99     0.97       5463.59|
|  8:  2.4815 -  2.3740  1277   140  0.92  14.19   1.00     0.98       4968.84|
|  9:  2.3740 -  2.2829  1276   144  0.91  14.64   1.01     0.98       4506.90|
| 10:  2.2829 -  2.2044  1235   133  0.91  14.71   1.01     0.97       4148.16|
| 11:  2.2044 -  2.1357  1273   148  0.91  15.49   1.01     0.98       4031.90|
| 12:  2.1357 -  2.0748  1252   131  0.92  13.98   1.02     1.00       3530.13|
| 13:  2.0748 -  2.0203  1240   142  0.91  14.84   1.02     1.01       3054.96|
| 14:  2.0203 -  1.9711   941   106  0.92  14.28   1.00     0.96       2431.64|
|alpha:            min =        0.96 max =            1.02 mean =         0.99|
|beta:             min =     2431.64 max =         9686.26 mean =      5859.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.25|
|phase err.(test): min =        0.00 max =           89.38 mean =        12.85|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.31    80.67   16.41    None  None   None       |
|    all(noH): 2823   0      1.31    80.67   16.41    None  None   None       |
|    Sol.    : 438    0      5.97    71.09   37.11    None  None   None       |
|    Mac.    : 2385   0      1.31    80.67   12.61    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:     1.311 -   9.247:  869   |   5:    40.992 -  48.928:  112        |
|      1:     9.247 -  17.183: 1188   |   6:    48.928 -  56.865:   73        |
|      2:    17.183 -  25.120:  283   |   7:    56.865 -  64.801:   23        |
|      3:    25.120 -  33.056:  124   |   8:    64.801 -  72.737:    6        |
|      4:    33.056 -  40.992:  140   |   9:    72.737 -  80.674:    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)= 270         
Filter by distance & map next to the model:
   mapped sites are within: 0.452 - 4.592
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 268 from: 270
   mapped sites are within: 0.753 - 4.592

peak=    5.918 closest distance to " O   HOH Z 126 " =    1.911
peak=    5.345 closest distance to " O   HOH Z 142 " =    1.724
peak=    5.324 closest distance to " NH2 ARG A  56 " =    2.166
peak=    5.216 closest distance to " CB  ARG A 275 " =    0.934
peak=    5.201 closest distance to " CB  SER A  63 " =    1.101
peak=    5.085 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.025 closest distance to " NE2 GLN A  11 " =    1.082
peak=    4.907 closest distance to " O   HOH Z 232 " =    2.414
peak=    4.889 closest distance to " O   HOH Z 193 " =    1.816
peak=    4.868 closest distance to " CB  GLU A 152 " =    1.192
peak=    4.855 closest distance to " O   HOH Z  78 " =    1.788
peak=    4.839 closest distance to " CB  GLN A 183 " =    1.241
peak=    4.763 closest distance to " C   PRO A 198 " =    1.465
peak=    4.757 closest distance to " CG  PRO A  54 " =    1.146
peak=    4.745 closest distance to " O   HOH Z 236 " =    1.951
peak=    4.594 closest distance to " O   HOH Z 427 " =    2.749
peak=    4.514 closest distance to " O   HOH Z  44 " =    1.968
peak=    4.488 closest distance to " O   HOH Z  93 " =    2.524
peak=    4.472 closest distance to " CB  ARG A  79 " =    1.449
peak=    4.414 closest distance to " CA  TYR A  30 " =    0.946
peak=    4.407 closest distance to " O   HOH Z 298 " =    1.867
peak=    4.330 closest distance to " CB  ASN A 148 " =    1.805
peak=    4.327 closest distance to " CB  TYR A 169 " =    0.754
peak=    4.296 closest distance to " O   HOH Z  54 " =    1.678
peak=    4.293 closest distance to " O   HOH Z 234 " =    3.639
peak=    4.291 closest distance to " OD1 ASN A  69 " =    2.616
peak=    4.285 closest distance to " O   HOH Z  78 " =    2.095
peak=    4.277 closest distance to " O   HOH Z 272 " =    1.862
peak=    4.269 closest distance to " O   HOH Z 303 " =    2.029
peak=    4.226 closest distance to " O   HOH Z 402 " =    1.458
peak=    4.214 closest distance to " ND2 ASN A 187 " =    1.463
peak=    4.184 closest distance to " O   HOH Z 403 " =    1.702
peak=    4.177 closest distance to " CG  PRO A 213 " =    1.216
peak=    4.168 closest distance to " O   HOH Z 344 " =    3.079
peak=    4.134 closest distance to " O   HOH Z 144 " =    2.190
peak=    4.131 closest distance to " O   HOH Z  40 " =    1.655
peak=    4.099 closest distance to " O   HOH Z 389 " =    1.833
peak=    4.090 closest distance to " O   HOH Z 392 " =    3.020
peak=    4.081 closest distance to " O   HOH Z 346 " =    1.745
peak=    4.081 closest distance to " CA  ALA A  21 " =    1.156
peak=    4.078 closest distance to " O   HOH Z 316 " =    3.007
peak=    4.067 closest distance to " CB  SER A   3 " =    1.290
peak=    4.064 closest distance to " CB  VAL A 265 " =    1.285
peak=    4.063 closest distance to " O   HOH Z  10 " =    1.843
peak=    4.062 closest distance to " O   HOH Z 368 " =    1.971
peak=    4.056 closest distance to " CD2 TRP A 179 " =    1.382
peak=    4.036 closest distance to " O   HOH Z 369 " =    2.052
peak=    4.028 closest distance to " O   SER A  87 " =    2.265
peak=    4.021 closest distance to " O   HOH Z  43 " =    1.993
peak=    4.018 closest distance to " O   HOH Z 203 " =    1.690
peak=    4.014 closest distance to " O   HOH Z  15 " =    2.226
peak=    4.001 closest distance to " OD2 ASP A 286 " =    2.763
peak=    3.958 closest distance to " O   HOH Z   6 " =    2.078
peak=    3.934 closest distance to " O   HOH Z 128 " =    1.946
peak=    3.916 closest distance to " CB  PRO A  54 " =    0.915
