# Date 2008-01-16 Time 06:52:54 PST -0800 (1200495174.34 s)
#phil __OFF__

Command line arguments: "../1321.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32478
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1321

-------------------------------------------------------------------------------
  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: (72.0062, 48.1033, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.9616
Completeness in resolution range: 0.904929
Completeness with d_max=infinity: 0.902303

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1768
                             d_min =   1.9616

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: (72.0062, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.9616
Completeness in resolution range: 0.904929
Completeness with d_max=infinity: 0.902303

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1772 -  4.1991 [2276/2305]  2049   227  10.0%
  bin  2:  4.1991 -  3.3447 [2174/2197]  1957   217  10.0%
  bin  3:  3.3447 -  2.9253 [2143/2168]  1925   218  10.2%
  bin  4:  2.9253 -  2.6594 [2148/2174]  1940   208   9.7%
  bin  5:  2.6594 -  2.4697 [2108/2142]  1899   209   9.9%
  bin  6:  2.4697 -  2.3246 [2111/2139]  1894   217  10.3%
  bin  7:  2.3246 -  2.2086 [2099/2135]  1884   215  10.2%
  bin  8:  2.2086 -  2.1127 [2091/2133]  1884   207   9.9%
  bin  9:  2.1127 -  2.0315 [1926/2140]  1736   190   9.9%
  bin 10:  2.0315 -  1.9616 [ 513/2114]   462    51   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1321/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 15
        2.02 -     2.74: 267
        2.74 -     3.46: 4561
        3.46 -     4.18: 9321
        4.18 -     4.90: 13908
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.300 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.367 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.367 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.380 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.591 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28067 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_1321/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1321/model_refine_001.geo

