# Date 2008-01-16 Time 06:35:03 PST -0800 (1200494103.30 s)
#phil __OFF__

Command line arguments: "../1200.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20635
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1200

-------------------------------------------------------------------------------
  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: (71.655, 48.1033, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


================================== 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: (71.655, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96159
Completeness in resolution range: 0.909045
Completeness with d_max=infinity: 0.906395

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1240
                             d_min =   1.9616

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96159
Completeness in resolution range: 0.909045
Completeness with d_max=infinity: 0.906395

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1245 -  4.1988 [2263/2292]  2039   224   9.9%
  bin  2:  4.1988 -  3.3446 [2168/2191]  1949   219  10.1%
  bin  3:  3.3446 -  2.9253 [2134/2159]  1918   216  10.1%
  bin  4:  2.9253 -  2.6594 [2130/2156]  1923   207   9.7%
  bin  5:  2.6594 -  2.4697 [2100/2134]  1892   208   9.9%
  bin  6:  2.4697 -  2.3246 [2107/2135]  1894   213  10.1%
  bin  7:  2.3246 -  2.2085 [2085/2121]  1874   211  10.1%
  bin  8:  2.2085 -  2.1127 [2079/2121]  1866   213  10.2%
  bin  9:  2.1127 -  2.0315 [1971/2123]  1779   192   9.7%
  bin 10:  2.0315 -  1.9616 [ 552/2117]   496    56  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1200/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 14
        2.02 -     2.74: 247
        2.74 -     3.46: 4571
        3.46 -     4.18: 9327
        4.18 -     4.90: 13936
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.295 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.337 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.399 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.511 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.529 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28090 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_1200/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1200/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 71.655 48.10325 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4887   r_free= 0.4739   ksol= 0.00   Bsol= 0.00   scale= 0.867    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.297536                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6838 0.99   1470  166 0.3905 0.4092      6.5969       6.606|
|  2:  4.6838 -  3.7362 0.99   1411  154 0.4325 0.4206      6.8707      6.8593|
|  3:  3.7362 -  3.2693 0.99   1378  148 0.4733 0.4234      6.6925      6.6633|
|  4:  3.2693 -  2.9729 0.98   1369  161 0.4954 0.4842      6.5247      6.5076|
|  5:  2.9729 -  2.7612 0.99   1385  150 0.5119 0.4904      6.3686      6.3523|
|  6:  2.7612 -  2.5992 0.99   1354  158 0.5297 0.5009      6.2823      6.1777|
|  7:  2.5992 -  2.4697 0.98   1354  137 0.5208 0.4743      6.2437      6.2068|
|  8:  2.4697 -  2.3626 0.98   1339  151 0.5252 0.5117      6.1448       6.198|
|  9:  2.3626 -  2.2719 0.99   1353  152 0.5502 0.5256      6.1542      6.0931|
| 10:  2.2719 -  2.1938 0.99   1342  159 0.5313 0.5256      6.0766      6.1199|
| 11:  2.1938 -  2.1254 0.97   1348  137 0.5333 0.5514      6.0216      5.9935|
| 12:  2.1254 -  2.0648 0.98   1324  150 0.5082 0.5153      5.9192      5.9532|
| 13:  2.0648 -  2.0105 0.72    956  116 0.5323 0.4438      5.8607      5.8478|
| 14:  2.0105 -  1.9616 0.18    247   20 0.5703 0.4713      5.7978      5.6922|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6838  1470   166  0.67  36.72   0.81     0.71      81201.66|
|  2:  4.6838 -  3.7362  1411   154  0.67  37.96   0.88     0.76     115544.58|
|  3:  3.7362 -  3.2693  1378   148  0.55  48.20   0.88     0.72     125497.47|
|  4:  3.2693 -  2.9729  1369   161  0.45  56.17   0.87     0.63     112227.33|
|  5:  2.9729 -  2.7612  1385   150  0.38  61.03   0.85     0.57      88084.36|
|  6:  2.7612 -  2.5992  1354   158  0.38  61.32   0.86     0.54      70900.38|
|  7:  2.5992 -  2.4697  1354   137  0.39  60.71   0.89     0.54      62194.41|
|  8:  2.4697 -  2.3626  1339   151  0.36  63.09   0.87     0.53      58964.98|
|  9:  2.3626 -  2.2719  1353   152  0.34  64.59   0.90     0.51      54559.88|
| 10:  2.2719 -  2.1938  1342   159  0.32  66.25   0.90     0.48      52443.55|
| 11:  2.1938 -  2.1254  1348   137  0.27  69.95   0.90     0.41      49733.59|
| 12:  2.1254 -  2.0648  1324   150  0.23  72.71   0.91     0.39      47538.00|
| 13:  2.0648 -  2.0105   956   116  0.25  71.33   0.91     0.41      39287.42|
| 14:  2.0105 -  1.9616   247    20  0.31  67.05   0.87     0.51      30731.02|
|alpha:            min =        0.39 max =            0.76 mean =         0.56|
|beta:             min =    30731.02 max =       125497.47 mean =     74274.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.99 mean =        58.80|
|phase err.(test): min =        0.00 max =           89.99 mean =        58.76|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.550039             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.640   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.487284              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.491   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.295 -  1.656:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.656 -  2.016:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.016 -  2.377:       23 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.377 -  2.737:      224 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.737 -  3.098:     2307 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.098 -  3.458:     2264 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.458 -  3.819:     4218 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.819 -  4.179:     5109 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.179 -  4.540:     6267 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.540 -  4.900:     7669 |
|-----------------------------------------------------------------------------|
|-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 |        0.197 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.295 |       0.666 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4887   r_free= 0.4739   ksol= 0.00   Bsol= 0.00   scale= 0.867    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.297536                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4826   r_free= 0.4664   ksol= 0.28   Bsol= 20.00   scale= 0.912   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.40,3.16,0.12,0.00,0.00,0.00); trace/3= 0.96                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.295304                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.203354              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.482   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.548376              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.253   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4826      final r-factor (work) = 0.4186          |
| start r-factor (free) = 0.4664      final r-factor (free) = 0.4439          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1470 = 9.20 * 0.50 * 6.2912 + 1.00 * 0.1969                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.7456 = 9.20 * 0.50 * 6.2223 + 1.00 * 0.1126                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4186      final r-factor (work) = 0.3861          |
| start r-factor (free) = 0.4439      final r-factor (free) = 0.4462          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6407 = 1.55 * 1.00 * 6.2223 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5937 = 1.55 * 1.00 * 6.1755 + 1.00 * 0.0317                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    151.15  18.88    None  None   None       |
|    all(noH): 2823   0      0.00    151.15  18.88    None  None   None       |
|    Sol.    : 438    0      0.00    73.81   36.04    None  None   None       |
|    Mac.    : 2385   0      0.00    151.15  15.73    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 -  15.115: 1325   |   5:    75.573 -  90.688:    0        |
|      1:    15.115 -  30.229:  999   |   6:    90.688 - 105.802:    0        |
|      2:    30.229 -  45.344:  351   |   7:   105.802 - 120.917:    0        |
|      3:    45.344 -  60.458:  132   |   8:   120.917 - 136.031:    0        |