peak=    3.907 closest distance to " O   HOH Z 371 " =    3.147
peak=    3.907 closest distance to " CA  ASN A 215 " =    1.172
peak=    3.891 closest distance to " O   HOH Z 158 " =    2.933
peak=    3.886 closest distance to " O   HOH Z 245 " =    1.319
peak=    3.881 closest distance to " NZ  LYS A 117 " =    3.278
peak=    3.880 closest distance to " CG1 ILE A  33 " =    1.202
peak=    3.878 closest distance to " O   HOH Z 327 " =    1.648
peak=    3.874 closest distance to " CB  TYR A 169 " =    0.851
peak=    3.868 closest distance to " O   HOH Z 250 " =    1.394
peak=    3.867 closest distance to " ND2 ASN A 110 " =    1.780
peak=    3.861 closest distance to " O   HOH Z  97 " =    1.890
peak=    3.833 closest distance to " O   HOH Z 124 " =    1.379
peak=    3.829 closest distance to " CB  SER A  26 " =    1.551
peak=    3.828 closest distance to " O   HOH Z  71 " =    2.037
peak=    3.820 closest distance to " CB  ARG A 190 " =    1.688
peak=    3.808 closest distance to " NH2BARG A 145 " =    2.004
peak=    3.806 closest distance to " CB  TRP A 179 " =    1.264
peak=    3.796 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.786 closest distance to " CG1BVAL A  72 " =    1.542
peak=    3.786 closest distance to " O   HOH Z 425 " =    1.988
peak=    3.782 closest distance to " CB  TRP A 266 " =    0.961
peak=    3.770 closest distance to " CB  GLU A 128 " =    1.055
peak=    3.759 closest distance to " CG  GLN A  77 " =    1.900
peak=    3.756 closest distance to " O   HOH Z 407 " =    2.522
peak=    3.747 closest distance to " O   HOH Z 426 " =    1.490
peak=    3.746 closest distance to " CB  LEU A 228 " =    1.065
peak=    3.740 closest distance to " O   HOH Z  66 " =    2.155
peak=    3.726 closest distance to " O   HOH Z 365 " =    2.953
peak=    3.724 closest distance to " O   HOH Z 132 " =    2.485
peak=    3.721 closest distance to " CB  ARG A 139 " =    0.984
peak=    3.711 closest distance to " CG2 ILE A  20 " =    1.431
peak=    3.710 closest distance to " O   HOH Z 193 " =    2.051
peak=    3.708 closest distance to " O   HOH Z 189 " =    1.916
peak=    3.695 closest distance to " CD1 ILE A 106 " =    0.936
peak=    3.677 closest distance to " OG BSER A 164 " =    2.296
peak=    3.674 closest distance to " O   HOH Z 173 " =    1.962
peak=    3.672 closest distance to " O   HOH Z 128 " =    2.204
peak=    3.666 closest distance to " CG2 ILE A 120 " =    1.099
peak=    3.664 closest distance to " O   HOH Z  21 " =    1.736
peak=    3.661 closest distance to " CB  VAL A 202 " =    1.534
peak=    3.657 closest distance to " O   HOH Z 147 " =    1.731
peak=    3.656 closest distance to " CA  THR A 221 " =    0.955
peak=    3.650 closest distance to " O   HOH Z 108 " =    2.339
peak=    3.645 closest distance to " O   HOH Z  59 " =    2.087
peak=    3.629 closest distance to " O   HOH Z 248 " =    1.665
peak=    3.615 closest distance to " CZ2 TRP A 179 " =    1.722
peak=    3.603 closest distance to " CG2 VAL A 257 " =    0.873
peak=    3.602 closest distance to " O   MET A 105 " =    1.827
peak=    3.596 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.594 closest distance to " CB  ASP A 140 " =    0.900
peak=    3.589 closest distance to " O   HOH Z 126 " =    2.167
peak=    3.584 closest distance to " O   HOH Z 263 " =    2.287
peak=    3.581 closest distance to " N   ASN A  39 " =    1.230
peak=    3.581 closest distance to " O   HOH Z 433 " =    1.713
peak=    3.577 closest distance to " CB  ASN A  39 " =    0.817
peak=    3.571 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.570 closest distance to " CB  GLU A 277 " =    3.462
peak=    3.565 closest distance to " O   HOH Z 214 " =    2.075
peak=    3.554 closest distance to " CG  ARG A  66 " =    2.515
peak=    3.553 closest distance to " O   HOH Z 423 " =    1.984
peak=    3.549 closest distance to " O   HOH Z 368 " =    3.629
peak=    3.545 closest distance to " O   HOH Z 284 " =    2.947
peak=    3.539 closest distance to " CB  ILE A 120 " =    1.295
peak=    3.535 closest distance to " O   HOH Z 163 " =    1.839
peak=    3.525 closest distance to " CG  LYS A  76 " =    1.026
peak=    3.524 closest distance to " O   HOH Z 172 " =    3.640
peak=    3.511 closest distance to " O   HOH Z 291 " =    1.582
peak=    3.509 closest distance to " OG  SER A  22 " =    2.588
peak=    3.501 closest distance to " O   HOH Z 227 " =    1.508
peak=    3.500 closest distance to " O   HOH Z 219 " =    1.983
peak=    3.494 closest distance to " CA  THR A 264 " =    0.913
peak=    3.492 closest distance to " CA  ASN A 176 " =    1.131
peak=    3.492 closest distance to " CB  ALA A 291 " =    1.347
peak=    3.491 closest distance to " O   HOH Z   1 " =    1.927
peak=    3.480 closest distance to " NH1BARG A 145 " =    1.358
peak=    3.476 closest distance to " O   HOH Z 417 " =    3.200
peak=    3.474 closest distance to " CA  ALA A  84 " =    1.364
peak=    3.474 closest distance to " O   TRP A 274 " =    1.914
peak=    3.470 closest distance to " CD2 LEU A 297 " =    0.862
peak=    3.462 closest distance to " O   HOH Z 299 " =    4.296
peak=    3.457 closest distance to " O   ALA A   1 " =    1.693
peak=    3.454 closest distance to " O   HOH Z  49 " =    2.073
peak=    3.451 closest distance to " O   HOH Z 427 " =    3.022
peak=    3.448 closest distance to " O   HOH Z 305 " =    3.616
