# Date 2008-01-16 Time 06:53:55 PST -0800 (1200495235.25 s)
#phil __OFF__

Command line arguments: "../1330.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 784
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1330

-------------------------------------------------------------------------------
  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, 88.5498, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 2.05
Completeness in resolution range: 0.985412
Completeness with d_max=infinity: 0.982249

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3688
                             d_min =   2.0500

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, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 2.05
Completeness in resolution range: 0.985412
Completeness with d_max=infinity: 0.982249

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3692 -  4.3856 [2087/2110]  1878   209  10.0%
  bin  2:  4.3856 -  3.4944 [2015/2035]  1813   202  10.0%
  bin  3:  3.4944 -  3.0567 [1978/1997]  1781   197  10.0%
  bin  4:  3.0567 -  2.7790 [1933/1963]  1740   193  10.0%
  bin  5:  2.7790 -  2.5808 [1963/1982]  1766   197  10.0%
  bin  6:  2.5808 -  2.4293 [1940/1965]  1747   193   9.9%
  bin  7:  2.4293 -  2.3080 [1926/1954]  1733   193  10.0%
  bin  8:  2.3080 -  2.2079 [1926/1962]  1734   192  10.0%
  bin  9:  2.2079 -  2.1231 [1921/1963]  1728   193  10.0%
  bin 10:  2.1231 -  2.0500 [1900/1948]  1710   190  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1330/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:
        1.44 -     2.13: 4
        2.13 -     2.82: 856
        2.82 -     3.52: 4295
        3.52 -     4.21: 9004
        4.21 -     4.90: 13234
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.439 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.836 3.040 -x+1/2,-y+1,z+1/2
  " OG  SER A 245 " - " O   HOH Z 202 "  2.052 3.040 -x+1/2,-y+1,z-1/2
  " OE1 GLN A  94 " - " O   HOH Z  43 "  2.144 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27388 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_1330/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1330/model_refine_001.geo

CPU time processing inputs: 9.01


============================ 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 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5152   r_free= 0.5023   ksol= 0.00   Bsol= 0.00   scale= 0.826    |
|                                                                             |
| 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:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.310342                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3692 -  4.8910 0.99   1363  152 0.4147 0.4176      6.6283      6.5867|
|  2:  4.8910 -  3.9031 0.99   1299  144 0.4744 0.4896      6.9333      6.9564|
|  3:  3.9031 -  3.4159 0.99   1272  141 0.5085 0.4559      6.7721      6.7329|
|  4:  3.4159 -  3.1064 0.99   1277  142 0.5165 0.5047      6.5962      6.5413|
|  5:  3.1064 -  2.8853 0.99   1255  140 0.5332 0.4989      6.4081      6.4145|
|  6:  2.8853 -  2.7162 0.99   1266  140 0.5406 0.5372      6.3182      6.2778|
|  7:  2.7162 -  2.5808 0.99   1246  139 0.5540 0.5233      6.2675      6.1871|
|  8:  2.5808 -  2.4689 0.98   1249  138 0.5489 0.4985      6.2158       6.221|
|  9:  2.4689 -  2.3742 0.98   1233  137 0.5496 0.5483      6.1363      6.1654|
| 10:  2.3742 -  2.2926 1.00   1237  138 0.5535 0.5558      6.1339      6.1621|
| 11:  2.2926 -  2.2211 0.97   1250  139 0.5570 0.5591       6.057      6.1005|
| 12:  2.2211 -  2.1578 0.97   1224  136 0.5392 0.5541      6.0199      6.0436|
| 13:  2.1578 -  2.1011 0.99   1229  136 0.5390 0.5096      5.9116      5.8723|
| 14:  2.1011 -  2.0500 0.97   1230  137 0.5355 0.5258      5.8541      5.8015|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3692 -  4.8910  1363   152  0.67  37.24   0.78     0.71      83818.76|
|  2:  4.8910 -  3.9031  1299   144  0.64  40.17   0.84     0.72     132075.31|
|  3:  3.9031 -  3.4159  1272   141  0.52  50.54   0.82     0.65     143755.53|
|  4:  3.4159 -  3.1064  1277   142  0.39  60.34   0.82     0.51     130235.39|
|  5:  3.1064 -  2.8853  1255   140  0.30  67.15   0.81     0.42      98911.72|
|  6:  2.8853 -  2.7162  1266   140  0.28  69.31   0.81     0.37      83167.17|
|  7:  2.7162 -  2.5808  1246   139  0.24  72.39   0.83     0.32      74490.93|
|  8:  2.5808 -  2.4689  1249   138  0.20  75.23   0.82     0.27      71078.70|
|  9:  2.4689 -  2.3742  1233   137  0.16  78.42   0.85     0.22      66005.42|
| 10:  2.3742 -  2.2926  1237   138  0.19  75.96   0.86     0.26      58881.75|
| 11:  2.2926 -  2.2211  1250   139  0.22  73.45   0.86     0.33      53472.81|
| 12:  2.2211 -  2.1578  1224   136  0.25  71.34   0.89     0.37      48276.15|
| 13:  2.1578 -  2.1011  1229   136  0.22  73.66   0.84     0.31      41931.48|
| 14:  2.1011 -  2.0500  1230   137  0.14  79.92   0.85     0.17      34771.29|
|alpha:            min =        0.17 max =            0.72 mean =         0.41|
|beta:             min =    34771.29 max =       143755.53 mean =     80570.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           89.98 mean =        65.75|
|phase err.(test): min =        0.00 max =           89.95 mean =        65.79|
|-----------------------------------------------------------------------------|

