# Date 2008-01-16 Time 05:48:39 PST -0800 (1200491319.64 s)
#phil __OFF__

Command line arguments: "../889.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29115
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 889

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.4607, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 1.9831
Completeness in resolution range: 0.942867
Completeness with d_max=infinity: 0.940061

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1841
                             d_min =   1.9831

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 1.9831
Completeness in resolution range: 0.942867
Completeness with d_max=infinity: 0.940061

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1846 -  4.2443 [2181/2206]  1961   220  10.1%
  bin  2:  4.2443 -  3.3810 [2100/2120]  1893   207   9.9%
  bin  3:  3.3810 -  2.9572 [2076/2095]  1869   207  10.0%
  bin  4:  2.9572 -  2.6885 [2040/2070]  1833   207  10.1%
  bin  5:  2.6885 -  2.4967 [2038/2057]  1840   198   9.7%
  bin  6:  2.4967 -  2.3501 [2034/2059]  1827   207  10.2%
  bin  7:  2.3501 -  2.2328 [2023/2051]  1816   207  10.2%
  bin  8:  2.2328 -  2.1358 [1997/2033]  1797   200  10.0%
  bin  9:  2.1358 -  2.0538 [2021/2063]  1824   197   9.7%
  bin 10:  2.0538 -  1.9831 [1079/2022]   970   109  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_889/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 21
        2.42 -     3.04: 2168
        3.04 -     3.66: 4664
        3.66 -     4.28: 8922
        4.28 -     4.90: 12274
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.957 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.065 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.065 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.085 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28044 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_889/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_889/model_refine_001.geo