peak=    3.438 closest distance to " O   HOH Z 279 " =    2.081
peak=    3.437 closest distance to " NH1AARG A 145 " =    1.163
peak=    3.430 closest distance to " CA  ALA A 291 " =    0.904
peak=    3.429 closest distance to " CD BLYS A 290 " =    1.277
peak=    3.427 closest distance to " CA  ASP A 162 " =    1.044
peak=    3.426 closest distance to " O   HOH Z  88 " =    2.757
peak=    3.422 closest distance to " CG  PRO A 243 " =    1.102
peak=    3.419 closest distance to " O   HOH Z 273 " =    2.593
peak=    3.414 closest distance to " O   HOH Z 209 " =    2.271
peak=    3.412 closest distance to " O   HOH Z  19 " =    2.281
peak=    3.400 closest distance to " O   HOH Z 187 " =    2.218
peak=    3.398 closest distance to " CA  LYS A 117 " =    1.194
peak=    3.398 closest distance to " O   HOH Z 337 " =    3.594
peak=    3.397 closest distance to " O   HOH Z 374 " =    2.498
peak=    3.397 closest distance to " O   HOH Z 411 " =    3.765
peak=    3.393 closest distance to " CG  MET A 185 " =    1.037
peak=    3.391 closest distance to " CA  MET A  40 " =    1.070
peak=    3.391 closest distance to " O   HOH Z 286 " =    2.179
peak=    3.384 closest distance to " O   HOH Z 406 " =    1.612
peak=    3.376 closest distance to " O   HOH Z   9 " =    2.152
peak=    3.373 closest distance to " CA  ASP A 140 " =    1.132
peak=    3.373 closest distance to " O   HOH Z 144 " =    1.797
peak=    3.372 closest distance to " CA  ARG A 195 " =    1.208
peak=    3.365 closest distance to " O   HOH Z  89 " =    2.177
peak=    3.364 closest distance to " O   HOH Z  35 " =    2.572
peak=    3.363 closest distance to " O   HOH Z 250 " =    1.883
peak=    3.351 closest distance to " CG  MET A 185 " =    1.111
peak=    3.351 closest distance to " CG  PRO A  90 " =    1.145
peak=    3.348 closest distance to " O   HOH Z 423 " =    3.086
peak=    3.344 closest distance to " N   ARG A 156 " =    1.279
peak=    3.336 closest distance to " O   HOH Z 180 " =    2.197
peak=    3.332 closest distance to " CA  ALA A 233 " =    1.179
peak=    3.328 closest distance to " O   HOH Z 368 " =    2.604
peak=    3.319 closest distance to " CA  ILE A  33 " =    1.430
peak=    3.315 closest distance to " CB  ASP A 171 " =    1.232
peak=    3.311 closest distance to " CB  ALA A  71 " =    1.350
peak=    3.310 closest distance to " CE BLYS A 290 " =    1.179
peak=    3.309 closest distance to " CE1 TYR A 186 " =    1.304
peak=    3.308 closest distance to " CZ  PHE A 218 " =    1.041
peak=    3.305 closest distance to " O   HOH Z 163 " =    1.700
peak=    3.304 closest distance to " O   HOH Z 185 " =    1.691
peak=    3.300 closest distance to " CA  ARG A  36 " =    1.043
peak=    3.299 closest distance to " CB  GLN A  88 " =    1.170
peak=    3.295 closest distance to " NE2 GLN A  73 " =    3.804
peak=    3.294 closest distance to " O   HOH Z 329 " =    3.760
peak=    3.288 closest distance to " CD1 LEU A 300 " =    1.315
peak=    3.288 closest distance to " O   HOH Z  47 " =    1.759
peak=    3.287 closest distance to " N   PHE A 130 " =    1.394
peak=    3.285 closest distance to " O   HOH Z 193 " =    1.596
peak=    3.285 closest distance to " OE2 GLU A  53 " =    2.103
peak=    3.284 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.277 closest distance to " O   ALA A 165 " =    1.488
peak=    3.273 closest distance to " CD  LYS A 166 " =    1.239
peak=    3.271 closest distance to " O   HOH Z 334 " =    1.374
peak=    3.270 closest distance to " CG  GLN A  11 " =    1.623
peak=    3.266 closest distance to " O   HOH Z 148 " =    3.167
peak=    3.260 closest distance to " O   HOH Z 175 " =    2.117
peak=    3.258 closest distance to " CA  GLY A  80 " =    0.807
peak=    3.257 closest distance to " O   HOH Z 326 " =    1.476
peak=    3.254 closest distance to " CB  GLN A  89 " =    1.288
peak=    3.248 closest distance to " CB  ASN A 110 " =    1.054
peak=    3.246 closest distance to " CG  GLU A 277 " =    2.187
peak=    3.240 closest distance to " O   HOH Z 286 " =    2.404
peak=    3.240 closest distance to " O   HOH Z  30 " =    2.130
peak=    3.236 closest distance to " O   HOH Z 342 " =    0.798
peak=    3.233 closest distance to " CG AARG A 275 " =    1.077
peak=    3.232 closest distance to " CG2BVAL A  41 " =    0.861
peak=    3.226 closest distance to " CB  ALA A  34 " =    1.119
peak=    3.223 closest distance to " CB  ALA A 248 " =    1.383
peak=    3.223 closest distance to " O   HOH Z 359 " =    1.482
peak=    3.221 closest distance to " O   HOH Z 266 " =    2.020
peak=    3.216 closest distance to " NH2 ARG A 219 " =    1.863
peak=    3.216 closest distance to " O   HOH Z  83 " =    1.774
peak=    3.216 closest distance to " NE AARG A 275 " =    2.204
peak=    3.215 closest distance to " O   HOH Z 380 " =    1.866
peak=    3.215 closest distance to " O   HOH Z 234 " =    1.790
peak=    3.211 closest distance to " CB  SER A 216 " =    0.753
peak=    3.209 closest distance to " CA  ASN A 217 " =    1.243
peak=    3.204 closest distance to " CB  SER A 141 " =    1.014
peak=    3.199 closest distance to " CD1 LEU A 228 " =    1.634
peak=    3.197 closest distance to " CB  ALA A  10 " =    1.324
peak=    3.193 closest distance to " CG2 THR A 221 " =    1.142
peak=    3.191 closest distance to " CB  GLU A  46 " =    1.027
peak=    3.188 closest distance to " CB  GLN A 278 " =    0.830