============================== 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 = 17.768978             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.769   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.480849              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.840   (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 |  1.439 -  1.785:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.785 -  2.131:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.131 -  2.477:       12 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.477 -  2.823:      844 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.823 -  3.170:     1973 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.170 -  3.516:     2322 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.516 -  3.862:     4477 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.862 -  4.208:     4527 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.208 -  4.554:     5972 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.554 -  4.900:     7262 |
|-----------------------------------------------------------------------------|
|-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 |        0.169 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.439 |       0.205 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5152   r_free= 0.5023   ksol= 0.00   Bsol= 0.00   scale= 0.826    |
|                                                                             |
| 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:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.310342                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5111   r_free= 0.4987   ksol= 0.27   Bsol= 65.66   scale= 0.868   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,1.58,2.14,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.309499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.694371             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.474   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.599914              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.243   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5111      final r-factor (work) = 0.4476          |
| start r-factor (free) = 0.4987      final r-factor (free) = 0.4760          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.5032 = 14.69 * 0.50 * 6.3065 + 1.00 * 0.1685                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.0715 = 14.69 * 0.50 * 6.2489 + 1.00 * 0.1597                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4476      final r-factor (work) = 0.4027          |
| start r-factor (free) = 0.4760      final r-factor (free) = 0.4745          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.2525 = 2.60 * 1.00 * 6.2489 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.1460 = 2.60 * 1.00 * 6.1968 + 1.00 * 0.0348                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    150.53  22.37    None  None   None       |
|    all(noH): 2823   0      0.00    150.53  22.37    None  None   None       |
|    Sol.    : 438    0      0.00    150.53  37.65    None  None   None       |
|    Mac.    : 2385   0      0.00    107.31  19.57    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 -  15.053: 1166   |   5:    75.265 -  90.318:   29        |
|      1:    15.053 -  30.106:  903   |   6:    90.318 - 105.371:   11        |
|      2:    30.106 -  45.159:  437   |   7:   105.371 - 120.424:    5        |
|      3:    45.159 -  60.212:  196   |   8:   120.424 - 135.477:    0        |
|      4:    60.212 -  75.265:   75   |   9:   135.477 - 150.530:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4027 r_free = 0.4745             target_work(ml) = 6.199         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4026 r_free = 0.4764             target_work(ml) = 6.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4026   r_free= 0.4764   ksol= 0.27   Bsol= 65.66   scale= 0.962   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,1.58,2.14,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.199630                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4030   r_free= 0.4749   ksol= 0.32   Bsol= 96.80   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.96,2.17,2.77,0.00,0.00,0.00); trace/3= 1.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.201129                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.163252             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.008   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.223154              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.134  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4030      final r-factor (work) = 0.3506          |
| start r-factor (free) = 0.4749      final r-factor (free) = 0.4292          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 65.7752 = 21.16 * 0.50 * 6.2009 + 1.00 * 0.1597                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 65.2551 = 21.16 * 0.50 * 6.1550 + 1.00 * 0.1247                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3506      final r-factor (work) = 0.3376          |
| start r-factor (free) = 0.4292      final r-factor (free) = 0.4142          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5634 = 1.22 * 1.00 * 6.1550 + 1.00 * 0.0348                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4762 = 1.22 * 1.00 * 6.0927 + 1.00 * 0.0239                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    157.99  20.51    None  None   None       |
|    all(noH): 2823   0      0.00    157.99  20.51    None  None   None       |
|    Sol.    : 438    0      0.00    157.99  36.94    None  None   None       |
|    Mac.    : 2385   0      0.00    101.72  17.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  15.799: 1340   |   5:    78.995 -  94.794:   24        |
|      1:    15.799 -  31.598:  924   |   6:    94.794 - 110.593:    6        |
|      2:    31.598 -  47.397:  362   |   7:   110.593 - 126.391:    1        |
|      3:    47.397 -  63.196:  115   |   8:   126.391 - 142.190:    0        |
|      4:    63.196 -  78.995:   50   |   9:   142.190 - 157.989:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3376 r_free = 0.4142             target_work(ml) = 6.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3374 r_free = 0.4143             target_work(ml) = 6.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3374   r_free= 0.4143   ksol= 0.32   Bsol= 96.80   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.96,2.17,2.77,0.00,0.00,0.00); trace/3= 1.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.079754                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3379   r_free= 0.4136   ksol= 0.34   Bsol= 92.74   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.86,2.08,2.11,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.080975                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.436795             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.456  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.604046              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.990  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3379      final r-factor (work) = 0.2823          |
| start r-factor (free) = 0.4136      final r-factor (free) = 0.3529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.2444 = 17.44 * 0.50 * 6.0928 + 1.00 * 0.1247                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.6167 = 17.44 * 0.50 * 6.0211 + 1.00 * 0.1221                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2823      final r-factor (work) = 0.2606          |
| start r-factor (free) = 0.3529      final r-factor (free) = 0.3321          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6622 = 0.60 * 1.00 * 6.0211 + 1.00 * 0.0252                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5795 = 0.60 * 1.00 * 5.9011 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    154.93  18.62    None  None   None       |
|    all(noH): 2823   0      0.00    154.93  18.62    None  None   None       |
|    Sol.    : 438    0      0.00    154.93  39.97    None  None   None       |
|    Mac.    : 2385   0      0.00    100.31  14.70    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 -  15.493: 1594   |   5:    77.466 -  92.959:   20        |
|      1:    15.493 -  30.986:  754   |   6:    92.959 - 108.452:    4        |
|      2:    30.986 -  46.479:  279   |   7:   108.452 - 123.945:    1        |
|      3:    46.479 -  61.973:  118   |   8:   123.945 - 139.438:    0        |
|      4:    61.973 -  77.466:   52   |   9:   139.438 - 154.931:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2606 r_free = 0.3321             target_work(ml) = 5.873         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2604 r_free = 0.3315             target_work(ml) = 5.872         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2604   r_free= 0.3315   ksol= 0.34   Bsol= 92.74   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.86,2.08,2.11,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.872348                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2602   r_free= 0.3311   ksol= 0.33   Bsol= 90.07   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,0.72,0.82,0.00,0.00,0.00); trace/3= 0.44                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.872742                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.162334             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.111  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.037289              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.081  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2602      final r-factor (work) = 0.2069          |
| start r-factor (free) = 0.3311      final r-factor (free) = 0.2612          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1070 = 10.16 * 0.50 * 5.9012 + 1.00 * 0.1221                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.5040 = 10.16 * 0.50 * 5.7837 + 1.00 * 0.1159                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2069      final r-factor (work) = 0.1829          |
| start r-factor (free) = 0.2612      final r-factor (free) = 0.2408          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0143 = 1.04 * 1.00 * 5.7837 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8290 = 1.04 * 1.00 * 5.6024 + 1.00 * 0.0177                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    149.66  18.51    None  None   None       |