CPU time processing inputs: 9.34


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.4607 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4024   r_free= 0.3924   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.195685                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1846 -  4.7343 0.99   1416  156 0.3246 0.2975       6.472      6.3462|
|  2:  4.7343 -  3.7768 0.99   1370  155 0.3203 0.3278      6.6406       6.618|
|  3:  3.7768 -  3.3050 0.99   1331  145 0.3545 0.3075       6.524      6.4764|
|  4:  3.3050 -  3.0054 0.99   1339  150 0.3884 0.4061      6.4095      6.4343|
|  5:  3.0054 -  2.7914 0.99   1319  149 0.4315 0.3817       6.267      6.2444|
|  6:  2.7914 -  2.6277 0.99   1315  144 0.4099 0.4442       6.151      6.1302|
|  7:  2.6277 -  2.4967 0.99   1306  140 0.4307 0.4060      6.1614      6.1112|
|  8:  2.4967 -  2.3885 0.98   1299  151 0.4659 0.4635      6.1227      6.1388|
|  9:  2.3885 -  2.2968 0.98   1287  142 0.4515 0.4226      6.0604      6.0518|
| 10:  2.2968 -  2.2178 1.00   1300  147 0.4700 0.4779      6.0531      6.0079|
| 11:  2.2178 -  2.1487 0.98   1308  143 0.4740 0.4733      6.0044       6.016|
| 12:  2.1487 -  2.0874 0.98   1274  141 0.4709 0.4348      5.9104      5.9379|
| 13:  2.0874 -  2.0326 0.99   1277  139 0.4605 0.4835       5.824      5.7703|
| 14:  2.0326 -  1.9831 0.37    489   57 0.4775 0.4609       5.844      5.7987|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1846 -  4.7343  1416   156  0.79  25.73   0.84     0.82      43266.22|
|  2:  4.7343 -  3.7768  1370   155  0.81  25.04   0.94     0.90      61791.78|
|  3:  3.7768 -  3.3050  1331   145  0.73  32.60   0.95     0.89      67180.26|
|  4:  3.3050 -  3.0054  1339   150  0.67  38.34   0.94     0.83      62946.17|
|  5:  3.0054 -  2.7914  1319   149  0.59  44.60   0.93     0.77      52347.72|
|  6:  2.7914 -  2.6277  1315   144  0.57  46.62   0.94     0.73      47095.28|
|  7:  2.6277 -  2.4967  1306   140  0.56  47.14   0.95     0.72      44255.09|
|  8:  2.4967 -  2.3885  1299   151  0.54  49.33   0.92     0.72      40908.62|
|  9:  2.3885 -  2.2968  1287   142  0.54  49.15   0.96     0.73      38302.41|
| 10:  2.2968 -  2.2178  1300   147  0.52  50.30   0.97     0.72      35234.87|
| 11:  2.2178 -  2.1487  1308   143  0.50  52.30   0.96     0.71      35786.64|
| 12:  2.1487 -  2.0874  1274   141  0.48  53.73   0.95     0.70      33467.87|
| 13:  2.0874 -  2.0326  1277   139  0.46  55.79   0.97     0.70      29592.19|
| 14:  2.0326 -  1.9831   489    57  0.52  50.98   0.96     0.70      23130.61|
|alpha:            min =        0.70 max =            0.90 mean =         0.77|
|beta:             min =    23130.61 max =        67180.26 mean =     45104.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.98 mean =        43.84|
|phase err.(test): min =        0.00 max =           89.99 mean =        43.57|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.200255              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.953   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.273066              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.491   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      195 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1973 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2823 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4582 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4340 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5587 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6687 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.179 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4024   r_free= 0.3924   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.195685                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3913   r_free= 0.3856   ksol= 0.32   Bsol= 58.42   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-0.89,3.85,-0.00,0.00,0.00); trace/3= 0.30                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.183485                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.904426              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.910   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.618947              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.169   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3913      final r-factor (work) = 0.2240          |
| start r-factor (free) = 0.3856      final r-factor (free) = 0.2555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4893 = 6.90 * 0.50 * 6.1774 + 1.00 * 0.1636                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.5754 = 6.90 * 0.50 * 5.9324 + 1.00 * 0.0954                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2240      final r-factor (work) = 0.2057          |
| start r-factor (free) = 0.2555      final r-factor (free) = 0.2603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6783 = 0.62 * 1.00 * 5.9324 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5341 = 0.62 * 1.00 * 5.6531 + 1.00 * 0.0351                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.96   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    66.96   16.85    None  None   None       |
|    Sol.    : 438    0      3.02    64.53   38.64    None  None   None       |
|    Mac.    : 2385   0      0.00    66.96   12.85    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 -   6.696:  384   |   5:    33.482 -  40.178:  104        |
|      1:     6.696 -  13.393: 1140   |   6:    40.178 -  46.874:   96        |
|      2:    13.393 -  20.089:  604   |   7:    46.874 -  53.571:   92        |
|      3:    20.089 -  26.785:  234   |   8:    53.571 -  60.267:   45        |
|      4:    26.785 -  33.482:  115   |   9:    60.267 -  66.963:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2057 r_free = 0.2603             target_work(ml) = 5.665         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2054 r_free = 0.2600             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2054   r_free= 0.2600   ksol= 0.32   Bsol= 58.42   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-0.89,3.85,-0.00,0.00,0.00); trace/3= 0.30                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.663811                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2029   r_free= 0.2574   ksol= 0.34   Bsol= 68.82   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.27,0.56,-0.00,0.00,0.00); trace/3= -1.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.661493                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.443174              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.969   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.349820              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.054   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2029      final r-factor (work) = 0.1454          |
| start r-factor (free) = 0.2574      final r-factor (free) = 0.1940          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6851 = 4.44 * 0.50 * 5.6670 + 1.00 * 0.0954                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3490 = 4.44 * 0.50 * 5.5282 + 1.00 * 0.0676                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1454      final r-factor (work) = 0.1342          |
| start r-factor (free) = 0.1940      final r-factor (free) = 0.1824          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0249 = 0.35 * 1.00 * 5.5282 + 1.00 * 0.0910                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8741 = 0.35 * 1.00 * 5.3312 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.01   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    71.01   17.20    None  None   None       |
|    Sol.    : 438    0      4.96    71.01   40.58    None  None   None       |
|    Mac.    : 2385   0      0.00    63.65   12.90    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 -   7.101:  372   |   5:    35.503 -  42.603:   89        |
|      1:     7.101 -  14.201: 1378   |   6:    42.603 -  49.704:   84        |
|      2:    14.201 -  21.302:  462   |   7:    49.704 -  56.804:   98        |
|      3:    21.302 -  28.402:  169   |   8:    56.804 -  63.905:   51        |
|      4:    28.402 -  35.503:   99   |   9:    63.905 -  71.005:   21        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1342 r_free = 0.1824             target_work(ml) = 5.298         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1340 r_free = 0.1821             target_work(ml) = 5.298         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1340   r_free= 0.1821   ksol= 0.34   Bsol= 68.82   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.27,0.56,-0.00,0.00,0.00); trace/3= -1.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.297546                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1339   r_free= 0.1813   ksol= 0.34   Bsol= 68.82   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.42,-0.22,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.294925                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.352083              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.191  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.615589              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.506  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1339      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1813      final r-factor (free) = 0.1655          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3369 = 2.35 * 0.50 * 5.3308 + 1.00 * 0.0676                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2406 = 2.35 * 0.50 * 5.2545 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1655      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2437 = 0.62 * 1.00 * 5.2545 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2101 = 0.62 * 1.00 * 5.1983 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.79   17.33    None  None   None       |
|    all(noH): 2823   0      0.00    82.79   17.33    None  None   None       |
|    Sol.    : 438    0      0.00    82.79   41.70    None  None   None       |
|    Mac.    : 2385   0      0.29    78.68   12.86    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 -   8.279:  656   |   5:    41.393 -  49.672:   83        |
|      1:     8.279 -  16.557: 1332   |   6:    49.672 -  57.950:   86        |
|      2:    16.557 -  24.836:  323   |   7:    57.950 -  66.229:   60        |
|      3:    24.836 -  33.114:  132   |   8:    66.229 -  74.507:   30        |