|      4:    60.458 -  75.573:   15   |   9:   136.031 - 151.146:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3861 r_free = 0.4462             target_work(ml) = 6.177         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3859 r_free = 0.4477             target_work(ml) = 6.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3859   r_free= 0.4477   ksol= 0.28   Bsol= 20.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.40,3.16,0.12,0.00,0.00,0.00); trace/3= 0.96                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.176782                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3861   r_free= 0.4459   ksol= 0.30   Bsol= 50.00   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,1.73,-0.24,0.00,-0.00,-0.00); trace/3= 0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.178223                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.977804             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.936  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.220930              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.397  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3861      final r-factor (work) = 0.3244          |
| start r-factor (free) = 0.4459      final r-factor (free) = 0.3972          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.1032 = 11.98 * 0.50 * 6.1764 + 1.00 * 0.1131                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.7211 = 11.98 * 0.50 * 6.1104 + 1.00 * 0.1266                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3244      final r-factor (work) = 0.3043          |
| start r-factor (free) = 0.3972      final r-factor (free) = 0.3890          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4827 = 1.22 * 1.00 * 6.1104 + 1.00 * 0.0223                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3853 = 1.22 * 1.00 * 6.0334 + 1.00 * 0.0189                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.29  20.11    None  None   None       |
|    all(noH): 2823   0      0.00    102.29  20.11    None  None   None       |
|    Sol.    : 438    0      0.00    102.29  38.25    None  None   None       |
|    Mac.    : 2385   0      0.00    85.37   16.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.229:  890   |   5:    51.146 -  61.375:   92        |
|      1:    10.229 -  20.458:  860   |   6:    61.375 -  71.604:   45        |
|      2:    20.458 -  30.688:  495   |   7:    71.604 -  81.834:   21        |
|      3:    30.688 -  40.917:  269   |   8:    81.834 -  92.063:    6        |
|      4:    40.917 -  51.146:  142   |   9:    92.063 - 102.292:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3043 r_free = 0.3890             target_work(ml) = 6.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3041 r_free = 0.3889             target_work(ml) = 6.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3041   r_free= 0.3889   ksol= 0.30   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,1.73,-0.24,0.00,-0.00,-0.00); trace/3= 0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.027634                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3047   r_free= 0.3883   ksol= 0.32   Bsol= 65.49   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,1.27,-0.50,0.00,-0.00,-0.00); trace/3= 0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.027863                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.745488              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.841   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.910924              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.076  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3047      final r-factor (work) = 0.2662          |
| start r-factor (free) = 0.3883      final r-factor (free) = 0.3433          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.4783 = 6.75 * 0.50 * 6.0341 + 1.00 * 0.1267                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2402 = 6.75 * 0.50 * 5.9798 + 1.00 * 0.0718                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2662      final r-factor (work) = 0.2536          |
| start r-factor (free) = 0.3433      final r-factor (free) = 0.3334          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4660 = 0.91 * 1.00 * 5.9798 + 1.00 * 0.0189                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3832 = 0.91 * 1.00 * 5.8917 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.59  19.69    None  None   None       |
|    all(noH): 2823   0      0.00    102.59  19.69    None  None   None       |
|    Sol.    : 438    0      1.18    102.59  41.47    None  None   None       |
|    Mac.    : 2385   0      0.00    94.06   15.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.259:  974   |   5:    51.293 -  61.552:   99        |
|      1:    10.259 -  20.517:  909   |   6:    61.552 -  71.810:   45        |
|      2:    20.517 -  30.776:  390   |   7:    71.810 -  82.069:   29        |
|      3:    30.776 -  41.034:  232   |   8:    82.069 -  92.327:   13        |
|      4:    41.034 -  51.293:  124   |   9:    92.327 - 102.586:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2536 r_free = 0.3334             target_work(ml) = 5.879         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2535 r_free = 0.3331             target_work(ml) = 5.879         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2535   r_free= 0.3331   ksol= 0.32   Bsol= 65.49   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,1.27,-0.50,0.00,-0.00,-0.00); trace/3= 0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.878809                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2537   r_free= 0.3325   ksol= 0.32   Bsol= 71.21   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,0.47,-1.08,0.00,-0.00,-0.00); trace/3= -0.51                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.878422                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.818903              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.676  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.579121              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.028  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2537      final r-factor (work) = 0.1973          |
| start r-factor (free) = 0.3325      final r-factor (free) = 0.2587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.9966 = 9.82 * 0.50 * 5.8916 + 1.00 * 0.0718                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.5316 = 9.82 * 0.50 * 5.7915 + 1.00 * 0.0984                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1973      final r-factor (work) = 0.1747          |
| start r-factor (free) = 0.2587      final r-factor (free) = 0.2299          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3703 = 0.58 * 1.00 * 5.7915 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2490 = 0.58 * 1.00 * 5.5885 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.16   18.80    None  None   None       |
|    all(noH): 2823   0      0.00    99.16   18.80    None  None   None       |
|    Sol.    : 438    0      5.62    96.07   45.01    None  None   None       |
|    Mac.    : 2385   0      0.00    99.16   13.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.916: 1027   |   5:    49.578 -  59.494:   85        |
|      1:     9.916 -  19.831: 1022   |   6:    59.494 -  69.410:   69        |
|      2:    19.831 -  29.747:  283   |   7:    69.410 -  79.325:   33        |
|      3:    29.747 -  39.663:  139   |   8:    79.325 -  89.241:   23        |
|      4:    39.663 -  49.578:  133   |   9:    89.241 -  99.157:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1747 r_free = 0.2299             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1745 r_free = 0.2299             target_work(ml) = 5.530         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1745   r_free= 0.2299   ksol= 0.32   Bsol= 71.21   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,0.47,-1.08,0.00,-0.00,-0.00); trace/3= -0.51                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.530326                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1743   r_free= 0.2285   ksol= 0.33   Bsol= 64.73   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-0.69,-1.60,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.528810                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.280389              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.627  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.343108              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.150  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1743      final r-factor (work) = 0.1567          |
| start r-factor (free) = 0.2285      final r-factor (free) = 0.2049          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4741 = 2.28 * 0.50 * 5.5917 + 1.00 * 0.0984                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3087 = 2.28 * 0.50 * 5.4842 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1567      final r-factor (work) = 0.1508          |