|    all(noH): 2823   0      0.00    149.66  18.51    None  None   None       |
|    Sol.    : 438    0      4.21    149.66  47.72    None  None   None       |
|    Mac.    : 2385   0      0.00    112.76  13.14    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 -  14.966: 1775   |   5:    74.828 -  89.794:   43        |
|      1:    14.966 -  29.931:  536   |   6:    89.794 - 104.759:    9        |
|      2:    29.931 -  44.897:  210   |   7:   104.759 - 119.725:    3        |
|      3:    44.897 -  59.863:  141   |   8:   119.725 - 134.691:    0        |
|      4:    59.863 -  74.828:  105   |   9:   134.691 - 149.656:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1829 r_free = 0.2408             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1828 r_free = 0.2408             target_work(ml) = 5.564         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1828   r_free= 0.2408   ksol= 0.33   Bsol= 90.07   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,0.72,0.82,0.00,0.00,0.00); trace/3= 0.44                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.564273                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1829   r_free= 0.2412   ksol= 0.34   Bsol= 87.77   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,0.15,0.70,0.00,0.00,0.00); trace/3= 0.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.564001                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.721926              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.982  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.046971              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.449  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1829      final r-factor (work) = 0.1681          |
| start r-factor (free) = 0.2412      final r-factor (free) = 0.2234          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7411 = 2.72 * 0.50 * 5.6029 + 1.00 * 0.1159                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5936 = 2.72 * 0.50 * 5.5315 + 1.00 * 0.0655                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1681      final r-factor (work) = 0.1666          |
| start r-factor (free) = 0.2234      final r-factor (free) = 0.2243          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8088 = 1.05 * 1.00 * 5.5315 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8157 = 1.05 * 1.00 * 5.4910 + 1.00 * 0.0668                               |
|-----------------------------------------------------------------------------|
| number of iterations = 1       |    number of function evaluations = 1      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    149.48  17.94    None  None   None       |
|    all(noH): 2823   0      0.00    149.48  17.94    None  None   None       |
|    Sol.    : 438    0      1.18    149.48  47.65    None  None   None       |
|    Mac.    : 2385   0      0.00    113.13  12.48    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 -  14.948: 1813   |   5:    74.741 -  89.689:   40        |
|      1:    14.948 -  29.896:  503   |   6:    89.689 - 104.637:   10        |
|      2:    29.896 -  44.844:  209   |   7:   104.637 - 119.585:    3        |
|      3:    44.844 -  59.793:  136   |   8:   119.585 - 134.533:    0        |
|      4:    59.793 -  74.741:  108   |   9:   134.533 - 149.481:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1666 r_free = 0.2243             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1663 r_free = 0.2247             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1663   r_free= 0.2247   ksol= 0.34   Bsol= 87.77   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,0.15,0.70,0.00,0.00,0.00); trace/3= 0.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.488723                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3692 -  4.8910 0.99   1363  152 0.1183 0.1632      5.5584      5.7381|
|  2:  4.8910 -  3.9031 0.99   1299  144 0.1111 0.1491      5.6832      5.9199|
|  3:  3.9031 -  3.4159 0.99   1272  141 0.1496 0.1839      5.7964      6.0338|
|  4:  3.4159 -  3.1064 0.99   1277  142 0.1767 0.2292      5.8019      6.0289|
|  5:  3.1064 -  2.8853 0.99   1255  140 0.2045 0.2457      5.7115      5.8864|
|  6:  2.8853 -  2.7162 0.99   1266  140 0.1919 0.2752      5.5933      5.8137|
|  7:  2.7162 -  2.5808 0.99   1246  139 0.1852 0.2452      5.5168      5.6876|
|  8:  2.5808 -  2.4689 0.98   1249  138 0.1821 0.2293      5.4679      5.6731|
|  9:  2.4689 -  2.3742 0.98   1233  137 0.1911 0.2729      5.4342      5.6867|
| 10:  2.3742 -  2.2926 1.00   1237  138 0.1726 0.2740      5.3477      5.5888|
| 11:  2.2926 -  2.2211 0.97   1250  139 0.1838 0.2238      5.3342      5.5059|
| 12:  2.2211 -  2.1578 0.97   1224  136 0.1653 0.2786      5.2266      5.7219|
| 13:  2.1578 -  2.1011 0.99   1229  136 0.1763 0.2342      5.2002      5.3256|
| 14:  2.1011 -  2.0500 0.97   1230  137 0.1820 0.2625      5.1231       5.337|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3692 -  4.8910  1363   152  0.91  12.98   0.94     0.91      11656.10|
|  2:  4.8910 -  3.9031  1299   144  0.93  11.94   1.00     0.98      15534.68|
|  3:  3.9031 -  3.4159  1272   141  0.89  16.86   1.02     1.00      19987.08|
|  4:  3.4159 -  3.1064  1277   142  0.86  20.21   0.99     0.95      20888.59|
|  5:  3.1064 -  2.8853  1255   140  0.81  24.96   0.98     0.94      18815.11|
|  6:  2.8853 -  2.7162  1266   140  0.83  23.65   0.95     0.89      14364.21|
|  7:  2.7162 -  2.5808  1246   139  0.83  23.29   0.97     0.94      12905.06|
|  8:  2.5808 -  2.4689  1249   138  0.83  23.23   0.95     0.90      11643.40|
|  9:  2.4689 -  2.3742  1233   137  0.82  24.96   0.96     0.87      11087.03|
| 10:  2.3742 -  2.2926  1237   138  0.84  23.18   0.95     0.87       9350.20|
| 11:  2.2926 -  2.2211  1250   139  0.82  24.28   0.94     0.86       9155.86|
| 12:  2.2211 -  2.1578  1224   136  0.84  22.53   0.94     0.90       7861.97|
| 13:  2.1578 -  2.1011  1229   136  0.82  24.38   0.92     0.89       7781.73|
| 14:  2.1011 -  2.0500  1230   137  0.82  24.55   0.89     0.82       6313.47|
|alpha:            min =        0.82 max =            1.00 mean =         0.91|
|beta:             min =     6313.47 max =        20888.59 mean =     12718.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.99 mean =        21.40|
|phase err.(test): min =        0.00 max =           89.66 mean =        20.49|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1659   r_free= 0.2239   ksol= 0.34   Bsol= 91.77   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.07,0.75,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.490079                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.05 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1659   r_free= 0.2239   ksol= 0.34   Bsol= 91.77   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.07,0.75,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.490079                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3692 -  4.8910 0.99   1363  152 0.1188 0.1655      5.5644      5.7512|
|  2:  4.8910 -  3.9031 0.99   1299  144 0.1127 0.1501       5.693      5.9287|
|  3:  3.9031 -  3.4159 0.99   1272  141 0.1502 0.1842      5.8003      6.0364|
|  4:  3.4159 -  3.1064 0.99   1277  142 0.1766 0.2294      5.8025      6.0303|
|  5:  3.1064 -  2.8853 0.99   1255  140 0.2048 0.2458      5.7117      5.8855|
|  6:  2.8853 -  2.7162 0.99   1266  140 0.1919 0.2749      5.5931      5.8131|
|  7:  2.7162 -  2.5808 0.99   1246  139 0.1853 0.2450      5.5165      5.6874|
|  8:  2.5808 -  2.4689 0.98   1249  138 0.1820 0.2291      5.4673      5.6712|
|  9:  2.4689 -  2.3742 0.98   1233  137 0.1910 0.2728       5.434      5.6864|
| 10:  2.3742 -  2.2926 1.00   1237  138 0.1725 0.2739      5.3478      5.5882|
| 11:  2.2926 -  2.2211 0.97   1250  139 0.1837 0.2242      5.3342      5.5069|
| 12:  2.2211 -  2.1578 0.97   1224  136 0.1652 0.2790      5.2261      5.7236|
| 13:  2.1578 -  2.1011 0.99   1229  136 0.1762 0.2334      5.1998      5.3246|
| 14:  2.1011 -  2.0500 0.97   1230  137 0.1820 0.2623      5.1227      5.3364|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3692 -  4.8910  1363   152  0.91  13.16   0.94     0.92      11868.39|
|  2:  4.8910 -  3.9031  1299   144  0.92  12.14   1.01     0.99      15847.07|
|  3:  3.9031 -  3.4159  1272   141  0.89  17.00   1.04     1.01      20225.59|
|  4:  3.4159 -  3.1064  1277   142  0.86  20.27   1.02     0.98      20990.33|
|  5:  3.1064 -  2.8853  1255   140  0.81  24.97   1.01     0.97      18798.69|
|  6:  2.8853 -  2.7162  1266   140  0.83  23.65   0.98     0.92      14352.15|
|  7:  2.7162 -  2.5808  1246   139  0.83  23.26   1.01     0.98      12874.92|
|  8:  2.5808 -  2.4689  1249   138  0.83  23.21   0.99     0.93      11622.26|
|  9:  2.4689 -  2.3742  1233   137  0.82  24.95   1.00     0.91      11075.09|
| 10:  2.3742 -  2.2926  1237   138  0.84  23.17   0.99     0.91       9338.90|
| 11:  2.2926 -  2.2211  1250   139  0.82  24.30   0.99     0.90       9167.84|
| 12:  2.2211 -  2.1578  1224   136  0.84  22.53   0.99     0.94       7853.52|
| 13:  2.1578 -  2.1011  1229   136  0.82  24.36   0.97     0.94       7773.13|
| 14:  2.1011 -  2.0500  1230   137  0.82  24.54   0.94     0.88       6306.59|
|alpha:            min =        0.88 max =            1.01 mean =         0.94|
|beta:             min =     6306.59 max =        20990.33 mean =     12773.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           90.00 mean =        21.44|
|phase err.(test): min =        0.00 max =           89.41 mean =        20.48|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.11    150.59  19.05    None  None   None       |
|    all(noH): 2823   0      1.11    150.59  19.05    None  None   None       |
|    Sol.    : 438    0      2.30    150.59  48.76    None  None   None       |
|    Mac.    : 2385   0      1.11    114.24  13.60    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.113 -  16.061: 1813   |   5:    75.854 -  90.802:   40        |
|      1:    16.061 -  31.010:  503   |   6:    90.802 - 105.750:   10        |
|      2:    31.010 -  45.958:  209   |   7:   105.750 - 120.698:    3        |
|      3:    45.958 -  60.906:  136   |   8:   120.698 - 135.646:    0        |
|      4:    60.906 -  75.854:  108   |   9:   135.646 - 150.595:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 355         
Filter by distance & map next to the model:
   mapped sites are within: 0.501 - 5.066
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 347 from: 355
   mapped sites are within: 0.707 - 5.066