CPU time processing inputs: 9.06


============================ 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 = 72.00625 48.10325 84.6622 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: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4981   r_free= 0.4833   ksol= 0.00   Bsol= 0.00   scale= 0.858    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.304420                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6843 0.99   1478  167 0.4000 0.4166      6.6147      6.6204|
|  2:  4.6843 -  3.7363 0.99   1420  158 0.4454 0.4387      6.8835      6.8834|
|  3:  3.7363 -  3.2694 0.99   1380  145 0.4887 0.4446      6.7047      6.6756|
|  4:  3.2694 -  2.9729 0.98   1389  166 0.5073 0.4854      6.5307      6.5174|
|  5:  2.9729 -  2.7612 0.99   1370  146 0.5232 0.5208      6.3757       6.352|
|  6:  2.7612 -  2.5993 0.99   1372  159 0.5380 0.5108      6.2903      6.1973|
|  7:  2.5993 -  2.4697 0.98   1361  138 0.5322 0.4835      6.2417      6.2106|
|  8:  2.4697 -  2.3626 0.98   1353  152 0.5273 0.5076      6.1407        6.19|
|  9:  2.3626 -  2.2719 0.99   1353  153 0.5553 0.5231      6.1571      6.1023|
| 10:  2.2719 -  2.1938 0.99   1348  160 0.5447 0.5385      6.0773      6.1097|
| 11:  2.1938 -  2.1254 0.97   1346  138 0.5307 0.5482      6.0123      5.9903|
| 12:  2.1254 -  2.0648 0.98   1330  145 0.5180 0.5358      5.9302      5.9662|
| 13:  2.0648 -  2.0105 0.67    906  114 0.5323 0.4492      5.8552      5.8409|
| 14:  2.0105 -  1.9616 0.16    224   18 0.5735 0.4119       5.788      5.7107|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6843  1478   167  0.66  37.42   0.81     0.71      83786.15|
|  2:  4.6843 -  3.7363  1420   158  0.65  39.45   0.87     0.74     123114.19|
|  3:  3.7363 -  3.2694  1380   145  0.51  50.91   0.87     0.68     135037.84|
|  4:  3.2694 -  2.9729  1389   166  0.40  59.38   0.85     0.59     121677.40|
|  5:  2.9729 -  2.7612  1370   146  0.33  65.18   0.84     0.49      95470.30|
|  6:  2.7612 -  2.5993  1372   159  0.33  65.51   0.86     0.48      77956.50|
|  7:  2.5993 -  2.4697  1361   138  0.33  65.14   0.87     0.46      66863.30|
|  8:  2.4697 -  2.3626  1353   152  0.32  66.05   0.87     0.48      62201.19|
|  9:  2.3626 -  2.2719  1353   153  0.30  67.55   0.90     0.45      56151.28|
| 10:  2.2719 -  2.1938  1348   160  0.26  70.46   0.89     0.40      55204.81|
| 11:  2.1938 -  2.1254  1346   138  0.19  76.19   0.90     0.28      53121.17|
| 12:  2.1254 -  2.0648  1330   145  0.16  78.01   0.90     0.27      50525.60|
| 13:  2.0648 -  2.0105   906   114  0.21  74.43   0.92     0.34      40455.78|
| 14:  2.0105 -  1.9616   224    18  0.32  66.28   0.84     0.53      29757.76|
|alpha:            min =        0.27 max =            0.74 mean =         0.50|
|beta:             min =    29757.76 max =       135037.84 mean =     79372.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           89.99 mean =        62.18|
|phase err.(test): min =        0.00 max =           89.92 mean =        62.11|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.262264             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.518   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.271273              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.592   (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 |  1.300 -  1.660:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.660 -  2.020:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.020 -  2.380:       23 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.380 -  2.740:      244 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.740 -  3.100:     2288 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.100 -  3.460:     2273 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.460 -  3.820:     4218 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.820 -  4.180:     5103 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.180 -  4.540:     6255 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.540 -  4.900:     7653 |
|-----------------------------------------------------------------------------|
|-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 |        0.200 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.300 |       0.703 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    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: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4981   r_free= 0.4833   ksol= 0.00   Bsol= 0.00   scale= 0.858    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.304420                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4925   r_free= 0.4762   ksol= 0.28   Bsol= 20.00   scale= 0.901   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.36,2.60,-0.20,0.00,-0.00,-0.00); trace/3= 0.92                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.303397                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.585161             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.422   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.816304              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.303   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4925      final r-factor (work) = 0.3994          |
| start r-factor (free) = 0.4762      final r-factor (free) = 0.4420          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 61.8843 = 19.59 * 0.50 * 6.2991 + 1.00 * 0.1996                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 60.9934 = 19.59 * 0.50 * 6.2089 + 1.00 * 0.1922                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3994      final r-factor (work) = 0.3694          |
| start r-factor (free) = 0.4420      final r-factor (free) = 0.4386          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2839 = 1.82 * 1.00 * 6.2089 + 1.00 * 0.0066                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2455 = 1.82 * 1.00 * 6.1445 + 1.00 * 0.0852                              |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    214.00  17.60    None  None   None       |
|    all(noH): 2823   0      0.00    214.00  17.60    None  None   None       |
|    Sol.    : 438    0      0.00    70.95   36.52    None  None   None       |
|    Mac.    : 2385   0      0.00    214.00  14.12    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 -  21.400: 1951   |   5:   107.002 - 128.402:    0        |
|      1:    21.400 -  42.801:  703   |   6:   128.402 - 149.803:    0        |
|      2:    42.801 -  64.201:  164   |   7:   149.803 - 171.203:    0        |
|      3:    64.201 -  85.602:    4   |   8:   171.203 - 192.603:    0        |
|      4:    85.602 - 107.002:    0   |   9:   192.603 - 214.004:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3694 r_free = 0.4386             target_work(ml) = 6.143         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3690 r_free = 0.4386             target_work(ml) = 6.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3690   r_free= 0.4386   ksol= 0.28   Bsol= 20.00   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.36,2.60,-0.20,0.00,-0.00,-0.00); trace/3= 0.92                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.141999                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3686   r_free= 0.4363   ksol= 0.33   Bsol= 65.23   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.63,2.17,0.71,0.00,0.00,0.00); trace/3= 1.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.142719                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.386668             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.749  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.461674              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.725   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3686      final r-factor (work) = 0.3093          |
| start r-factor (free) = 0.4363      final r-factor (free) = 0.3738          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.1891 = 11.39 * 0.50 * 6.1468 + 1.00 * 0.1932                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.7376 = 11.39 * 0.50 * 6.0836 + 1.00 * 0.1018                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3093      final r-factor (work) = 0.2852          |
| start r-factor (free) = 0.3738      final r-factor (free) = 0.3811          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.0807 = 3.46 * 1.00 * 6.0836 + 1.00 * 0.0214                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.7476 = 3.46 * 1.00 * 5.9840 + 1.00 * 0.0328                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.75  21.25    None  None   None       |
|    all(noH): 2823   0      0.00    124.75  21.25    None  None   None       |
|    Sol.    : 438    0      0.00    117.46  44.48    None  None   None       |
|    Mac.    : 2385   0      0.00    124.75  16.98    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 -  12.475: 1223   |   5:    62.373 -  74.848:   77        |
|      1:    12.475 -  24.949:  739   |   6:    74.848 -  87.323:   44        |
|      2:    24.949 -  37.424:  377   |   7:    87.323 -  99.797:   26        |
|      3:    37.424 -  49.899:  201   |   8:    99.797 - 112.272:   11        |
|      4:    49.899 -  62.373:  119   |   9:   112.272 - 124.746:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2852 r_free = 0.3811             target_work(ml) = 5.991         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2852 r_free = 0.3811             target_work(ml) = 5.991         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2852   r_free= 0.3811   ksol= 0.33   Bsol= 65.23   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.63,2.17,0.71,0.00,0.00,0.00); trace/3= 1.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 5.990754                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2858   r_free= 0.3814   ksol= 0.34   Bsol= 77.55   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.62,1.80,0.38,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 5.991160                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.977546              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.983  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.546049              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.556  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2858      final r-factor (work) = 0.2501          |
| start r-factor (free) = 0.3814      final r-factor (free) = 0.3321          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9702 = 7.98 * 0.50 * 5.9839 + 1.00 * 0.1018                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7798 = 7.98 * 0.50 * 5.9420 + 1.00 * 0.0786                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2501      final r-factor (work) = 0.2390          |
| start r-factor (free) = 0.3321      final r-factor (free) = 0.3075          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2771 = 0.55 * 1.00 * 5.9420 + 1.00 * 0.0325                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2086 = 0.55 * 1.00 * 5.8475 + 1.00 * 0.0156                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.89  18.71    None  None   None       |
|    all(noH): 2823   0      0.00    108.89  18.71    None  None   None       |
|    Sol.    : 438    0      2.62    108.89  42.24    None  None   None       |
|    Mac.    : 2385   0      0.00    100.93  14.39    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 -  10.889: 1219   |   5:    54.446 -  65.336:   73        |
|      1:    10.889 -  21.779:  826   |   6:    65.336 -  76.225:   39        |
|      2:    21.779 -  32.668:  302   |   7:    76.225 -  87.114:   27        |
|      3:    32.668 -  43.557:  210   |   8:    87.114 -  98.004:    9        |