|      4:    33.114 -  41.393:  110   |   9:    74.507 -  82.786:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1638             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1638             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1638   ksol= 0.34   Bsol= 68.82   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.42,-0.22,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.191846                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1637   ksol= 0.34   Bsol= 68.82   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.38,-0.36,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.191710                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.515796              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.099  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.143881              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.662  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0007 = 1.52 * 0.50 * 5.1980 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9871 = 1.52 * 0.50 * 5.1916 + 1.00 * 0.0524                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7570 = 0.14 * 1.00 * 5.1916 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7559 = 0.14 * 1.00 * 5.2016 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.31    79.65   16.55    None  None   None       |
|    all(noH): 2823   0      1.31    79.65   16.55    None  None   None       |
|    Sol.    : 438    0      1.31    79.65   38.08    None  None   None       |
|    Mac.    : 2385   0      1.36    75.64   12.60    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:     1.307 -   9.141:  849   |   5:    40.476 -  48.310:   84        |
|      1:     9.141 -  16.975: 1193   |   6:    48.310 -  56.144:   86        |
|      2:    16.975 -  24.808:  299   |   7:    56.144 -  63.977:   35        |
|      3:    24.808 -  32.642:  132   |   8:    63.977 -  71.811:   16        |
|      4:    32.642 -  40.476:  121   |   9:    71.811 -  79.645:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1193 r_free = 0.1628             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1192 r_free = 0.1627             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1627   ksol= 0.34   Bsol= 68.82   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.38,-0.36,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.197505                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1627   ksol= 0.34   Bsol= 68.82   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.40,-0.43,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.197477                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.447232              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.619  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.354557              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.574  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1627      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4165 = 2.45 * 0.50 * 5.2011 + 1.00 * 0.0524                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4011 = 2.45 * 0.50 * 5.1767 + 1.00 * 0.0669                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1602      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8429 = 0.35 * 1.00 * 5.1767 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8387 = 0.35 * 1.00 * 5.1627 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.85    80.04   16.49    None  None   None       |
|    all(noH): 2823   0      0.85    80.04   16.49    None  None   None       |
|    Sol.    : 438    0      3.00    80.04   38.41    None  None   None       |
|    Mac.    : 2385   0      0.85    76.21   12.47    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:     0.854 -   8.773:  809   |   5:    40.446 -  48.364:   85        |
|      1:     8.773 -  16.691: 1216   |   6:    48.364 -  56.282:   90        |
|      2:    16.691 -  24.609:  308   |   7:    56.282 -  64.201:   37        |
|      3:    24.609 -  32.527:  131   |   8:    64.201 -  72.119:   16        |
|      4:    32.527 -  40.446:  123   |   9:    72.119 -  80.037:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1605             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1129 r_free = 0.1606             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1606   ksol= 0.34   Bsol= 68.82   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.40,-0.43,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163813                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1846 -  4.7343 0.99   1416  156 0.1014 0.1349      5.4209      5.5931|
|  2:  4.7343 -  3.7768 0.99   1370  155 0.0876 0.1161       5.464      5.6559|
|  3:  3.7768 -  3.3050 0.99   1331  145 0.1079 0.1529      5.4897      5.8283|
|  4:  3.3050 -  3.0054 0.99   1339  150 0.1221 0.1722      5.4554      5.6235|
|  5:  3.0054 -  2.7914 0.99   1319  149 0.1347 0.1703      5.3285      5.5701|
|  6:  2.7914 -  2.6277 0.99   1315  144 0.1240 0.1910      5.2143      5.4874|
|  7:  2.6277 -  2.4967 0.99   1306  140 0.1287 0.1635       5.188      5.3349|
|  8:  2.4967 -  2.3885 0.98   1299  151 0.1176 0.1607      5.0781      5.3152|
|  9:  2.3885 -  2.2968 0.98   1287  142 0.1191 0.1897      5.0462      5.3309|
| 10:  2.2968 -  2.2178 1.00   1300  147 0.1139 0.1732      4.9462      5.2143|
| 11:  2.2178 -  2.1487 0.98   1308  143 0.1113 0.1792      4.9419      5.3065|
| 12:  2.1487 -  2.0874 0.98   1274  141 0.1147 0.1760      4.8746      5.1664|
| 13:  2.0874 -  2.0326 0.99   1277  139 0.1099 0.1715      4.7891      5.0284|
| 14:  2.0326 -  1.9831 0.37    489   57 0.1009 0.1557      4.6898      4.8967|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1846 -  4.7343  1416   156  0.94   9.54   0.97     0.94       7741.85|
|  2:  4.7343 -  3.7768  1370   155  0.95   8.27   1.00     0.99       9683.33|
|  3:  3.7768 -  3.3050  1331   145  0.93  11.67   1.01     1.01      10671.75|
|  4:  3.3050 -  3.0054  1339   150  0.91  14.19   1.00     0.97      10419.18|
|  5:  3.0054 -  2.7914  1319   149  0.90  15.75   0.99     0.97       8355.86|
|  6:  2.7914 -  2.6277  1315   144  0.89  16.55   0.98     0.95       7158.60|
|  7:  2.6277 -  2.4967  1306   140  0.90  15.74   0.98     0.95       6458.27|
|  8:  2.4967 -  2.3885  1299   151  0.90  15.78   0.98     0.95       5490.98|
|  9:  2.3885 -  2.2968  1287   142  0.90  15.77   0.99     0.95       5123.48|
| 10:  2.2968 -  2.2178  1300   147  0.90  15.64   0.99     0.96       4308.27|
| 11:  2.2178 -  2.1487  1308   143  0.90  15.91   0.97     0.92       4241.80|
| 12:  2.1487 -  2.0874  1274   141  0.91  15.82   0.99     0.99       3972.67|
| 13:  2.0874 -  2.0326  1277   139  0.89  17.08   0.98     0.97       3531.43|
| 14:  2.0326 -  1.9831   489    57  0.92  14.38   0.96     0.93       2763.11|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2763.11 max =        10671.75 mean =      6639.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.80 mean =        14.37|
|phase err.(test): min =        0.00 max =           88.78 mean =        13.81|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1594   ksol= 0.34   Bsol= 68.79   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.29,-0.33,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.160204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1594   ksol= 0.34   Bsol= 68.79   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.29,-0.33,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.160204                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1846 -  4.7343 0.99   1416  156 0.1009 0.1254      5.3892      5.5327|
|  2:  4.7343 -  3.7768 0.99   1370  155 0.0879 0.1143      5.4515      5.6418|
|  3:  3.7768 -  3.3050 0.99   1331  145 0.1083 0.1517      5.4873      5.8232|
|  4:  3.3050 -  3.0054 0.99   1339  150 0.1220 0.1730      5.4545      5.6249|
|  5:  3.0054 -  2.7914 0.99   1319  149 0.1347 0.1709      5.3286      5.5719|
|  6:  2.7914 -  2.6277 0.99   1315  144 0.1240 0.1907      5.2142      5.4868|
|  7:  2.6277 -  2.4967 0.99   1306  140 0.1286 0.1637      5.1886      5.3358|
|  8:  2.4967 -  2.3885 0.98   1299  151 0.1175 0.1614      5.0785      5.3168|
|  9:  2.3885 -  2.2968 0.98   1287  142 0.1190 0.1897      5.0465      5.3308|
| 10:  2.2968 -  2.2178 1.00   1300  147 0.1138 0.1733      4.9464      5.2148|
| 11:  2.2178 -  2.1487 0.98   1308  143 0.1113 0.1792      4.9422      5.3066|
| 12:  2.1487 -  2.0874 0.98   1274  141 0.1147 0.1761      4.8748      5.1668|
| 13:  2.0874 -  2.0326 0.99   1277  139 0.1098 0.1715       4.789      5.0284|
| 14:  2.0326 -  1.9831 0.37    489   57 0.1009 0.1557      4.6901       4.897|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1846 -  4.7343  1416   156  0.94   8.73   0.97     0.94       6723.05|
|  2:  4.7343 -  3.7768  1370   155  0.95   7.91   1.00     0.99       8983.68|
|  3:  3.7768 -  3.3050  1331   145  0.93  11.52   1.01     1.01      10475.19|
|  4:  3.3050 -  3.0054  1339   150  0.91  14.17   1.00     0.97      10402.33|
|  5:  3.0054 -  2.7914  1319   149  0.90  15.75   0.99     0.98       8360.75|
|  6:  2.7914 -  2.6277  1315   144  0.90  16.54   0.98     0.95       7160.25|
|  7:  2.6277 -  2.4967  1306   140  0.90  15.77   0.99     0.95       6471.40|
|  8:  2.4967 -  2.3885  1299   151  0.90  15.80   0.99     0.96       5501.16|
|  9:  2.3885 -  2.2968  1287   142  0.90  15.78   1.00     0.96       5130.56|
| 10:  2.2968 -  2.2178  1300   147  0.90  15.65   1.00     0.97       4312.82|
| 11:  2.2178 -  2.1487  1308   143  0.90  15.92   0.97     0.92       4245.26|
| 12:  2.1487 -  2.0874  1274   141  0.91  15.83   1.00     0.99       3977.39|
| 13:  2.0874 -  2.0326  1277   139  0.89  17.09   0.99     0.97       3533.16|
| 14:  2.0326 -  1.9831   489    57  0.92  14.38   0.96     0.93       2764.53|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2764.53 max =        10475.19 mean =      6490.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.78 mean =        14.27|
|phase err.(test): min =        0.00 max =           88.60 mean =        13.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.099)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    80.01   16.46    None  None   None       |
|    all(noH): 2823   0      0.83    80.01   16.46    None  None   None       |
|    Sol.    : 438    0      2.97    80.01   38.38    None  None   None       |
|    Mac.    : 2385   0      0.83    76.18   12.44    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:     0.825 -   8.743:  809   |   5:    40.417 -  48.335:   85        |
|      1:     8.743 -  16.662: 1216   |   6:    48.335 -  56.253:   90        |
|      2:    16.662 -  24.580:  308   |   7:    56.253 -  64.172:   37        |
|      3:    24.580 -  32.498:  131   |   8:    64.172 -  72.090:   16        |
|      4:    32.498 -  40.417:  123   |   9:    72.090 -  80.008:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.565 - 4.756
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 299
   mapped sites are within: 0.705 - 4.756