| start r-factor (free) = 0.2049      final r-factor (free) = 0.1990          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8942 = 0.34 * 1.00 * 5.4842 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8710 = 0.34 * 1.00 * 5.4202 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.11  18.24    None  None   None       |
|    all(noH): 2823   0      0.00    101.11  18.24    None  None   None       |
|    Sol.    : 438    0      5.19    98.02   44.76    None  None   None       |
|    Mac.    : 2385   0      0.00    101.11  13.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.111: 1071   |   5:    50.555 -  60.666:   94        |
|      1:    10.111 -  20.222: 1059   |   6:    60.666 -  70.776:   56        |
|      2:    20.222 -  30.333:  245   |   7:    70.776 -  80.887:   33        |
|      3:    30.333 -  40.444:  117   |   8:    80.887 -  90.998:   17        |
|      4:    40.444 -  50.555:  124   |   9:    90.998 - 101.109:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1508 r_free = 0.1990             target_work(ml) = 5.408         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1507 r_free = 0.1988             target_work(ml) = 5.408         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1507   r_free= 0.1988   ksol= 0.33   Bsol= 64.73   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-0.69,-1.60,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.407579                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6838 0.99   1470  166 0.1068 0.1364      5.4659      5.6485|
|  2:  4.6838 -  3.7362 0.99   1411  154 0.1015 0.1263      5.5684      5.7924|
|  3:  3.7362 -  3.2693 0.99   1378  148 0.1385 0.1986       5.683      6.0162|
|  4:  3.2693 -  2.9729 0.98   1369  161 0.1780 0.1984       5.718      5.8478|
|  5:  2.9729 -  2.7612 0.99   1385  150 0.1859 0.2206      5.6078      5.7239|
|  6:  2.7612 -  2.5992 0.99   1354  158 0.1667 0.2505       5.476      5.6693|
|  7:  2.5992 -  2.4697 0.98   1354  137 0.1719 0.2147      5.4291      5.6167|
|  8:  2.4697 -  2.3626 0.98   1339  151 0.1771 0.2172      5.3765      5.5819|
|  9:  2.3626 -  2.2719 0.99   1353  152 0.1700 0.2484      5.3052      5.5169|
| 10:  2.2719 -  2.1938 0.99   1342  159 0.1620 0.2232      5.2605      5.4844|
| 11:  2.1938 -  2.1254 0.97   1348  137 0.1542 0.2135      5.1687      5.3894|
| 12:  2.1254 -  2.0648 0.98   1324  150 0.1621 0.2577      5.1346       5.399|
| 13:  2.0648 -  2.0105 0.72    956  116 0.1620 0.2075      5.0508      5.2554|
| 14:  2.0105 -  1.9616 0.18    247   20 0.1604 0.1965      4.9455      5.1907|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6838  1470   166  0.93  10.28   0.96     0.93       8476.39|
|  2:  4.6838 -  3.7362  1411   154  0.94   9.77   1.01     0.99      11246.19|
|  3:  3.7362 -  3.2693  1378   148  0.91  14.99   1.03     1.02      14791.04|
|  4:  3.2693 -  2.9729  1369   161  0.87  19.39   1.01     0.98      16628.42|
|  5:  2.9729 -  2.7612  1385   150  0.84  22.32   1.01     0.99      14673.87|
|  6:  2.7612 -  2.5992  1354   158  0.85  21.93   1.00     0.96      12395.75|
|  7:  2.5992 -  2.4697  1354   137  0.86  21.06   0.99     0.94      10187.07|
|  8:  2.4697 -  2.3626  1339   151  0.84  22.41   1.01     0.97      10057.79|
|  9:  2.3626 -  2.2719  1353   152  0.85  21.88   1.00     0.94       8323.64|
| 10:  2.2719 -  2.1938  1342   159  0.85  21.64   0.99     0.93       7949.94|
| 11:  2.1938 -  2.1254  1348   137  0.86  21.07   0.99     0.94       6894.63|
| 12:  2.1254 -  2.0648  1324   150  0.85  22.42   0.99     0.95       6831.25|
| 13:  2.0648 -  2.0105   956   116  0.84  23.12   0.99     0.98       5886.31|
| 14:  2.0105 -  1.9616   247    20  0.83  22.81   0.98     0.95       4655.32|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     4655.32 max =        16628.42 mean =     10373.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           90.00 mean =        19.27|
|phase err.(test): min =        0.00 max =           89.58 mean =        18.48|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1511   r_free= 0.1999   ksol= 0.33   Bsol= 69.59   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-1.18,-1.82,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.410712                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1511   r_free= 0.1999   ksol= 0.33   Bsol= 69.59   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-1.18,-1.82,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.410712                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6838 0.99   1470  166 0.1086 0.1422      5.4888      5.6771|
|  2:  4.6838 -  3.7362 0.99   1411  154 0.1026 0.1288      5.5816        5.81|
|  3:  3.7362 -  3.2693 0.99   1378  148 0.1390 0.1981      5.6896      6.0107|
|  4:  3.2693 -  2.9729 0.98   1369  161 0.1778 0.1985      5.7187      5.8492|
|  5:  2.9729 -  2.7612 0.99   1385  150 0.1858 0.2213      5.6075      5.7267|
|  6:  2.7612 -  2.5992 0.99   1354  158 0.1666 0.2500      5.4756      5.6676|
|  7:  2.5992 -  2.4697 0.98   1354  137 0.1715 0.2148      5.4273      5.6159|
|  8:  2.4697 -  2.3626 0.98   1339  151 0.1769 0.2171      5.3756      5.5821|
|  9:  2.3626 -  2.2719 0.99   1353  152 0.1697 0.2484      5.3039      5.5157|
| 10:  2.2719 -  2.1938 0.99   1342  159 0.1620 0.2236      5.2602      5.4857|
| 11:  2.1938 -  2.1254 0.97   1348  137 0.1541 0.2134       5.168      5.3885|
| 12:  2.1254 -  2.0648 0.98   1324  150 0.1621 0.2581      5.1353      5.4011|
| 13:  2.0648 -  2.0105 0.72    956  116 0.1619 0.2074      5.0505      5.2545|
| 14:  2.0105 -  1.9616 0.18    247   20 0.1604 0.1959      4.9449      5.1852|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6838  1470   166  0.93  10.88   0.95     0.93       9106.48|
|  2:  4.6838 -  3.7362  1411   154  0.94  10.09   1.01     0.99      11828.27|
|  3:  3.7362 -  3.2693  1378   148  0.90  15.18   1.02     1.02      15131.94|
|  4:  3.2693 -  2.9729  1369   161  0.87  19.40   1.00     0.98      16672.14|
|  5:  2.9729 -  2.7612  1385   150  0.84  22.30   1.00     0.98      14661.14|
|  6:  2.7612 -  2.5992  1354   158  0.85  21.90   0.99     0.95      12374.45|
|  7:  2.5992 -  2.4697  1354   137  0.86  21.01   0.98     0.93      10155.29|
|  8:  2.4697 -  2.3626  1339   151  0.84  22.37   1.00     0.95      10039.60|
|  9:  2.3626 -  2.2719  1353   152  0.85  21.86   0.99     0.92       8322.95|
| 10:  2.2719 -  2.1938  1342   159  0.85  21.62   0.97     0.91       7947.67|
| 11:  2.1938 -  2.1254  1348   137  0.86  21.05   0.98     0.92       6892.60|
| 12:  2.1254 -  2.0648  1324   150  0.85  22.43   0.97     0.93       6844.43|
| 13:  2.0648 -  2.0105   956   116  0.84  23.11   0.97     0.96       5879.62|
| 14:  2.0105 -  1.9616   247    20  0.83  22.79   0.97     0.93       4638.36|
|alpha:            min =        0.91 max =            1.02 mean =         0.95|
|beta:             min =     4638.36 max =        16672.14 mean =     10496.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.98 mean =        19.34|
|phase err.(test): min =        0.00 max =           89.93 mean =        18.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.11  18.25    None  None   None       |
|    all(noH): 2823   0      0.00    101.11  18.25    None  None   None       |
|    Sol.    : 438    0      5.19    98.02   44.76    None  None   None       |
|    Mac.    : 2385   0      0.00    101.11  13.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.114: 1071   |   5:    50.558 -  60.668:   94        |
|      1:    10.114 -  20.225: 1059   |   6:    60.668 -  70.779:   56        |
|      2:    20.225 -  30.336:  245   |   7:    70.779 -  80.890:   33        |
|      3:    30.336 -  40.447:  117   |   8:    80.890 -  91.001:   17        |
|      4:    40.447 -  50.558:  124   |   9:    91.001 - 101.112:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 356         
Filter by distance & map next to the model:
   mapped sites are within: 0.724 - 5.969
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 355 from: 356
   mapped sites are within: 0.724 - 5.969

peak=    7.331 closest distance to " O   HOH Z  41 " =    1.510
peak=    6.692 closest distance to " O   HOH Z 400 " =    1.193
peak=    6.623 closest distance to " O   ARG A 275 " =    0.892
peak=    5.868 closest distance to " O   HOH Z 130 " =    1.099
peak=    5.708 closest distance to " CG  GLN A  77 " =    1.038
peak=    5.667 closest distance to " O   HOH Z 426 " =    1.372
peak=    5.656 closest distance to " O   HOH Z 120 " =    1.216
peak=    5.653 closest distance to " O   HOH Z 159 " =    1.251
peak=    5.597 closest distance to " N   ARG A 275 " =    0.946
peak=    5.381 closest distance to " CB  GLN A  73 " =    1.151
peak=    5.373 closest distance to " NE2 HIS A 115 " =    1.036