peak=    3.180 closest distance to " O   HOH Z 421 " =    1.682
peak=    3.179 closest distance to " CG2 THR A 294 " =    1.582
peak=    3.179 closest distance to " OG  SER A  62 " =    2.824
peak=    3.178 closest distance to " O   HOH Z 419 " =    1.939
peak=    3.176 closest distance to " O   HOH Z 345 " =    3.198
peak=    3.172 closest distance to " OD1 ASP A 231 " =    1.907
peak=    3.171 closest distance to " CD2 LEU A 255 " =    1.262
peak=    3.167 closest distance to " CB  ALA A   1 " =    1.097
peak=    3.166 closest distance to " CD1AILE A 234 " =    0.996
peak=    3.166 closest distance to " O   HOH Z  49 " =    2.449
peak=    3.166 closest distance to " O   HOH Z 336 " =    1.760
peak=    3.154 closest distance to " O   HOH Z 287 " =    2.246
peak=    3.153 closest distance to " O   HOH Z  48 " =    1.491
peak=    3.151 closest distance to " O   HOH Z 227 " =    1.685
peak=    3.150 closest distance to " CB  THR A  31 " =    1.722
peak=    3.149 closest distance to " CB  VAL A 126 " =    1.118
peak=    3.146 closest distance to " O   HOH Z  59 " =    2.381
peak=    3.145 closest distance to " ND1 HIS A  81 " =    1.566
peak=    3.140 closest distance to " O   HOH Z 302 " =    1.973
peak=    3.140 closest distance to " O   ALA A   1 " =    1.456
peak=    3.135 closest distance to " CB  ALA A   1 " =    4.592
peak=    3.134 closest distance to " N   HIS A  86 " =    1.857
peak=    3.132 closest distance to " CB  MET A  40 " =    0.863
peak=    3.132 closest distance to " O   HOH Z  73 " =    1.681
peak=    3.131 closest distance to " CA  ALA A  51 " =    0.889
peak=    3.116 closest distance to " O   HOH Z 410 " =    1.967
peak=    3.108 closest distance to " C   TYR A 214 " =    1.429
peak=    3.107 closest distance to " NH2AARG A 190 " =    1.095
peak=    3.101 closest distance to " O   HOH Z 119 " =    1.689
peak=    3.093 closest distance to " O   HOH Z 411 " =    1.695
peak=    3.092 closest distance to " O   HOH Z 371 " =    1.620
peak=    3.084 closest distance to " O   HOH Z 112 " =    2.698
peak=    3.080 closest distance to " N   TYR A 116 " =    1.650
peak=    3.074 closest distance to " CG  GLN A  77 " =    1.779
peak=    3.074 closest distance to " CD  LYS A 119 " =    1.324
peak=    3.069 closest distance to " CD2 HIS A  81 " =    1.128
peak=    3.068 closest distance to " O   HOH Z 357 " =    1.708
peak=    3.066 closest distance to " O   HOH Z 409 " =    3.047
peak=    3.061 closest distance to " CE  LYS A 119 " =    1.152
peak=    3.059 closest distance to " O   HOH Z 132 " =    2.534
peak=    3.055 closest distance to " O   HOH Z 250 " =    1.509
peak=    3.054 closest distance to " O   HOH Z 367 " =    3.529
peak=    3.054 closest distance to " OD1BASN A 224 " =    2.306
peak=    3.041 closest distance to " O   HOH Z  88 " =    2.178
peak=    3.029 closest distance to " CB  LEU A 255 " =    0.797

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.651 - 5.984
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.801 - 5.984

peak=   -5.077 closest distance to " O   HOH Z 266 " =    4.516
peak=   -4.463 closest distance to " C   HIS A 108 " =    1.108
peak=   -4.462 closest distance to " CD  ARG A 156 " =    2.003
peak=   -4.430 closest distance to " O   VAL A  67 " =    2.680
peak=   -4.338 closest distance to " SG  CYS A 254 " =    3.334
peak=   -4.334 closest distance to " CB  PRO A 243 " =    2.594
peak=   -4.247 closest distance to " O   HOH Z 290 " =    1.089
peak=   -4.236 closest distance to " CG1 VAL A 112 " =    2.724
peak=   -4.227 closest distance to " O   HOH Z 372 " =    2.356
peak=   -4.185 closest distance to " CB  ALA A 161 " =    2.521
peak=   -4.180 closest distance to " CA  VAL A  67 " =    2.673
peak=   -4.126 closest distance to " CG  GLN A 223 " =    1.938
peak=   -4.076 closest distance to " O   HOH Z 126 " =    1.788
peak=   -4.049 closest distance to " CD  ARG A 139 " =    1.503
peak=   -4.048 closest distance to " OG  SER A  97 " =    2.132
peak=   -4.040 closest distance to " CZ  TYR A 169 " =    1.702
peak=   -4.027 closest distance to " OG BSER A 134 " =    1.192
peak=   -4.018 closest distance to " O   HOH Z 198 " =    2.038
peak=   -4.012 closest distance to " N   GLN A  58 " =    1.602
peak=   -4.011 closest distance to " O   HOH Z 353 " =    2.189
peak=   -3.993 closest distance to " CB  PRO A 280 " =    2.133
peak=   -3.955 closest distance to " CZ3 TRP A 179 " =    1.213
peak=   -3.924 closest distance to " OXT GLY A 302 " =    2.719
peak=   -3.895 closest distance to " O   HOH Z 407 " =    2.901
peak=   -3.875 closest distance to " CD  GLN A  58 " =    1.162
peak=   -3.830 closest distance to " CB  ASN A  39 " =    2.246
peak=   -3.818 closest distance to " O   HOH Z 389 " =    1.780
peak=   -3.805 closest distance to " O   HOH Z 185 " =    2.139
peak=   -3.797 closest distance to " CD1 PHE A  59 " =    1.856
peak=   -3.796 closest distance to " CD2 LEU A 300 " =    2.972
peak=   -3.770 closest distance to " CG  PHE A 283 " =    2.705
peak=   -3.740 closest distance to " O   HOH Z  47 " =    1.640
peak=   -3.740 closest distance to " O   HOH Z 435 " =    2.686
peak=   -3.731 closest distance to " ND2 ASN A  45 " =    1.817
peak=   -3.726 closest distance to " O   HOH Z 211 " =    1.762
peak=   -3.718 closest distance to " CB  ASP A 132 " =    2.266
peak=   -3.715 closest distance to " O   HOH Z  13 " =    1.490