peak=    9.443 closest distance to " O   HOH Z  57 " =    2.013
peak=    8.681 closest distance to " O   HOH Z 103 " =    1.257
peak=    8.152 closest distance to " O   SER A   3 " =    1.463
peak=    7.097 closest distance to " O   HOH Z 138 " =    1.429
peak=    6.700 closest distance to " O   HOH Z 332 " =    1.298
peak=    6.521 closest distance to " O   HOH Z 369 " =    1.265
peak=    6.474 closest distance to " O   HOH Z 426 " =    1.405
peak=    6.333 closest distance to " O   HOH Z  69 " =    1.129
peak=    5.696 closest distance to " O   HOH Z  41 " =    1.661
peak=    5.690 closest distance to " O   HOH Z  70 " =    1.502
peak=    5.438 closest distance to " O   HOH Z 279 " =    1.557
peak=    5.323 closest distance to " NH1BARG A 275 " =    1.364
peak=    5.320 closest distance to " CG AARG A 275 " =    1.323
peak=    5.281 closest distance to " CG  GLN A  77 " =    0.813
peak=    5.209 closest distance to " O   HOH Z 117 " =    1.719
peak=    5.200 closest distance to " CD  ARG A 269 " =    0.827
peak=    5.183 closest distance to " NH1 ARG A 269 " =    0.819
peak=    5.163 closest distance to " OH  TYR A  68 " =    1.001
peak=    5.025 closest distance to " CG  ASN A  69 " =    1.263
peak=    5.014 closest distance to " O   HOH Z  54 " =    1.554
peak=    4.964 closest distance to " O   HOH Z 425 " =    2.093
peak=    4.674 closest distance to " O   HOH Z  67 " =    1.248
peak=    4.560 closest distance to " CB  SER A  63 " =    1.353
peak=    4.557 closest distance to " OD1 ASN A 301 " =    0.994
peak=    4.488 closest distance to " CD ALYS A 290 " =    1.072
peak=    4.477 closest distance to " O   HOH Z 190 " =    0.773
peak=    4.452 closest distance to " N   ARG A 275 " =    0.789
peak=    4.424 closest distance to " O   GLN A  73 " =    0.994
peak=    4.412 closest distance to " CB AVAL A  41 " =    0.765
peak=    4.401 closest distance to " CZ  PHE A 218 " =    1.178
peak=    4.389 closest distance to " CG  PRO A  90 " =    1.242
peak=    4.355 closest distance to " ND2 ASN A 301 " =    0.980
peak=    4.344 closest distance to " O   HOH Z 174 " =    1.784
peak=    4.342 closest distance to " CB  SER A  26 " =    0.802
peak=    4.312 closest distance to " O   HOH Z  53 " =    0.819
peak=    4.282 closest distance to " O   HOH Z 422 " =    1.215
peak=    4.276 closest distance to " NH2AARG A 145 " =    1.041
peak=    4.233 closest distance to " CB  TRP A 266 " =    0.953
peak=    4.223 closest distance to " O   GLN A  11 " =    0.842
peak=    4.208 closest distance to " NH1AARG A 145 " =    1.498
peak=    4.180 closest distance to " O   HOH Z 417 " =    1.020
peak=    4.155 closest distance to " CG  PRO A  54 " =    1.420
peak=    4.146 closest distance to " CG  ARG A 269 " =    1.076
peak=    4.140 closest distance to " O   HOH Z 394 " =    1.844
peak=    4.097 closest distance to " OE1 GLN A  58 " =    1.249
peak=    4.080 closest distance to " CZ  PHE A 192 " =    0.920
peak=    4.065 closest distance to " O   HOH Z  65 " =    1.143
peak=    4.061 closest distance to " CG1 VAL A 153 " =    1.316
peak=    4.054 closest distance to " O   HOH Z 131 " =    0.951
peak=    4.044 closest distance to " O   HOH Z 437 " =    2.095
peak=    4.042 closest distance to " N   SER A 164 " =    0.893
peak=    4.022 closest distance to " O   HOH Z 130 " =    1.151
peak=    4.020 closest distance to " CB  ASN A  39 " =    0.774
peak=    4.004 closest distance to " CG  GLN A  11 " =    1.042
peak=    3.979 closest distance to " CA  GLY A 196 " =    0.948
peak=    3.970 closest distance to " O   HOH Z 120 " =    1.032
peak=    3.967 closest distance to " CB  GLN A 223 " =    1.439
peak=    3.962 closest distance to " O   HOH Z 223 " =    1.053
peak=    3.955 closest distance to " CA  ALA A 154 " =    0.990
peak=    3.942 closest distance to " CD1 LEU A   5 " =    1.249
peak=    3.920 closest distance to " O   HOH Z 104 " =    2.540
peak=    3.904 closest distance to " O   HOH Z 396 " =    0.988
peak=    3.895 closest distance to " CA  TRP A 274 " =    0.917
peak=    3.894 closest distance to " O   HOH Z 411 " =    3.561
peak=    3.893 closest distance to " O   HOH Z 291 " =    1.328
peak=    3.892 closest distance to " O   THR A 220 " =    1.456
peak=    3.875 closest distance to " O   HOH Z  69 " =    1.902
peak=    3.869 closest distance to " N   TYR A  15 " =    1.068
peak=    3.867 closest distance to " CB  SER A   3 " =    1.098
peak=    3.856 closest distance to " CA  GLY A 133 " =    3.903
peak=    3.852 closest distance to " O   HOH Z 134 " =    1.919
peak=    3.849 closest distance to " O   HOH Z 137 " =    1.220
peak=    3.843 closest distance to " NH1 ARG A  14 " =    1.040
peak=    3.838 closest distance to " CB  VAL A 296 " =    1.562
peak=    3.836 closest distance to " NZ  LYS A 181 " =    0.769
peak=    3.832 closest distance to " NZ  LYS A 289 " =    1.179
peak=    3.818 closest distance to " CB  ARG A 275 " =    0.905
peak=    3.814 closest distance to " ND2 ASN A 249 " =    2.375
peak=    3.806 closest distance to " CG  LYS A  76 " =    1.234
peak=    3.801 closest distance to " C   GLN A  58 " =    1.080
peak=    3.796 closest distance to " CA  ARG A  36 " =    1.005
peak=    3.794 closest distance to " CG  PRO A 213 " =    1.364
peak=    3.793 closest distance to " CB  ARG A 269 " =    0.879
peak=    3.788 closest distance to " O   HOH Z 159 " =    0.969
peak=    3.780 closest distance to " O   HOH Z 330 " =    1.113
peak=    3.779 closest distance to " CB  MET A  40 " =    0.934
peak=    3.778 closest distance to " O   HOH Z 222 " =    1.087
peak=    3.778 closest distance to " CD1 LEU A 300 " =    1.175
peak=    3.776 closest distance to " O   ASP A 200 " =    1.682
peak=    3.764 closest distance to " OD1 ASN A  60 " =    0.930
peak=    3.746 closest distance to " CB  ASP A 140 " =    0.999
peak=    3.736 closest distance to " CG2 THR A  31 " =    1.027
peak=    3.733 closest distance to " CB  GLU A 128 " =    1.092
peak=    3.725 closest distance to " O   HOH Z 408 " =    3.265
peak=    3.721 closest distance to " O   HOH Z 272 " =    1.399
peak=    3.714 closest distance to " O   HOH Z 107 " =    1.389
peak=    3.708 closest distance to " NE2 HIS A 108 " =    0.732
peak=    3.706 closest distance to " CA  ALA A 100 " =    1.069
peak=    3.704 closest distance to " N   GLU A 277 " =    0.830
peak=    3.700 closest distance to " O   HOH Z 123 " =    1.482
peak=    3.698 closest distance to " O   HOH Z 261 " =    1.746
peak=    3.696 closest distance to " CA  GLY A   6 " =    0.915
peak=    3.694 closest distance to " N   GLN A  11 " =    0.804
peak=    3.687 closest distance to " CA  ASP A 149 " =    1.769
peak=    3.686 closest distance to " O   HOH Z 331 " =    1.188
peak=    3.663 closest distance to " CA  ARG A 102 " =    1.183
peak=    3.656 closest distance to " O   GLN A  55 " =    1.628
peak=    3.650 closest distance to " CB  SER A 141 " =    1.099
peak=    3.649 closest distance to " O   HOH Z 145 " =    1.637
peak=    3.646 closest distance to " CG  PRO A 280 " =    0.862
peak=    3.646 closest distance to " O   HOH Z 392 " =    1.151
peak=    3.645 closest distance to " CA  ARG A 195 " =    1.101
peak=    3.642 closest distance to " O   HOH Z 407 " =    2.132
peak=    3.632 closest distance to " CG1 ILE A 120 " =    1.170
peak=    3.632 closest distance to " OE1 GLN A 240 " =    0.977
peak=    3.627 closest distance to " O   HOH Z 278 " =    1.112