peak=    5.618 closest distance to " NH2 ARG A  56 " =    2.141
peak=    5.410 closest distance to " NE2 GLN A  11 " =    1.195
peak=    5.343 closest distance to " CG  PRO A  54 " =    1.339
peak=    5.135 closest distance to " O   HOH Z 144 " =    1.882
peak=    5.036 closest distance to " CB  GLN A 223 " =    1.461
peak=    4.868 closest distance to " O   HOH Z 369 " =    2.107
peak=    4.821 closest distance to " O   HOH Z 232 " =    2.330
peak=    4.743 closest distance to " CB  GLN A 183 " =    1.222
peak=    4.677 closest distance to " O   HOH Z 126 " =    1.867
peak=    4.670 closest distance to " CB  PRO A  54 " =    1.011
peak=    4.660 closest distance to " CB  ARG A 190 " =    1.536
peak=    4.620 closest distance to " CZ  PHE A 218 " =    1.057
peak=    4.586 closest distance to " CB  ARG A 275 " =    0.899
peak=    4.542 closest distance to " CG  PRO A 213 " =    1.212
peak=    4.514 closest distance to " O   HOH Z 298 " =    2.050
peak=    4.478 closest distance to " CB  ASN A 148 " =    1.414
peak=    4.474 closest distance to " O   HOH Z 423 " =    1.551
peak=    4.459 closest distance to " CB  ARG A  79 " =    1.462
peak=    4.450 closest distance to " CB  SER A  63 " =    1.260
peak=    4.429 closest distance to " O   HOH Z  78 " =    1.784
peak=    4.402 closest distance to " ND2 ASN A 187 " =    1.547
peak=    4.273 closest distance to " O   HOH Z 189 " =    2.871
peak=    4.270 closest distance to " O   HOH Z 406 " =    1.694
peak=    4.268 closest distance to " O   HOH Z 287 " =    2.022
peak=    4.249 closest distance to " CB  VAL A 265 " =    1.343
peak=    4.239 closest distance to " CG2 VAL A 257 " =    0.927
peak=    4.206 closest distance to " CD  ARG A 159 " =    0.770
peak=    4.201 closest distance to " CG  PRO A 198 " =    1.296
peak=    4.195 closest distance to " CE  LYS A  76 " =    0.892
peak=    4.195 closest distance to " CB  TRP A 266 " =    1.017
peak=    4.151 closest distance to " O   HOH Z  21 " =    1.772
peak=    4.132 closest distance to " CB  LEU A 228 " =    1.059
peak=    4.124 closest distance to " CD2 TRP A 179 " =    1.280
peak=    4.104 closest distance to " O   HOH Z 303 " =    2.227
peak=    4.077 closest distance to " CB  ASN A 142 " =    0.993
peak=    4.070 closest distance to " O   HOH Z 133 " =    2.640
peak=    4.050 closest distance to " CG  PRO A 280 " =    0.860
peak=    4.033 closest distance to " O   HOH Z 180 " =    2.115
peak=    4.032 closest distance to " O   HOH Z  10 " =    1.790
peak=    4.023 closest distance to " NH1AARG A 145 " =    1.312
peak=    4.006 closest distance to " CG  LEU A 167 " =    1.293
peak=    3.994 closest distance to " CB  SER A 212 " =    1.233
peak=    3.989 closest distance to " CB  GLU A 152 " =    1.206
peak=    3.987 closest distance to " O   HOH Z 427 " =    2.935
peak=    3.984 closest distance to " CA  SER A  87 " =    0.947
peak=    3.983 closest distance to " O   HOH Z 234 " =    3.797
peak=    3.957 closest distance to " O   HOH Z 419 " =    2.202
peak=    3.938 closest distance to " CB  ASN A  39 " =    0.928
peak=    3.926 closest distance to " O   HOH Z 368 " =    2.000
peak=    3.924 closest distance to " CA  TYR A  30 " =    0.978
peak=    3.894 closest distance to " O   HOH Z  61 " =    1.664
peak=    3.889 closest distance to " O   HOH Z 214 " =    2.171
peak=    3.882 closest distance to " O   HOH Z 158 " =    3.167
peak=    3.875 closest distance to " O   HOH Z 285 " =    2.190
peak=    3.866 closest distance to " O   PRO A 198 " =    1.588
peak=    3.853 closest distance to " O   HOH Z  40 " =    2.156
peak=    3.849 closest distance to " CA  ARG A 195 " =    1.270
peak=    3.848 closest distance to " CB  GLU A  46 " =    0.969
peak=    3.844 closest distance to " CB  GLU A 277 " =    3.669
peak=    3.842 closest distance to " CG  PRO A 243 " =    1.090
peak=    3.831 closest distance to " O   HOH Z 394 " =    4.044
peak=    3.830 closest distance to " CB  GLU A 128 " =    0.908
peak=    3.811 closest distance to " CA  THR A 264 " =    0.910
peak=    3.792 closest distance to " O   HOH Z 265 " =    2.174
peak=    3.784 closest distance to " O   HOH Z 380 " =    1.692
peak=    3.774 closest distance to " O   HOH Z  68 " =    2.153
peak=    3.773 closest distance to " O   HOH Z   9 " =    2.025
peak=    3.769 closest distance to " N   PHE A 130 " =    1.224
peak=    3.761 closest distance to " NE2 HIS A 207 " =    1.227
peak=    3.754 closest distance to " O   HOH Z 193 " =    1.729
peak=    3.750 closest distance to " CA  ALA A  51 " =    0.927
peak=    3.750 closest distance to " CB  ASN A 187 " =    1.137
peak=    3.749 closest distance to " O   HOH Z 346 " =    1.669
peak=    3.739 closest distance to " O   HOH Z 353 " =    2.608
peak=    3.724 closest distance to " O   HOH Z 261 " =    2.029
peak=    3.720 closest distance to " CA  TYR A 116 " =    1.368
peak=    3.713 closest distance to " O   HOH Z 422 " =    2.708
peak=    3.710 closest distance to " CA  ALA A 233 " =    1.264
peak=    3.709 closest distance to " ND1 HIS A  86 " =    1.728
peak=    3.708 closest distance to " CB  ASN A 110 " =    1.129
peak=    3.704 closest distance to " O   HOH Z   1 " =    1.997
peak=    3.703 closest distance to " O   HOH Z 313 " =    2.072
peak=    3.703 closest distance to " O   HOH Z 368 " =    3.625
peak=    3.688 closest distance to " O   HOH Z  53 " =    2.527
peak=    3.682 closest distance to " CB  TYR A 169 " =    0.705
peak=    3.681 closest distance to " OD1 ASN A  69 " =    2.631
peak=    3.661 closest distance to " CB  ASP A 124 " =    0.777
peak=    3.646 closest distance to " CD  LYS A 166 " =    1.268
peak=    3.646 closest distance to " O   SER A  87 " =    2.205
peak=    3.644 closest distance to " O   HOH Z 128 " =    2.226
peak=    3.633 closest distance to " O   HOH Z 126 " =    1.573
peak=    3.625 closest distance to " O   ALA A 165 " =    1.558
peak=    3.622 closest distance to " O   HOH Z 294 " =    1.544
peak=    3.615 closest distance to " CA  VAL A 125 " =    1.113
peak=    3.610 closest distance to " CE1 PHE A 218 " =    0.980
peak=    3.607 closest distance to " CA  ILE A 234 " =    0.976
peak=    3.598 closest distance to " CD1 LEU A 300 " =    1.143
peak=    3.592 closest distance to " CA  ASN A 215 " =    1.140
peak=    3.592 closest distance to " O   HOH Z 352 " =    1.858
peak=    3.582 closest distance to " O   HOH Z 250 " =    1.472
peak=    3.571 closest distance to " CB  SER A 216 " =    0.879
peak=    3.561 closest distance to " O   TYR A 116 " =    1.330
peak=    3.556 closest distance to " O   HOH Z 209 " =    2.240
peak=    3.555 closest distance to " CB  MET A  40 " =    0.779
peak=    3.555 closest distance to " O   HOH Z 148 " =    3.439
peak=    3.551 closest distance to " CB  PRO A  90 " =    1.178
peak=    3.550 closest distance to " O   HOH Z 272 " =    1.824
peak=    3.548 closest distance to " CZ3 TRP A 266 " =    1.136
peak=    3.543 closest distance to " O   HOH Z 172 " =    2.984
peak=    3.542 closest distance to " CB  SER A 210 " =    0.771
peak=    3.542 closest distance to " O   HOH Z 391 " =    2.843
peak=    3.536 closest distance to " CA  ALA A 158 " =    1.198
peak=    3.531 closest distance to " CD  ARG A 269 " =    0.866
peak=    3.529 closest distance to " CG2 THR A 221 " =    0.988
peak=    3.524 closest distance to " N   ALA A   1 " =    2.223
peak=    3.522 closest distance to " O   HOH Z  61 " =    1.533
peak=    3.519 closest distance to " NZ  LYS A 117 " =    3.127
peak=    3.519 closest distance to " O   HOH Z  43 " =    1.917
peak=    3.516 closest distance to " O   HOH Z 171 " =    4.166
peak=    3.516 closest distance to " CB  LEU A  83 " =    0.749
peak=    3.515 closest distance to " O   HOH Z 365 " =    2.868
peak=    3.513 closest distance to " CB  SER A   3 " =    1.376
peak=    3.502 closest distance to " CG  LYS A 119 " =    1.185
peak=    3.492 closest distance to " CG AARG A 275 " =    1.189
peak=    3.492 closest distance to " O   HOH Z 386 " =    2.967
peak=    3.480 closest distance to " CB  VAL A 202 " =    1.619
peak=    3.479 closest distance to " CB  MET A  47 " =    1.208
peak=    3.477 closest distance to " O   ASN A  74 " =    1.455
peak=    3.475 closest distance to " CB  TYR A 116 " =    0.845
peak=    3.474 closest distance to " O   HOH Z 327 " =    1.784
peak=    3.473 closest distance to " O   HOH Z 147 " =    1.841
peak=    3.473 closest distance to " O   HOH Z 183 " =    1.436
peak=    3.472 closest distance to " O   HOH Z   9 " =    1.357
peak=    3.460 closest distance to " O   HOH Z 193 " =    2.044
peak=    3.458 closest distance to " O   HOH Z 405 " =    1.337
peak=    3.456 closest distance to " CB  LYS A 117 " =    1.208
peak=    3.452 closest distance to " N   ARG A 156 " =    1.322
peak=    3.451 closest distance to " O   HOH Z 116 " =    3.140
peak=    3.447 closest distance to " CB  TYR A 169 " =    0.787
peak=    3.445 closest distance to " O   HOH Z 132 " =    2.576
peak=    3.441 closest distance to " CA  ARG A  36 " =    1.053
peak=    3.440 closest distance to " O   HOH Z 213 " =    2.856
peak=    3.440 closest distance to " O   HOH Z 371 " =    2.882
peak=    3.440 closest distance to " O   HOH Z 213 " =    2.239
peak=    3.437 closest distance to " CB  GLN A 103 " =    0.893
peak=    3.432 closest distance to " CB  ASP A 140 " =    0.995
peak=    3.431 closest distance to " O   HOH Z  88 " =    3.910
peak=    3.430 closest distance to " CB  ARG A 138 " =    1.033