peak=   -3.705 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.700 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.687 closest distance to " O   HOH Z 114 " =    3.162
peak=   -3.685 closest distance to " N   ALA A 248 " =    1.584
peak=   -3.684 closest distance to " N   ALA A  43 " =    2.491
peak=   -3.683 closest distance to " O   HOH Z 231 " =    2.295
peak=   -3.676 closest distance to " CA  GLY A 203 " =    2.269
peak=   -3.674 closest distance to " O   HOH Z 313 " =    2.023
peak=   -3.672 closest distance to " CB  PHE A 192 " =    1.908
peak=   -3.661 closest distance to " CB  ALA A 291 " =    2.419
peak=   -3.652 closest distance to " O   HOH Z 166 " =    1.445
peak=   -3.649 closest distance to " CE2 TYR A  30 " =    2.765
peak=   -3.645 closest distance to " CZ  PHE A  59 " =    1.560
peak=   -3.625 closest distance to " O   HOH Z 385 " =    2.029
peak=   -3.622 closest distance to " O   ALA A 161 " =    1.591
peak=   -3.621 closest distance to " CB  ASP A 132 " =    2.348
peak=   -3.619 closest distance to " O   PRO A 163 " =    2.025
peak=   -3.600 closest distance to " OG  SER A   3 " =    1.720
peak=   -3.598 closest distance to " CD1 LEU A 228 " =    2.087
peak=   -3.591 closest distance to " C   LEU A 143 " =    0.991
peak=   -3.588 closest distance to " CG  GLU A   2 " =    1.920
peak=   -3.587 closest distance to " CB  PRO A 163 " =    2.484
peak=   -3.587 closest distance to " C   ALA A 158 " =    1.203
peak=   -3.575 closest distance to " O   MET A  40 " =    2.748
peak=   -3.573 closest distance to " SG ACYS A 201 " =    1.844
peak=   -3.557 closest distance to " O   HOH Z  10 " =    1.431
peak=   -3.542 closest distance to " NH1 ARG A 195 " =    2.519
peak=   -3.540 closest distance to " OD1 ASN A 148 " =    1.607
peak=   -3.540 closest distance to " O   HOH Z 362 " =    5.984
peak=   -3.535 closest distance to " O   HOH Z 196 " =    2.102
peak=   -3.533 closest distance to " O   HOH Z 351 " =    1.480
peak=   -3.531 closest distance to " O   HOH Z 198 " =    1.343
peak=   -3.522 closest distance to " O   SER A 210 " =    2.030
peak=   -3.516 closest distance to " OD2 ASP A 171 " =    2.339
peak=   -3.503 closest distance to " O   SER A 135 " =    1.532
peak=   -3.490 closest distance to " CB  ALA A 248 " =    2.031
peak=   -3.488 closest distance to " NE2 GLN A  88 " =    1.853
peak=   -3.485 closest distance to " ND2 ASN A  45 " =    0.990
peak=   -3.483 closest distance to " OG BSER A 134 " =    1.661
peak=   -3.481 closest distance to " NH2 ARG A  79 " =    1.930
peak=   -3.476 closest distance to " C   PRO A  90 " =    1.491
peak=   -3.470 closest distance to " O   HOH Z 311 " =    3.559
peak=   -3.467 closest distance to " O   HOH Z 385 " =    1.944
peak=   -3.465 closest distance to " CD2 LEU A 237 " =    2.620
peak=   -3.465 closest distance to " CB  ALA A 248 " =    2.282
peak=   -3.462 closest distance to " CB  TYR A  15 " =    2.154
peak=   -3.459 closest distance to " CD1 LEU A 101 " =    2.371
peak=   -3.452 closest distance to " N   HIS A 115 " =    1.989
peak=   -3.451 closest distance to " O   VAL A 174 " =    2.030
peak=   -3.444 closest distance to " N   THR A 235 " =    1.339
peak=   -3.441 closest distance to " O   HOH Z  52 " =    1.326
peak=   -3.438 closest distance to " OD1 ASP A 171 " =    1.673
peak=   -3.437 closest distance to " O   VAL A 153 " =    2.389
peak=   -3.432 closest distance to " N   GLN A 122 " =    1.425
peak=   -3.429 closest distance to " CG  GLU A 152 " =    0.953
peak=   -3.428 closest distance to " O   HOH Z  43 " =    1.742
peak=   -3.426 closest distance to " CG1 VAL A 230 " =    1.906
peak=   -3.426 closest distance to " CG  ARG A  66 " =    2.457
peak=   -3.416 closest distance to " CB  ASP A 286 " =    2.062
peak=   -3.413 closest distance to " O   SER A 146 " =    1.129
peak=   -3.410 closest distance to " O   HOH Z 298 " =    1.259
peak=   -3.408 closest distance to " CB  CYS A 201 " =    2.620
peak=   -3.404 closest distance to " N   ASP A 286 " =    2.372
peak=   -3.404 closest distance to " O   HOH Z 102 " =    1.625
peak=   -3.391 closest distance to " O   LYS A 117 " =    1.586
peak=   -3.390 closest distance to " O   SER A  95 " =    1.525
peak=   -3.388 closest distance to " OD1 ASP A 191 " =    1.503
peak=   -3.388 closest distance to " CE  MET A 105 " =    1.958
peak=   -3.385 closest distance to " NH2AARG A 275 " =    5.102
peak=   -3.384 closest distance to " CG2 ILE A 263 " =    2.206
peak=   -3.377 closest distance to " OXT GLY A 302 " =    3.319
peak=   -3.376 closest distance to " O   HOH Z  11 " =    1.731
peak=   -3.354 closest distance to " CG2 THR A 178 " =    2.215
peak=   -3.353 closest distance to " OG  SER A  62 " =    1.474
peak=   -3.352 closest distance to " O   HOH Z 200 " =    4.865
peak=   -3.344 closest distance to " CB  ALA A  43 " =    2.317
peak=   -3.341 closest distance to " O   HOH Z 417 " =    2.494
peak=   -3.341 closest distance to " O   HOH Z  15 " =    1.560
peak=   -3.337 closest distance to " CG1 VAL A  78 " =    3.202
peak=   -3.336 closest distance to " NZ  LYS A 119 " =    3.426
peak=   -3.333 closest distance to " OD1 ASN A 176 " =    1.269
peak=   -3.330 closest distance to " O   HOH Z  11 " =    2.027
peak=   -3.329 closest distance to " O   GLY A 196 " =    0.987
peak=   -3.324 closest distance to " CD1 ILE A 239 " =    2.572
peak=   -3.322 closest distance to " O   LEU A 167 " =    1.492