peak=    3.626 closest distance to " O   THR A 251 " =    1.173
peak=    3.621 closest distance to " O   HOH Z 311 " =    4.474
peak=    3.620 closest distance to " CA  ARG A 156 " =    0.982
peak=    3.616 closest distance to " CB  MET A  47 " =    1.125
peak=    3.615 closest distance to " CB  TRP A 179 " =    1.425
peak=    3.614 closest distance to " O   HOH Z 362 " =    3.115
peak=    3.613 closest distance to " O   HOH Z 404 " =    1.822
peak=    3.610 closest distance to " CB  ALA A  10 " =    1.422
peak=    3.606 closest distance to " CB  ARG A 190 " =    1.868
peak=    3.601 closest distance to " ND2 ASN A  69 " =    1.705
peak=    3.597 closest distance to " CB  TYR A  30 " =    1.091
peak=    3.595 closest distance to " OD1 ASN A 148 " =    0.873
peak=    3.587 closest distance to " OG  SER A  22 " =    2.629
peak=    3.587 closest distance to " NE2 GLN A  77 " =    3.115
peak=    3.580 closest distance to " NH2 ARG A  56 " =    1.406
peak=    3.579 closest distance to " O   HOH Z 277 " =    1.497
peak=    3.577 closest distance to " O   LEU A  25 " =    0.874
peak=    3.576 closest distance to " O   HOH Z 174 " =    1.629
peak=    3.572 closest distance to " O   HOH Z  49 " =    1.480
peak=    3.562 closest distance to " O   GLN A  58 " =    1.979
peak=    3.560 closest distance to " N   ASN A 187 " =    0.859
peak=    3.557 closest distance to " C   ALA A 137 " =    1.700
peak=    3.555 closest distance to " CD  LYS A 289 " =    1.125
peak=    3.546 closest distance to " O   HOH Z 359 " =    1.569
peak=    3.539 closest distance to " O   GLU A 152 " =    1.431
peak=    3.536 closest distance to " N   GLU A  53 " =    1.846
peak=    3.529 closest distance to " CA  PRO A 198 " =    1.001
peak=    3.529 closest distance to " O   PRO A 198 " =    1.650
peak=    3.523 closest distance to " O   HOH Z 235 " =    2.027
peak=    3.523 closest distance to " CG  GLN A  55 " =    0.937
peak=    3.520 closest distance to " CA  LEU A   5 " =    0.920
peak=    3.505 closest distance to " OD1 ASN A 217 " =    1.553
peak=    3.500 closest distance to " CB  ASN A 176 " =    1.009
peak=    3.491 closest distance to " CB  THR A 235 " =    1.424
peak=    3.491 closest distance to " O   HOH Z  48 " =    2.162
peak=    3.489 closest distance to " N   HIS A 108 " =    1.788
peak=    3.486 closest distance to " O   SER A 206 " =    0.991
peak=    3.485 closest distance to " NE2 HIS A 115 " =    1.275
peak=    3.482 closest distance to " O   HOH Z 271 " =    2.556
peak=    3.475 closest distance to " O   HOH Z 417 " =    2.503
peak=    3.475 closest distance to " CA  TYR A  30 " =    1.148
peak=    3.465 closest distance to " CB  THR A  52 " =    0.924
peak=    3.462 closest distance to " CD1 ILE A 199 " =    1.553
peak=    3.461 closest distance to " OG BSER A  99 " =    3.282
peak=    3.460 closest distance to " CA  THR A 246 " =    1.162
peak=    3.457 closest distance to " CB  VAL A 202 " =    1.256
peak=    3.456 closest distance to " CA  SER A  87 " =    1.158
peak=    3.447 closest distance to " CG2 ILE A 120 " =    1.181
peak=    3.446 closest distance to " CB  SER A  62 " =    0.957
peak=    3.446 closest distance to " CG  PRO A 198 " =    1.427
peak=    3.446 closest distance to " O   HOH Z 371 " =    2.654
peak=    3.445 closest distance to " O   HOH Z 316 " =    3.120
peak=    3.443 closest distance to " O   HOH Z 133 " =    3.034
peak=    3.443 closest distance to " CG2 THR A 221 " =    1.054
peak=    3.439 closest distance to " CB  LEU A 281 " =    0.902
peak=    3.435 closest distance to " O   HOH Z 184 " =    2.037
peak=    3.434 closest distance to " CA  ARG A  66 " =    0.950
peak=    3.427 closest distance to " O   VAL A 112 " =    2.593
peak=    3.427 closest distance to " CA  GLU A 277 " =    0.920
peak=    3.423 closest distance to " N   LYS A 166 " =    0.918
peak=    3.423 closest distance to " O   HOH Z 296 " =    1.839
peak=    3.423 closest distance to " O   HOH Z 293 " =    2.193
peak=    3.415 closest distance to " O   HOH Z 126 " =    1.660
peak=    3.414 closest distance to " O   ALA A 233 " =    1.925
peak=    3.411 closest distance to " O   HOH Z 380 " =    2.623
peak=    3.409 closest distance to " O   LEU A  83 " =    1.012
peak=    3.406 closest distance to " CG2 VAL A 268 " =    1.005
peak=    3.406 closest distance to " CB  ALA A 114 " =    0.717
peak=    3.405 closest distance to " CG2 ILE A 106 " =    1.236
peak=    3.404 closest distance to " CB  ILE A 263 " =    1.044
peak=    3.404 closest distance to " CB  GLU A   2 " =    0.962
peak=    3.398 closest distance to " N   TYR A 247 " =    1.488
peak=    3.395 closest distance to " O   HOH Z 377 " =    1.863
peak=    3.394 closest distance to " CG2BVAL A 121 " =    0.781
peak=    3.392 closest distance to " O   HOH Z 210 " =    1.569
peak=    3.392 closest distance to " O   HOH Z  85 " =    2.232
peak=    3.391 closest distance to " O   HOH Z 395 " =    1.629
peak=    3.389 closest distance to " O   HOH Z 139 " =    5.066
peak=    3.387 closest distance to " O   HOH Z 403 " =    2.213
peak=    3.387 closest distance to " CB  GLU A 277 " =    4.209
peak=    3.386 closest distance to " CA  GLN A  11 " =    1.001
peak=    3.382 closest distance to " CG  MET A 185 " =    0.847
peak=    3.380 closest distance to " CG  ARG A 138 " =    1.489
peak=    3.380 closest distance to " N   ALA A 256 " =    1.905
peak=    3.378 closest distance to " CB  LEU A  83 " =    0.808
peak=    3.378 closest distance to " O   HOH Z  80 " =    2.498
peak=    3.377 closest distance to " O   GLY A 133 " =    1.753
peak=    3.377 closest distance to " O   VAL A 121 " =    0.759
peak=    3.376 closest distance to " CA  GLU A 152 " =    0.933
peak=    3.372 closest distance to " CA  TYR A 172 " =    1.030
peak=    3.371 closest distance to " CB  PHE A  59 " =    0.799
peak=    3.370 closest distance to " CB  ALA A 233 " =    0.993
peak=    3.363 closest distance to " O   HOH Z 248 " =    1.433
peak=    3.359 closest distance to " OD2 ASP A 272 " =    1.357
peak=    3.355 closest distance to " N   ALA A 180 " =    0.773
peak=    3.352 closest distance to " CG1BVAL A  72 " =    0.866
peak=    3.351 closest distance to " CA  ASP A 132 " =    1.431
peak=    3.349 closest distance to " OG  SER A 271 " =    1.866
peak=    3.348 closest distance to " O   HOH Z 209 " =    1.129
peak=    3.341 closest distance to " OG  SER A  62 " =    4.179
peak=    3.338 closest distance to " O   HOH Z 325 " =    2.319
peak=    3.334 closest distance to " OE1 GLU A   2 " =    1.008
peak=    3.330 closest distance to " O   HOH Z  54 " =    1.885
peak=    3.329 closest distance to " CG  GLU A  44 " =    0.948
peak=    3.326 closest distance to " NH1 ARG A  56 " =    1.109
peak=    3.326 closest distance to " O   HOH Z 303 " =    1.393
peak=    3.324 closest distance to " O   HOH Z 343 " =    2.548
peak=    3.323 closest distance to " CB  ASN A 187 " =    1.171
peak=    3.321 closest distance to " CA  CYS A 260 " =    1.264
peak=    3.319 closest distance to " CG1 VAL A 257 " =    1.265
peak=    3.319 closest distance to " NH2AARG A 190 " =    1.133
peak=    3.317 closest distance to " CD2 TRP A 179 " =    1.403
peak=    3.314 closest distance to " CE1 PHE A 225 " =    1.099
peak=    3.312 closest distance to " O   HOH Z 149 " =    2.398
peak=    3.311 closest distance to " CD2 HIS A  86 " =    1.859