peak=    3.423 closest distance to " O   HOH Z 188 " =    2.004
peak=    3.418 closest distance to " O   HOH Z 316 " =    3.083
peak=    3.416 closest distance to " CG2AVAL A  72 " =    1.503
peak=    3.413 closest distance to " CE1 TYR A 186 " =    1.400
peak=    3.408 closest distance to " O   HOH Z 425 " =    1.307
peak=    3.406 closest distance to " O   HOH Z 154 " =    2.024
peak=    3.400 closest distance to " O   HOH Z 187 " =    2.329
peak=    3.400 closest distance to " CA  ASN A 217 " =    1.275
peak=    3.400 closest distance to " O   HOH Z 258 " =    2.138
peak=    3.393 closest distance to " O   HOH Z 411 " =    3.766
peak=    3.392 closest distance to " CA  MET A  40 " =    1.212
peak=    3.391 closest distance to " O  BHOH Z 338 " =    2.394
peak=    3.387 closest distance to " CB  ALA A   1 " =    4.756
peak=    3.385 closest distance to " O   HOH Z 193 " =    1.871
peak=    3.381 closest distance to " O   THR A 251 " =    1.149
peak=    3.376 closest distance to " CG  GLN A  11 " =    1.726
peak=    3.376 closest distance to " O   HOH Z 325 " =    2.351
peak=    3.373 closest distance to " NE  ARG A  79 " =    1.162
peak=    3.364 closest distance to " O   HOH Z 248 " =    1.618
peak=    3.361 closest distance to " O   HOH Z 280 " =    3.099
peak=    3.355 closest distance to " CB  GLN A  88 " =    1.241
peak=    3.352 closest distance to " O   HOH Z  88 " =    3.451
peak=    3.349 closest distance to " O   HOH Z 106 " =    4.171
peak=    3.341 closest distance to " CB  ALA A  34 " =    0.985
peak=    3.339 closest distance to " NH1 ARG A 138 " =    1.062
peak=    3.337 closest distance to " OG BSER A 134 " =    2.855
peak=    3.335 closest distance to " OG BSER A 164 " =    2.404
peak=    3.334 closest distance to " CZ  PHE A  38 " =    1.235
peak=    3.330 closest distance to " CA  GLU A  46 " =    0.904
peak=    3.322 closest distance to " CD1 LEU A  96 " =    0.739
peak=    3.318 closest distance to " O   HOH Z  44 " =    2.794
peak=    3.313 closest distance to " CA  THR A 221 " =    1.027
peak=    3.312 closest distance to " O   PHE A 192 " =    1.364
peak=    3.312 closest distance to " O   HOH Z 287 " =    2.224
peak=    3.310 closest distance to " O   HOH Z 291 " =    1.554
peak=    3.310 closest distance to " CB  PRO A 243 " =    1.423
peak=    3.309 closest distance to " O   HOH Z 403 " =    1.481
peak=    3.303 closest distance to " ND2 ASN A 249 " =    0.836
peak=    3.300 closest distance to " CG2 ILE A  20 " =    1.436
peak=    3.299 closest distance to " O   HOH Z   1 " =    1.681
peak=    3.298 closest distance to " O   HOH Z 368 " =    4.250
peak=    3.295 closest distance to " CD2 TYR A 186 " =    1.043
peak=    3.295 closest distance to " CA  GLY A 267 " =    1.166
peak=    3.292 closest distance to " CG1 VAL A 153 " =    0.889
peak=    3.291 closest distance to " O   HOH Z 345 " =    1.891
peak=    3.287 closest distance to " OG  SER A 135 " =    1.182
peak=    3.287 closest distance to " CG2 ILE A 120 " =    1.313
peak=    3.284 closest distance to " CB  ALA A 248 " =    0.941
peak=    3.282 closest distance to " CG2 ILE A 239 " =    0.744
peak=    3.279 closest distance to " CB  PHE A 204 " =    0.768
peak=    3.276 closest distance to " N   ASP A 162 " =    1.202
peak=    3.275 closest distance to " CB  ALA A  43 " =    0.757
peak=    3.271 closest distance to " O   HOH Z 417 " =    3.643
peak=    3.265 closest distance to " CB  ILE A 120 " =    1.249
peak=    3.265 closest distance to " O   HOH Z 302 " =    1.957
peak=    3.263 closest distance to " O   HOH Z 310 " =    2.167
peak=    3.261 closest distance to " CG  ARG A 159 " =    0.852
peak=    3.255 closest distance to " O   HOH Z 286 " =    2.298
peak=    3.252 closest distance to " OG  SER A  62 " =    2.926
peak=    3.250 closest distance to " O   HOH Z 218 " =    4.563
peak=    3.250 closest distance to " O   HOH Z 421 " =    2.198
peak=    3.249 closest distance to " OE2 GLU A  53 " =    2.010
peak=    3.248 closest distance to " CB  ALA A 160 " =    1.267
peak=    3.247 closest distance to " O   HOH Z  66 " =    2.259
peak=    3.242 closest distance to " N   ASN A  39 " =    1.271
peak=    3.240 closest distance to " CA  ALA A 154 " =    1.066
peak=    3.236 closest distance to " CA  ASP A 162 " =    0.989
peak=    3.235 closest distance to " NE2 GLN A  73 " =    3.932
peak=    3.234 closest distance to " O   HOH Z 234 " =    1.805
peak=    3.233 closest distance to " CB  TRP A 150 " =    1.258
peak=    3.230 closest distance to " O   HOH Z 359 " =    1.509
peak=    3.226 closest distance to " CG  MET A 113 " =    1.274
peak=    3.226 closest distance to " NH2 ARG A 156 " =    1.128
peak=    3.225 closest distance to " O   THR A 220 " =    1.352
peak=    3.222 closest distance to " CG1 VAL A 189 " =    1.956
peak=    3.222 closest distance to " CB  ALA A 114 " =    0.800
peak=    3.221 closest distance to " CA  GLY A 241 " =    0.823
peak=    3.221 closest distance to " O   HOH Z 305 " =    3.648
peak=    3.220 closest distance to " CA  ARG A 159 " =    1.292
peak=    3.220 closest distance to " O   HOH Z 248 " =    1.676
peak=    3.218 closest distance to " CA  SER A  95 " =    0.992
peak=    3.218 closest distance to " O   HOH Z 152 " =    2.702
peak=    3.217 closest distance to " O   HOH Z 371 " =    1.874
peak=    3.215 closest distance to " O   HOH Z 273 " =    2.832
peak=    3.207 closest distance to " O   HOH Z 426 " =    1.959
peak=    3.203 closest distance to " CB  THR A  31 " =    1.589
peak=    3.200 closest distance to " O   HOH Z 234 " =    2.317
peak=    3.197 closest distance to " CD BLYS A 290 " =    1.047
peak=    3.197 closest distance to " O   HOH Z 251 " =    1.696
peak=    3.196 closest distance to " O   HOH Z 271 " =    2.776
peak=    3.194 closest distance to " O   HOH Z  94 " =    2.204
peak=    3.193 closest distance to " CB  SER A  62 " =    1.041
peak=    3.191 closest distance to " OD2 ASP A 286 " =    3.304
peak=    3.189 closest distance to " O   HOH Z 299 " =    4.418
peak=    3.189 closest distance to " O   HOH Z 343 " =    3.360
peak=    3.189 closest distance to " CA  ALA A 291 " =    0.832
peak=    3.186 closest distance to " CD1 ILE A 263 " =    1.265
peak=    3.185 closest distance to " O   HOH Z 233 " =    1.605
peak=    3.182 closest distance to " CA  ASN A 127 " =    1.088
peak=    3.178 closest distance to " O   HOH Z 343 " =    2.741
peak=    3.177 closest distance to " O   HOH Z 369 " =    1.748
peak=    3.177 closest distance to " N   ASN A 127 " =    1.282
peak=    3.177 closest distance to " O   PRO A  90 " =    1.497
peak=    3.175 closest distance to " O   HOH Z 389 " =    1.854
peak=    3.171 closest distance to " O   ASN A 209 " =    1.268
peak=    3.171 closest distance to " CA  ALA A 100 " =    1.114
peak=    3.170 closest distance to " NE AARG A 275 " =    1.348
peak=    3.168 closest distance to " O   HOH Z 124 " =    1.951
peak=    3.166 closest distance to " O   MET A 105 " =    1.879
peak=    3.165 closest distance to " NH2AARG A 275 " =    3.567
peak=    3.165 closest distance to " CG  GLN A 144 " =    0.834
peak=    3.165 closest distance to " O   HOH Z 344 " =    3.179
peak=    3.165 closest distance to " CG2 ILE A 151 " =    0.871
peak=    3.163 closest distance to " N   CYS A 260 " =    0.905
peak=    3.162 closest distance to " CB  ARG A 139 " =    0.999
peak=    3.159 closest distance to " CG  GLU A  37 " =    0.929
peak=    3.158 closest distance to " CG  MET A 185 " =    1.225
peak=    3.156 closest distance to " CG  PHE A 204 " =    0.863
peak=    3.152 closest distance to " O   HOH Z 358 " =    3.705
peak=    3.152 closest distance to " O   HOH Z   7 " =    1.325
peak=    3.150 closest distance to " CD  PRO A 243 " =    1.566
peak=    3.147 closest distance to " CB  TRP A 179 " =    1.477
peak=    3.145 closest distance to " CG  GLN A 278 " =    1.365
peak=    3.142 closest distance to " N   GLU A 152 " =    1.458
peak=    3.141 closest distance to " CD1 ILE A 106 " =    0.804
peak=    3.137 closest distance to " O   HOH Z 421 " =    2.995
peak=    3.136 closest distance to " CG  GLN A  89 " =    1.552
peak=    3.135 closest distance to " CG1 ILE A  49 " =    1.539
peak=    3.134 closest distance to " O   HOH Z 409 " =    2.553
peak=    3.133 closest distance to " O   HOH Z 188 " =    1.432
peak=    3.132 closest distance to " OG  SER A  62 " =    2.946
peak=    3.131 closest distance to " CB  ALA A   9 " =    1.644
peak=    3.130 closest distance to " CA  GLY A 136 " =    0.994
peak=    3.123 closest distance to " CB  ARG A 102 " =    0.729
peak=    3.121 closest distance to " CB  ASN A 215 " =    1.121
peak=    3.116 closest distance to " CA  ARG A 102 " =    1.118
peak=    3.107 closest distance to " O   HOH Z 128 " =    2.143
peak=    3.103 closest distance to " CA  ALA A  84 " =    1.379
peak=    3.100 closest distance to " O   HOH Z 437 " =    1.336
peak=    3.090 closest distance to " O   HOH Z 113 " =    2.182
peak=    3.086 closest distance to " CA  ILE A 106 " =    0.830
peak=    3.072 closest distance to " O   SER A 164 " =    1.380
peak=    3.061 closest distance to " O   HOH Z  97 " =    2.908
peak=    3.060 closest distance to " CD1 LEU A 261 " =    1.288
peak=    3.058 closest distance to " CB  ALA A 291 " =    1.315
peak=    3.045 closest distance to " CG2 ILE A 234 " =    0.837
peak=    3.043 closest distance to " CA  ALA A 299 " =    0.950
peak=    3.011 closest distance to " CB  ASP A 171 " =    0.742