|      4:    43.557 -  54.446:  110   |   9:    98.004 - 108.893:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2390 r_free = 0.3075             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2388 r_free = 0.3074             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2388   r_free= 0.3074   ksol= 0.34   Bsol= 77.55   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.62,1.80,0.38,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.812070                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2388   r_free= 0.3068   ksol= 0.33   Bsol= 72.01   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.00,0.84,-0.26,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.811589                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.514680              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.489  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.774489              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.695  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2388      final r-factor (work) = 0.1871          |
| start r-factor (free) = 0.3068      final r-factor (free) = 0.2403          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1264 = 6.51 * 0.50 * 5.8477 + 1.00 * 0.0786                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7283 = 6.51 * 0.50 * 5.7221 + 1.00 * 0.0896                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1871      final r-factor (work) = 0.1679          |
| start r-factor (free) = 0.2403      final r-factor (free) = 0.2225          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4475 = 0.77 * 1.00 * 5.7221 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3030 = 0.77 * 1.00 * 5.5369 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.45  18.38    None  None   None       |
|    all(noH): 2823   0      0.00    114.45  18.38    None  None   None       |
|    Sol.    : 438    0      4.55    101.62  47.23    None  None   None       |
|    Mac.    : 2385   0      0.00    114.45  13.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.445: 1427   |   5:    57.226 -  68.671:   88        |
|      1:    11.445 -  22.890:  767   |   6:    68.671 -  80.116:   57        |
|      2:    22.890 -  34.335:  216   |   7:    80.116 -  91.561:   27        |
|      3:    34.335 -  45.781:  126   |   8:    91.561 - 103.006:   11        |
|      4:    45.781 -  57.226:  100   |   9:   103.006 - 114.451:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1679 r_free = 0.2225             target_work(ml) = 5.500         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1678 r_free = 0.2224             target_work(ml) = 5.500         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1678   r_free= 0.2224   ksol= 0.33   Bsol= 72.01   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.00,0.84,-0.26,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.499766                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1679   r_free= 0.2226   ksol= 0.33   Bsol= 73.01   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,0.05,-0.72,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.500993                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.815684              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.380   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.180421              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.940  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1679      final r-factor (work) = 0.1448          |
| start r-factor (free) = 0.2226      final r-factor (free) = 0.1982          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6580 = 3.82 * 0.50 * 5.5394 + 1.00 * 0.0896                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4558 = 3.82 * 0.50 * 5.4416 + 1.00 * 0.0741                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1448      final r-factor (work) = 0.1409          |
| start r-factor (free) = 0.1982      final r-factor (free) = 0.1887          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9965 = 0.18 * 1.00 * 5.4416 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9794 = 0.18 * 1.00 * 5.3724 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    109.99  17.12    None  None   None       |
|    all(noH): 2823   0      0.93    109.99  17.12    None  None   None       |
|    Sol.    : 438    0      4.14    100.63  43.40    None  None   None       |
|    Mac.    : 2385   0      0.93    109.99  12.30    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:     0.934 -  11.840: 1555   |   5:    55.461 -  66.366:   69        |
|      1:    11.840 -  22.745:  741   |   6:    66.366 -  77.271:   48        |
|      2:    22.745 -  33.650:  152   |   7:    77.271 -  88.176:   15        |
|      3:    33.650 -  44.555:  124   |   8:    88.176 -  99.082:    8        |
|      4:    44.555 -  55.461:  106   |   9:    99.082 - 109.987:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1409 r_free = 0.1887             target_work(ml) = 5.349         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1408 r_free = 0.1886             target_work(ml) = 5.348         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1408   r_free= 0.1886   ksol= 0.33   Bsol= 73.01   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,0.05,-0.72,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.348421                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6843 0.99   1478  167 0.1037 0.1408      5.4549      5.6832|
|  2:  4.6843 -  3.7363 0.99   1420  158 0.0963 0.1233      5.5423      5.7764|
|  3:  3.7363 -  3.2694 0.99   1380  145 0.1279 0.1906      5.6281      5.9797|
|  4:  3.2694 -  2.9729 0.98   1389  166 0.1687 0.1986      5.6644      5.8082|
|  5:  2.9729 -  2.7612 0.99   1370  146 0.1711 0.2124      5.5377      5.6837|
|  6:  2.7612 -  2.5993 0.99   1372  159 0.1619 0.2269      5.4269      5.5945|
|  7:  2.5993 -  2.4697 0.98   1361  138 0.1586 0.2104      5.3524      5.5848|
|  8:  2.4697 -  2.3626 0.98   1353  152 0.1627 0.2068      5.2961      5.4765|
|  9:  2.3626 -  2.2719 0.99   1353  153 0.1540 0.2287      5.2355      5.4668|
| 10:  2.2719 -  2.1938 0.99   1348  160 0.1505 0.2116      5.1902      5.4363|
| 11:  2.1938 -  2.1254 0.97   1346  138 0.1433 0.2012      5.1015      5.3017|
| 12:  2.1254 -  2.0648 0.98   1330  145 0.1469 0.2268      5.0415      5.2917|
| 13:  2.0648 -  2.0105 0.67    906  114 0.1510 0.1891      4.9639      5.1504|
| 14:  2.0105 -  1.9616 0.16    224   18 0.1505 0.1652      4.8833      5.0401|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6843  1478   167  0.93  10.60   0.96     0.94       9208.98|
|  2:  4.6843 -  3.7363  1420   158  0.94   9.86   1.01     0.99      11577.65|
|  3:  3.7363 -  3.2694  1380   145  0.91  14.59   1.03     1.02      14125.93|
|  4:  3.2694 -  2.9729  1389   166  0.88  18.63   1.01     0.98      15129.00|
|  5:  2.9729 -  2.7612  1370   146  0.85  20.94   1.01     0.98      13063.31|
|  6:  2.7612 -  2.5993  1372   159  0.86  20.58   1.00     0.97      10789.34|
|  7:  2.5993 -  2.4697  1361   138  0.87  19.74   0.99     0.96       9079.39|
|  8:  2.4697 -  2.3626  1353   152  0.86  20.46   1.01     0.97       8485.21|
|  9:  2.3626 -  2.2719  1353   153  0.86  20.85   1.01     0.95       7586.38|
| 10:  2.2719 -  2.1938  1348   160  0.86  20.35   0.99     0.93       6892.00|
| 11:  2.1938 -  2.1254  1346   138  0.87  20.02   1.00     0.95       6169.76|
| 12:  2.1254 -  2.0648  1330   145  0.86  20.68   0.99     0.97       5622.54|
| 13:  2.0648 -  2.0105   906   114  0.86  20.73   1.00     0.98       4745.84|
| 14:  2.0105 -  1.9616   224    18  0.86  20.52   0.98     0.96       3889.71|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3889.71 max =        15129.00 mean =      9506.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.92 mean =        18.19|
|phase err.(test): min =        0.00 max =           89.65 mean =        17.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1411   r_free= 0.1890   ksol= 0.33   Bsol= 66.96   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,-0.48,-0.93,-0.00,-0.00,-0.00); trace/3= -0.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.349761                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1411   r_free= 0.1890   ksol= 0.33   Bsol= 66.96   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,-0.48,-0.93,-0.00,-0.00,-0.00); trace/3= -0.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.349761                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6843 0.99   1478  167 0.1052 0.1416      5.4665      5.6799|
|  2:  4.6843 -  3.7363 0.99   1420  158 0.0964 0.1242      5.5447      5.7804|
|  3:  3.7363 -  3.2694 0.99   1380  145 0.1280 0.1902      5.6294       5.979|
|  4:  3.2694 -  2.9729 0.98   1389  166 0.1690 0.1982      5.6651      5.8063|
|  5:  2.9729 -  2.7612 0.99   1370  146 0.1712 0.2130      5.5383      5.6864|
|  6:  2.7612 -  2.5993 0.99   1372  159 0.1621 0.2265      5.4272      5.5941|
|  7:  2.5993 -  2.4697 0.98   1361  138 0.1587 0.2104      5.3524      5.5845|
|  8:  2.4697 -  2.3626 0.98   1353  152 0.1626 0.2073      5.2955       5.478|
|  9:  2.3626 -  2.2719 0.99   1353  153 0.1538 0.2285      5.2347      5.4661|
| 10:  2.2719 -  2.1938 0.99   1348  160 0.1505 0.2118      5.1898      5.4372|
| 11:  2.1938 -  2.1254 0.97   1346  138 0.1432 0.2016      5.1012      5.3018|
| 12:  2.1254 -  2.0648 0.98   1330  145 0.1470 0.2273       5.043      5.2946|
| 13:  2.0648 -  2.0105 0.67    906  114 0.1509 0.1886      4.9641      5.1493|
| 14:  2.0105 -  1.9616 0.16    224   18 0.1506 0.1651      4.8825      5.0366|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6843  1478   167  0.93  10.91   0.96     0.93       9339.48|
|  2:  4.6843 -  3.7363  1420   158  0.94   9.87   1.00     0.98      11629.62|
|  3:  3.7363 -  3.2694  1380   145  0.91  14.54   1.02     1.02      14121.88|
|  4:  3.2694 -  2.9729  1389   166  0.88  18.60   1.00     0.97      15105.22|
|  5:  2.9729 -  2.7612  1370   146  0.85  20.92   1.00     0.97      13053.30|
|  6:  2.7612 -  2.5993  1372   159  0.86  20.56   0.99     0.96      10777.51|
|  7:  2.5993 -  2.4697  1361   138  0.87  19.72   0.98     0.94       9075.15|
|  8:  2.4697 -  2.3626  1353   152  0.86  20.45   0.99     0.95       8480.89|
|  9:  2.3626 -  2.2719  1353   153  0.86  20.84   0.99     0.94       7593.52|
| 10:  2.2719 -  2.1938  1348   160  0.86  20.35   0.97     0.91       6895.84|
| 11:  2.1938 -  2.1254  1346   138  0.87  20.02   0.98     0.93       6174.70|
| 12:  2.1254 -  2.0648  1330   145  0.86  20.70   0.97     0.95       5641.94|
| 13:  2.0648 -  2.0105   906   114  0.86  20.73   0.97     0.96       4746.90|
| 14:  2.0105 -  1.9616   224    18  0.86  20.51   0.97     0.94       3876.23|
|alpha:            min =        0.91 max =            1.02 mean =         0.95|
|beta:             min =     3876.23 max =        15105.22 mean =      9519.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.96 mean =        18.20|
|phase err.(test): min =        0.00 max =           90.00 mean =        17.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.187)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.90    109.95  17.09    None  None   None       |
|    all(noH): 2823   0      0.90    109.95  17.09    None  None   None       |
|    Sol.    : 438    0      4.11    100.60  43.37    None  None   None       |
|    Mac.    : 2385   0      0.90    109.95  12.26    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:     0.902 -  11.807: 1555   |   5:    55.428 -  66.334:   69        |
|      1:    11.807 -  22.713:  741   |   6:    66.334 -  77.239:   48        |
|      2:    22.713 -  33.618:  152   |   7:    77.239 -  88.144:   15        |
|      3:    33.618 -  44.523:  124   |   8:    88.144 -  99.050:    8        |
|      4:    44.523 -  55.428:  106   |   9:    99.050 - 109.955:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 367         
Filter by distance & map next to the model:
   mapped sites are within: 0.654 - 5.875
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 362 from: 367
   mapped sites are within: 0.717 - 5.875