peak=    3.309 closest distance to " O   HOH Z 335 " =    0.930
peak=    3.308 closest distance to " CA  ALA A 227 " =    1.461
peak=    3.307 closest distance to " O   HOH Z 411 " =    1.755
peak=    3.302 closest distance to " O   HOH Z 134 " =    2.493
peak=    3.301 closest distance to " CD  PRO A 213 " =    1.252
peak=    3.301 closest distance to " CD1 LEU A  96 " =    0.707
peak=    3.301 closest distance to " O   HOH Z 297 " =    2.131
peak=    3.296 closest distance to " CB  ASP A 124 " =    0.952
peak=    3.293 closest distance to " O   HOH Z 124 " =    1.101
peak=    3.291 closest distance to " CB  LYS A 289 " =    1.324
peak=    3.287 closest distance to " O   HOH Z  99 " =    2.187
peak=    3.285 closest distance to " O   HOH Z 269 " =    1.878
peak=    3.285 closest distance to " O   HOH Z  15 " =    2.407
peak=    3.280 closest distance to " CD  ARG A 159 " =    0.861
peak=    3.279 closest distance to " O   HOH Z 132 " =    3.943
peak=    3.277 closest distance to " CD1 LEU A 222 " =    1.018
peak=    3.274 closest distance to " CB  TRP A 274 " =    1.112
peak=    3.271 closest distance to " O   HOH Z 147 " =    1.446
peak=    3.269 closest distance to " NZ  LYS A 117 " =    3.932
peak=    3.260 closest distance to " O   TYR A 116 " =    1.275
peak=    3.260 closest distance to " CB  SER A 258 " =    0.960
peak=    3.258 closest distance to " O   THR A 182 " =    1.450
peak=    3.254 closest distance to " O   HOH Z 379 " =    2.841
peak=    3.252 closest distance to " CA  ASP A 191 " =    0.914
peak=    3.244 closest distance to " CD  ARG A  36 " =    0.864
peak=    3.244 closest distance to " O   HOH Z 183 " =    1.620
peak=    3.239 closest distance to " CD1 TRP A 274 " =    1.008
peak=    3.236 closest distance to " CB  TRP A 150 " =    1.517
peak=    3.234 closest distance to " CA  TYR A 116 " =    1.603
peak=    3.232 closest distance to " CE  LYS A  76 " =    0.936
peak=    3.230 closest distance to " N   ASN A  39 " =    1.325
peak=    3.230 closest distance to " CB  SER A 273 " =    0.767
peak=    3.227 closest distance to " O   HOH Z 343 " =    1.922
peak=    3.227 closest distance to " CD1AILE A 234 " =    1.104
peak=    3.219 closest distance to " CG  GLU A 277 " =    2.760
peak=    3.217 closest distance to " CA  GLY A 262 " =    0.912
peak=    3.217 closest distance to " O   HOH Z 434 " =    1.767
peak=    3.216 closest distance to " O   HOH Z 134 " =    1.915
peak=    3.207 closest distance to " CB  ALA A 248 " =    1.456
peak=    3.207 closest distance to " O   HOH Z 329 " =    2.680
peak=    3.205 closest distance to " CG  LEU A 167 " =    0.984
peak=    3.205 closest distance to " O   GLY A 211 " =    0.851
peak=    3.204 closest distance to " O   HOH Z 106 " =    3.446
peak=    3.204 closest distance to " O   HOH Z 287 " =    1.831
peak=    3.200 closest distance to " O   HOH Z 201 " =    2.637
peak=    3.198 closest distance to " CE3 TRP A 150 " =    1.332
peak=    3.194 closest distance to " O   GLU A   2 " =    1.711
peak=    3.193 closest distance to " O   HOH Z 214 " =    2.055
peak=    3.193 closest distance to " CB  ASN A 148 " =    1.624
peak=    3.191 closest distance to " CB  PRO A  54 " =    0.765
peak=    3.190 closest distance to " CG  LYS A 193 " =    1.294
peak=    3.190 closest distance to " CB  ILE A 234 " =    0.902
peak=    3.187 closest distance to " O   HOH Z 189 " =    3.595
peak=    3.187 closest distance to " CE3 TRP A  85 " =    1.050
peak=    3.184 closest distance to " CA  ALA A   9 " =    0.836
peak=    3.181 closest distance to " O   HOH Z  53 " =    1.788
peak=    3.181 closest distance to " O   HOH Z 207 " =    1.302
peak=    3.179 closest distance to " O   HOH Z 189 " =    3.052
peak=    3.178 closest distance to " CA  LYS A 117 " =    1.611
peak=    3.169 closest distance to " CB  ALA A 114 " =    1.567
peak=    3.169 closest distance to " O   HOH Z 200 " =    1.863
peak=    3.169 closest distance to " NE  ARG A 138 " =    1.107
peak=    3.167 closest distance to " O   HOH Z 139 " =    4.474
peak=    3.167 closest distance to " O   HOH Z  58 " =    1.981
peak=    3.166 closest distance to " O   ASP A 231 " =    1.852
peak=    3.164 closest distance to " CA  GLY A 267 " =    0.875
peak=    3.157 closest distance to " CA  ALA A 160 " =    1.215
peak=    3.156 closest distance to " N   LYS A 193 " =    1.209
peak=    3.156 closest distance to " CG2 ILE A  20 " =    1.223
peak=    3.155 closest distance to " O   HOH Z 213 " =    1.732
peak=    3.153 closest distance to " O   HOH Z 256 " =    1.962
peak=    3.153 closest distance to " CG  GLU A 277 " =    3.285
peak=    3.151 closest distance to " O   VAL A 112 " =    1.818
peak=    3.151 closest distance to " CG2 THR A 157 " =    0.786
peak=    3.146 closest distance to " O   HOH Z 217 " =    1.571
peak=    3.145 closest distance to " O   SER A  26 " =    1.398
peak=    3.143 closest distance to " CG2 THR A 264 " =    1.364
peak=    3.143 closest distance to " O   VAL A  72 " =    1.005
peak=    3.140 closest distance to " N   ASN A 252 " =    1.507
peak=    3.140 closest distance to " CG2 VAL A 197 " =    1.315
peak=    3.139 closest distance to " CG  GLN A 183 " =    1.439
peak=    3.136 closest distance to " O   HOH Z 182 " =    1.416
peak=    3.133 closest distance to " O   HOH Z  88 " =    2.106
peak=    3.131 closest distance to " O   HOH Z  32 " =    2.274
peak=    3.125 closest distance to " O   HOH Z   7 " =    1.965
peak=    3.123 closest distance to " O   HOH Z 341 " =    2.671
peak=    3.120 closest distance to " O   HOH Z 234 " =    1.884
peak=    3.118 closest distance to " O   HOH Z 435 " =    2.704
peak=    3.117 closest distance to " O   ASP A 191 " =    1.215
peak=    3.117 closest distance to " O   HOH Z 341 " =    1.410
peak=    3.116 closest distance to " O   GLN A  58 " =    1.094
peak=    3.116 closest distance to " CD  ARG A  24 " =    1.413
peak=    3.113 closest distance to " O   HOH Z 124 " =    1.337
peak=    3.112 closest distance to " OG1 THR A 264 " =    0.825
peak=    3.108 closest distance to " O   HOH Z   2 " =    3.093
peak=    3.107 closest distance to " CB  ALA A 291 " =    1.296
peak=    3.103 closest distance to " CB  LEU A 228 " =    1.329
peak=    3.098 closest distance to " CG2 VAL A  67 " =    1.055
peak=    3.096 closest distance to " CA  ALA A 295 " =    0.790
peak=    3.095 closest distance to " CB  ALA A 131 " =    1.932
peak=    3.095 closest distance to " O   HOH Z 197 " =    4.794
peak=    3.092 closest distance to " O   HOH Z 350 " =    1.175
peak=    3.091 closest distance to " O   ALA A 104 " =    1.655
peak=    3.089 closest distance to " CD  ARG A  66 " =    2.048
peak=    3.084 closest distance to " O   HOH Z 146 " =    1.549
peak=    3.083 closest distance to " CG ALYS A 290 " =    1.324
peak=    3.082 closest distance to " O   HOH Z 371 " =    2.572
peak=    3.079 closest distance to " CA  ASN A  74 " =    0.829
peak=    3.071 closest distance to " O   HOH Z  97 " =    0.835
peak=    3.069 closest distance to " CG  GLN A  58 " =    2.396
peak=    3.068 closest distance to " O   HOH Z 410 " =    1.138
peak=    3.065 closest distance to " CA  HIS A 115 " =    1.166
peak=    3.064 closest distance to " CB  PHE A  16 " =    0.842
peak=    3.060 closest distance to " O   ALA A  84 " =    1.173
peak=    3.026 closest distance to " CA  VAL A 125 " =    1.210
peak=    3.007 closest distance to " CD  LYS A  76 " =    1.786