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.506 - 5.627
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 206
   mapped sites are within: 0.733 - 5.627

peak=   -4.404 closest distance to " CD  ARG A  14 " =    3.574
peak=   -4.386 closest distance to " CD  ARG A 156 " =    2.110
peak=   -4.369 closest distance to " CZ3 TRP A 179 " =    1.167
peak=   -4.314 closest distance to " O   HOH Z 377 " =    2.166
peak=   -4.301 closest distance to " O   HOH Z 211 " =    1.157
peak=   -4.275 closest distance to " CB  PRO A 243 " =    2.641
peak=   -4.237 closest distance to " O   HOH Z 231 " =    2.229
peak=   -4.217 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -4.214 closest distance to " OG BSER A 134 " =    1.311
peak=   -4.207 closest distance to " O   PRO A 198 " =    1.249
peak=   -4.103 closest distance to " O   VAL A  67 " =    2.639
peak=   -3.987 closest distance to " O   HOH Z 351 " =    1.436
peak=   -3.985 closest distance to " O   HOH Z 266 " =    5.556
peak=   -3.963 closest distance to " CB  ALA A  43 " =    2.552
peak=   -3.961 closest distance to " OG  SER A  97 " =    2.219
peak=   -3.960 closest distance to " N   ALA A  43 " =    2.584
peak=   -3.957 closest distance to " O   HOH Z  38 " =    1.455
peak=   -3.905 closest distance to " CD  GLN A  58 " =    0.861
peak=   -3.890 closest distance to " CE BMET A  47 " =    1.381
peak=   -3.877 closest distance to " O   HOH Z 290 " =    1.105
peak=   -3.860 closest distance to " CD2 PHE A 192 " =    2.046
peak=   -3.852 closest distance to " O   HOH Z 359 " =    3.194
peak=   -3.851 closest distance to " CD2 TYR A 293 " =    1.978
peak=   -3.846 closest distance to " O   HOH Z 185 " =    2.371
peak=   -3.838 closest distance to " O   HOH Z 372 " =    2.504
peak=   -3.832 closest distance to " O   HOH Z 407 " =    3.263
peak=   -3.814 closest distance to " CG  GLN A 223 " =    2.000
peak=   -3.779 closest distance to " CD1 LEU A 255 " =    2.963
peak=   -3.768 closest distance to " O   TYR A 247 " =    2.899
peak=   -3.743 closest distance to " O   HOH Z 389 " =    2.082
peak=   -3.742 closest distance to " C   HIS A 108 " =    1.169
peak=   -3.738 closest distance to " O   HOH Z  73 " =    2.137
peak=   -3.732 closest distance to " O   HOH Z 131 " =    4.095
peak=   -3.714 closest distance to " O   HOH Z 111 " =    1.681
peak=   -3.704 closest distance to " CE2 TYR A  30 " =    2.697
peak=   -3.701 closest distance to " CB  ALA A 291 " =    2.281
peak=   -3.686 closest distance to " CG1 VAL A 112 " =    2.998
peak=   -3.686 closest distance to " CA  GLY A 241 " =    2.337
peak=   -3.660 closest distance to " CD1 LEU A 101 " =    2.359
peak=   -3.659 closest distance to " O   ALA A  10 " =    1.657
peak=   -3.657 closest distance to " O   HOH Z  22 " =    2.353
peak=   -3.649 closest distance to " N   THR A 157 " =    1.588
peak=   -3.647 closest distance to " ND2 ASN A  45 " =    2.041
peak=   -3.630 closest distance to " NH2AARG A 275 " =    5.549
peak=   -3.622 closest distance to " O   PRO A 163 " =    1.983
peak=   -3.613 closest distance to " CG  GLN A  88 " =    0.829
peak=   -3.609 closest distance to " CG1 VAL A 250 " =    2.697
peak=   -3.601 closest distance to " O   HOH Z 176 " =    0.733
peak=   -3.586 closest distance to " OXT GLY A 302 " =    3.085
peak=   -3.585 closest distance to " CE  MET A 105 " =    2.408
peak=   -3.569 closest distance to " CA  GLY A 241 " =    3.206
peak=   -3.559 closest distance to " ND2 ASN A 249 " =    2.255
peak=   -3.544 closest distance to " CA  VAL A  67 " =    2.974
peak=   -3.544 closest distance to " CB  PRO A 163 " =    2.475
peak=   -3.540 closest distance to " ND2 ASN A  60 " =    1.526
peak=   -3.537 closest distance to " CA  ASP A 298 " =    1.106
peak=   -3.533 closest distance to " O   HOH Z 313 " =    1.902
peak=   -3.528 closest distance to " OD1 ASP A 171 " =    1.663
peak=   -3.528 closest distance to " O   HOH Z 196 " =    2.124
peak=   -3.526 closest distance to " OG BSER A 134 " =    1.789
peak=   -3.519 closest distance to " CB  ALA A 291 " =    2.024
peak=   -3.511 closest distance to " O   HOH Z 395 " =    5.248
peak=   -3.508 closest distance to " CG  MET A 105 " =    0.976
peak=   -3.498 closest distance to " CB  ALA A 100 " =    2.231
peak=   -3.494 closest distance to " O   HOH Z 191 " =    5.627
peak=   -3.482 closest distance to " O   HOH Z 198 " =    1.774
peak=   -3.482 closest distance to " C   LEU A 222 " =    0.750
peak=   -3.481 closest distance to " CA  GLY A  98 " =    1.914
peak=   -3.470 closest distance to " CG2 ILE A 263 " =    2.315
peak=   -3.463 closest distance to " O   SER A 210 " =    1.964
peak=   -3.460 closest distance to " O   HOH Z  60 " =    2.491
peak=   -3.456 closest distance to " O   PHE A 218 " =    1.520
peak=   -3.455 closest distance to " O   HOH Z 174 " =    2.683
peak=   -3.451 closest distance to " CG2 THR A  18 " =    2.846
peak=   -3.442 closest distance to " CB  ASN A  39 " =    2.217
peak=   -3.442 closest distance to " O   HOH Z 429 " =    1.924
peak=   -3.438 closest distance to " ND2 ASN A  45 " =    1.308
peak=   -3.430 closest distance to " CB  TRP A  85 " =    2.476
peak=   -3.425 closest distance to " ND2 ASN A  60 " =    4.113
peak=   -3.423 closest distance to " N   THR A  52 " =    1.779
peak=   -3.420 closest distance to " CB  ASP A 286 " =    2.134
peak=   -3.417 closest distance to " OH  TYR A 172 " =    1.811
peak=   -3.416 closest distance to " CA  GLY A 203 " =    2.378
peak=   -3.411 closest distance to " CD2 PHE A  61 " =    2.091
peak=   -3.399 closest distance to " O   HOH Z 298 " =    1.230
peak=   -3.388 closest distance to " CG  GLU A 277 " =    1.253
peak=   -3.388 closest distance to " CG2 ILE A  49 " =    2.736
peak=   -3.385 closest distance to " CD1 PHE A  59 " =    2.026
peak=   -3.378 closest distance to " O   HOH Z 417 " =    2.901
peak=   -3.377 closest distance to " ND2 ASN A 187 " =    1.508
peak=   -3.370 closest distance to " O   HOH Z  51 " =    1.403
peak=   -3.369 closest distance to " CA  GLY A 133 " =    2.065
peak=   -3.367 closest distance to " NH2BARG A 275 " =    1.834
peak=   -3.361 closest distance to " O   GLY A 211 " =    1.305
peak=   -3.361 closest distance to " O   HOH Z 394 " =    1.473
peak=   -3.352 closest distance to " CB  ASP A 132 " =    2.400
peak=   -3.348 closest distance to " C   MET A 188 " =    1.446
peak=   -3.345 closest distance to " O   VAL A 189 " =    2.576
peak=   -3.342 closest distance to " O   SER A 135 " =    1.419
peak=   -3.340 closest distance to " O   HOH Z   9 " =    1.828
peak=   -3.338 closest distance to " O   ARG A 145 " =    1.516