peak=    8.651 closest distance to " O   HOH Z  41 " =    1.801
peak=    6.433 closest distance to " O   HOH Z 400 " =    1.189
peak=    6.264 closest distance to " O   HOH Z 120 " =    1.259
peak=    6.251 closest distance to " O   HOH Z 130 " =    1.164
peak=    5.686 closest distance to " NH2AARG A 102 " =    1.105
peak=    5.653 closest distance to " O   HOH Z 342 " =    1.054
peak=    5.644 closest distance to " O   ARG A 275 " =    0.823
peak=    5.522 closest distance to " O   HOH Z 210 " =    1.662
peak=    5.361 closest distance to " O   HOH Z 404 " =    1.546
peak=    5.275 closest distance to " CG  PRO A  54 " =    1.263
peak=    5.149 closest distance to " O   HOH Z 111 " =    1.996
peak=    5.086 closest distance to " CB  SER A  63 " =    1.418
peak=    5.062 closest distance to " O   HOH Z  49 " =    1.248
peak=    5.043 closest distance to " O   HOH Z 117 " =    1.420
peak=    4.973 closest distance to " O   HOH Z 182 " =    1.581
peak=    4.879 closest distance to " O   HOH Z 192 " =    1.792
peak=    4.776 closest distance to " O   HOH Z  61 " =    1.678
peak=    4.713 closest distance to " NE2 HIS A 115 " =    1.049
peak=    4.680 closest distance to " CB  SER A  62 " =    1.005
peak=    4.670 closest distance to " O   HOH Z  54 " =    1.369
peak=    4.667 closest distance to " CB  GLN A 223 " =    1.554
peak=    4.652 closest distance to " O   HOH Z 350 " =    1.216
peak=    4.633 closest distance to " O   HOH Z 127 " =    1.360
peak=    4.621 closest distance to " CA  TYR A  30 " =    1.077
peak=    4.546 closest distance to " O   PRO A 198 " =    1.600
peak=    4.539 closest distance to " O   HOH Z 132 " =    1.832
peak=    4.516 closest distance to " O   HOH Z 102 " =    1.387
peak=    4.516 closest distance to " CG  PRO A 213 " =    1.290
peak=    4.511 closest distance to " O   HOH Z 124 " =    1.375
peak=    4.443 closest distance to " CB  ARG A 275 " =    0.948
peak=    4.432 closest distance to " O   HOH Z  41 " =    1.252
peak=    4.424 closest distance to " CA  GLU A 277 " =    1.127
peak=    4.418 closest distance to " CB  GLN A  73 " =    1.012
peak=    4.401 closest distance to " O   HOH Z 134 " =    2.184
peak=    4.390 closest distance to " CG  PRO A 198 " =    1.451
peak=    4.380 closest distance to " O   HOH Z 217 " =    1.577
peak=    4.378 closest distance to " CB  TRP A 179 " =    1.520
peak=    4.376 closest distance to " O   HOH Z  15 " =    1.933
peak=    4.324 closest distance to " CG  PRO A 280 " =    1.054
peak=    4.320 closest distance to " O   HOH Z 234 " =    3.708
peak=    4.307 closest distance to " O   HOH Z 426 " =    1.378
peak=    4.279 closest distance to " OG  SER A 276 " =    0.959
peak=    4.273 closest distance to " O   HOH Z   4 " =    1.262
peak=    4.256 closest distance to " CG1 VAL A 153 " =    1.069
peak=    4.242 closest distance to " N   ARG A 275 " =    0.913
peak=    4.232 closest distance to " CG  PRO A 243 " =    1.121
peak=    4.230 closest distance to " CA  GLY A 196 " =    1.060
peak=    4.228 closest distance to " CB  GLU A 152 " =    1.235
peak=    4.220 closest distance to " O   HOH Z  63 " =    1.584
peak=    4.214 closest distance to " CG1 ILE A  33 " =    1.300
peak=    4.211 closest distance to " O   HOH Z  47 " =    1.718
peak=    4.196 closest distance to " O   HOH Z  80 " =    2.357
peak=    4.192 closest distance to " CB  TRP A 266 " =    1.007
peak=    4.190 closest distance to " CG AARG A 275 " =    1.133
peak=    4.189 closest distance to " O   HOH Z 292 " =    1.528
peak=    4.173 closest distance to " OE1 GLN A  11 " =    2.039
peak=    4.170 closest distance to " O   HOH Z 411 " =    2.861
peak=    4.168 closest distance to " CB  GLU A 277 " =    0.890
peak=    4.163 closest distance to " O   HOH Z 214 " =    1.371
peak=    4.149 closest distance to " O   HOH Z 406 " =    1.539
peak=    4.148 closest distance to " CG  GLN A  77 " =    0.812
peak=    4.139 closest distance to " CB  GLN A 194 " =    0.886
peak=    4.115 closest distance to " O   HOH Z  44 " =    2.461
peak=    4.106 closest distance to " O   HOH Z 431 " =    1.440
peak=    4.097 closest distance to " O   HOH Z 272 " =    1.409
peak=    4.081 closest distance to " O   HOH Z 433 " =    2.060
peak=    4.070 closest distance to " O   HOH Z 126 " =    2.095
peak=    4.069 closest distance to " OE1 GLN A  88 " =    0.895
peak=    4.065 closest distance to " O   HOH Z  11 " =    1.199
peak=    4.061 closest distance to " O   HOH Z 389 " =    1.850
peak=    4.059 closest distance to " O   HOH Z 207 " =    1.656
peak=    4.051 closest distance to " CG  PRO A  90 " =    1.268
peak=    4.036 closest distance to " O   HOH Z 418 " =    1.828
peak=    4.030 closest distance to " O   HOH Z 193 " =    1.867
peak=    4.022 closest distance to " O   HOH Z 335 " =    0.951
peak=    4.022 closest distance to " O   HOH Z  47 " =    1.700
peak=    4.018 closest distance to " O   HOH Z 261 " =    1.596
peak=    4.013 closest distance to " O  BHOH Z 338 " =    1.067
peak=    4.012 closest distance to " CG2BVAL A  41 " =    1.014
peak=    4.008 closest distance to " CB  TRP A 179 " =    1.648
peak=    3.995 closest distance to " O   HOH Z  39 " =    2.163
peak=    3.990 closest distance to " O   HOH Z  97 " =    1.865
peak=    3.989 closest distance to " O   HOH Z  68 " =    1.931
peak=    3.989 closest distance to " O   HOH Z 352 " =    1.567
peak=    3.988 closest distance to " O   HOH Z 174 " =    1.626
peak=    3.988 closest distance to " CG2 VAL A  78 " =    1.037
peak=    3.970 closest distance to " O   HOH Z 132 " =    1.631
peak=    3.968 closest distance to " CB  PHE A  61 " =    0.913
peak=    3.956 closest distance to " CD BLYS A 290 " =    1.054
peak=    3.947 closest distance to " CB  ASN A 187 " =    1.227
peak=    3.943 closest distance to " CG2 VAL A 197 " =    1.349
peak=    3.934 closest distance to " O   HOH Z  14 " =    1.765
peak=    3.931 closest distance to " O   SER A 276 " =    1.152
peak=    3.926 closest distance to " CB  GLN A  58 " =    0.977
peak=    3.917 closest distance to " CB  SER A 276 " =    1.085
peak=    3.915 closest distance to " O   HOH Z   7 " =    1.270
peak=    3.902 closest distance to " NH2AARG A 145 " =    0.955
peak=    3.897 closest distance to " CA  ASN A 176 " =    1.854
peak=    3.892 closest distance to " O   HOH Z 394 " =    1.662
peak=    3.888 closest distance to " O   HOH Z 316 " =    3.240
peak=    3.876 closest distance to " CE  LYS A 119 " =    1.414
peak=    3.875 closest distance to " O   HOH Z 422 " =    1.196
peak=    3.861 closest distance to " O   HOH Z 112 " =    1.509
peak=    3.859 closest distance to " O   HOH Z 172 " =    5.812
peak=    3.855 closest distance to " O   HOH Z 324 " =    1.624
peak=    3.848 closest distance to " O   HOH Z 343 " =    2.335
peak=    3.847 closest distance to " CB  ASN A 285 " =    0.818
peak=    3.845 closest distance to " CB  LEU A 228 " =    1.164
peak=    3.834 closest distance to " CD1 TRP A 274 " =    1.055
peak=    3.831 closest distance to " CA  SER A  87 " =    0.810
peak=    3.829 closest distance to " CE3 TRP A 274 " =    3.633
peak=    3.826 closest distance to " CD  LYS A 119 " =    1.215
peak=    3.824 closest distance to " CD  ARG A  66 " =    2.978
peak=    3.802 closest distance to " O   GLY A  91 " =    1.207
peak=    3.798 closest distance to " CA  ALA A  21 " =    1.480
peak=    3.797 closest distance to " CB  VAL A 202 " =    1.408
peak=    3.792 closest distance to " O   HOH Z 203 " =    1.846
peak=    3.786 closest distance to " O   THR A 251 " =    1.374
peak=    3.769 closest distance to " CA  ASP A 191 " =    0.878
peak=    3.763 closest distance to " O   HOH Z 411 " =    1.471
peak=    3.760 closest distance to " CZ  PHE A 218 " =    1.175