peak=    5.217 closest distance to " NH2BARG A 102 " =    1.161
peak=    5.168 closest distance to " OG  SER A 276 " =    0.932
peak=    5.009 closest distance to " N   GLU A 277 " =    1.115
peak=    4.920 closest distance to " OD2 ASP A  65 " =    1.208
peak=    4.903 closest distance to " CG  PRO A  54 " =    1.267
peak=    4.856 closest distance to " CB  ARG A 275 " =    0.998
peak=    4.790 closest distance to " CB  SER A  63 " =    1.467
peak=    4.752 closest distance to " CG  PRO A 280 " =    1.024
peak=    4.725 closest distance to " O   HOH Z 342 " =    0.936
peak=    4.706 closest distance to " O   HOH Z  61 " =    1.619
peak=    4.699 closest distance to " NH2 ARG A  56 " =    2.120
peak=    4.598 closest distance to " NH2AARG A 145 " =    1.048
peak=    4.598 closest distance to " CB  SER A  62 " =    1.093
peak=    4.583 closest distance to " O   VAL A  72 " =    1.071
peak=    4.561 closest distance to " CB  ASN A 285 " =    0.968
peak=    4.515 closest distance to " CA  TYR A  30 " =    1.119
peak=    4.512 closest distance to " CD BLYS A 290 " =    0.995
peak=    4.496 closest distance to " O   HOH Z 404 " =    1.542
peak=    4.479 closest distance to " O   HOH Z 210 " =    1.716
peak=    4.444 closest distance to " O   HOH Z 124 " =    1.487
peak=    4.420 closest distance to " O   HOH Z 117 " =    1.447
peak=    4.410 closest distance to " O   HOH Z 126 " =    2.256
peak=    4.372 closest distance to " O   HOH Z 272 " =    1.555
peak=    4.368 closest distance to " CG  PRO A 198 " =    1.459
peak=    4.339 closest distance to " OD1 ASP A 238 " =    0.962
peak=    4.331 closest distance to " CB  GLU A 277 " =    1.003
peak=    4.328 closest distance to " O   HOH Z  83 " =    1.220
peak=    4.283 closest distance to " CG  PRO A  90 " =    1.268
peak=    4.280 closest distance to " O   HOH Z  80 " =    2.397
peak=    4.279 closest distance to " CB  TRP A 179 " =    1.476
peak=    4.263 closest distance to " O   HOH Z 433 " =    2.146
peak=    4.261 closest distance to " O   HOH Z 221 " =    1.380
peak=    4.259 closest distance to " O   HOH Z 335 " =    1.052
peak=    4.243 closest distance to " O   HOH Z 182 " =    1.446
peak=    4.243 closest distance to " CB  PRO A 198 " =    0.997
peak=    4.237 closest distance to " CG AARG A 275 " =    1.092
peak=    4.233 closest distance to " CB  GLN A 223 " =    1.371
peak=    4.230 closest distance to " O   HOH Z  78 " =    2.161
peak=    4.229 closest distance to " CD  ARG A 269 " =    0.929
peak=    4.225 closest distance to " O   HOH Z 422 " =    1.347
peak=    4.218 closest distance to " CA  VAL A  41 " =    0.752
peak=    4.210 closest distance to " O   HOH Z 431 " =    1.535
peak=    4.202 closest distance to " N   VAL A 121 " =    0.776
peak=    4.198 closest distance to " NH1 ARG A 269 " =    0.938
peak=    4.188 closest distance to " O   HOH Z 127 " =    1.341
peak=    4.181 closest distance to " CB  PHE A  61 " =    0.880
peak=    4.177 closest distance to " OE1 GLN A  11 " =    2.084
peak=    4.174 closest distance to " O   HOH Z 103 " =    0.976
peak=    4.161 closest distance to " O   PRO A 198 " =    1.600
peak=    4.147 closest distance to " CB  SER A 276 " =    1.156
peak=    4.144 closest distance to " O   HOH Z  15 " =    1.977
peak=    4.122 closest distance to " O   HOH Z 102 " =    1.238
peak=    4.118 closest distance to " OE1 GLN A  77 " =    1.094
peak=    4.108 closest distance to " O   GLN A  55 " =    0.858
peak=    4.107 closest distance to " O   HOH Z 350 " =    1.158
peak=    4.063 closest distance to " O   HOH Z  97 " =    1.890
peak=    4.057 closest distance to " CB  ALA A   1 " =    1.487
peak=    4.053 closest distance to " O   HOH Z 203 " =    1.823
peak=    4.046 closest distance to " CG2BVAL A  41 " =    1.225
peak=    4.042 closest distance to " NE2 GLN A  89 " =    1.266
peak=    4.036 closest distance to " O   HOH Z 234 " =    3.718
peak=    4.029 closest distance to " CB  MET A  47 " =    1.052
peak=    4.026 closest distance to " O   HOH Z 272 " =    2.068
peak=    4.012 closest distance to " CB  SER A  26 " =    0.955
peak=    4.005 closest distance to " O   HOH Z 193 " =    1.994
peak=    4.000 closest distance to " O   HOH Z   4 " =    1.371
peak=    3.989 closest distance to " CG1 VAL A 153 " =    1.234
peak=    3.985 closest distance to " O   HOH Z 411 " =    1.475
peak=    3.973 closest distance to " O   HOH Z 214 " =    1.461
peak=    3.973 closest distance to " O   HOH Z 207 " =    2.097
peak=    3.968 closest distance to " CA  ALA A 100 " =    1.153
peak=    3.963 closest distance to " CD1 TRP A 274 " =    1.067
peak=    3.960 closest distance to " O   HOH Z 142 " =    1.800
peak=    3.956 closest distance to " O   HOH Z 398 " =    1.607
peak=    3.955 closest distance to " O   HOH Z 371 " =    3.271
peak=    3.951 closest distance to " O   HOH Z 192 " =    1.525
peak=    3.949 closest distance to " CG1 ILE A 120 " =    1.161
peak=    3.948 closest distance to " O   HOH Z 132 " =    1.937
peak=    3.947 closest distance to " O   HOH Z 261 " =    1.433
peak=    3.942 closest distance to " CA  GLY A 196 " =    0.978
peak=    3.937 closest distance to " O   HOH Z  89 " =    3.563
peak=    3.923 closest distance to " O   HOH Z 411 " =    2.955
peak=    3.922 closest distance to " N   ILE A  33 " =    1.167
peak=    3.919 closest distance to " CB  TRP A 179 " =    1.625
peak=    3.917 closest distance to " CB  SER A  28 " =    1.071
peak=    3.910 closest distance to " NH2 ARG A 156 " =    1.210
peak=    3.889 closest distance to " CG1 ILE A  33 " =    1.362
peak=    3.883 closest distance to " CB  TYR A 247 " =    1.144
peak=    3.877 closest distance to " O   HOH Z 139 " =    4.390
peak=    3.873 closest distance to " CG  PRO A 213 " =    1.334
peak=    3.862 closest distance to " O   ARG A  56 " =    1.107
peak=    3.850 closest distance to " O   HOH Z 211 " =    1.493
peak=    3.847 closest distance to " O   GLN A  11 " =    0.941
peak=    3.839 closest distance to " O   HOH Z  54 " =    1.120
peak=    3.838 closest distance to " NH1AARG A 145 " =    1.153
peak=    3.835 closest distance to " O   HOH Z  47 " =    1.835
peak=    3.828 closest distance to " O   HOH Z 133 " =    1.767
peak=    3.823 closest distance to " O   HOH Z 189 " =    2.183
peak=    3.821 closest distance to " CB  ALA A 137 " =    1.363
peak=    3.821 closest distance to " OH  TYR A  68 " =    1.246
peak=    3.817 closest distance to " O   HOH Z 406 " =    1.674
peak=    3.813 closest distance to " N   LYS A 166 " =    0.882
peak=    3.811 closest distance to " CG  PRO A 243 " =    1.266
peak=    3.801 closest distance to " O   HOH Z  39 " =    2.372
peak=    3.794 closest distance to " OD1 ASN A 217 " =    1.655
peak=    3.790 closest distance to " N   ASN A  39 " =    1.246
peak=    3.789 closest distance to " O   GLY A  57 " =    1.065
peak=    3.788 closest distance to " O   HOH Z 258 " =    2.009
peak=    3.786 closest distance to " O   HOH Z 428 " =    1.211
peak=    3.770 closest distance to " CD  GLN A  77 " =    1.352
peak=    3.759 closest distance to " O   HOH Z  68 " =    1.824
peak=    3.759 closest distance to " CA  ARG A 102 " =    1.385
peak=    3.753 closest distance to " CB  TRP A 266 " =    1.015
peak=    3.740 closest distance to " O   PHE A  61 " =    0.931
peak=    3.730 closest distance to " CA  GLN A 223 " =    0.837
peak=    3.727 closest distance to " O   HOH Z 174 " =    1.556
peak=    3.723 closest distance to " CG2 VAL A  78 " =    0.984
peak=    3.722 closest distance to " CZ3 TRP A 274 " =    4.868
peak=    3.718 closest distance to " CB  ASP A 132 " =    3.864
peak=    3.713 closest distance to " CB  PRO A  54 " =    0.844
peak=    3.708 closest distance to " CB  GLN A 194 " =    0.932
peak=    3.705 closest distance to " O   HOH Z 215 " =    1.528
peak=    3.702 closest distance to " CD  LYS A 119 " =    1.214
peak=    3.692 closest distance to " CB  SER A 141 " =    1.032
peak=    3.692 closest distance to " NH1 ARG A  36 " =    1.178
peak=    3.687 closest distance to " O   HOH Z 272 " =    1.527
peak=    3.678 closest distance to " O   HOH Z 250 " =    1.595
peak=    3.675 closest distance to " O   HOH Z  49 " =    1.074
peak=    3.672 closest distance to " O   HOH Z 131 " =    0.997
peak=    3.672 closest distance to " CB  PHE A  16 " =    1.473
peak=    3.671 closest distance to " O   SER A 276 " =    1.101
peak=    3.656 closest distance to " CA  TRP A 274 " =    0.973
peak=    3.652 closest distance to " CG  TRP A 150 " =    1.101
peak=    3.647 closest distance to " N   GLN A  55 " =    0.864
peak=    3.641 closest distance to " O   HOH Z 394 " =    1.643
peak=    3.627 closest distance to " N   PHE A  61 " =    0.724
peak=    3.621 closest distance to " O   HOH Z 292 " =    1.643
peak=    3.619 closest distance to " O  BHOH Z 338 " =    1.087