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.355 - 5.856
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 206
   mapped sites are within: 0.706 - 5.856

peak=   -4.763 closest distance to " CD  GLN A 223 " =    1.341
peak=   -4.429 closest distance to " CD1 PHE A  59 " =    1.955
peak=   -4.427 closest distance to " O   HOH Z 114 " =    1.675
peak=   -4.411 closest distance to " N   ARG A 275 " =    0.935
peak=   -4.315 closest distance to " O   HOH Z 400 " =    1.298
peak=   -4.284 closest distance to " N   ASP A 272 " =    1.262
peak=   -4.218 closest distance to " O   HOH Z 137 " =    1.568
peak=   -4.217 closest distance to " O   ASN A 285 " =    2.128
peak=   -4.168 closest distance to " CG  GLU A  53 " =    1.353
peak=   -4.138 closest distance to " O   HOH Z   5 " =    1.367
peak=   -4.134 closest distance to " O   HOH Z 166 " =    1.120
peak=   -4.078 closest distance to " O   HOH Z 400 " =    0.752
peak=   -3.987 closest distance to " N   SER A 134 " =    1.140
peak=   -3.973 closest distance to " O   HOH Z  38 " =    0.915
peak=   -3.905 closest distance to " O   SER A 276 " =    1.847
peak=   -3.900 closest distance to " O   HOH Z 411 " =    5.259
peak=   -3.879 closest distance to " O   HOH Z 211 " =    0.841
peak=   -3.873 closest distance to " O   SER A   3 " =    0.918
peak=   -3.867 closest distance to " O   HOH Z  19 " =    1.678
peak=   -3.863 closest distance to " CG1BVAL A  72 " =    2.633
peak=   -3.851 closest distance to " CD2 LEU A 237 " =    2.551
peak=   -3.840 closest distance to " O   HOH Z  33 " =    1.499
peak=   -3.819 closest distance to " CD  GLN A  88 " =    0.847
peak=   -3.816 closest distance to " O   HOH Z 113 " =    2.044
peak=   -3.807 closest distance to " CD  ARG A  14 " =    3.274
peak=   -3.807 closest distance to " SD  MET A 105 " =    0.904
peak=   -3.799 closest distance to " CG  PRO A 243 " =    1.765
peak=   -3.790 closest distance to " O   HOH Z 151 " =    1.533
peak=   -3.767 closest distance to " O   VAL A 121 " =    0.953
peak=   -3.763 closest distance to " O   HOH Z 205 " =    1.501
peak=   -3.758 closest distance to " OE1 GLU A 236 " =    0.956
peak=   -3.756 closest distance to " O   GLN A  11 " =    1.319
peak=   -3.753 closest distance to " CB  ALA A 291 " =    2.597
peak=   -3.741 closest distance to " O   PRO A 198 " =    1.248
peak=   -3.733 closest distance to " CD2 TYR A 293 " =    1.643
peak=   -3.721 closest distance to " N   SER A 212 " =    1.606
peak=   -3.719 closest distance to " CD2 LEU A 237 " =    2.673
peak=   -3.708 closest distance to " CB  ALA A 291 " =    2.510
peak=   -3.702 closest distance to " O   HOH Z 340 " =    0.966
peak=   -3.696 closest distance to " CA  GLY A 229 " =    2.518
peak=   -3.690 closest distance to " N   ALA A  19 " =    2.350
peak=   -3.674 closest distance to " CG  LEU A 281 " =    1.979
peak=   -3.672 closest distance to " O   HOH Z 407 " =    0.935
peak=   -3.671 closest distance to " CB  PHE A 130 " =    1.170
peak=   -3.662 closest distance to " CE3 TRP A 150 " =    1.510
peak=   -3.660 closest distance to " O   HOH Z  54 " =    0.950
peak=   -3.646 closest distance to " NH2 ARG A  66 " =    1.515
peak=   -3.642 closest distance to " CD2 TYR A  30 " =    2.629
peak=   -3.630 closest distance to " N   ALA A 184 " =    1.015
peak=   -3.612 closest distance to " ND2 ASN A 285 " =    2.367
peak=   -3.609 closest distance to " NH1 ARG A 219 " =    2.147
peak=   -3.607 closest distance to " O   HOH Z 191 " =    5.856
peak=   -3.605 closest distance to " CD  GLN A  55 " =    1.210
peak=   -3.569 closest distance to " O   HOH Z 185 " =    2.713
peak=   -3.561 closest distance to " NE1 TRP A 274 " =    1.120
peak=   -3.554 closest distance to " CE3 TRP A 274 " =    2.295
peak=   -3.551 closest distance to " CB  ALA A 100 " =    2.153
peak=   -3.550 closest distance to " CA  TRP A 274 " =    0.945
peak=   -3.549 closest distance to " O   HOH Z 186 " =    3.798
peak=   -3.548 closest distance to " CD1 ILE A 109 " =    2.267
peak=   -3.543 closest distance to " ND2 ASN A 209 " =    2.052
peak=   -3.542 closest distance to " O   HOH Z 150 " =    1.934
peak=   -3.539 closest distance to " CD  LYS A 289 " =    2.232
peak=   -3.535 closest distance to " C   SER A 273 " =    0.984
peak=   -3.525 closest distance to " OG  SER A 276 " =    0.962
peak=   -3.519 closest distance to " O   HOH Z  33 " =    1.754
peak=   -3.513 closest distance to " O   HOH Z 103 " =    1.030
peak=   -3.511 closest distance to " O   HOH Z 198 " =    1.639
peak=   -3.509 closest distance to " O   HOH Z  70 " =    2.099
peak=   -3.508 closest distance to " CB  ASP A 171 " =    2.297
peak=   -3.506 closest distance to " CG2 THR A 251 " =    1.627
peak=   -3.506 closest distance to " CA  GLU A 277 " =    1.090
peak=   -3.505 closest distance to " O   HOH Z 257 " =    1.263
peak=   -3.502 closest distance to " N   ASP A 191 " =    1.216
peak=   -3.502 closest distance to " O   HOH Z 155 " =    2.081
peak=   -3.501 closest distance to " O   VAL A  72 " =    1.093
peak=   -3.496 closest distance to " C   LEU A 101 " =    1.261
peak=   -3.493 closest distance to " NH1 ARG A 259 " =    2.576
peak=   -3.488 closest distance to " O   HOH Z 138 " =    1.765
peak=   -3.483 closest distance to " O   HOH Z 132 " =    0.954
peak=   -3.475 closest distance to " O   HOH Z 139 " =    5.547
peak=   -3.466 closest distance to " O   HOH Z 412 " =    1.860
peak=   -3.465 closest distance to " OD1 ASN A 148 " =    1.331
peak=   -3.457 closest distance to " O   HOH Z 148 " =    2.006
peak=   -3.457 closest distance to " O   HOH Z 124 " =    1.799
peak=   -3.455 closest distance to " CG  LEU A  83 " =    2.435
peak=   -3.452 closest distance to " O   HOH Z 118 " =    1.498
peak=   -3.449 closest distance to " O   HOH Z 418 " =    1.215
peak=   -3.446 closest distance to " OE1 GLN A 122 " =    2.450
peak=   -3.444 closest distance to " O   HOH Z 278 " =    0.944
peak=   -3.443 closest distance to " CG1 VAL A 125 " =    1.939
peak=   -3.436 closest distance to " CZ  ARG A 259 " =    0.865
peak=   -3.435 closest distance to " O   HOH Z 377 " =    1.867
peak=   -3.431 closest distance to " CG BMET A  47 " =    1.235
peak=   -3.431 closest distance to " O   HOH Z  37 " =    1.781
peak=   -3.428 closest distance to " CD2 HIS A  81 " =    2.406
peak=   -3.424 closest distance to " C   VAL A 265 " =    0.991
peak=   -3.422 closest distance to " N   GLN A  58 " =    1.349
peak=   -3.420 closest distance to " OG  SER A  32 " =    1.342
peak=   -3.412 closest distance to " O   HOH Z  67 " =    1.250
peak=   -3.410 closest distance to " CG1BVAL A  72 " =    1.774
peak=   -3.409 closest distance to " O   HOH Z 332 " =    1.296
peak=   -3.397 closest distance to " O   HOH Z 281 " =    2.074
peak=   -3.396 closest distance to " CB  ASP A 286 " =    1.988
peak=   -3.395 closest distance to " CG2 VAL A 202 " =    2.207
peak=   -3.394 closest distance to " CG  GLN A  11 " =    0.997
peak=   -3.392 closest distance to " CA  GLY A 241 " =    2.308
peak=   -3.384 closest distance to " O   SER A  12 " =    1.265
peak=   -3.381 closest distance to " N   ALA A 242 " =    1.229
peak=   -3.375 closest distance to " CG  ARG A 269 " =    2.527
peak=   -3.368 closest distance to " SG  CYS A 254 " =    3.296
peak=   -3.365 closest distance to " O   HOH Z 109 " =    1.251
peak=   -3.363 closest distance to " O   HOH Z  88 " =    3.011
peak=   -3.362 closest distance to " O   HOH Z  97 " =    1.627
peak=   -3.362 closest distance to " CE  MET A  93 " =    1.939
peak=   -3.347 closest distance to " OD2 ASP A  50 " =    2.231
peak=   -3.344 closest distance to " O   HOH Z 261 " =    1.089
peak=   -3.343 closest distance to " O   HOH Z 156 " =    3.539
peak=   -3.340 closest distance to " O   HOH Z 438 " =    2.815
peak=   -3.339 closest distance to " CG  PRO A 163 " =    1.908
peak=   -3.336 closest distance to " OG  SER A  28 " =    2.194
peak=   -3.323 closest distance to " CD1 TYR A 247 " =    2.696
peak=   -3.318 closest distance to " O   HOH Z 368 " =    2.080
peak=   -3.310 closest distance to " CB  SER A 206 " =    1.224
peak=   -3.307 closest distance to " O   HOH Z 362 " =    3.714
peak=   -3.307 closest distance to " N   GLN A  11 " =    1.388
peak=   -3.298 closest distance to " O   HOH Z 396 " =    1.706
peak=   -3.296 closest distance to " CG1 VAL A 112 " =    3.140
peak=   -3.293 closest distance to " CA  MET A  47 " =    1.238
peak=   -3.292 closest distance to " NE2 HIS A 115 " =    1.195
peak=   -3.291 closest distance to " CD  GLN A  77 " =    1.026
peak=   -3.291 closest distance to " N   GLY A 302 " =    1.796
peak=   -3.291 closest distance to " O   ASN A  74 " =    1.939
peak=   -3.288 closest distance to " O  BHOH Z 338 " =    0.706
peak=   -3.285 closest distance to " CG  LEU A 282 " =    2.448
peak=   -3.282 closest distance to " CZ  TYR A  68 " =    1.122
peak=   -3.277 closest distance to " O   HOH Z 174 " =    2.430
peak=   -3.276 closest distance to " O   HOH Z 179 " =    2.164
peak=   -3.275 closest distance to " O   ASP A 171 " =    1.042
peak=   -3.274 closest distance to " O   GLN A  73 " =    1.440
peak=   -3.273 closest distance to " CD1 PHE A 130 " =    2.319
peak=   -3.271 closest distance to " O   HOH Z 250 " =    1.415
peak=   -3.271 closest distance to " CE1 PHE A 225 " =    2.580
peak=   -3.270 closest distance to " CA  ASP A  65 " =    1.260
peak=   -3.270 closest distance to " NZ  LYS A 119 " =    2.188
peak=   -3.265 closest distance to " O   HOH Z 108 " =    2.891
peak=   -3.264 closest distance to " O   HOH Z   7 " =    1.327
peak=   -3.261 closest distance to " C   SER A  28 " =    1.242
peak=   -3.261 closest distance to " O   HOH Z 210 " =    1.335
peak=   -3.261 closest distance to " CZ  PHE A 155 " =    1.392
peak=   -3.260 closest distance to " O   HOH Z 109 " =    3.903
peak=   -3.259 closest distance to " OG1 THR A 251 " =    2.309
peak=   -3.254 closest distance to " O   HOH Z 177 " =    1.729
peak=   -3.244 closest distance to " CG1 VAL A 153 " =    2.047
peak=   -3.237 closest distance to " OG  SER A 245 " =    0.950
peak=   -3.236 closest distance to " CD1 LEU A 167 " =    1.785
peak=   -3.233 closest distance to " O   HOH Z  43 " =    1.320
peak=   -3.225 closest distance to " C   SER A   3 " =    1.002
peak=   -3.225 closest distance to " O   THR A  82 " =    1.654
peak=   -3.221 closest distance to " O   HOH Z 174 " =    1.449
peak=   -3.220 closest distance to " O   HOH Z 221 " =    0.873
peak=   -3.217 closest distance to " CH2 TRP A 179 " =    1.130
peak=   -3.214 closest distance to " CZ  PHE A  38 " =    1.100
peak=   -3.214 closest distance to " CA  GLY A 241 " =    2.998
peak=   -3.210 closest distance to " O   HOH Z  38 " =    1.553
peak=   -3.205 closest distance to " O   HOH Z 394 " =    1.816
peak=   -3.205 closest distance to " CA  SER A  62 " =    2.857
peak=   -3.199 closest distance to " C   SER A   3 " =    1.065
peak=   -3.196 closest distance to " OG1 THR A   4 " =    1.478
peak=   -3.189 closest distance to " C   MET A 188 " =    1.301
peak=   -3.187 closest distance to " CG1 VAL A 202 " =    1.213
peak=   -3.184 closest distance to " O   HOH Z  90 " =    3.156
peak=   -3.182 closest distance to " O   HOH Z  41 " =    2.917
peak=   -3.176 closest distance to " CZ2 TRP A 179 " =    1.818
peak=   -3.170 closest distance to " NH2BARG A 102 " =    1.416
peak=   -3.164 closest distance to " CB  ASN A 224 " =    2.625
peak=   -3.155 closest distance to " CD  GLN A  58 " =    1.044
peak=   -3.151 closest distance to " O   PHE A  59 " =    2.091
peak=   -3.150 closest distance to " O   ASN A 127 " =    2.150
peak=   -3.146 closest distance to " O   VAL A 174 " =    2.188
peak=   -3.143 closest distance to " O   HOH Z 437 " =    1.441
peak=   -3.142 closest distance to " O   HOH Z 203 " =    1.175
peak=   -3.142 closest distance to " O   SER A  26 " =    1.630
peak=   -3.139 closest distance to " CG  ARG A 269 " =    1.897
peak=   -3.135 closest distance to " O   HOH Z  19 " =    2.258
peak=   -3.134 closest distance to " N   HIS A 115 " =    1.281
peak=   -3.133 closest distance to " O   HOH Z  60 " =    1.719
peak=   -3.127 closest distance to " O   HOH Z 424 " =    3.182
peak=   -3.123 closest distance to " N   PHE A 283 " =    1.228
peak=   -3.119 closest distance to " CD1 LEU A 101 " =    2.813
peak=   -3.104 closest distance to " CB  PRO A 243 " =    2.977
peak=   -3.098 closest distance to " O   HOH Z   7 " =    0.807
peak=   -3.096 closest distance to " N   ALA A  43 " =    2.815
peak=   -3.093 closest distance to " NH1 ARG A 139 " =    2.026
peak=   -3.093 closest distance to " CG  ARG A 259 " =    2.530
peak=   -3.089 closest distance to " CG1 VAL A 112 " =    2.699
peak=   -3.078 closest distance to " NE1 TRP A 150 " =    1.103
peak=   -3.066 closest distance to " CD2 TYR A 169 " =    2.653
peak=   -3.060 closest distance to " O   HOH Z 243 " =    1.266
peak=   -3.059 closest distance to " O   HOH Z   4 " =    2.145
peak=   -3.047 closest distance to " O   ARG A 275 " =    0.855