peak=   -3.335 closest distance to " O   HOH Z 357 " =    2.068
peak=   -3.335 closest distance to " O   SER A  22 " =    2.558
peak=   -3.326 closest distance to " O   HOH Z 140 " =    1.494
peak=   -3.312 closest distance to " CA  ASP A  27 " =    2.466
peak=   -3.312 closest distance to " CD  GLN A 223 " =    0.957
peak=   -3.312 closest distance to " O   HOH Z 152 " =    0.907
peak=   -3.310 closest distance to " O   HOH Z 275 " =    1.509
peak=   -3.310 closest distance to " O   HOH Z 216 " =    1.209
peak=   -3.306 closest distance to " NE2 GLN A 278 " =    1.607
peak=   -3.302 closest distance to " CE3 TRP A 274 " =    1.007
peak=   -3.299 closest distance to " NH2 ARG A  79 " =    1.631
peak=   -3.298 closest distance to " OH  TYR A 247 " =    2.151
peak=   -3.295 closest distance to " CE2 PHE A 218 " =    2.389
peak=   -3.295 closest distance to " CD2 TYR A 247 " =    2.539
peak=   -3.287 closest distance to " O   HOH Z  53 " =    1.723
peak=   -3.284 closest distance to " O   PRO A 198 " =    1.370
peak=   -3.284 closest distance to " O   GLN A 240 " =    2.126
peak=   -3.281 closest distance to " O   HOH Z 345 " =    2.217
peak=   -3.277 closest distance to " O   GLY A  17 " =    1.159
peak=   -3.274 closest distance to " O   HOH Z 219 " =    4.381
peak=   -3.260 closest distance to " N   SER A 276 " =    1.330
peak=   -3.260 closest distance to " O   HOH Z 275 " =    1.727
peak=   -3.259 closest distance to " O   HOH Z 253 " =    3.955
peak=   -3.259 closest distance to " O   HOH Z  11 " =    1.791
peak=   -3.256 closest distance to " O   HOH Z 421 " =    2.945
peak=   -3.253 closest distance to " CB  ALA A   9 " =    2.362
peak=   -3.253 closest distance to " O   HOH Z 103 " =    1.821
peak=   -3.251 closest distance to " O   HOH Z 252 " =    4.194
peak=   -3.250 closest distance to " O   HOH Z 100 " =    1.258
peak=   -3.248 closest distance to " O   HOH Z 348 " =    2.247
peak=   -3.245 closest distance to " CG  HIS A  86 " =    1.123
peak=   -3.243 closest distance to " CB  TYR A  15 " =    2.292
peak=   -3.242 closest distance to " O   HOH Z 108 " =    1.605
peak=   -3.238 closest distance to " OD1 ASN A 148 " =    1.499
peak=   -3.237 closest distance to " O   HOH Z 426 " =    1.617
peak=   -3.231 closest distance to " O   HOH Z 323 " =    1.442
peak=   -3.229 closest distance to " O   ILE A 106 " =    2.056
peak=   -3.226 closest distance to " CG  LEU A 167 " =    0.848
peak=   -3.224 closest distance to " O   HOH Z 174 " =    4.042
peak=   -3.221 closest distance to " CE3 TRP A 150 " =    2.249
peak=   -3.216 closest distance to " C   ASN A 285 " =    2.381
peak=   -3.215 closest distance to " O   HOH Z 266 " =    5.180
peak=   -3.211 closest distance to " CG2 THR A 178 " =    2.298
peak=   -3.211 closest distance to " CG1 VAL A 125 " =    1.834
peak=   -3.204 closest distance to " O   HOH Z 412 " =    4.448
peak=   -3.202 closest distance to " CB  GLN A  11 " =    1.739
peak=   -3.199 closest distance to " CD2 PHE A 192 " =    2.241
peak=   -3.199 closest distance to " OD1AASN A 224 " =    1.812
peak=   -3.198 closest distance to " O   HOH Z 114 " =    1.506
peak=   -3.194 closest distance to " O   VAL A 189 " =    1.640
peak=   -3.194 closest distance to " O   HOH Z  10 " =    1.482
peak=   -3.186 closest distance to " CG  PHE A 283 " =    2.634
peak=   -3.186 closest distance to " O   HOH Z   6 " =    1.414
peak=   -3.181 closest distance to " OD2 ASP A 140 " =    1.615
peak=   -3.176 closest distance to " CD1 LEU A 297 " =    2.643
peak=   -3.173 closest distance to " O   HOH Z  52 " =    1.481
peak=   -3.172 closest distance to " O   HOH Z  63 " =    1.906
peak=   -3.168 closest distance to " CG2 VAL A 189 " =    1.952
peak=   -3.166 closest distance to " OE1 GLN A  88 " =    1.077
peak=   -3.164 closest distance to " CG  GLU A  53 " =    1.444
peak=   -3.162 closest distance to " CZ  PHE A  38 " =    2.080
peak=   -3.162 closest distance to " CD2 PHE A 225 " =    1.086
peak=   -3.158 closest distance to " C   GLY A  13 " =    0.884
peak=   -3.155 closest distance to " OH  TYR A 247 " =    1.853
peak=   -3.155 closest distance to " O   LYS A 289 " =    3.067
peak=   -3.150 closest distance to " N   SER A 141 " =    1.845
peak=   -3.149 closest distance to " CB  ALA A 114 " =    2.534
peak=   -3.143 closest distance to " CD1 LEU A 228 " =    2.358
peak=   -3.141 closest distance to " C   ALA A 114 " =    2.340
peak=   -3.136 closest distance to " O   HOH Z 241 " =    1.274
peak=   -3.132 closest distance to " C   ALA A 158 " =    1.636
peak=   -3.131 closest distance to " O   GLN A 240 " =    2.404
peak=   -3.130 closest distance to " O   HOH Z  60 " =    1.376
peak=   -3.124 closest distance to " O   HOH Z 134 " =    3.359
peak=   -3.123 closest distance to " CA  GLY A 241 " =    2.904
peak=   -3.123 closest distance to " CB  ALA A 129 " =    2.402
peak=   -3.121 closest distance to " C   PHE A  59 " =    1.312
peak=   -3.120 closest distance to " O   HOH Z  43 " =    1.603
peak=   -3.119 closest distance to " CG1 VAL A 197 " =    2.250
peak=   -3.119 closest distance to " CG  TRP A 266 " =    1.752
peak=   -3.118 closest distance to " CZ  TYR A 169 " =    1.688
peak=   -3.118 closest distance to " NE2 GLN A  58 " =    2.625
peak=   -3.113 closest distance to " CA  GLY A  57 " =    2.151
peak=   -3.109 closest distance to " O   HOH Z   9 " =    2.395
peak=   -3.108 closest distance to " CA  GLY A 287 " =    1.395
peak=   -3.101 closest distance to " O   HOH Z 281 " =    2.714
peak=   -3.099 closest distance to " CE1 TYR A 247 " =    2.818
peak=   -3.093 closest distance to " OG  SER A  87 " =    1.288
peak=   -3.091 closest distance to " O   GLU A 152 " =    1.373
peak=   -3.089 closest distance to " O   TRP A  70 " =    1.423
peak=   -3.087 closest distance to " CB  PRO A  54 " =    2.479
peak=   -3.083 closest distance to " CB  ALA A 248 " =    2.458
peak=   -3.082 closest distance to " CD2 TYR A 293 " =    2.129
peak=   -3.082 closest distance to " O   HOH Z 184 " =    1.670
peak=   -3.077 closest distance to " N   MET A 105 " =    2.534
peak=   -3.075 closest distance to " C   ASP A 270 " =    1.281
peak=   -3.056 closest distance to " CA  SER A 135 " =    1.276
peak=   -3.051 closest distance to " SD  MET A 188 " =    2.303
peak=   -3.051 closest distance to " O   HOH Z 281 " =    2.804
peak=   -3.051 closest distance to " CD1 ILE A 199 " =    2.632
peak=   -3.051 closest distance to " C   LEU A 222 " =    0.755
peak=   -3.038 closest distance to " O   HOH Z 318 " =    1.957
peak=   -3.018 closest distance to " O   HOH Z 236 " =    1.454