peak=    3.750 closest distance to " O   HOH Z 128 " =    2.190
peak=    3.750 closest distance to " N   ASN A  39 " =    1.210
peak=    3.749 closest distance to " CA  GLN A 223 " =    0.845
peak=    3.741 closest distance to " CB  GLN A 183 " =    1.181
peak=    3.739 closest distance to " O   HOH Z 287 " =    1.780
peak=    3.728 closest distance to " O   HOH Z 371 " =    3.171
peak=    3.715 closest distance to " OE1 GLN A  77 " =    0.865
peak=    3.714 closest distance to " N   ILE A  33 " =    1.203
peak=    3.712 closest distance to " CG2 THR A 221 " =    1.087
peak=    3.707 closest distance to " CB  MET A  47 " =    1.041
peak=    3.706 closest distance to " O   HOH Z 243 " =    1.241
peak=    3.698 closest distance to " O   HOH Z 131 " =    1.027
peak=    3.682 closest distance to " CB  ALA A 256 " =    1.392
peak=    3.681 closest distance to " NZ  LYS A 193 " =    1.503
peak=    3.680 closest distance to " CA  GLU A 152 " =    0.972
peak=    3.680 closest distance to " CB  PRO A 198 " =    1.106
peak=    3.674 closest distance to " O   HOH Z 437 " =    1.806
peak=    3.667 closest distance to " O   HOH Z 104 " =    3.557
peak=    3.665 closest distance to " O   HOH Z 232 " =    2.072
peak=    3.665 closest distance to " CB  SER A 141 " =    1.001
peak=    3.664 closest distance to " O   HOH Z 133 " =    1.583
peak=    3.658 closest distance to " O   HOH Z 139 " =    4.612
peak=    3.647 closest distance to " O   HOH Z 118 " =    2.135
peak=    3.639 closest distance to " O   HOH Z  78 " =    1.384
peak=    3.636 closest distance to " CB  TYR A  30 " =    1.110
peak=    3.635 closest distance to " O   HOH Z 117 " =    2.162
peak=    3.631 closest distance to " O   HOH Z 221 " =    1.285
peak=    3.629 closest distance to " CB  ASN A 148 " =    1.285
peak=    3.628 closest distance to " CD  PRO A  54 " =    1.052
peak=    3.623 closest distance to " O   HOH Z 363 " =    1.246
peak=    3.621 closest distance to " O   HOH Z 178 " =    1.147
peak=    3.621 closest distance to " O   HOH Z 246 " =    1.506
peak=    3.615 closest distance to " N   GLN A  55 " =    0.845
peak=    3.611 closest distance to " CB  TYR A 116 " =    1.363
peak=    3.610 closest distance to " OG  SER A  97 " =    3.378
peak=    3.606 closest distance to " O   HOH Z 108 " =    1.567
peak=    3.602 closest distance to " O   HOH Z 369 " =    2.046
peak=    3.598 closest distance to " CD  ARG A 159 " =    0.796
peak=    3.594 closest distance to " O   HOH Z  22 " =    2.354
peak=    3.587 closest distance to " CZ  PHE A 192 " =    0.993
peak=    3.583 closest distance to " CB  ALA A 137 " =    1.329
peak=    3.583 closest distance to " O   HOH Z 189 " =    2.160
peak=    3.582 closest distance to " CB  PRO A  54 " =    0.717
peak=    3.579 closest distance to " O   HOH Z 139 " =    3.341
peak=    3.578 closest distance to " O   HOH Z 184 " =    1.146
peak=    3.575 closest distance to " O   HOH Z 149 " =    2.105
peak=    3.568 closest distance to " O   HOH Z 410 " =    1.452
peak=    3.566 closest distance to " CB  SER A  26 " =    0.937
peak=    3.562 closest distance to " O   HOH Z 272 " =    1.920
peak=    3.555 closest distance to " O   HOH Z 145 " =    2.016
peak=    3.553 closest distance to " O   HOH Z 387 " =    2.428
peak=    3.546 closest distance to " N   LYS A 166 " =    0.774
peak=    3.544 closest distance to " O   HOH Z 207 " =    1.757
peak=    3.539 closest distance to " O   HOH Z 175 " =    3.826
peak=    3.537 closest distance to " O   HOH Z 202 " =    1.601
peak=    3.537 closest distance to " OE1 GLN A  58 " =    1.226
peak=    3.534 closest distance to " NZ  LYS A 119 " =    1.548
peak=    3.533 closest distance to " N   PHE A 130 " =    1.291
peak=    3.515 closest distance to " N   ASN A 252 " =    1.150
peak=    3.514 closest distance to " O   HOH Z 425 " =    1.733
peak=    3.513 closest distance to " O   HOH Z 250 " =    1.348
peak=    3.512 closest distance to " O   HOH Z 432 " =    1.961
peak=    3.510 closest distance to " O   HOH Z 144 " =    1.681
peak=    3.509 closest distance to " CD1 LEU A  96 " =    0.852
peak=    3.501 closest distance to " CA  ALA A 100 " =    1.126
peak=    3.497 closest distance to " O   HOH Z   1 " =    3.070
peak=    3.495 closest distance to " O   HOH Z 132 " =    2.163
peak=    3.495 closest distance to " O   HOH Z 154 " =    1.396
peak=    3.489 closest distance to " O   HOH Z 183 " =    1.568
peak=    3.476 closest distance to " N   SER A 164 " =    0.970
peak=    3.476 closest distance to " O   HOH Z 377 " =    1.690
peak=    3.474 closest distance to " NH1 ARG A 269 " =    0.842
peak=    3.473 closest distance to " O   HOH Z 374 " =    2.722
peak=    3.472 closest distance to " CA  LEU A 282 " =    0.950
peak=    3.472 closest distance to " CB  GLU A 128 " =    1.176
peak=    3.469 closest distance to " O   HOH Z 418 " =    5.656
peak=    3.466 closest distance to " CA  VAL A  41 " =    0.755
peak=    3.463 closest distance to " O   HOH Z 344 " =    3.458
peak=    3.461 closest distance to " O   HOH Z 163 " =    1.998
peak=    3.454 closest distance to " CE  MET A 188 " =    1.585
peak=    3.454 closest distance to " CA  ARG A 139 " =    1.459
peak=    3.453 closest distance to " O   HOH Z 379 " =    1.640
peak=    3.451 closest distance to " O   HOH Z 298 " =    4.428
peak=    3.442 closest distance to " O   HOH Z 108 " =    2.289
peak=    3.440 closest distance to " O   ALA A 165 " =    1.259
peak=    3.438 closest distance to " CB  MET A 105 " =    1.137
peak=    3.437 closest distance to " CA  LYS A  48 " =    1.422
peak=    3.428 closest distance to " O   HOH Z 162 " =    1.972
peak=    3.424 closest distance to " CB  GLN A  88 " =    1.139
peak=    3.422 closest distance to " CG2AVAL A 121 " =    1.927
peak=    3.420 closest distance to " O   PHE A  16 " =    1.504
peak=    3.419 closest distance to " O   HOH Z 345 " =    3.464
peak=    3.415 closest distance to " CA  GLY A  75 " =    1.223
peak=    3.412 closest distance to " O   HOH Z 150 " =    1.867
peak=    3.411 closest distance to " O   HOH Z 423 " =    1.381
peak=    3.407 closest distance to " O   HOH Z 361 " =    3.140
peak=    3.405 closest distance to " ND2 ASN A  45 " =    1.157
peak=    3.403 closest distance to " O   HOH Z   6 " =    1.746
peak=    3.400 closest distance to " CA  ALA A 299 " =    1.172
peak=    3.399 closest distance to " CB  LEU A  83 " =    0.763
peak=    3.399 closest distance to " CB  ASP A 132 " =    3.857
peak=    3.398 closest distance to " CA  THR A  42 " =    1.086
peak=    3.392 closest distance to " CA  ASP A 149 " =    1.520
peak=    3.391 closest distance to " O   HOH Z 196 " =    2.503
peak=    3.390 closest distance to " CB  ASN A 217 " =    1.029
peak=    3.387 closest distance to " CD2 LEU A 255 " =    1.220
peak=    3.384 closest distance to " CG  GLN A  77 " =    1.105
peak=    3.381 closest distance to " CA  GLY A 241 " =    0.754
peak=    3.378 closest distance to " CB  ALA A 100 " =    1.552
peak=    3.374 closest distance to " NE2 GLN A  89 " =    1.184
peak=    3.367 closest distance to " O   VAL A  72 " =    1.161
peak=    3.366 closest distance to " O   HOH Z 174 " =    1.681
peak=    3.364 closest distance to " CD  LYS A 166 " =    1.468
peak=    3.364 closest distance to " CA  ALA A 295 " =    0.973
peak=    3.361 closest distance to " NH2 ARG A 156 " =    1.207
peak=    3.360 closest distance to " CG  ARG A  36 " =    1.474
peak=    3.353 closest distance to " CB  LEU A 261 " =    1.189
peak=    3.352 closest distance to " NE AARG A 275 " =    1.755
peak=    3.349 closest distance to " O   HOH Z  35 " =    2.204
peak=    3.347 closest distance to " O   HOH Z  66 " =    2.048