================= 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    :  0.5152 0.5023   6.310342e+00   6.296537e+00
   1_bss:  0.5111 0.4987   6.309499e+00   6.292903e+00
   1_xyz:  0.4476 0.4760   6.236071e+00   6.260593e+00
   1_adp:  0.4027 0.4745   6.199325e+00   6.262535e+00
   1_occ:  0.4026 0.4764   6.199630e+00   6.263038e+00
   2_bss:  0.4030 0.4749   6.201129e+00   6.262600e+00
   2_xyz:  0.3506 0.4292   6.104188e+00   6.215217e+00
   2_adp:  0.3376 0.4142   6.080352e+00   6.198390e+00
   2_occ:  0.3374 0.4143   6.079754e+00   6.197806e+00
   3_bss:  0.3379 0.4136   6.080975e+00   6.196928e+00
   3_xyz:  0.2823 0.3529   5.933821e+00   6.089215e+00
   3_adp:  0.2606 0.3321   5.873243e+00   6.041710e+00
   3_occ:  0.2604 0.3315   5.872348e+00   6.041567e+00
   4_bss:  0.2602 0.3311   5.872742e+00   6.042054e+00
   4_xyz:  0.2069 0.2612   5.658738e+00   5.846153e+00
   4_adp:  0.1829 0.2408   5.564792e+00   5.777853e+00
   4_occ:  0.1828 0.2408   5.564273e+00   5.777349e+00
   5_bss:  0.1829 0.2412   5.564001e+00   5.777360e+00
   5_xyz:  0.1681 0.2234   5.496400e+00   5.716412e+00
   5_adp:  0.1666 0.2243   5.489332e+00   5.713800e+00
   5_occ:  0.1663 0.2247   5.488723e+00   5.713278e+00
   5_bss:  0.1659 0.2239   5.490079e+00   5.714979e+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:  0.272  65.662  -0.800   1.579   2.137   0.000   0.000   0.000
   1_xyz:  0.272  65.662  -0.800   1.579   2.137   0.000   0.000   0.000
   1_adp:  0.272  65.662  -0.800   1.579   2.137   0.000   0.000   0.000
   1_occ:  0.272  65.662  -0.800   1.579   2.137   0.000   0.000   0.000
   2_bss:  0.324  96.795   0.957   2.172   2.772   0.000   0.000   0.000
   2_xyz:  0.324  96.795   0.957   2.172   2.772   0.000   0.000   0.000
   2_adp:  0.324  96.795   0.957   2.172   2.772   0.000   0.000   0.000
   2_occ:  0.324  96.795   0.957   2.172   2.772   0.000   0.000   0.000
   3_bss:  0.337  92.741   0.858   2.077   2.110   0.000   0.000   0.000
   3_xyz:  0.337  92.741   0.858   2.077   2.110   0.000   0.000   0.000
   3_adp:  0.337  92.741   0.858   2.077   2.110   0.000   0.000   0.000
   3_occ:  0.337  92.741   0.858   2.077   2.110   0.000   0.000   0.000
   4_bss:  0.334  90.073  -0.232   0.719   0.819   0.000   0.000   0.000
   4_xyz:  0.334  90.073  -0.232   0.719   0.819   0.000   0.000   0.000
   4_adp:  0.334  90.073  -0.232   0.719   0.819   0.000   0.000   0.000
   4_occ:  0.334  90.073  -0.232   0.719   0.819   0.000   0.000   0.000
   5_bss:  0.337  87.770  -0.607   0.153   0.698   0.000   0.000   0.000
   5_xyz:  0.337  87.770  -0.607   0.153   0.698   0.000   0.000   0.000
   5_adp:  0.337  87.770  -0.607   0.153   0.698   0.000   0.000   0.000
   5_occ:  0.337  87.770  -0.607   0.153   0.698   0.000   0.000   0.000
   5_bss:  0.336  91.773  -0.680  -0.068   0.748   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.750 0.3184  0.4051    80568.666
   1_bss:  65.218 0.3247  0.4342    79639.507
   1_xyz:  57.972 0.4184  0.5542    67645.664
   1_adp:  58.426 0.4124  0.5525    68555.750
   1_occ:  58.544 0.4109  0.5506    68929.031
   2_bss:  58.504 0.4114  0.5685    68749.164
   2_xyz:  50.603 0.5112  0.7111    54210.154
   2_adp:  48.187 0.5417  0.7404    50369.398
   2_occ:  48.111 0.5426  0.7412    50250.688
   3_bss:  48.082 0.5430  0.7357    50227.051
   3_xyz:  38.188 0.6637  0.8861    34701.197
   3_adp:  34.599 0.7064  0.9052    30041.321
   3_occ:  34.571 0.7066  0.9053    29981.277
   4_bss:  34.554 0.7068  0.8677    29969.006
   4_xyz:  26.268 0.7981  0.9424    17946.934
   4_adp:  23.565 0.8267  0.9369    14918.713
   4_occ:  23.553 0.8268  0.9371    14914.318
   5_bss:  23.532 0.8270  0.9258    14873.373
   5_xyz:  21.543 0.8471  0.9372    12745.774
   5_adp:  21.321 0.8496  0.9089    12715.265
   5_occ:  21.310 0.8497  0.9089    12717.972
   5_bss:  21.343 0.8495  0.9416    12773.868
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6855e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6855e-01
   1_xyz:   1.625  0.013  0.102 15.900  0.006  4.113   1.5971e-01
   1_adp:   1.625  0.013  0.102 15.900  0.006  4.113   1.5971e-01
   1_occ:   1.625  0.013  0.102 15.900  0.006  4.113   1.5971e-01
   2_bss:   1.625  0.013  0.102 15.900  0.006  4.113   1.5971e-01
   2_xyz:   1.483  0.011  0.104 15.827  0.006  4.115   1.2472e-01
   2_adp:   1.483  0.011  0.104 15.827  0.006  4.115   1.2472e-01
   2_occ:   1.483  0.011  0.104 15.827  0.006  4.115   1.2472e-01
   3_bss:   1.483  0.011  0.104 15.827  0.006  4.115   1.2472e-01
   3_xyz:   1.451  0.012  0.095 15.606  0.005  4.111   1.2208e-01
   3_adp:   1.451  0.012  0.095 15.606  0.005  4.111   1.2208e-01
   3_occ:   1.451  0.012  0.095 15.606  0.005  4.111   1.2208e-01
   4_bss:   1.451  0.012  0.095 15.606  0.005  4.111   1.2208e-01
   4_xyz:   1.365  0.013  0.096 15.059  0.005  4.117   1.1588e-01
   4_adp:   1.365  0.013  0.096 15.059  0.005  4.117   1.1588e-01
   4_occ:   1.365  0.013  0.096 15.059  0.005  4.117   1.1588e-01
   5_bss:   1.365  0.013  0.096 15.059  0.005  4.117   1.1588e-01
   5_xyz:   1.033  0.009  0.072 14.393  0.004  4.129   6.5457e-02
   5_adp:   1.033  0.009  0.072 14.393  0.004  4.129   6.5457e-02
   5_occ:   1.033  0.009  0.072 14.393  0.004  4.129   6.5457e-02
   5_bss:   1.033  0.009  0.072 14.393  0.004  4.129   6.5457e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.439   2.4742e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.439   2.4742e-01
   1_xyz:  11.509  0.095  0.386 87.074  0.043  1.839   2.3028e-01
   1_adp:  11.509  0.095  0.386 87.074  0.043  1.839   2.3028e-01
   1_occ:  11.509  0.095  0.386 87.074  0.043  1.839   2.3028e-01
   2_bss:  11.509  0.095  0.386 87.074  0.043  1.839   2.3028e-01
   2_xyz:   8.992  0.062  0.368 89.378  0.044  2.063   1.0428e-01
   2_adp:   8.992  0.062  0.368 89.378  0.044  2.063   1.0428e-01
   2_occ:   8.992  0.062  0.368 89.378  0.044  2.063   1.0428e-01
   3_bss:   8.992  0.062  0.368 89.378  0.044  2.063   1.0428e-01
   3_xyz:  10.152  0.062  0.317 88.202  0.034  2.010   1.0040e-01
   3_adp:  10.152  0.062  0.317 88.202  0.034  2.010   1.0040e-01
   3_occ:  10.152  0.062  0.317 88.202  0.034  2.010   1.0040e-01
   4_bss:  10.152  0.062  0.317 88.202  0.034  2.010   1.0040e-01
   4_xyz:   9.307  0.079  0.292 89.110  0.027  2.042   1.6034e-01
   4_adp:   9.307  0.079  0.292 89.110  0.027  2.042   1.6034e-01
   4_occ:   9.307  0.079  0.292 89.110  0.027  2.042   1.6034e-01
   5_bss:   9.307  0.079  0.292 89.110  0.027  2.042   1.6034e-01
   5_xyz:   8.655  0.044  0.286 88.779  0.043  2.163   3.9441e-02
   5_adp:   8.655  0.044  0.286 88.779  0.043  2.163   3.9441e-02
   5_occ:   8.655  0.044  0.286 88.779  0.043  2.163   3.9441e-02
   5_bss:   8.655  0.044  0.286 88.779  0.043  2.163   3.9441e-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: 150.53   0.00  22.37 107.31   0.00  19.57 150.53   0.00  37.65
   1_occ: 150.53   0.00  22.37 107.31   0.00  19.57 150.53   0.00  37.65
   2_bss: 150.53   0.00  22.37 107.31   0.00  19.57 150.53   0.00  37.65
   2_xyz: 150.53   0.00  22.37 107.31   0.00  19.57 150.53   0.00  37.65
   2_adp: 157.99   0.00  20.51 101.72   0.00  17.49 157.99   0.00  36.94
   2_occ: 157.99   0.00  20.51 101.72   0.00  17.49 157.99   0.00  36.94
   3_bss: 157.99   0.00  20.51 101.72   0.00  17.49 157.99   0.00  36.94
   3_xyz: 157.99   0.00  20.51 101.72   0.00  17.49 157.99   0.00  36.94
   3_adp: 154.93   0.00  18.62 100.31   0.00  14.70 154.93   0.00  39.97
   3_occ: 154.93   0.00  18.62 100.31   0.00  14.70 154.93   0.00  39.97
   4_bss: 154.93   0.00  18.62 100.31   0.00  14.70 154.93   0.00  39.97
   4_xyz: 154.93   0.00  18.62 100.31   0.00  14.70 154.93   0.00  39.97
   4_adp: 149.66   0.00  18.51 112.76   0.00  13.14 149.66   4.21  47.72
   4_occ: 149.66   0.00  18.51 112.76   0.00  13.14 149.66   4.21  47.72
   5_bss: 149.66   0.00  18.51 112.76   0.00  13.14 149.66   4.21  47.72
   5_xyz: 149.66   0.00  18.51 112.76   0.00  13.14 149.66   4.21  47.72
   5_adp: 149.48   0.00  17.94 113.13   0.00  12.48 149.48   1.18  47.65
   5_occ: 149.48   0.00  17.94 113.13   0.00  12.48 149.48   1.18  47.65
   5_bss: 150.59   1.11  19.05 114.24   1.11  13.60 150.59   2.30  48.76
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.754    0.016    0.334
   1_adp:    1.754    0.016    0.334
   1_occ:    1.754    0.016    0.334
   2_bss:    1.754    0.016    0.334
   2_xyz:    1.613    0.034    0.576
   2_adp:    1.613    0.034    0.576
   2_occ:    1.613    0.034    0.576
   3_bss:    1.613    0.034    0.576
   3_xyz:    1.820    0.079    0.790
   3_adp:    1.820    0.079    0.790
   3_occ:    1.820    0.079    0.790
   4_bss:    1.820    0.079    0.790
   4_xyz:    2.111    0.064    0.943
   4_adp:    2.111    0.064    0.943
   4_occ:    2.111    0.064    0.943
   5_bss:    2.111    0.064    0.943
   5_xyz:    2.130    0.046    0.982
   5_adp:    2.130    0.046    0.982
   5_occ:    2.130    0.046    0.982
   5_bss:    2.130    0.046    0.982
------------------------------------------------------------------------

CPU time actual refinement: 347.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1330/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_1330/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1330/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1330/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1330/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.51 
  Macro-tasks:
    bulk solvent and scale       = 58.66  
    individual site refinement   = 140.03 
    weights calculation          = 28.32  
    collect and process          = 6.16   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 233.26 
  Micro-tasks:
    mask                            = 2.83   
    f_calc                          = 104.45 
    alpha_beta                      = 8.23   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 114.55 
    fmodel                         = 9.06   
    r_factors                      = 0.30   
    phase_errors                   = 9.61   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 250.39 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.914 micro seconds
Total CPU time: 6.01 minutes
from_scatterers_fft:    629 calls, 104.15 s
gradients_fft:          575 calls, 101.64 s

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

# Date 2008-01-16 Time 06:59:54 PST -0800 (1200495594.66 s)
Start R-work = 0.5152, R-free = 0.5023 (no bulk solvent and anisotropic scale)
Final R-work = 0.1800, R-free = 0.2374 (no bulk solvent and anisotropic scale)

Start R-work = 0.5111, R-free = 0.4987
Final R-work = 0.1659, R-free = 0.2239