peak=   -3.317 closest distance to " O   HOH Z 353 " =    2.104
peak=   -3.316 closest distance to " CB  ALA A 291 " =    2.206
peak=   -3.307 closest distance to " CG  ARG A 269 " =    2.282
peak=   -3.307 closest distance to " C   MET A 188 " =    1.488
peak=   -3.305 closest distance to " O   PHE A 218 " =    1.676
peak=   -3.302 closest distance to " O   HOH Z  24 " =    1.457
peak=   -3.295 closest distance to " CD1 LEU A 297 " =    2.263
peak=   -3.284 closest distance to " ND2 ASN A 187 " =    1.469
peak=   -3.281 closest distance to " O   HOH Z 281 " =    2.667
peak=   -3.277 closest distance to " CA  GLY A  98 " =    1.891
peak=   -3.272 closest distance to " O   HOH Z 263 " =    2.876
peak=   -3.271 closest distance to " O   GLY A  80 " =    2.536
peak=   -3.267 closest distance to " CE  MET A  93 " =    1.206
peak=   -3.266 closest distance to " CG  GLU A 277 " =    1.218
peak=   -3.260 closest distance to " O   HOH Z 395 " =    5.185
peak=   -3.259 closest distance to " CG  GLU A 152 " =    2.537
peak=   -3.256 closest distance to " CG  PRO A 163 " =    2.663
peak=   -3.256 closest distance to " N   PHE A  59 " =    2.106
peak=   -3.253 closest distance to " OD2 ASP A 191 " =    1.453
peak=   -3.253 closest distance to " O   HOH Z 134 " =    2.828
peak=   -3.251 closest distance to " O   ALA A  51 " =    1.362
peak=   -3.250 closest distance to " CG  ASP A  50 " =    2.357
peak=   -3.246 closest distance to " O   HOH Z  90 " =    2.727
peak=   -3.238 closest distance to " O   ASP A 162 " =    2.238
peak=   -3.238 closest distance to " O   HOH Z 359 " =    3.010
peak=   -3.234 closest distance to " O   HOH Z  37 " =    1.800
peak=   -3.234 closest distance to " O   HOH Z  63 " =    1.518
peak=   -3.232 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.228 closest distance to " O   HOH Z 388 " =    2.087
peak=   -3.223 closest distance to " O   VAL A 189 " =    2.536
peak=   -3.222 closest distance to " CB  ALA A 131 " =    2.014
peak=   -3.222 closest distance to " OG1 THR A 178 " =    1.267
peak=   -3.220 closest distance to " CD1 ILE A 239 " =    2.104
peak=   -3.220 closest distance to " O   HOH Z 250 " =    1.416
peak=   -3.219 closest distance to " O   HOH Z 137 " =    1.488
peak=   -3.216 closest distance to " CG1 VAL A 197 " =    2.144
peak=   -3.215 closest distance to " CA  ASP A 298 " =    1.050
peak=   -3.214 closest distance to " CB  GLN A  11 " =    1.826
peak=   -3.214 closest distance to " CB  ALA A 100 " =    2.521
peak=   -3.211 closest distance to " O   HOH Z 421 " =    3.086
peak=   -3.209 closest distance to " O   ALA A  34 " =    2.526
peak=   -3.203 closest distance to " OD2 ASP A  50 " =    1.451
peak=   -3.202 closest distance to " O   ILE A 120 " =    1.441
peak=   -3.198 closest distance to " O   HOH Z  76 " =    1.857
peak=   -3.197 closest distance to " O   PRO A  90 " =    1.785
peak=   -3.197 closest distance to " N   GLY A  23 " =    2.320
peak=   -3.197 closest distance to " CA  GLY A 133 " =    1.982
peak=   -3.193 closest distance to " O   HOH Z 317 " =    2.408
peak=   -3.192 closest distance to " NH2BARG A 275 " =    2.125
peak=   -3.192 closest distance to " CD  GLN A  58 " =    1.211
peak=   -3.188 closest distance to " ND2 ASN A 249 " =    2.254
peak=   -3.187 closest distance to " OG ASER A 134 " =    1.108
peak=   -3.187 closest distance to " CD1 TYR A 247 " =    2.519
peak=   -3.180 closest distance to " NH2 ARG A  79 " =    1.692
peak=   -3.180 closest distance to " OG  SER A  26 " =    1.246
peak=   -3.179 closest distance to " OH  TYR A 214 " =    1.226
peak=   -3.177 closest distance to " CB  TRP A  85 " =    2.630
peak=   -3.173 closest distance to " O   HOH Z 234 " =    3.984
peak=   -3.173 closest distance to " O   HOH Z 369 " =    2.131
peak=   -3.161 closest distance to " CG1AVAL A  41 " =    2.882
peak=   -3.157 closest distance to " O   HOH Z 244 " =    2.050
peak=   -3.154 closest distance to " OG  SER A 206 " =    1.650
peak=   -3.151 closest distance to " O   HOH Z 210 " =    1.184
peak=   -3.148 closest distance to " O   GLN A 240 " =    1.843
peak=   -3.148 closest distance to " O   LYS A 289 " =    2.913
peak=   -3.137 closest distance to " CD  GLN A  88 " =    0.817
peak=   -3.136 closest distance to " O   HOH Z 361 " =    3.500
peak=   -3.134 closest distance to " O   ASN A  45 " =    1.884
peak=   -3.131 closest distance to " CG2 VAL A 189 " =    2.101
peak=   -3.124 closest distance to " CD2 TYR A 293 " =    2.028
peak=   -3.123 closest distance to " OE2 GLU A 152 " =    1.219
peak=   -3.123 closest distance to " CG  GLU A  53 " =    1.487
peak=   -3.123 closest distance to " O   HOH Z 166 " =    1.960
peak=   -3.120 closest distance to " O   HOH Z   6 " =    1.530
peak=   -3.115 closest distance to " NH2 ARG A  66 " =    4.994
peak=   -3.110 closest distance to " CZ  ARG A 259 " =    0.832
peak=   -3.108 closest distance to " C   TRP A 274 " =    1.442
peak=   -3.099 closest distance to " O   HOH Z 283 " =    5.821
peak=   -3.096 closest distance to " CE  LYS A  76 " =    2.978
peak=   -3.095 closest distance to " ND2 ASN A  60 " =    1.446
peak=   -3.081 closest distance to " CG  ASN A 301 " =    1.960
peak=   -3.075 closest distance to " O   ASN A 249 " =    1.462
peak=   -3.068 closest distance to " O   HOH Z  41 " =    2.404
peak=   -3.059 closest distance to " CB  PHE A 208 " =    2.206