peak=    3.344 closest distance to " O   HOH Z 186 " =    1.386
peak=    3.342 closest distance to " CA  ASP A 124 " =    0.837
peak=    3.337 closest distance to " O   HOH Z 211 " =    1.433
peak=    3.328 closest distance to " O   HOH Z 259 " =    1.933
peak=    3.326 closest distance to " O   HOH Z 155 " =    3.212
peak=    3.324 closest distance to " CG1 ILE A  49 " =    1.647
peak=    3.324 closest distance to " CB  ASP A 253 " =    1.133
peak=    3.320 closest distance to " CD1 LEU A 222 " =    0.850
peak=    3.320 closest distance to " CG2 THR A 220 " =    0.805
peak=    3.319 closest distance to " N   TYR A 116 " =    1.899
peak=    3.317 closest distance to " O   GLY A  23 " =    2.459
peak=    3.315 closest distance to " CA  VAL A 197 " =    1.246
peak=    3.314 closest distance to " CA  ARG A 195 " =    1.111
peak=    3.311 closest distance to " CD1 TRP A 266 " =    1.182
peak=    3.310 closest distance to " CA  ASN A 127 " =    1.071
peak=    3.310 closest distance to " OH  TYR A  68 " =    1.260
peak=    3.307 closest distance to " CA  ARG A  36 " =    0.938
peak=    3.305 closest distance to " CA  ALA A  43 " =    1.183
peak=    3.304 closest distance to " OG  SER A 245 " =    1.616
peak=    3.303 closest distance to " CG2 ILE A 106 " =    1.060
peak=    3.303 closest distance to " OD1 ASN A  69 " =    2.310
peak=    3.302 closest distance to " C   VAL A 265 " =    1.169
peak=    3.300 closest distance to " O   HOH Z  63 " =    2.006
peak=    3.297 closest distance to " CE BMET A  47 " =    1.210
peak=    3.294 closest distance to " O   HOH Z 152 " =    1.471
peak=    3.293 closest distance to " O   HOH Z 240 " =    2.043
peak=    3.290 closest distance to " CB  TRP A 150 " =    0.995
peak=    3.288 closest distance to " O   HOH Z 368 " =    2.035
peak=    3.287 closest distance to " CB  ALA A  71 " =    1.326
peak=    3.281 closest distance to " CA  ARG A 102 " =    1.369
peak=    3.276 closest distance to " CB  VAL A 257 " =    0.937
peak=    3.273 closest distance to " CB  ILE A 120 " =    1.353
peak=    3.269 closest distance to " CB  ASP A 124 " =    0.953
peak=    3.269 closest distance to " O   HOH Z 326 " =    1.340
peak=    3.266 closest distance to " CZ3 TRP A 274 " =    4.826
peak=    3.260 closest distance to " OD1 ASP A 238 " =    0.912
peak=    3.256 closest distance to " O   HOH Z 298 " =    2.003
peak=    3.256 closest distance to " CB  ARG A 190 " =    1.807
peak=    3.253 closest distance to " OE1 GLU A 277 " =    1.676
peak=    3.252 closest distance to " CD  ARG A 269 " =    0.764
peak=    3.249 closest distance to " CG ALYS A 290 " =    1.176
peak=    3.247 closest distance to " NH1 ARG A  56 " =    1.578
peak=    3.244 closest distance to " CB  ALA A   1 " =    1.247
peak=    3.244 closest distance to " N   VAL A 296 " =    1.645
peak=    3.244 closest distance to " O   HOH Z 336 " =    1.560
peak=    3.243 closest distance to " O   HOH Z 299 " =    2.266
peak=    3.243 closest distance to " CA  TRP A 274 " =    1.067
peak=    3.241 closest distance to " O   HOH Z  87 " =    2.130
peak=    3.238 closest distance to " NH2AARG A 190 " =    1.533
peak=    3.234 closest distance to " O   HOH Z  54 " =    1.651
peak=    3.234 closest distance to " SD  MET A  93 " =    1.450
peak=    3.233 closest distance to " CB  ARG A  79 " =    1.542
peak=    3.233 closest distance to " CA  GLY A 229 " =    0.863
peak=    3.231 closest distance to " O   HOH Z 301 " =    1.771
peak=    3.231 closest distance to " CG1 ILE A 120 " =    1.161
peak=    3.230 closest distance to " O   HOH Z  19 " =    2.385
peak=    3.229 closest distance to " CB  ASN A 148 " =    1.961
peak=    3.229 closest distance to " CA  SER A  32 " =    1.635
peak=    3.227 closest distance to " CA  MET A  40 " =    1.113
peak=    3.227 closest distance to " O   HOH Z  43 " =    2.000
peak=    3.226 closest distance to " O   HOH Z 272 " =    1.381
peak=    3.225 closest distance to " O   HOH Z 152 " =    1.581
peak=    3.223 closest distance to " CB  SER A  28 " =    1.106
peak=    3.214 closest distance to " CD2 TRP A 179 " =    1.341
peak=    3.212 closest distance to " O   HOH Z 368 " =    4.282
peak=    3.210 closest distance to " OD2 ASP A 286 " =    3.007
peak=    3.207 closest distance to " O   HOH Z 395 " =    1.361
peak=    3.207 closest distance to " O   HOH Z 327 " =    2.693
peak=    3.207 closest distance to " CD  ARG A 195 " =    0.969
peak=    3.206 closest distance to " CE2 PHE A 204 " =    0.997
peak=    3.205 closest distance to " O   HOH Z 402 " =    1.733
peak=    3.205 closest distance to " O   HOH Z 128 " =    1.588
peak=    3.203 closest distance to " CD2 LEU A 297 " =    0.952
peak=    3.201 closest distance to " CG  LEU A 167 " =    1.104
peak=    3.196 closest distance to " O   HOH Z 135 " =    2.288
peak=    3.196 closest distance to " O   HOH Z 260 " =    1.437
peak=    3.192 closest distance to " O   HOH Z 142 " =    1.719
peak=    3.191 closest distance to " CD2 TYR A  68 " =    1.253
peak=    3.190 closest distance to " O   HOH Z  87 " =    1.743
peak=    3.190 closest distance to " O   HOH Z 282 " =    2.301
peak=    3.186 closest distance to " CD1 LEU A 300 " =    1.179
peak=    3.186 closest distance to " NH2BARG A 145 " =    1.781
peak=    3.184 closest distance to " O   GLY A  57 " =    0.947
peak=    3.183 closest distance to " CA  ASP A 270 " =    1.126
peak=    3.183 closest distance to " O   HOH Z 128 " =    2.326
peak=    3.183 closest distance to " NE AARG A 102 " =    1.389
peak=    3.181 closest distance to " O   HOH Z  78 " =    2.348
peak=    3.181 closest distance to " O   HOH Z  39 " =    2.194
peak=    3.180 closest distance to " OE1 GLN A  58 " =    5.875
peak=    3.172 closest distance to " CB  TYR A 293 " =    1.666
peak=    3.170 closest distance to " CD  PRO A 280 " =    0.940
peak=    3.167 closest distance to " CD1 PHE A  59 " =    1.752
peak=    3.167 closest distance to " CD  ARG A 219 " =    1.029
peak=    3.165 closest distance to " O   HOH Z 427 " =    1.186
peak=    3.164 closest distance to " CA  THR A 221 " =    0.924
peak=    3.157 closest distance to " O   HOH Z 126 " =    1.831
peak=    3.153 closest distance to " CE2 TYR A 186 " =    1.003
peak=    3.150 closest distance to " CG  ARG A  66 " =    0.942
peak=    3.148 closest distance to " CA  ALA A 248 " =    1.235
peak=    3.146 closest distance to " CG  LYS A 166 " =    1.436
peak=    3.137 closest distance to " O   HOH Z  64 " =    1.997
peak=    3.131 closest distance to " CB  LYS A  76 " =    0.920
peak=    3.128 closest distance to " ND2 ASN A 209 " =    1.395
peak=    3.127 closest distance to " O   ASN A  74 " =    1.720
peak=    3.126 closest distance to " O   HOH Z 126 " =    1.717
peak=    3.121 closest distance to " O   PHE A  61 " =    0.948
peak=    3.116 closest distance to " CA  ALA A 158 " =    1.119
peak=    3.105 closest distance to " CB  ASN A 170 " =    1.170
peak=    3.104 closest distance to " CA  ALA A 160 " =    1.051
peak=    3.100 closest distance to " O   HOH Z 214 " =    2.018
peak=    3.098 closest distance to " CB  ASN A  45 " =    0.849
peak=    3.093 closest distance to " O   HOH Z 119 " =    2.619
peak=    3.090 closest distance to " NZ  LYS A 117 " =    3.028
peak=    3.078 closest distance to " CB  THR A 235 " =    1.281
peak=    3.074 closest distance to " NE2 GLN A 278 " =    2.477
peak=    3.072 closest distance to " O   HOH Z 372 " =    1.219
peak=    3.062 closest distance to " CB  LEU A 167 " =    1.138
peak=    3.054 closest distance to " CA  GLU A 152 " =    1.535
peak=    3.052 closest distance to " CD  GLN A  77 " =    1.202
peak=    3.041 closest distance to " CG2 VAL A 112 " =    1.489
peak=    3.040 closest distance to " CB  PRO A  90 " =    1.429