peak=    3.616 closest distance to " CB  LYS A  76 " =    1.100
peak=    3.614 closest distance to " CZ  PHE A 192 " =    1.060
peak=    3.604 closest distance to " OG  SER A  97 " =    3.438
peak=    3.603 closest distance to " CB  ASP A  65 " =    0.991
peak=    3.601 closest distance to " CB  ASN A 187 " =    1.187
peak=    3.597 closest distance to " O   HOH Z 134 " =    2.443
peak=    3.592 closest distance to " O   HOH Z 108 " =    2.394
peak=    3.589 closest distance to " O   HOH Z 117 " =    2.247
peak=    3.588 closest distance to " O   HOH Z 324 " =    1.723
peak=    3.586 closest distance to " O   HOH Z 387 " =    2.454
peak=    3.582 closest distance to " CG2 VAL A 197 " =    1.329
peak=    3.574 closest distance to " CB  TYR A 116 " =    1.642
peak=    3.572 closest distance to " O   HOH Z 327 " =    2.635
peak=    3.571 closest distance to " OD2 ASP A 286 " =    2.205
peak=    3.560 closest distance to " CB  GLN A  58 " =    1.054
peak=    3.555 closest distance to " CE  MET A 188 " =    1.520
peak=    3.552 closest distance to " CB  ARG A 190 " =    1.779
peak=    3.548 closest distance to " CB  TRP A 123 " =    1.460
peak=    3.547 closest distance to " OG BSER A 258 " =    1.199
peak=    3.546 closest distance to " O   HOH Z 352 " =    1.414
peak=    3.546 closest distance to " O   HOH Z 163 " =    1.897
peak=    3.544 closest distance to " O   VAL A 121 " =    0.980
peak=    3.541 closest distance to " CG1BVAL A 121 " =    1.242
peak=    3.541 closest distance to " CB  MET A 113 " =    1.491
peak=    3.540 closest distance to " O   HOH Z  63 " =    1.358
peak=    3.539 closest distance to " N   GLY A  75 " =    3.501
peak=    3.538 closest distance to " O   HOH Z 369 " =    2.306
peak=    3.537 closest distance to " O   HOH Z  47 " =    1.787
peak=    3.534 closest distance to " O   HOH Z  98 " =    2.148
peak=    3.532 closest distance to " N   ASP A 286 " =    1.124
peak=    3.527 closest distance to " OD2 ASP A  50 " =    1.259
peak=    3.526 closest distance to " CD2 TYR A  68 " =    1.065
peak=    3.524 closest distance to " CA  ARG A 195 " =    1.087
peak=    3.520 closest distance to " CB  GLU A 175 " =    1.314
peak=    3.513 closest distance to " CA  ILE A 120 " =    1.256
peak=    3.508 closest distance to " O   HOH Z 410 " =    1.492
peak=    3.504 closest distance to " N   SER A 164 " =    0.997
peak=    3.494 closest distance to " O   HOH Z 344 " =    3.552
peak=    3.489 closest distance to " O   HOH Z 225 " =    2.182
peak=    3.481 closest distance to " O   HOH Z 200 " =    4.035
peak=    3.480 closest distance to " ND2 ASN A 209 " =    1.429
peak=    3.479 closest distance to " CB  GLU A 128 " =    1.114
peak=    3.478 closest distance to " CB  ASN A  69 " =    1.014
peak=    3.478 closest distance to " CZ  PHE A 218 " =    1.018
peak=    3.476 closest distance to " O   HOH Z 389 " =    1.786
peak=    3.468 closest distance to " CD  GLN A  88 " =    0.884
peak=    3.465 closest distance to " CA  GLY A 267 " =    1.695
peak=    3.463 closest distance to " ND2 ASN A 285 " =    1.093
peak=    3.457 closest distance to " CB  GLN A  88 " =    1.254
peak=    3.446 closest distance to " N   ALA A 100 " =    0.837
peak=    3.444 closest distance to " O   HOH Z  44 " =    1.632
peak=    3.438 closest distance to " O   HOH Z  47 " =    1.490
peak=    3.437 closest distance to " OG  SER A 245 " =    1.619
peak=    3.435 closest distance to " O   HOH Z 217 " =    1.470
peak=    3.434 closest distance to " CG2 THR A 221 " =    1.177
peak=    3.430 closest distance to " O   HOH Z  66 " =    2.063
peak=    3.429 closest distance to " O   HOH Z  43 " =    1.979
peak=    3.426 closest distance to " CA  ARG A 139 " =    1.508
peak=    3.426 closest distance to " OG ASER A 210 " =    0.913
peak=    3.416 closest distance to " O   HOH Z 418 " =    1.706
peak=    3.413 closest distance to " O   HOH Z 427 " =    3.620
peak=    3.413 closest distance to " CB  PRO A  90 " =    1.489
peak=    3.413 closest distance to " CB  ASN A 148 " =    2.106
peak=    3.407 closest distance to " O   HOH Z 420 " =    5.720
peak=    3.403 closest distance to " O   HOH Z 437 " =    1.740
peak=    3.403 closest distance to " CA  ARG A  36 " =    1.151
peak=    3.398 closest distance to " O   HOH Z 132 " =    1.525
peak=    3.397 closest distance to " NH1 ARG A  56 " =    1.798
peak=    3.396 closest distance to " O   HOH Z 196 " =    2.568
peak=    3.394 closest distance to " O   HOH Z  14 " =    1.830
peak=    3.393 closest distance to " O   HOH Z  22 " =    2.133
peak=    3.393 closest distance to " CB  ARG A 269 " =    0.993
peak=    3.393 closest distance to " CB  VAL A 202 " =    1.423
peak=    3.392 closest distance to " CD2 LEU A 255 " =    1.225
peak=    3.392 closest distance to " CA  GLU A 152 " =    1.028
peak=    3.387 closest distance to " O   HOH Z 332 " =    1.098
peak=    3.387 closest distance to " CA  GLN A  11 " =    1.567
peak=    3.385 closest distance to " CA  ILE A 263 " =    1.058
peak=    3.385 closest distance to " CG ALYS A 290 " =    1.330
peak=    3.378 closest distance to " OE1 GLU A 277 " =    1.530
peak=    3.377 closest distance to " O   HOH Z   1 " =    3.129
peak=    3.373 closest distance to " O   HOH Z 358 " =    1.706
peak=    3.372 closest distance to " O   HOH Z 343 " =    2.257
peak=    3.369 closest distance to " CB  ILE A 199 " =    0.977
peak=    3.368 closest distance to " O   HOH Z 368 " =    3.123
peak=    3.368 closest distance to " CB  SER A 273 " =    0.805
peak=    3.367 closest distance to " CE BMET A  47 " =    1.287
peak=    3.361 closest distance to " O   HOH Z 128 " =    2.239
peak=    3.361 closest distance to " CB  ASP A 140 " =    0.812
peak=    3.360 closest distance to " C   GLY A  80 " =    1.211
peak=    3.358 closest distance to " O   ILE A 106 " =    1.823
peak=    3.345 closest distance to " CB  ALA A 129 " =    0.987
peak=    3.345 closest distance to " O   HOH Z  87 " =    2.225
peak=    3.344 closest distance to " CB  ASN A 217 " =    1.014
peak=    3.342 closest distance to " CA  ALA A  21 " =    1.654
peak=    3.342 closest distance to " CG2 VAL A 112 " =    1.365
peak=    3.339 closest distance to " CD  LYS A 166 " =    1.699
peak=    3.336 closest distance to " O   HOH Z 363 " =    1.211
peak=    3.336 closest distance to " NH2AARG A 190 " =    1.571
peak=    3.335 closest distance to " O   SER A 164 " =    1.532
peak=    3.332 closest distance to " CB  MET A 105 " =    1.208
peak=    3.328 closest distance to " O   HOH Z 149 " =    2.084
peak=    3.325 closest distance to " O   LYS A 289 " =    1.103
peak=    3.324 closest distance to " O   GLY A  91 " =    1.275
peak=    3.319 closest distance to " O   HOH Z 108 " =    1.537
peak=    3.310 closest distance to " O   HOH Z  50 " =    3.443
peak=    3.309 closest distance to " CB  ALA A 244 " =    1.079
peak=    3.308 closest distance to " CG2AVAL A 121 " =    1.821
peak=    3.308 closest distance to " NZ  LYS A 117 " =    3.040
peak=    3.306 closest distance to " O   HOH Z 118 " =    2.123
peak=    3.306 closest distance to " CA  ALA A 295 " =    1.004
peak=    3.305 closest distance to " CA  ARG A  66 " =    1.062
peak=    3.304 closest distance to " CA  ALA A 248 " =    1.251
peak=    3.304 closest distance to " OH  TYR A 247 " =    1.100
peak=    3.301 closest distance to " O   HOH Z 295 " =    2.473
peak=    3.300 closest distance to " O   HOH Z 145 " =    2.125
peak=    3.297 closest distance to " O   HOH Z 162 " =    2.536
peak=    3.297 closest distance to " CA  ASP A 191 " =    0.842
peak=    3.296 closest distance to " CG2 THR A 220 " =    0.750
peak=    3.295 closest distance to " O   HOH Z 207 " =    1.692
peak=    3.295 closest distance to " CB  ASN A 127 " =    0.736
peak=    3.291 closest distance to " O   HOH Z 132 " =    2.327
peak=    3.289 closest distance to " CA  SER A  87 " =    0.820
peak=    3.289 closest distance to " O   HOH Z 172 " =    5.969
peak=    3.287 closest distance to " CA  GLY A   6 " =    0.953
peak=    3.286 closest distance to " O   HOH Z 414 " =    1.631
peak=    3.282 closest distance to " CD  ARG A 159 " =    0.802
peak=    3.281 closest distance to " CD1 LEU A  96 " =    0.826
peak=    3.277 closest distance to " O   HOH Z 112 " =    1.489
peak=    3.275 closest distance to " CB  TYR A  30 " =    1.247
peak=    3.275 closest distance to " CD  ARG A  24 " =    1.572
peak=    3.273 closest distance to " CA  ASP A 149 " =    1.634
peak=    3.263 closest distance to " O   THR A 251 " =    1.298
peak=    3.260 closest distance to " O   HOH Z 202 " =    2.421
peak=    3.257 closest distance to " CA  TRP A  85 " =    1.020
peak=    3.253 closest distance to " O   HOH Z 194 " =    1.959
peak=    3.246 closest distance to " O   HOH Z 184 " =    1.273
peak=    3.245 closest distance to " CG  PHE A 283 " =    1.070
peak=    3.241 closest distance to " CA  ASP A 124 " =    0.772