peak=   -3.057 closest distance to " CA  GLY A 241 " =    3.147
peak=   -3.033 closest distance to " OE2 GLU A   2 " =    1.199

================= 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    :  0.3125 0.3118   6.009720e+00   6.012395e+00
   1_bss:  0.2967 0.2930   5.984997e+00   5.970095e+00
   1_xyz:  0.1875 0.2066   5.550829e+00   5.634488e+00
   1_adp:  0.1737 0.2126   5.505044e+00   5.662362e+00
   1_occ:  0.1733 0.2132   5.503913e+00   5.662564e+00
   2_bss:  0.1712 0.2112   5.496976e+00   5.656823e+00
   2_xyz:  0.1267 0.1653   5.223033e+00   5.425722e+00
   2_adp:  0.1184 0.1593   5.168257e+00   5.383618e+00
   2_occ:  0.1182 0.1592   5.167340e+00   5.382819e+00
   3_bss:  0.1185 0.1585   5.166593e+00   5.378666e+00
   3_xyz:  0.1099 0.1517   5.116059e+00   5.349211e+00
   3_adp:  0.1080 0.1525   5.110202e+00   5.352660e+00
   3_occ:  0.1079 0.1524   5.110117e+00   5.352807e+00
   4_bss:  0.1079 0.1524   5.109802e+00   5.352489e+00
   4_xyz:  0.1074 0.1522   5.108972e+00   5.353807e+00
   4_adp:  0.1092 0.1515   5.114085e+00   5.349888e+00
   4_occ:  0.1091 0.1515   5.113950e+00   5.350137e+00
   5_bss:  0.1091 0.1516   5.114204e+00   5.350433e+00
   5_xyz:  0.1045 0.1516   5.091557e+00   5.347337e+00
   5_adp:  0.1035 0.1523   5.089529e+00   5.351682e+00
   5_occ:  0.1035 0.1522   5.089476e+00   5.351678e+00
   5_bss:  0.1034 0.1522   5.089262e+00   5.351449e+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:  0.313  26.003  -2.174  -2.834   1.225  -0.000   0.000   0.000
   1_xyz:  0.313  26.003  -2.174  -2.834   1.225  -0.000   0.000   0.000
   1_adp:  0.313  26.003  -2.174  -2.834   1.225  -0.000   0.000   0.000
   1_occ:  0.313  26.003  -2.174  -2.834   1.225  -0.000   0.000   0.000
   2_bss:  0.309  33.065  -3.041  -2.869  -1.157  -0.000  -0.000  -0.000
   2_xyz:  0.309  33.065  -3.041  -2.869  -1.157  -0.000  -0.000  -0.000
   2_adp:  0.309  33.065  -3.041  -2.869  -1.157  -0.000  -0.000  -0.000
   2_occ:  0.309  33.065  -3.041  -2.869  -1.157  -0.000  -0.000  -0.000
   3_bss:  0.315  35.667  -2.935  -2.522  -1.562  -0.000  -0.000  -0.000
   3_xyz:  0.315  35.667  -2.935  -2.522  -1.562  -0.000  -0.000  -0.000
   3_adp:  0.315  35.667  -2.935  -2.522  -1.562  -0.000  -0.000  -0.000
   3_occ:  0.315  35.667  -2.935  -2.522  -1.562  -0.000  -0.000  -0.000
   4_bss:  0.316  36.995  -2.801  -2.302  -1.572  -0.000  -0.000  -0.000
   4_xyz:  0.316  36.995  -2.801  -2.302  -1.572  -0.000  -0.000  -0.000
   4_adp:  0.316  36.995  -2.801  -2.302  -1.572  -0.000  -0.000  -0.000
   4_occ:  0.316  36.995  -2.801  -2.302  -1.572  -0.000  -0.000  -0.000
   5_bss:  0.321  36.995  -2.753  -2.190  -1.522  -0.000  -0.000  -0.000
   5_xyz:  0.321  36.995  -2.753  -2.190  -1.522  -0.000  -0.000  -0.000
   5_adp:  0.321  36.995  -2.753  -2.190  -1.522  -0.000  -0.000  -0.000
   5_occ:  0.321  36.995  -2.753  -2.190  -1.522  -0.000  -0.000  -0.000
   5_bss:  0.324  39.156  -2.546  -1.990  -1.333  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.915 0.7401  0.9330    28046.714
   1_bss:  30.256 0.7566  0.9119    24028.102
   1_xyz:  19.193 0.8706  1.0003    10603.230
   1_adp:  20.074 0.8615  0.9972    11238.293
   1_occ:  20.075 0.8615  0.9971    11238.935
   2_bss:  19.818 0.8640  0.9604    11029.708
   2_xyz:  14.978 0.9063  0.9844     6782.302
   2_adp:  14.060 0.9142  0.9845     6294.405
   2_occ:  14.049 0.9143  0.9844     6279.578
   3_bss:  13.963 0.9150  0.9854     6222.830
   3_xyz:  13.272 0.9205  0.9870     5824.851
   3_adp:  13.307 0.9205  0.9818     5871.981
   3_occ:  13.306 0.9205  0.9817     5870.886
   4_bss:  13.302 0.9205  0.9859     5869.599
   4_xyz:  13.316 0.9204  0.9852     5872.038
   4_adp:  13.202 0.9214  0.9823     5837.036
   4_occ:  13.206 0.9213  0.9821     5837.200
   5_bss:  13.212 0.9213  0.9846     5844.422
   5_xyz:  13.126 0.9220  0.9851     5828.786
   5_adp:  13.215 0.9213  0.9795     5859.953
   5_occ:  13.216 0.9213  0.9794     5859.050
   5_bss:  13.211 0.9213  0.9851     5858.719
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6824e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6824e-01
   1_xyz:   1.002  0.007  0.062 14.828  0.004  4.109   5.9646e-02
   1_adp:   1.002  0.007  0.062 14.828  0.004  4.109   5.9646e-02
   1_occ:   1.002  0.007  0.062 14.828  0.004  4.109   5.9646e-02
   2_bss:   1.002  0.007  0.062 14.828  0.004  4.109   5.9646e-02
   2_xyz:   0.961  0.006  0.068 14.525  0.004  4.111   5.3753e-02
   2_adp:   0.961  0.006  0.068 14.525  0.004  4.111   5.3753e-02
   2_occ:   0.961  0.006  0.068 14.525  0.004  4.111   5.3753e-02
   3_bss:   0.961  0.006  0.068 14.525  0.004  4.111   5.3753e-02
   3_xyz:   0.961  0.006  0.072 14.728  0.004  4.110   5.6051e-02
   3_adp:   0.961  0.006  0.072 14.728  0.004  4.110   5.6051e-02
   3_occ:   0.961  0.006  0.072 14.728  0.004  4.110   5.6051e-02
   4_bss:   0.961  0.006  0.072 14.728  0.004  4.110   5.6051e-02
   4_xyz:   0.919  0.005  0.069 14.491  0.004  4.109   5.1587e-02
   4_adp:   0.919  0.005  0.069 14.491  0.004  4.109   5.1587e-02
   4_occ:   0.919  0.005  0.069 14.491  0.004  4.109   5.1587e-02
   5_bss:   0.919  0.005  0.069 14.491  0.004  4.109   5.1587e-02
   5_xyz:   1.101  0.008  0.082 14.964  0.005  4.109   7.0329e-02
   5_adp:   1.101  0.008  0.082 14.964  0.005  4.109   7.0329e-02
   5_occ:   1.101  0.008  0.082 14.964  0.005  4.109   7.0329e-02