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.315 - 5.606
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 218
   mapped sites are within: 0.707 - 5.606

peak=   -5.574 closest distance to " N   ARG A 275 " =    0.742
peak=   -5.125 closest distance to " CB  SER A 276 " =    0.909
peak=   -4.656 closest distance to " O   HOH Z 166 " =    1.658
peak=   -4.397 closest distance to " C   ASN A 285 " =    2.673
peak=   -4.239 closest distance to " O   HOH Z  13 " =    1.410
peak=   -4.211 closest distance to " O   HOH Z  38 " =    0.911
peak=   -4.164 closest distance to " O   HOH Z 290 " =    0.860
peak=   -4.142 closest distance to " O   HOH Z  83 " =    0.769
peak=   -4.123 closest distance to " NH2 ARG A  66 " =    0.932
peak=   -4.095 closest distance to " O   HOH Z 151 " =    1.598
peak=   -4.091 closest distance to " CG1 VAL A 112 " =    2.632
peak=   -4.082 closest distance to " CB  LEU A 167 " =    2.042
peak=   -4.076 closest distance to " O   HOH Z 184 " =    0.899
peak=   -4.072 closest distance to " CD  GLN A  88 " =    0.880
peak=   -4.055 closest distance to " N   ALA A  43 " =    2.682
peak=   -4.044 closest distance to " O   HOH Z  19 " =    1.701
peak=   -4.021 closest distance to " CA  GLU A 277 " =    1.114
peak=   -3.998 closest distance to " OG1 THR A  82 " =    1.788
peak=   -3.997 closest distance to " O   HOH Z 350 " =    0.871
peak=   -3.970 closest distance to " O   HOH Z 411 " =    4.554
peak=   -3.924 closest distance to " CD2 PHE A  59 " =    2.276
peak=   -3.873 closest distance to " O   HOH Z 377 " =    1.674
peak=   -3.873 closest distance to " O   HOH Z 207 " =    1.544
peak=   -3.868 closest distance to " CG2 ILE A  49 " =    2.653
peak=   -3.866 closest distance to " O   HOH Z 120 " =    0.896
peak=   -3.864 closest distance to " O   HOH Z 210 " =    0.920
peak=   -3.858 closest distance to " O   HOH Z 221 " =    1.109
peak=   -3.850 closest distance to " OG  SER A  97 " =    2.340
peak=   -3.850 closest distance to " O   HOH Z  37 " =    1.363
peak=   -3.850 closest distance to " N   SER A 134 " =    1.183
peak=   -3.829 closest distance to " CE  MET A  93 " =    1.298
peak=   -3.825 closest distance to " O   HOH Z 198 " =    1.485
peak=   -3.823 closest distance to " O   HOH Z  52 " =    2.043
peak=   -3.814 closest distance to " CA  VAL A  67 " =    2.745
peak=   -3.811 closest distance to " O   HOH Z 340 " =    0.800
peak=   -3.807 closest distance to " O   HOH Z 400 " =    0.955
peak=   -3.793 closest distance to " O   HOH Z  33 " =    0.807
peak=   -3.787 closest distance to " O   HOH Z 335 " =    1.008
peak=   -3.775 closest distance to " N   GLU A 277 " =    0.707
peak=   -3.766 closest distance to " CD  GLN A 223 " =    0.768
peak=   -3.756 closest distance to " CA  GLY A  23 " =    2.337
peak=   -3.756 closest distance to " ND2 ASN A 285 " =    2.442
peak=   -3.740 closest distance to " CD2 LEU A 237 " =    2.438
peak=   -3.740 closest distance to " CD2 TRP A 274 " =    2.282
peak=   -3.736 closest distance to " O   THR A  52 " =    2.188
peak=   -3.730 closest distance to " OD2 ASP A 171 " =    2.349
peak=   -3.721 closest distance to " CD  GLN A  77 " =    0.940
peak=   -3.709 closest distance to " CB  ALA A 161 " =    2.619
peak=   -3.709 closest distance to " O   HOH Z 430 " =    1.099
peak=   -3.708 closest distance to " NH2 ARG A  66 " =    0.800
peak=   -3.707 closest distance to " CA  ASN A 127 " =    1.148
peak=   -3.703 closest distance to " C   SER A 271 " =    1.326
peak=   -3.702 closest distance to " O   HOH Z 292 " =    1.336
peak=   -3.699 closest distance to " O   HOH Z 222 " =    1.296
peak=   -3.691 closest distance to " O   TYR A  15 " =    1.435
peak=   -3.687 closest distance to " O   HOH Z 117 " =    0.872
peak=   -3.686 closest distance to " O   HOH Z 130 " =    1.265
peak=   -3.674 closest distance to " NZ  LYS A 119 " =    1.309
peak=   -3.667 closest distance to " CG  GLN A  58 " =    1.078
peak=   -3.648 closest distance to " CD  LYS A 119 " =    0.874
peak=   -3.635 closest distance to " O   HOH Z 352 " =    0.990
peak=   -3.633 closest distance to " O   HOH Z  71 " =    1.360
peak=   -3.633 closest distance to " O   HOH Z 128 " =    4.290
peak=   -3.630 closest distance to " O   HOH Z  11 " =    1.158
peak=   -3.630 closest distance to " O   HOH Z 124 " =    1.165
peak=   -3.624 closest distance to " CB  ALA A 227 " =    2.388
peak=   -3.616 closest distance to " C   ASN A 187 " =    1.909
peak=   -3.615 closest distance to " OH  TYR A 169 " =    0.948
peak=   -3.613 closest distance to " OD1 ASN A 148 " =    1.596
peak=   -3.610 closest distance to " O   HOH Z 396 " =    1.492
peak=   -3.607 closest distance to " O   ALA A  34 " =    1.970
peak=   -3.602 closest distance to " CA  VAL A 197 " =    0.975
peak=   -3.596 closest distance to " CB  GLN A  55 " =    1.494
peak=   -3.588 closest distance to " O   HOH Z 325 " =    1.958
peak=   -3.588 closest distance to " O   HOH Z 221 " =    1.689
peak=   -3.568 closest distance to " O   HOH Z 414 " =    1.423
peak=   -3.561 closest distance to " CD1 LEU A  25 " =    2.580
peak=   -3.556 closest distance to " O   HOH Z 378 " =    1.093
peak=   -3.550 closest distance to " CD2 HIS A 115 " =    1.059
peak=   -3.549 closest distance to " O   GLY A 196 " =    1.206
peak=   -3.543 closest distance to " O   ALA A 256 " =    1.610
peak=   -3.542 closest distance to " O   ARG A 275 " =    0.878
peak=   -3.535 closest distance to " CD1 PHE A  59 " =    1.930
peak=   -3.533 closest distance to " O   HOH Z  38 " =    5.606
peak=   -3.530 closest distance to " O   HOH Z  17 " =    0.888
peak=   -3.524 closest distance to " O   VAL A 125 " =    2.155
peak=   -3.514 closest distance to " CB  PHE A 130 " =    1.274
peak=   -3.511 closest distance to " CD1 TYR A 186 " =    2.165
peak=   -3.507 closest distance to " CA  ALA A 137 " =    2.621
peak=   -3.505 closest distance to " O   HOH Z  53 " =    2.470
peak=   -3.487 closest distance to " O   HOH Z 423 " =    1.076
peak=   -3.477 closest distance to " O   HOH Z 231 " =    1.822
peak=   -3.475 closest distance to " O   HOH Z 406 " =    1.312
peak=   -3.475 closest distance to " CD  ARG A  14 " =    3.205
peak=   -3.467 closest distance to " O   HOH Z 150 " =    1.808
peak=   -3.462 closest distance to " OG  SER A  63 " =    1.380
peak=   -3.461 closest distance to " O   HOH Z   7 " =    0.901
peak=   -3.446 closest distance to " CG  ARG A 269 " =    2.446
peak=   -3.443 closest distance to " OE1 GLN A  88 " =    0.999
peak=   -3.441 closest distance to " O   PRO A 198 " =    1.345
peak=   -3.437 closest distance to " SG ACYS A 201 " =    1.055
peak=   -3.437 closest distance to " CG  ASP A 298 " =    0.990
peak=   -3.435 closest distance to " SD  MET A  93 " =    1.560
peak=   -3.430 closest distance to " O   HOH Z 148 " =    3.072
peak=   -3.429 closest distance to " O   HOH Z 414 " =    1.736
peak=   -3.422 closest distance to " O   THR A  18 " =    1.592
peak=   -3.415 closest distance to " ND2 ASN A  60 " =    1.332
peak=   -3.410 closest distance to " CA  TYR A  68 " =    2.873
peak=   -3.391 closest distance to " O   ALA A   1 " =    2.126
peak=   -3.391 closest distance to " O   HOH Z 120 " =    0.887
peak=   -3.391 closest distance to " O   HOH Z 428 " =    1.321
peak=   -3.390 closest distance to " O   GLY A 118 " =    2.467
peak=   -3.383 closest distance to " N   ALA A 226 " =    2.252
peak=   -3.381 closest distance to " O   HOH Z 418 " =    1.597
peak=   -3.379 closest distance to " O   HOH Z 399 " =    2.313
peak=   -3.377 closest distance to " NH1AARG A 275 " =    1.503
peak=   -3.371 closest distance to " O   HOH Z 422 " =    1.008
peak=   -3.369 closest distance to " O   HOH Z 140 " =    0.976
peak=   -3.367 closest distance to " CD2 TYR A  68 " =    2.412
peak=   -3.367 closest distance to " N   GLN A  58 " =    1.448
peak=   -3.364 closest distance to " SG  CYS A 254 " =    3.258
peak=   -3.361 closest distance to " O   VAL A 174 " =    2.029
peak=   -3.352 closest distance to " O   HOH Z 136 " =    1.503
peak=   -3.349 closest distance to " O   HOH Z  91 " =    2.250
peak=   -3.344 closest distance to " O   HOH Z  93 " =    1.993
peak=   -3.342 closest distance to " CB  ALA A  43 " =    2.655
peak=   -3.339 closest distance to " O   HOH Z 313 " =    1.256
peak=   -3.335 closest distance to " CZ  ARG A 259 " =    0.835
peak=   -3.333 closest distance to " CA  GLY A 203 " =    2.217
peak=   -3.329 closest distance to " O   HOH Z 109 " =    3.367
peak=   -3.328 closest distance to " O   SER A 276 " =    1.882
peak=   -3.325 closest distance to " CG  GLU A   2 " =    1.372
peak=   -3.323 closest distance to " O   HOH Z  60 " =    1.971
peak=   -3.317 closest distance to " O   HOH Z 158 " =    1.647
peak=   -3.305 closest distance to " CZ  PHE A 218 " =    1.288
peak=   -3.304 closest distance to " O   GLY A 211 " =    1.451
peak=   -3.302 closest distance to " O   HOH Z 127 " =    1.435
peak=   -3.296 closest distance to " O   LEU A 143 " =    1.262
peak=   -3.295 closest distance to " O   SER A 164 " =    2.035
peak=   -3.294 closest distance to " CB  ASN A 215 " =    1.830
peak=   -3.287 closest distance to " O   HOH Z 300 " =    1.435
peak=   -3.285 closest distance to " OD2 ASP A 171 " =    1.815
peak=   -3.279 closest distance to " CA  HIS A  86 " =    2.212
peak=   -3.264 closest distance to " O   HOH Z 186 " =    1.008
peak=   -3.257 closest distance to " O   HOH Z   7 " =    1.623
peak=   -3.256 closest distance to " O   HOH Z 134 " =    2.010
peak=   -3.254 closest distance to " CD1 TRP A 179 " =    0.989
peak=   -3.250 closest distance to " OG  SER A  32 " =    1.164
peak=   -3.250 closest distance to " CG  LEU A 101 " =    2.523
peak=   -3.246 closest distance to " N   ASP A 286 " =    1.288
peak=   -3.245 closest distance to " OG ASER A 134 " =    1.182
peak=   -3.237 closest distance to " O   HOH Z 380 " =    4.151
peak=   -3.232 closest distance to " CA  SER A 164 " =    1.953
peak=   -3.229 closest distance to " CD  LYS A 289 " =    2.351
peak=   -3.228 closest distance to " CG2 THR A 221 " =    2.162
peak=   -3.227 closest distance to " CE2 TYR A  30 " =    2.715
peak=   -3.225 closest distance to " O   HOH Z 389 " =    2.062
peak=   -3.220 closest distance to " O   TYR A 186 " =    2.543
peak=   -3.210 closest distance to " C   LEU A 143 " =    1.843
peak=   -3.207 closest distance to " C   PRO A 213 " =    2.111
peak=   -3.206 closest distance to " NE1 TRP A  85 " =    1.185
peak=   -3.205 closest distance to " O   HOH Z 423 " =    2.053
peak=   -3.199 closest distance to " O   HOH Z 147 " =    0.903
peak=   -3.199 closest distance to " O   PHE A 218 " =    1.438
peak=   -3.198 closest distance to " OE2 GLU A   2 " =    1.510
peak=   -3.183 closest distance to " CB  SER A  63 " =    3.335
peak=   -3.181 closest distance to " CD2 PHE A 225 " =    1.159
peak=   -3.174 closest distance to " O   HOH Z 213 " =    1.573
peak=   -3.169 closest distance to " O   ARG A 275 " =    1.692
peak=   -3.169 closest distance to " C   THR A 279 " =    1.227
peak=   -3.168 closest distance to " O   GLN A  11 " =    1.310
peak=   -3.165 closest distance to " O   HOH Z 200 " =    1.417
peak=   -3.161 closest distance to " O   GLN A  55 " =    1.186
peak=   -3.160 closest distance to " O   HOH Z 409 " =    3.059
peak=   -3.156 closest distance to " O   HOH Z 342 " =    1.823
peak=   -3.155 closest distance to " CA  ALA A  34 " =    2.355
peak=   -3.154 closest distance to " CG  GLU A  53 " =    1.318
peak=   -3.154 closest distance to " CB  ALA A 291 " =    2.270
peak=   -3.145 closest distance to " ND1 HIS A 115 " =    0.892
peak=   -3.145 closest distance to " CA  SER A 276 " =    1.319
peak=   -3.144 closest distance to " OG  SER A  63 " =    1.076
peak=   -3.144 closest distance to " O   GLY A 262 " =    2.152
peak=   -3.143 closest distance to " O   HOH Z 274 " =    2.943
peak=   -3.140 closest distance to " O   HOH Z 402 " =    1.055
peak=   -3.138 closest distance to " CB  CYS A 254 " =    2.199
peak=   -3.135 closest distance to " CD2 LEU A 300 " =    2.771
peak=   -3.126 closest distance to " N   LEU A 261 " =    1.263
peak=   -3.124 closest distance to " O   ARG A 275 " =    1.050
peak=   -3.120 closest distance to " O   HOH Z 290 " =    1.100
peak=   -3.117 closest distance to " OG ASER A  12 " =    1.649
peak=   -3.117 closest distance to " O   HOH Z 231 " =    1.427
peak=   -3.110 closest distance to " CD1 TYR A 247 " =    2.285
peak=   -3.109 closest distance to " CD  PRO A 198 " =    1.019
peak=   -3.105 closest distance to " O   HOH Z 111 " =    1.149
peak=   -3.101 closest distance to " OE2 GLU A  37 " =    2.642
peak=   -3.099 closest distance to " O   HOH Z  51 " =    1.350
peak=   -3.094 closest distance to " CE  MET A 105 " =    2.203
peak=   -3.091 closest distance to " OE1 GLU A 277 " =    1.993
peak=   -3.089 closest distance to " SG ACYS A 201 " =    2.213
peak=   -3.080 closest distance to " N   THR A 157 " =    1.898
peak=   -3.080 closest distance to " O   HOH Z 351 " =    1.137
peak=   -3.074 closest distance to " O   HOH Z 422 " =    1.716
peak=   -3.059 closest distance to " OD2 ASP A 171 " =    2.937
peak=   -3.058 closest distance to " CA  VAL A 232 " =    2.432
peak=   -3.009 closest distance to " O   HOH Z 423 " =    1.014