peak=    3.241 closest distance to " O   HOH Z 250 " =    1.964
peak=    3.240 closest distance to " O   HOH Z  44 " =    2.465
peak=    3.239 closest distance to " O   HOH Z 166 " =    1.601
peak=    3.239 closest distance to " O   HOH Z 316 " =    3.061
peak=    3.238 closest distance to " CG2 THR A  18 " =    0.872
peak=    3.233 closest distance to " CG  GLU A 277 " =    3.018
peak=    3.233 closest distance to " N   VAL A 268 " =    1.320
peak=    3.232 closest distance to " NH1BARG A 145 " =    1.899
peak=    3.230 closest distance to " O   HOH Z  37 " =    1.045
peak=    3.229 closest distance to " N   ASN A  74 " =    0.966
peak=    3.228 closest distance to " CB  VAL A 257 " =    1.077
peak=    3.226 closest distance to " CB  ASN A 148 " =    1.406
peak=    3.218 closest distance to " O   HOH Z 287 " =    1.826
peak=    3.217 closest distance to " O   HOH Z  97 " =    2.469
peak=    3.216 closest distance to " NZ  LYS A  76 " =    1.027
peak=    3.215 closest distance to " CA  ALA A  43 " =    1.348
peak=    3.214 closest distance to " CB  GLN A 240 " =    1.762
peak=    3.209 closest distance to " CD  ARG A  66 " =    3.082
peak=    3.209 closest distance to " CB  GLU A 152 " =    1.207
peak=    3.207 closest distance to " O   HOH Z 271 " =    1.194
peak=    3.206 closest distance to " CG2 ILE A 120 " =    0.968
peak=    3.197 closest distance to " O   HOH Z  20 " =    4.008
peak=    3.188 closest distance to " O   HOH Z  54 " =    2.091
peak=    3.187 closest distance to " O   HOH Z  22 " =    1.112
peak=    3.185 closest distance to " CG2 ILE A 106 " =    1.102
peak=    3.184 closest distance to " CA  LEU A 282 " =    1.164
peak=    3.182 closest distance to " O   HOH Z  91 " =    2.387
peak=    3.182 closest distance to " CB  ALA A 256 " =    1.307
peak=    3.177 closest distance to " O   HOH Z 380 " =    1.975
peak=    3.176 closest distance to " O   HOH Z   7 " =    1.427
peak=    3.172 closest distance to " O   HOH Z 299 " =    1.690
peak=    3.168 closest distance to " O   HOH Z 368 " =    1.639
peak=    3.168 closest distance to " O   HOH Z 432 " =    1.718
peak=    3.164 closest distance to " O   HOH Z  52 " =    1.428
peak=    3.159 closest distance to " CG2 ILE A  49 " =    2.196
peak=    3.158 closest distance to " CB  ALA A  71 " =    1.269
peak=    3.148 closest distance to " CE2 TYR A 293 " =    1.071
peak=    3.146 closest distance to " OG1 THR A 157 " =    1.005
peak=    3.146 closest distance to " CB  ALA A 114 " =    1.203
peak=    3.139 closest distance to " ND1 HIS A  81 " =    1.471
peak=    3.138 closest distance to " O   HOH Z   4 " =    2.037
peak=    3.135 closest distance to " O   HOH Z 297 " =    1.214
peak=    3.133 closest distance to " N   TYR A 116 " =    1.899
peak=    3.130 closest distance to " O   HOH Z 172 " =    1.990
peak=    3.130 closest distance to " CD1 ILE A 120 " =    1.080
peak=    3.130 closest distance to " CB  ALA A 248 " =    1.307
peak=    3.122 closest distance to " O   SER A 273 " =    1.078
peak=    3.118 closest distance to " O   HOH Z 417 " =    3.334
peak=    3.115 closest distance to " O   HOH Z 329 " =    2.779
peak=    3.114 closest distance to " NE  ARG A 138 " =    1.079
peak=    3.112 closest distance to " CA  ILE A  33 " =    1.642
peak=    3.102 closest distance to " OE1 GLU A 175 " =    1.081
peak=    3.099 closest distance to " CD  LYS A 289 " =    1.039
peak=    3.098 closest distance to " O   HOH Z 151 " =    1.753
peak=    3.092 closest distance to " CE1 TYR A 116 " =    1.230
peak=    3.083 closest distance to " O   HOH Z 214 " =    2.085
peak=    3.083 closest distance to " CB ASER A 164 " =    0.945
peak=    3.081 closest distance to " CA  SER A  12 " =    1.290
peak=    3.077 closest distance to " O   HOH Z 211 " =    1.456
peak=    3.076 closest distance to " O   GLY A  23 " =    2.629
peak=    3.063 closest distance to " CA  ASP A 270 " =    1.141
peak=    3.058 closest distance to " O   HOH Z 259 " =    1.929
peak=    3.049 closest distance to " O   HOH Z 250 " =    1.046
peak=    3.038 closest distance to " CG1 ILE A  49 " =    1.659
peak=    3.036 closest distance to " O   HOH Z 200 " =    1.208
peak=    3.007 closest distance to " CA  LYS A 166 " =    1.269
peak=    3.007 closest distance to " O   HOH Z 237 " =    2.134

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.512 - 5.668
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 209
   mapped sites are within: 0.761 - 5.668

peak=   -5.399 closest distance to " N   ARG A 275 " =    0.772
peak=   -5.036 closest distance to " CB  SER A 276 " =    1.004
peak=   -4.473 closest distance to " C   ASN A 285 " =    2.465
peak=   -4.410 closest distance to " NH2 ARG A  66 " =    0.934
peak=   -4.347 closest distance to " N   ARG A 275 " =    1.038
peak=   -4.257 closest distance to " O   HOH Z 198 " =    1.419
peak=   -4.209 closest distance to " O   HOH Z 166 " =    1.523
peak=   -4.175 closest distance to " O   HOH Z 151 " =    1.416
peak=   -4.168 closest distance to " O   HOH Z 411 " =    4.515
peak=   -4.163 closest distance to " OG  SER A  32 " =    1.088
peak=   -4.153 closest distance to " O   GLN A  55 " =    1.123
peak=   -4.136 closest distance to " O   HOH Z  52 " =    1.807
peak=   -4.133 closest distance to " CD  LYS A 289 " =    2.405
peak=   -4.129 closest distance to " O   HOH Z 222 " =    1.252
peak=   -4.121 closest distance to " CA  GLU A 277 " =    1.026
peak=   -4.112 closest distance to " N   VAL A  72 " =    1.040
peak=   -4.072 closest distance to " O   TYR A  15 " =    1.376
peak=   -4.039 closest distance to " CA  SER A 276 " =    1.224
peak=   -4.029 closest distance to " CD2 PHE A  59 " =    2.325
peak=   -4.013 closest distance to " O   VAL A 121 " =    0.880
peak=   -3.996 closest distance to " CE2 TRP A  85 " =    1.125
peak=   -3.984 closest distance to " CB  ALA A 161 " =    2.638
peak=   -3.976 closest distance to " O   HOH Z  38 " =    0.861
peak=   -3.967 closest distance to " N   ARG A 275 " =    1.140
peak=   -3.966 closest distance to " O   HOH Z  53 " =    2.427
peak=   -3.958 closest distance to " O   ARG A 275 " =    1.026
peak=   -3.956 closest distance to " C   SER A 271 " =    1.263
peak=   -3.930 closest distance to " CB  LEU A 167 " =    2.033
peak=   -3.915 closest distance to " O   HOH Z  13 " =    1.349
peak=   -3.902 closest distance to " CA  VAL A 197 " =    1.042
peak=   -3.871 closest distance to " CD2 LEU A 237 " =    2.476
peak=   -3.863 closest distance to " CG2BVAL A  41 " =    2.636
peak=   -3.830 closest distance to " O   HOH Z 400 " =    0.805
peak=   -3.830 closest distance to " CG2 ILE A  49 " =    2.596
peak=   -3.829 closest distance to " N   ALA A  43 " =    2.524
peak=   -3.828 closest distance to " O   HOH Z  37 " =    1.303
peak=   -3.814 closest distance to " CG  GLU A   2 " =    1.302
peak=   -3.811 closest distance to " O   HOH Z 186 " =    1.251
peak=   -3.805 closest distance to " N   ASP A 286 " =    1.132
peak=   -3.789 closest distance to " O   HOH Z 335 " =    0.992
peak=   -3.783 closest distance to " O   HOH Z 426 " =    0.818
peak=   -3.777 closest distance to " CD  GLN A  77 " =    0.862
peak=   -3.757 closest distance to " O   HOH Z 184 " =    0.849
peak=   -3.754 closest distance to " O   ALA A   1 " =    2.262
peak=   -3.750 closest distance to " CG  GLN A  58 " =    1.162
peak=   -3.743 closest distance to " CG  ASP A 231 " =    0.761
peak=   -3.732 closest distance to " O   HOH Z 221 " =    1.062
peak=   -3.731 closest distance to " SD  MET A  93 " =    1.448
peak=   -3.728 closest distance to " CD  GLN A  88 " =    0.868
peak=   -3.726 closest distance to " O   ALA A 256 " =    1.718
peak=   -3.724 closest distance to " CE  MET A  93 " =    1.325
peak=   -3.723 closest distance to " O   HOH Z  15 " =    1.622
peak=   -3.700 closest distance to " O   HOH Z 351 " =    1.677
peak=   -3.697 closest distance to " CA  ARG A  24 " =    1.283
peak=   -3.696 closest distance to " O   GLN A  11 " =    1.164
peak=   -3.693 closest distance to " C   GLY A  23 " =    2.221
peak=   -3.693 closest distance to " O   HOH Z  86 " =    2.659
peak=   -3.690 closest distance to " O   PHE A 218 " =    1.428
peak=   -3.675 closest distance to " NH2 ARG A  36 " =    1.156
peak=   -3.675 closest distance to " CG  GLN A  73 " =    0.935
peak=   -3.664 closest distance to " O   PRO A 198 " =    1.390
peak=   -3.659 closest distance to " CB  PHE A 130 " =    1.216
peak=   -3.657 closest distance to " O   HOH Z  11 " =    1.053
peak=   -3.654 closest distance to " N   SER A 134 " =    1.188
peak=   -3.640 closest distance to " OE2 GLU A   2 " =    1.649
peak=   -3.634 closest distance to " NH2 ARG A  66 " =    1.727
peak=   -3.623 closest distance to " O   HOH Z 430 " =    1.151
peak=   -3.623 closest distance to " CD2 HIS A 115 " =    1.068
peak=   -3.623 closest distance to " CE  MET A 105 " =    2.196