   5_bss:   1.101  0.008  0.082 14.964  0.005  4.109   7.0329e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.690   2.3895e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.690   2.3895e-01
   1_xyz:   8.418  0.034  0.269 84.796  0.041  2.290   6.0330e-02
   1_adp:   8.418  0.034  0.269 84.796  0.041  2.290   6.0330e-02
   1_occ:   8.418  0.034  0.269 84.796  0.041  2.290   6.0330e-02
   2_bss:   8.418  0.034  0.269 84.796  0.041  2.290   6.0330e-02
   2_xyz:   6.135  0.036  0.222 82.636  0.035  2.317   3.8249e-02
   2_adp:   6.135  0.036  0.222 82.636  0.035  2.317   3.8249e-02
   2_occ:   6.135  0.036  0.222 82.636  0.035  2.317   3.8249e-02
   3_bss:   6.135  0.036  0.222 82.636  0.035  2.317   3.8249e-02
   3_xyz:   6.510  0.040  0.245 82.244  0.039  2.318   3.9672e-02
   3_adp:   6.510  0.040  0.245 82.244  0.039  2.318   3.9672e-02
   3_occ:   6.510  0.040  0.245 82.244  0.039  2.318   3.9672e-02
   4_bss:   6.510  0.040  0.245 82.244  0.039  2.318   3.9672e-02
   4_xyz:   6.149  0.040  0.230 82.213  0.037  2.340   3.4084e-02
   4_adp:   6.149  0.040  0.230 82.213  0.037  2.340   3.4084e-02
   4_occ:   6.149  0.040  0.230 82.213  0.037  2.340   3.4084e-02
   5_bss:   6.149  0.040  0.230 82.213  0.037  2.340   3.4084e-02
   5_xyz:   7.069  0.047  0.267 82.765  0.038  2.214   5.8158e-02
   5_adp:   7.069  0.047  0.267 82.765  0.038  2.214   5.8158e-02
   5_occ:   7.069  0.047  0.267 82.765  0.038  2.214   5.8158e-02
   5_bss:   7.069  0.047  0.267 82.765  0.038  2.214   5.8158e-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:  72.02   0.00  16.78  72.02   0.00  12.95  62.21   7.59  37.62
   1_occ:  72.02   0.00  16.78  72.02   0.00  12.95  62.21   7.59  37.62
   2_bss:  72.02   0.00  16.78  72.02   0.00  12.95  62.21   7.59  37.62
   2_xyz:  72.02   0.00  16.78  72.02   0.00  12.95  62.21   7.59  37.62
   2_adp:  70.02   0.00  16.99  70.02   0.00  13.07  67.19   5.41  38.31
   2_occ:  70.02   0.00  16.99  70.02   0.00  13.07  67.19   5.41  38.31
   3_bss:  70.02   0.00  16.99  70.02   0.00  13.07  67.19   5.41  38.31
   3_xyz:  70.02   0.00  16.99  70.02   0.00  13.07  67.19   5.41  38.31
   3_adp:  83.63   0.00  17.09  83.63   0.00  13.03  72.82   3.69  39.18
   3_occ:  83.63   0.00  17.09  83.63   0.00  13.03  72.82   3.69  39.18
   4_bss:  83.63   0.00  17.09  83.63   0.00  13.03  72.82   3.69  39.18
   4_xyz:  83.63   0.00  17.09  83.63   0.00  13.03  72.82   3.69  39.18
   4_adp:  79.15   2.07  16.39  79.15   2.07  12.76  71.27   5.22  36.16
   4_occ:  79.15   2.07  16.39  79.15   2.07  12.76  71.27   5.22  36.16
   5_bss:  79.15   2.07  16.39  79.15   2.07  12.76  71.27   5.22  36.16
   5_xyz:  79.15   2.07  16.39  79.15   2.07  12.76  71.27   5.22  36.16
   5_adp:  80.72   1.36  16.46  80.72   1.36  12.66  71.14   6.02  37.15
   5_occ:  80.72   1.36  16.46  80.72   1.36  12.66  71.14   6.02  37.15
   5_bss:  80.67   1.31  16.41  80.67   1.31  12.61  71.09   5.97  37.11
------------------------------------------------------------------------
 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:    1.453    0.005    0.231
   1_adp:    1.453    0.005    0.231
   1_occ:    1.453    0.005    0.231
   2_bss:    1.453    0.005    0.231
   2_xyz:    0.961    0.015    0.321
   2_adp:    0.961    0.015    0.321
   2_occ:    0.961    0.015    0.321
   3_bss:    0.961    0.015    0.321
   3_xyz:    1.128    0.024    0.347
   3_adp:    1.128    0.024    0.347
   3_occ:    1.128    0.024    0.347
   4_bss:    1.128    0.024    0.347
   4_xyz:    1.186    0.008    0.357
   4_adp:    1.186    0.008    0.357
   4_occ:    1.186    0.008    0.357
   5_bss:    1.186    0.008    0.357
   5_xyz:    1.204    0.028    0.363
   5_adp:    1.204    0.028    0.363
   5_occ:    1.204    0.028    0.363
   5_bss:    1.204    0.028    0.363
------------------------------------------------------------------------

CPU time actual refinement: 324.81


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_420/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_420/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_420/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_420/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_420/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.67 
  Macro-tasks:
    bulk solvent and scale       = 38.24  
    individual site refinement   = 131.44 
    weights calculation          = 29.69  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 206.04 
  Micro-tasks:
    mask                            = 1.18   
    f_calc                          = 103.15 
    alpha_beta                      = 7.83   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 111.88 
    fmodel                         = 6.57   
    r_factors                      = 0.14   
    phase_errors                   = 11.23  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 243.39 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.645 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    637 calls, 102.79 s
gradients_fft:          582 calls,  98.73 s

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

# Date 2008-01-16 Time 04:47:41 PST -0800 (1200487661.65 s)
Start R-work = 0.3125, R-free = 0.3118 (no bulk solvent and anisotropic scale)
Final R-work = 0.1297, R-free = 0.1730 (no bulk solvent and anisotropic scale)

Start R-work = 0.2967, R-free = 0.2930
Final R-work = 0.1034, R-free = 0.1522