================= 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    :  0.4981 0.4833   6.304420e+00   6.291668e+00
   1_bss:  0.4925 0.4762   6.303397e+00   6.284588e+00
   1_xyz:  0.3994 0.4420   6.177734e+00   6.237698e+00
   1_adp:  0.3694 0.4386   6.142603e+00   6.235058e+00
   1_occ:  0.3690 0.4386   6.141999e+00   6.235236e+00
   2_bss:  0.3686 0.4363   6.142719e+00   6.233136e+00
   2_xyz:  0.3093 0.3738   6.014800e+00   6.145942e+00
   2_adp:  0.2852 0.3811   5.990758e+00   6.153118e+00
   2_occ:  0.2852 0.3811   5.990754e+00   6.153408e+00
   3_bss:  0.2858 0.3814   5.991160e+00   6.153789e+00
   3_xyz:  0.2501 0.3321   5.859226e+00   6.052717e+00
   3_adp:  0.2390 0.3075   5.812367e+00   5.994406e+00
   3_occ:  0.2388 0.3074   5.812070e+00   5.994104e+00
   4_bss:  0.2388 0.3068   5.811589e+00   5.993847e+00
   4_xyz:  0.1871 0.2403   5.584209e+00   5.783794e+00
   4_adp:  0.1679 0.2225   5.500003e+00   5.714340e+00
   4_occ:  0.1678 0.2224   5.499766e+00   5.714072e+00
   5_bss:  0.1679 0.2226   5.500993e+00   5.714765e+00
   5_xyz:  0.1448 0.1982   5.378956e+00   5.606144e+00
   5_adp:  0.1409 0.1887   5.348709e+00   5.563354e+00
   5_occ:  0.1408 0.1886   5.348421e+00   5.563296e+00
   5_bss:  0.1411 0.1890   5.349761e+00   5.563523e+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:  0.279  20.001   0.355   2.601  -0.203   0.000  -0.000  -0.000
   1_xyz:  0.279  20.001   0.355   2.601  -0.203   0.000  -0.000  -0.000
   1_adp:  0.279  20.001   0.355   2.601  -0.203   0.000  -0.000  -0.000
   1_occ:  0.279  20.001   0.355   2.601  -0.203   0.000  -0.000  -0.000
   2_bss:  0.330  65.230   0.632   2.168   0.707   0.000   0.000   0.000
   2_xyz:  0.330  65.230   0.632   2.168   0.707   0.000   0.000   0.000
   2_adp:  0.330  65.230   0.632   2.168   0.707   0.000   0.000   0.000
   2_occ:  0.330  65.230   0.632   2.168   0.707   0.000   0.000   0.000
   3_bss:  0.336  77.546   0.621   1.802   0.384   0.000   0.000   0.000
   3_xyz:  0.336  77.546   0.621   1.802   0.384   0.000   0.000   0.000
   3_adp:  0.336  77.546   0.621   1.802   0.384   0.000   0.000   0.000
   3_occ:  0.336  77.546   0.621   1.802   0.384   0.000   0.000   0.000
   4_bss:  0.330  72.009  -0.000   0.844  -0.262   0.000  -0.000  -0.000
   4_xyz:  0.330  72.009  -0.000   0.844  -0.262   0.000  -0.000  -0.000
   4_adp:  0.330  72.009  -0.000   0.844  -0.262   0.000  -0.000  -0.000
   4_occ:  0.330  72.009  -0.000   0.844  -0.262   0.000  -0.000  -0.000
   5_bss:  0.332  73.007  -0.759   0.046  -0.721   0.000  -0.000  -0.000
   5_xyz:  0.332  73.007  -0.759   0.046  -0.721   0.000  -0.000  -0.000
   5_adp:  0.332  73.007  -0.759   0.046  -0.721   0.000  -0.000  -0.000
   5_occ:  0.332  73.007  -0.759   0.046  -0.721   0.000  -0.000  -0.000
   5_bss:  0.326  66.958  -1.086  -0.481  -0.933  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.173 0.3654  0.4976    79371.320
   1_bss:  61.531 0.3722  0.5242    76610.428
   1_xyz:  52.441 0.4884  0.6832    59654.704
   1_adp:  51.968 0.4940  0.6853    58562.411
   1_occ:  52.028 0.4931  0.6825    58550.705
   2_bss:  51.814 0.4957  0.6938    57977.192
   2_xyz:  42.336 0.6133  0.8402    41252.824
   2_adp:  43.240 0.6017  0.8156    42540.234
   2_occ:  43.271 0.6013  0.8148    42578.345
   3_bss:  43.236 0.6017  0.8081    42524.710
   3_xyz:  36.166 0.6860  0.9007    30647.740
   3_adp:  32.383 0.7308  0.9264    26184.448
   3_occ:  32.394 0.7306  0.9260    26183.306
   4_bss:  32.322 0.7314  0.9042    26096.559
   4_xyz:  24.275 0.8179  0.9702    15223.276
   4_adp:  22.014 0.8413  0.9709    13047.543
   4_occ:  22.013 0.8414  0.9708    13051.014
   5_bss:  22.020 0.8414  0.9485    13062.798
   5_xyz:  19.237 0.8684  0.9659    10207.491
   5_adp:  18.115 0.8796  0.9674     9495.602
   5_occ:  18.107 0.8797  0.9674     9507.280
   5_bss:  18.120 0.8796  0.9549     9520.433
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9956e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9956e-01
   1_xyz:   1.836  0.015  0.113 16.785  0.008  4.109   1.9220e-01
   1_adp:   1.836  0.015  0.113 16.785  0.008  4.109   1.9220e-01
   1_occ:   1.836  0.015  0.113 16.785  0.008  4.109   1.9220e-01
   2_bss:   1.836  0.015  0.113 16.785  0.008  4.109   1.9220e-01
   2_xyz:   1.393  0.010  0.089 15.144  0.006  4.131   1.0180e-01
   2_adp:   1.393  0.010  0.089 15.144  0.006  4.131   1.0180e-01
   2_occ:   1.393  0.010  0.089 15.144  0.006  4.131   1.0180e-01
   3_bss:   1.393  0.010  0.089 15.144  0.006  4.131   1.0180e-01
   3_xyz:   1.211  0.008  0.077 14.946  0.004  4.113   7.8556e-02
   3_adp:   1.211  0.008  0.077 14.946  0.004  4.113   7.8556e-02
   3_occ:   1.211  0.008  0.077 14.946  0.004  4.113   7.8556e-02
   4_bss:   1.211  0.008  0.077 14.946  0.004  4.113   7.8556e-02
   4_xyz:   1.231  0.010  0.081 14.732  0.005  4.115   8.9639e-02
   4_adp:   1.231  0.010  0.081 14.732  0.005  4.115   8.9639e-02
   4_occ:   1.231  0.010  0.081 14.732  0.005  4.115   8.9639e-02
   5_bss:   1.231  0.010  0.081 14.732  0.005  4.115   8.9639e-02
   5_xyz:   1.132  0.009  0.078 14.676  0.004  4.126   7.4070e-02
   5_adp:   1.132  0.009  0.078 14.676  0.004  4.126   7.4070e-02
   5_occ:   1.132  0.009  0.078 14.676  0.004  4.126   7.4070e-02
   5_bss:   1.132  0.009  0.078 14.676  0.004  4.126   7.4070e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.300   2.4506e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.300   2.4506e-01
   1_xyz:  10.773  0.089  0.476 89.880  0.045  1.870   1.2942e-01
   1_adp:  10.773  0.089  0.476 89.880  0.045  1.870   1.2942e-01
   1_occ:  10.773  0.089  0.476 89.880  0.045  1.870   1.2942e-01
   2_bss:  10.773  0.089  0.476 89.880  0.045  1.870   1.2942e-01
   2_xyz:   8.199  0.076  0.254 85.289  0.051  2.190   8.6944e-02
   2_adp:   8.199  0.076  0.254 85.289  0.051  2.190   8.6944e-02
   2_occ:   8.199  0.076  0.254 85.289  0.051  2.190   8.6944e-02
   3_bss:   8.199  0.076  0.254 85.289  0.051  2.190   8.6944e-02
   3_xyz:   8.850  0.049  0.270 87.727  0.014  2.103   5.1297e-02
   3_adp:   8.850  0.049  0.270 87.727  0.014  2.103   5.1297e-02
   3_occ:   8.850  0.049  0.270 87.727  0.014  2.103   5.1297e-02
   4_bss:   8.850  0.049  0.270 87.727  0.014  2.103   5.1297e-02
   4_xyz:   7.858  0.065  0.250 84.527  0.041  2.232   1.6945e-01
   4_adp:   7.858  0.065  0.250 84.527  0.041  2.232   1.6945e-01
   4_occ:   7.858  0.065  0.250 84.527  0.041  2.232   1.6945e-01
   5_bss:   7.858  0.065  0.250 84.527  0.041  2.232   1.6945e-01
   5_xyz:   8.448  0.052  0.236 82.712  0.030  2.253   5.3549e-02
   5_adp:   8.448  0.052  0.236 82.712  0.030  2.253   5.3549e-02
   5_occ:   8.448  0.052  0.236 82.712  0.030  2.253   5.3549e-02
   5_bss:   8.448  0.052  0.236 82.712  0.030  2.253   5.3549e-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: 214.00   0.00  17.60 214.00   0.00  14.12  70.95   0.00  36.52
   1_occ: 214.00   0.00  17.60 214.00   0.00  14.12  70.95   0.00  36.52
   2_bss: 214.00   0.00  17.60 214.00   0.00  14.12  70.95   0.00  36.52
   2_xyz: 214.00   0.00  17.60 214.00   0.00  14.12  70.95   0.00  36.52
   2_adp: 124.75   0.00  21.25 124.75   0.00  16.98 117.46   0.00  44.48
   2_occ: 124.75   0.00  21.25 124.75   0.00  16.98 117.46   0.00  44.48
   3_bss: 124.75   0.00  21.25 124.75   0.00  16.98 117.46   0.00  44.48
   3_xyz: 124.75   0.00  21.25 124.75   0.00  16.98 117.46   0.00  44.48
   3_adp: 108.89   0.00  18.71 100.93   0.00  14.39 108.89   2.62  42.24
   3_occ: 108.89   0.00  18.71 100.93   0.00  14.39 108.89   2.62  42.24
   4_bss: 108.89   0.00  18.71 100.93   0.00  14.39 108.89   2.62  42.24
   4_xyz: 108.89   0.00  18.71 100.93   0.00  14.39 108.89   2.62  42.24
   4_adp: 114.45   0.00  18.38 114.45   0.00  13.09 101.62   4.55  47.23
   4_occ: 114.45   0.00  18.38 114.45   0.00  13.09 101.62   4.55  47.23
   5_bss: 114.45   0.00  18.38 114.45   0.00  13.09 101.62   4.55  47.23
   5_xyz: 114.45   0.00  18.38 114.45   0.00  13.09 101.62   4.55  47.23
   5_adp: 109.99   0.93  17.12 109.99   0.93  12.30 100.63   4.14  43.40
   5_occ: 109.99   0.93  17.12 109.99   0.93  12.30 100.63   4.14  43.40
   5_bss: 109.95   0.90  17.09 109.95   0.90  12.26 100.60   4.11  43.37
------------------------------------------------------------------------
 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:    2.701    0.042    0.446
   1_adp:    2.701    0.042    0.446
   1_occ:    2.701    0.042    0.446
   2_bss:    2.701    0.042    0.446
   2_xyz:    2.603    0.028    0.611
   2_adp:    2.603    0.028    0.611
   2_occ:    2.603    0.028    0.611
   3_bss:    2.603    0.028    0.611
   3_xyz:    2.572    0.101    0.765
   3_adp:    2.572    0.101    0.765
   3_occ:    2.572    0.101    0.765
   4_bss:    2.572    0.101    0.765
   4_xyz:    2.466    0.050    0.903
   4_adp:    2.466    0.050    0.903
   4_occ:    2.466    0.050    0.903
   5_bss:    2.466    0.050    0.903
   5_xyz:    2.417    0.083    0.956
   5_adp:    2.417    0.083    0.956
   5_occ:    2.417    0.083    0.956
   5_bss:    2.417    0.083    0.956
------------------------------------------------------------------------

CPU time actual refinement: 360.50


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1321/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_1321/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1321/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1321/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1321/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 360.36 
  Macro-tasks:
    bulk solvent and scale       = 49.97  
    individual site refinement   = 146.45 
    weights calculation          = 29.76  
    collect and process          = 6.23   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 232.50 
  Micro-tasks:
    mask                            = 3.04   
    f_calc                          = 115.98 
    alpha_beta                      = 8.28   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 123.36 
    fmodel                         = 8.03   
    r_factors                      = 0.19   
    phase_errors                   = 9.78   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 270.03 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.137 micro seconds
Total CPU time: 6.23 minutes
from_scatterers_fft:    630 calls, 115.70 s
gradients_fft:          575 calls, 110.79 s

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

# Date 2008-01-16 Time 06:59:06 PST -0800 (1200495546.79 s)
Start R-work = 0.4981, R-free = 0.4833 (no bulk solvent and anisotropic scale)
Final R-work = 0.1572, R-free = 0.2052 (no bulk solvent and anisotropic scale)

Start R-work = 0.4925, R-free = 0.4762
Final R-work = 0.1411, R-free = 0.1890