peak=   -3.613 closest distance to " O   HOH Z 120 " =    0.956
peak=   -3.612 closest distance to " O   HOH Z  83 " =    0.922
peak=   -3.608 closest distance to " O   VAL A  72 " =    0.957
peak=   -3.603 closest distance to " O   HOH Z 418 " =    1.354
peak=   -3.597 closest distance to " N   THR A 235 " =    1.172
peak=   -3.597 closest distance to " O   HOH Z 159 " =    0.861
peak=   -3.596 closest distance to " OG BSER A 258 " =    2.188
peak=   -3.590 closest distance to " CD1 PHE A  59 " =    1.878
peak=   -3.582 closest distance to " O   HOH Z 401 " =    1.292
peak=   -3.575 closest distance to " O   HOH Z  71 " =    1.349
peak=   -3.570 closest distance to " O   HOH Z 210 " =    0.937
peak=   -3.552 closest distance to " CD2 TRP A 274 " =    2.307
peak=   -3.546 closest distance to " O   MET A 113 " =    1.048
peak=   -3.531 closest distance to " N   GLN A  55 " =    1.668
peak=   -3.526 closest distance to " CB  TRP A 150 " =    1.694
peak=   -3.522 closest distance to " O   HOH Z 139 " =    3.712
peak=   -3.505 closest distance to " CA  TRP A 274 " =    1.265
peak=   -3.504 closest distance to " O   HOH Z 423 " =    0.940
peak=   -3.496 closest distance to " O   ARG A 275 " =    1.468
peak=   -3.490 closest distance to " O   HOH Z 118 " =    5.668
peak=   -3.480 closest distance to " CA  VAL A  67 " =    2.911
peak=   -3.452 closest distance to " C   LEU A 101 " =    1.107
peak=   -3.449 closest distance to " O   HOH Z  93 " =    1.782
peak=   -3.443 closest distance to " O   VAL A 174 " =    1.964
peak=   -3.434 closest distance to " O   HOH Z 377 " =    1.799
peak=   -3.427 closest distance to " O   HOH Z 414 " =    1.698
peak=   -3.416 closest distance to " O   HOH Z 282 " =    1.903
peak=   -3.415 closest distance to " OG1 THR A  82 " =    1.963
peak=   -3.412 closest distance to " O   THR A  52 " =    2.143
peak=   -3.410 closest distance to " ND2 ASN A  60 " =    1.157
peak=   -3.405 closest distance to " OD2 ASP A 270 " =    2.337
peak=   -3.402 closest distance to " O   HOH Z 380 " =    4.255
peak=   -3.398 closest distance to " OH  TYR A 169 " =    1.006
peak=   -3.397 closest distance to " CG  PRO A 243 " =    1.514
peak=   -3.395 closest distance to " CD  ARG A  14 " =    3.183
peak=   -3.394 closest distance to " CB  ALA A  43 " =    2.600
peak=   -3.388 closest distance to " O   HOH Z 423 " =    2.334
peak=   -3.385 closest distance to " NZ  LYS A 119 " =    1.469
peak=   -3.381 closest distance to " O   HOH Z 130 " =    1.083
peak=   -3.380 closest distance to " N   GLY A  17 " =    1.511
peak=   -3.374 closest distance to " O   HOH Z 109 " =    3.371
peak=   -3.374 closest distance to " O   HOH Z 132 " =    1.345
peak=   -3.368 closest distance to " CA  ALA A 137 " =    2.686
peak=   -3.367 closest distance to " CE3 TRP A  85 " =    2.631
peak=   -3.363 closest distance to " OG  SER A  97 " =    2.358
peak=   -3.363 closest distance to " O   HOH Z 292 " =    1.368
peak=   -3.360 closest distance to " CG2 VAL A 296 " =    1.820
peak=   -3.358 closest distance to " O   HOH Z 158 " =    1.582
peak=   -3.349 closest distance to " CG1 VAL A 232 " =    2.234
peak=   -3.343 closest distance to " N   GLU A   2 " =    1.109
peak=   -3.343 closest distance to " CA  ALA A 114 " =    1.127
peak=   -3.342 closest distance to " OG ASER A 134 " =    1.020
peak=   -3.340 closest distance to " NE1 TRP A 150 " =    2.242
peak=   -3.340 closest distance to " O   ALA A  34 " =    1.839
peak=   -3.333 closest distance to " O   HOH Z  66 " =    1.930
peak=   -3.332 closest distance to " CA  ASN A 127 " =    1.094
peak=   -3.327 closest distance to " SG  CYS A 254 " =    3.289
peak=   -3.326 closest distance to " O   HOH Z 124 " =    1.252
peak=   -3.324 closest distance to " O   HOH Z   7 " =    1.106
peak=   -3.324 closest distance to " O   HOH Z 300 " =    1.580
peak=   -3.321 closest distance to " O   HOH Z  23 " =    1.295
peak=   -3.319 closest distance to " OG  SER A  63 " =    1.447
peak=   -3.311 closest distance to " CD2 LEU A  96 " =    2.140
peak=   -3.307 closest distance to " CG  LEU A  83 " =    2.188
peak=   -3.305 closest distance to " CE3 TRP A 150 " =    1.207
peak=   -3.305 closest distance to " O   TYR A 186 " =    2.504
peak=   -3.301 closest distance to " N   GLU A 277 " =    0.951
peak=   -3.299 closest distance to " CA  ALA A   8 " =    1.423
peak=   -3.293 closest distance to " O   HOH Z 134 " =    1.932
peak=   -3.293 closest distance to " OD1 ASN A  69 " =    1.073
peak=   -3.292 closest distance to " CD  PRO A 198 " =    1.044
peak=   -3.292 closest distance to " O   HOH Z 290 " =    1.079
peak=   -3.285 closest distance to " O   HOH Z  29 " =    1.622
peak=   -3.283 closest distance to " CA  SER A 164 " =    1.667
peak=   -3.280 closest distance to " O   HOH Z 127 " =    1.386
peak=   -3.279 closest distance to " O   HOH Z 231 " =    1.391
peak=   -3.277 closest distance to " CD1 LEU A  25 " =    2.637
peak=   -3.272 closest distance to " O   HOH Z 148 " =    3.185
peak=   -3.268 closest distance to " O   HOH Z  19 " =    1.736
peak=   -3.265 closest distance to " O   HOH Z 136 " =    1.477
peak=   -3.259 closest distance to " OD2 ASP A 270 " =    1.143
peak=   -3.259 closest distance to " O   HOH Z   7 " =    1.436
peak=   -3.256 closest distance to " O   HOH Z 128 " =    4.296
peak=   -3.248 closest distance to " OD1 ASN A 148 " =    1.519
peak=   -3.248 closest distance to " C   GLN A 240 " =    2.379
peak=   -3.243 closest distance to " O   HOH Z 348 " =    2.131
peak=   -3.240 closest distance to " NE2 GLN A  58 " =    0.886
peak=   -3.232 closest distance to " O   HOH Z 118 " =    2.001
peak=   -3.231 closest distance to " C   THR A 279 " =    1.261
peak=   -3.228 closest distance to " NH1AARG A 275 " =    1.417
peak=   -3.223 closest distance to " O   HOH Z 332 " =    0.905
peak=   -3.221 closest distance to " C   LEU A   5 " =    1.176
peak=   -3.217 closest distance to " O   ASN A 110 " =    1.625
peak=   -3.217 closest distance to " O   HOH Z 428 " =    1.515
peak=   -3.212 closest distance to " O   HOH Z  17 " =    1.113
peak=   -3.210 closest distance to " O   HOH Z 351 " =    1.329
peak=   -3.206 closest distance to " CA  GLY A 241 " =    2.296
peak=   -3.205 closest distance to " O   HOH Z 402 " =    1.146
peak=   -3.205 closest distance to " NE2 GLN A 223 " =    1.128
peak=   -3.203 closest distance to " CG1AVAL A 121 " =    1.070
peak=   -3.202 closest distance to " O   HOH Z 326 " =    4.612
peak=   -3.201 closest distance to " O   HOH Z  50 " =    1.333
peak=   -3.199 closest distance to " O   THR A  31 " =    1.957
peak=   -3.186 closest distance to " N   SER A   3 " =    1.193
peak=   -3.185 closest distance to " CD2 LEU A 237 " =    2.866
peak=   -3.183 closest distance to " O   HOH Z 388 " =    1.958
peak=   -3.179 closest distance to " OE1 GLN A  88 " =    3.032
peak=   -3.174 closest distance to " O   HOH Z 414 " =    1.555
peak=   -3.173 closest distance to " C   SER A 206 " =    1.494
peak=   -3.168 closest distance to " CB  ALA A 227 " =    2.392
peak=   -3.165 closest distance to " N   PHE A  61 " =    1.034
peak=   -3.162 closest distance to " O   HOH Z 231 " =    1.875
peak=   -3.162 closest distance to " O   HOH Z 241 " =    1.022
peak=   -3.161 closest distance to " O   HOH Z 393 " =    1.237
peak=   -3.161 closest distance to " O   ALA A 291 " =    2.876
peak=   -3.155 closest distance to " CG  ASP A  50 " =    2.352
peak=   -3.152 closest distance to " O   HOH Z 325 " =    1.799
peak=   -3.152 closest distance to " OG  SER A  87 " =    1.440
peak=   -3.145 closest distance to " SG ACYS A 201 " =    2.283
peak=   -3.142 closest distance to " N   GLY A  75 " =    1.119
peak=   -3.141 closest distance to " O   HOH Z 150 " =    1.839
peak=   -3.134 closest distance to " O   GLY A  80 " =    1.731
peak=   -3.132 closest distance to " O   HOH Z 422 " =    1.766
peak=   -3.131 closest distance to " OD2 ASP A 171 " =    1.814
peak=   -3.121 closest distance to " O   HOH Z 119 " =    3.042
peak=   -3.115 closest distance to " CA  GLY A 118 " =    2.418
peak=   -3.112 closest distance to " O   HOH Z 424 " =    1.216
peak=   -3.109 closest distance to " O   HOH Z  94 " =    1.994
peak=   -3.108 closest distance to " CB  ALA A 100 " =    2.002
peak=   -3.104 closest distance to " O   THR A  18 " =    1.484
peak=   -3.097 closest distance to " O   HOH Z 174 " =    2.108
peak=   -3.089 closest distance to " CG  GLU A  53 " =    1.249
peak=   -3.087 closest distance to " O   HOH Z 140 " =    1.016
peak=   -3.084 closest distance to " CA  SER A  63 " =    1.266
peak=   -3.081 closest distance to " OD2 ASP A 171 " =    2.394
peak=   -3.046 closest distance to " N   ALA A 184 " =    1.030
peak=   -3.034 closest distance to " CA  SER A 273 " =    2.411