================= 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    :  0.4024 0.3924   6.195685e+00   6.170666e+00
   1_bss:  0.3913 0.3856   6.183485e+00   6.155259e+00
   1_xyz:  0.2240 0.2555   5.711918e+00   5.800632e+00
   1_adp:  0.2057 0.2603   5.664737e+00   5.829185e+00
   1_occ:  0.2054 0.2600   5.663811e+00   5.828883e+00
   2_bss:  0.2029 0.2574   5.661493e+00   5.827448e+00
   2_xyz:  0.1454 0.1940   5.366419e+00   5.575331e+00
   2_adp:  0.1342 0.1824   5.298438e+00   5.517195e+00
   2_occ:  0.1340 0.1821   5.297546e+00   5.516566e+00
   3_bss:  0.1339 0.1813   5.294925e+00   5.512579e+00
   3_xyz:  0.1211 0.1655   5.210255e+00   5.436741e+00
   3_adp:  0.1180 0.1638   5.191900e+00   5.424355e+00
   3_occ:  0.1179 0.1638   5.191846e+00   5.424502e+00
   4_bss:  0.1179 0.1637   5.191710e+00   5.424567e+00
   4_xyz:  0.1178 0.1643   5.193706e+00   5.427367e+00
   4_adp:  0.1193 0.1628   5.197743e+00   5.422286e+00
   4_occ:  0.1192 0.1627   5.197505e+00   5.422543e+00
   5_bss:  0.1192 0.1627   5.197477e+00   5.422566e+00
   5_xyz:  0.1139 0.1602   5.167228e+00   5.408464e+00
   5_adp:  0.1130 0.1605   5.163698e+00   5.408766e+00
   5_occ:  0.1129 0.1606   5.163813e+00   5.409003e+00
   5_bss:  0.1130 0.1594   5.160204e+00   5.403173e+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:  0.324  58.416  -2.051  -0.893   3.853  -0.000   0.000   0.000
   1_xyz:  0.324  58.416  -2.051  -0.893   3.853  -0.000   0.000   0.000
   1_adp:  0.324  58.416  -2.051  -0.893   3.853  -0.000   0.000   0.000
   1_occ:  0.324  58.416  -2.051  -0.893   3.853  -0.000   0.000   0.000
   2_bss:  0.336  68.822  -2.516  -2.269   0.562  -0.000   0.000   0.000
   2_xyz:  0.336  68.822  -2.516  -2.269   0.562  -0.000   0.000   0.000
   2_adp:  0.336  68.822  -2.516  -2.269   0.562  -0.000   0.000   0.000
   2_occ:  0.336  68.822  -2.516  -2.269   0.562  -0.000   0.000   0.000
   3_bss:  0.336  68.822  -2.449  -2.424  -0.220  -0.000  -0.000  -0.000
   3_xyz:  0.336  68.822  -2.449  -2.424  -0.220  -0.000  -0.000  -0.000
   3_adp:  0.336  68.822  -2.449  -2.424  -0.220  -0.000  -0.000  -0.000
   3_occ:  0.336  68.822  -2.449  -2.424  -0.220  -0.000  -0.000  -0.000
   4_bss:  0.336  68.822  -2.263  -2.380  -0.361  -0.000  -0.000  -0.000
   4_xyz:  0.336  68.822  -2.263  -2.380  -0.361  -0.000  -0.000  -0.000
   4_adp:  0.336  68.822  -2.263  -2.380  -0.361  -0.000  -0.000  -0.000
   4_occ:  0.336  68.822  -2.263  -2.380  -0.361  -0.000  -0.000  -0.000
   5_bss:  0.336  68.822  -2.263  -2.400  -0.428  -0.000  -0.000  -0.000
   5_xyz:  0.336  68.822  -2.263  -2.400  -0.428  -0.000  -0.000  -0.000
   5_adp:  0.336  68.822  -2.263  -2.400  -0.428  -0.000  -0.000  -0.000
   5_occ:  0.336  68.822  -2.263  -2.400  -0.428  -0.000  -0.000  -0.000
   5_bss:  0.336  68.793  -2.116  -2.286  -0.332  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.814 0.5980  0.7657    45103.630
   1_bss:  42.763 0.6093  0.7934    42610.782
   1_xyz:  24.365 0.8193  0.9943    15946.700
   1_adp:  25.470 0.8069  0.9836    16931.346
   1_occ:  25.478 0.8067  0.9830    16891.704
   2_bss:  25.267 0.8093  0.9301    16856.567
   2_xyz:  18.424 0.8760  0.9764     9441.476
   2_adp:  16.907 0.8903  0.9790     8423.941
   2_occ:  16.891 0.8904  0.9789     8403.949
   3_bss:  16.806 0.8911  0.9694     8307.545
   3_xyz:  15.028 0.9064  0.9748     6991.903
   3_adp:  14.696 0.9095  0.9687     6798.531
   3_occ:  14.700 0.9095  0.9687     6800.446
   4_bss:  14.698 0.9095  0.9698     6802.575
   4_xyz:  14.725 0.9095  0.9707     6846.935
   4_adp:  14.591 0.9107  0.9676     6822.656
   4_occ:  14.600 0.9106  0.9674     6824.146
   5_bss:  14.599 0.9106  0.9665     6824.318
   5_xyz:  14.308 0.9129  0.9682     6652.849
   5_adp:  14.306 0.9129  0.9623     6635.871
   5_occ:  14.315 0.9128  0.9622     6639.194
   5_bss:  14.214 0.9135  0.9655     6490.703
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6365e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6365e-01
   1_xyz:   1.311  0.011  0.086 15.845  0.006  4.115   9.5445e-02
   1_adp:   1.311  0.011  0.086 15.845  0.006  4.115   9.5445e-02
   1_occ:   1.311  0.011  0.086 15.845  0.006  4.115   9.5445e-02
   2_bss:   1.311  0.011  0.086 15.845  0.006  4.115   9.5445e-02
   2_xyz:   1.083  0.009  0.079 14.935  0.004  4.129   6.7572e-02
   2_adp:   1.083  0.009  0.079 14.935  0.004  4.129   6.7572e-02
   2_occ:   1.083  0.009  0.079 14.935  0.004  4.129   6.7572e-02
   3_bss:   1.083  0.009  0.079 14.935  0.004  4.129   6.7572e-02
   3_xyz:   1.007  0.008  0.076 14.781  0.003  4.114   6.1108e-02
   3_adp:   1.007  0.008  0.076 14.781  0.003  4.114   6.1108e-02
   3_occ:   1.007  0.008  0.076 14.781  0.003  4.114   6.1108e-02
   4_bss:   1.007  0.008  0.076 14.781  0.003  4.114   6.1108e-02
   4_xyz:   0.919  0.007  0.071 14.458  0.003  4.116   5.2431e-02
   4_adp:   0.919  0.007  0.071 14.458  0.003  4.116   5.2431e-02
   4_occ:   0.919  0.007  0.071 14.458  0.003  4.116   5.2431e-02
   5_bss:   0.919  0.007  0.071 14.458  0.003  4.116   5.2431e-02
   5_xyz:   1.053  0.009  0.079 14.725  0.003  4.119   6.6860e-02
   5_adp:   1.053  0.009  0.079 14.725  0.003  4.119   6.6860e-02
   5_occ:   1.053  0.009  0.079 14.725  0.003  4.119   6.6860e-02
   5_bss:   1.053  0.009  0.079 14.725  0.003  4.119   6.6860e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4258e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4258e-01
   1_xyz:   9.316  0.065  0.331 81.912  0.051  2.104   9.5743e-02
   1_adp:   9.316  0.065  0.331 81.912  0.051  2.104   9.5743e-02
   1_occ:   9.316  0.065  0.331 81.912  0.051  2.104   9.5743e-02
   2_bss:   9.316  0.065  0.331 81.912  0.051  2.104   9.5743e-02
   2_xyz:   6.928  0.058  0.247 83.603  0.027  2.319   5.8239e-02
   2_adp:   6.928  0.058  0.247 83.603  0.027  2.319   5.8239e-02
   2_occ:   6.928  0.058  0.247 83.603  0.027  2.319   5.8239e-02
   3_bss:   6.928  0.058  0.247 83.603  0.027  2.319   5.8239e-02
   3_xyz:   7.344  0.043  0.243 83.253  0.027  2.386   3.9988e-02
   3_adp:   7.344  0.043  0.243 83.253  0.027  2.386   3.9988e-02
   3_occ:   7.344  0.043  0.243 83.253  0.027  2.386   3.9988e-02
   4_bss:   7.344  0.043  0.243 83.253  0.027  2.386   3.9988e-02
   4_xyz:   7.439  0.048  0.210 82.769  0.031  2.402   3.2417e-02
   4_adp:   7.439  0.048  0.210 82.769  0.031  2.402   3.2417e-02
   4_occ:   7.439  0.048  0.210 82.769  0.031  2.402   3.2417e-02
   5_bss:   7.439  0.048  0.210 82.769  0.031  2.402   3.2417e-02
   5_xyz:   7.329  0.046  0.264 84.351  0.026  2.304   4.9239e-02
   5_adp:   7.329  0.046  0.264 84.351  0.026  2.304   4.9239e-02
   5_occ:   7.329  0.046  0.264 84.351  0.026  2.304   4.9239e-02
   5_bss:   7.329  0.046  0.264 84.351  0.026  2.304   4.9239e-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:  66.96   0.00  16.85  66.96   0.00  12.85  64.53   3.02  38.64
   1_occ:  66.96   0.00  16.85  66.96   0.00  12.85  64.53   3.02  38.64
   2_bss:  66.96   0.00  16.85  66.96   0.00  12.85  64.53   3.02  38.64
   2_xyz:  66.96   0.00  16.85  66.96   0.00  12.85  64.53   3.02  38.64
   2_adp:  71.01   0.00  17.20  63.65   0.00  12.90  71.01   4.96  40.58
   2_occ:  71.01   0.00  17.20  63.65   0.00  12.90  71.01   4.96  40.58
   3_bss:  71.01   0.00  17.20  63.65   0.00  12.90  71.01   4.96  40.58
   3_xyz:  71.01   0.00  17.20  63.65   0.00  12.90  71.01   4.96  40.58
   3_adp:  82.79   0.00  17.33  78.68   0.29  12.86  82.79   0.00  41.70
   3_occ:  82.79   0.00  17.33  78.68   0.29  12.86  82.79   0.00  41.70
   4_bss:  82.79   0.00  17.33  78.68   0.29  12.86  82.79   0.00  41.70
   4_xyz:  82.79   0.00  17.33  78.68   0.29  12.86  82.79   0.00  41.70
   4_adp:  79.65   1.31  16.55  75.64   1.36  12.60  79.65   1.31  38.08
   4_occ:  79.65   1.31  16.55  75.64   1.36  12.60  79.65   1.31  38.08
   5_bss:  79.65   1.31  16.55  75.64   1.36  12.60  79.65   1.31  38.08
   5_xyz:  79.65   1.31  16.55  75.64   1.36  12.60  79.65   1.31  38.08
   5_adp:  80.04   0.85  16.49  76.21   0.85  12.47  80.04   3.00  38.41
   5_occ:  80.04   0.85  16.49  76.21   0.85  12.47  80.04   3.00  38.41
   5_bss:  80.01   0.83  16.46  76.18   0.83  12.44  80.01   2.97  38.38
------------------------------------------------------------------------
 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:    1.300    0.026    0.420
   1_adp:    1.300    0.026    0.420
   1_occ:    1.300    0.026    0.420
   2_bss:    1.300    0.026    0.420
   2_xyz:    1.191    0.055    0.489
   2_adp:    1.191    0.055    0.489
   2_occ:    1.191    0.055    0.489
   3_bss:    1.191    0.055    0.489
   3_xyz:    1.184    0.045    0.533
   3_adp:    1.184    0.045    0.533
   3_occ:    1.184    0.045    0.533
   4_bss:    1.184    0.045    0.533
   4_xyz:    1.332    0.050    0.543
   4_adp:    1.332    0.050    0.543
   4_occ:    1.332    0.050    0.543
   5_bss:    1.332    0.050    0.543
   5_xyz:    1.481    0.036    0.553
   5_adp:    1.481    0.036    0.553
   5_occ:    1.481    0.036    0.553
   5_bss:    1.481    0.036    0.553
------------------------------------------------------------------------

CPU time actual refinement: 327.98


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_889/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_889/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_889/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_889/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_889/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.83 
  Macro-tasks:
    bulk solvent and scale       = 36.57  
    individual site refinement   = 142.18 
    weights calculation          = 28.24  
    collect and process          = 6.40   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 213.49 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 105.06 
    alpha_beta                      = 8.13   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 115.71 
    fmodel                         = 6.39   
    r_factors                      = 0.20   
    phase_errors                   = 10.70  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 249.43 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.546 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    665 calls, 104.72 s
gradients_fft:          610 calls, 101.26 s

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

# Date 2008-01-16 Time 05:54:19 PST -0800 (1200491659.14 s)
Start R-work = 0.4024, R-free = 0.3924 (no bulk solvent and anisotropic scale)
Final R-work = 0.1353, R-free = 0.1784 (no bulk solvent and anisotropic scale)

Start R-work = 0.3913, R-free = 0.3856
Final R-work = 0.1130, R-free = 0.1594