================= 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    :  0.4887 0.4739   6.297536e+00   6.282524e+00
   1_bss:  0.4826 0.4664   6.295304e+00   6.274512e+00
   1_xyz:  0.4186 0.4439   6.211679e+00   6.245796e+00
   1_adp:  0.3861 0.4462   6.177278e+00   6.247174e+00
   1_occ:  0.3859 0.4477   6.176782e+00   6.247668e+00
   2_bss:  0.3861 0.4459   6.178223e+00   6.246338e+00
   2_xyz:  0.3244 0.3972   6.056561e+00   6.178375e+00
   2_adp:  0.3043 0.3890   6.027704e+00   6.173191e+00
   2_occ:  0.3041 0.3889   6.027634e+00   6.173355e+00
   3_bss:  0.3047 0.3883   6.027863e+00   6.173104e+00
   3_xyz:  0.2662 0.3433   5.908276e+00   6.081401e+00
   3_adp:  0.2536 0.3334   5.879152e+00   6.059882e+00
   3_occ:  0.2535 0.3331   5.878809e+00   6.059290e+00
   4_bss:  0.2537 0.3325   5.878422e+00   6.059806e+00
   4_xyz:  0.1973 0.2587   5.638725e+00   5.842361e+00
   4_adp:  0.1747 0.2299   5.530879e+00   5.737895e+00
   4_occ:  0.1745 0.2299   5.530326e+00   5.737249e+00
   5_bss:  0.1743 0.2285   5.528810e+00   5.734057e+00
   5_xyz:  0.1567 0.2049   5.433758e+00   5.639522e+00
   5_adp:  0.1508 0.1990   5.407764e+00   5.615425e+00
   5_occ:  0.1507 0.1988   5.407579e+00   5.615347e+00
   5_bss:  0.1511 0.1999   5.410712e+00   5.618897e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.279  20.000  -0.402   3.160   0.116   0.000   0.000   0.000
   1_xyz:  0.279  20.000  -0.402   3.160   0.116   0.000   0.000   0.000
   1_adp:  0.279  20.000  -0.402   3.160   0.116   0.000   0.000   0.000
   1_occ:  0.279  20.000  -0.402   3.160   0.116   0.000   0.000   0.000
   2_bss:  0.300  50.000  -0.819   1.726  -0.237   0.000  -0.000  -0.000
   2_xyz:  0.300  50.000  -0.819   1.726  -0.237   0.000  -0.000  -0.000
   2_adp:  0.300  50.000  -0.819   1.726  -0.237   0.000  -0.000  -0.000
   2_occ:  0.300  50.000  -0.819   1.726  -0.237   0.000  -0.000  -0.000
   3_bss:  0.325  65.488  -0.616   1.270  -0.497   0.000  -0.000  -0.000
   3_xyz:  0.325  65.488  -0.616   1.270  -0.497   0.000  -0.000  -0.000
   3_adp:  0.325  65.488  -0.616   1.270  -0.497   0.000  -0.000  -0.000
   3_occ:  0.325  65.488  -0.616   1.270  -0.497   0.000  -0.000  -0.000
   4_bss:  0.325  71.213  -0.931   0.471  -1.079   0.000  -0.000  -0.000
   4_xyz:  0.325  71.213  -0.931   0.471  -1.079   0.000  -0.000  -0.000
   4_adp:  0.325  71.213  -0.931   0.471  -1.079   0.000  -0.000  -0.000
   4_occ:  0.325  71.213  -0.931   0.471  -1.079   0.000  -0.000  -0.000
   5_bss:  0.332  64.727  -1.717  -0.687  -1.598  -0.000  -0.000  -0.000
   5_xyz:  0.332  64.727  -1.717  -0.687  -1.598  -0.000  -0.000  -0.000
   5_adp:  0.332  64.727  -1.717  -0.687  -1.598  -0.000  -0.000  -0.000
   5_occ:  0.332  64.727  -1.717  -0.687  -1.598  -0.000  -0.000  -0.000
   5_bss:  0.329  69.587  -2.054  -1.182  -1.818  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.800 0.4095  0.5581    74274.734
   1_bss:  58.008 0.4182  0.5894    71301.299
   1_xyz:  52.763 0.4849  0.6778    61313.979
   1_adp:  53.531 0.4746  0.6794    61789.112
   1_occ:  53.647 0.4730  0.6752    61962.691
   2_bss:  53.413 0.4760  0.6660    61536.912
   2_xyz:  45.796 0.5706  0.7962    46949.888
   2_adp:  44.814 0.5828  0.8022    45473.436
   2_occ:  44.847 0.5824  0.8009    45527.790
   3_bss:  44.779 0.5831  0.7972    45339.544
   3_xyz:  37.712 0.6684  0.8904    33388.078
   3_adp:  36.039 0.6885  0.8907    31470.757
   3_occ:  36.023 0.6887  0.8908    31449.189
   4_bss:  35.956 0.6894  0.8748    31381.156
   4_xyz:  26.514 0.7940  0.9678    17570.990
   4_adp:  22.879 0.8327  0.9803    13918.812
   4_occ:  22.867 0.8328  0.9804    13908.681
   5_bss:  22.742 0.8339  0.9539    13718.755
   5_xyz:  20.019 0.8607  0.9665    10877.345
   5_adp:  19.193 0.8694  0.9630    10372.040
   5_occ:  19.188 0.8694  0.9628    10375.358
   5_bss:  19.267 0.8689  0.9514    10498.024
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9694e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9694e-01
   1_xyz:   1.425  0.011  0.088 15.597  0.005  4.107   1.1262e-01
   1_adp:   1.425  0.011  0.088 15.597  0.005  4.107   1.1262e-01
   1_occ:   1.425  0.011  0.088 15.597  0.005  4.107   1.1262e-01
   2_bss:   1.425  0.011  0.088 15.597  0.005  4.107   1.1262e-01
   2_xyz:   1.525  0.011  0.095 15.690  0.006  4.108   1.2659e-01
   2_adp:   1.525  0.011  0.095 15.690  0.006  4.108   1.2659e-01
   2_occ:   1.525  0.011  0.095 15.690  0.006  4.108   1.2659e-01
   3_bss:   1.525  0.011  0.095 15.690  0.006  4.108   1.2659e-01
   3_xyz:   1.143  0.008  0.074 14.770  0.004  4.113   7.1840e-02
   3_adp:   1.143  0.008  0.074 14.770  0.004  4.113   7.1840e-02
   3_occ:   1.143  0.008  0.074 14.770  0.004  4.113   7.1840e-02
   4_bss:   1.143  0.008  0.074 14.770  0.004  4.113   7.1840e-02
   4_xyz:   1.323  0.011  0.089 14.982  0.005  4.113   9.8432e-02
   4_adp:   1.323  0.011  0.089 14.982  0.005  4.113   9.8432e-02
   4_occ:   1.323  0.011  0.089 14.982  0.005  4.113   9.8432e-02
   5_bss:   1.323  0.011  0.089 14.982  0.005  4.113   9.8432e-02
   5_xyz:   0.961  0.006  0.067 14.248  0.004  4.120   5.5589e-02
   5_adp:   0.961  0.006  0.067 14.248  0.004  4.120   5.5589e-02
   5_occ:   0.961  0.006  0.067 14.248  0.004  4.120   5.5589e-02
   5_bss:   0.961  0.006  0.067 14.248  0.004  4.120   5.5589e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.295   2.4474e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.295   2.4474e-01
   1_xyz:   9.000  0.061  0.307 88.671  0.023  1.956   9.2171e-02
   1_adp:   9.000  0.061  0.307 88.671  0.023  1.956   9.2171e-02
   1_occ:   9.000  0.061  0.307 88.671  0.023  1.956   9.2171e-02
   2_bss:   9.000  0.061  0.307 88.671  0.023  1.956   9.2171e-02
   2_xyz:   9.430  0.055  0.277 83.195  0.056  1.740   1.0999e-01
   2_adp:   9.430  0.055  0.277 83.195  0.056  1.740   1.0999e-01
   2_occ:   9.430  0.055  0.277 83.195  0.056  1.740   1.0999e-01
   3_bss:   9.430  0.055  0.277 83.195  0.056  1.740   1.0999e-01
   3_xyz:   9.531  0.050  0.340 75.783  0.033  2.315   7.4992e-02
   3_adp:   9.531  0.050  0.340 75.783  0.033  2.315   7.4992e-02
   3_occ:   9.531  0.050  0.340 75.783  0.033  2.315   7.4992e-02
   4_bss:   9.531  0.050  0.340 75.783  0.033  2.315   7.4992e-02
   4_xyz:   7.984  0.079  0.279 83.472  0.034  2.114   1.0704e-01
   4_adp:   7.984  0.079  0.279 83.472  0.034  2.114   1.0704e-01
   4_occ:   7.984  0.079  0.279 83.472  0.034  2.114   1.0704e-01
   5_bss:   7.984  0.079  0.279 83.472  0.034  2.114   1.0704e-01
   5_xyz:   7.800  0.036  0.253 86.388  0.046  2.346   3.8189e-02
   5_adp:   7.800  0.036  0.253 86.388  0.046  2.346   3.8189e-02
   5_occ:   7.800  0.036  0.253 86.388  0.046  2.346   3.8189e-02
   5_bss:   7.800  0.036  0.253 86.388  0.046  2.346   3.8189e-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: 151.15   0.00  18.88 151.15   0.00  15.73  73.81   0.00  36.04
   1_occ: 151.15   0.00  18.88 151.15   0.00  15.73  73.81   0.00  36.04
   2_bss: 151.15   0.00  18.88 151.15   0.00  15.73  73.81   0.00  36.04
   2_xyz: 151.15   0.00  18.88 151.15   0.00  15.73  73.81   0.00  36.04
   2_adp: 102.29   0.00  20.11  85.37   0.00  16.78 102.29   0.00  38.25
   2_occ: 102.29   0.00  20.11  85.37   0.00  16.78 102.29   0.00  38.25
   3_bss: 102.29   0.00  20.11  85.37   0.00  16.78 102.29   0.00  38.25
   3_xyz: 102.29   0.00  20.11  85.37   0.00  16.78 102.29   0.00  38.25
   3_adp: 102.59   0.00  19.69  94.06   0.00  15.69 102.59   1.18  41.47
   3_occ: 102.59   0.00  19.69  94.06   0.00  15.69 102.59   1.18  41.47
   4_bss: 102.59   0.00  19.69  94.06   0.00  15.69 102.59   1.18  41.47
   4_xyz: 102.59   0.00  19.69  94.06   0.00  15.69 102.59   1.18  41.47
   4_adp:  99.16   0.00  18.80  99.16   0.00  13.98  96.07   5.62  45.01
   4_occ:  99.16   0.00  18.80  99.16   0.00  13.98  96.07   5.62  45.01
   5_bss:  99.16   0.00  18.80  99.16   0.00  13.98  96.07   5.62  45.01
   5_xyz:  99.16   0.00  18.80  99.16   0.00  13.98  96.07   5.62  45.01
   5_adp: 101.11   0.00  18.24 101.11   0.00  13.37  98.02   5.19  44.76
   5_occ: 101.11   0.00  18.24 101.11   0.00  13.37  98.02   5.19  44.76
   5_bss: 101.11   0.00  18.25 101.11   0.00  13.38  98.02   5.19  44.76
------------------------------------------------------------------------
 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:    2.279    0.012    0.266
   1_adp:    2.279    0.012    0.266
   1_occ:    2.279    0.012    0.266
   2_bss:    2.279    0.012    0.266
   2_xyz:    2.132    0.051    0.551
   2_adp:    2.132    0.051    0.551
   2_occ:    2.132    0.051    0.551
   3_bss:    2.132    0.051    0.551
   3_xyz:    2.084    0.051    0.663
   3_adp:    2.084    0.051    0.663
   3_occ:    2.084    0.051    0.663
   4_bss:    2.084    0.051    0.663
   4_xyz:    1.999    0.076    0.856
   4_adp:    1.999    0.076    0.856
   4_occ:    1.999    0.076    0.856
   5_bss:    1.999    0.076    0.856
   5_xyz:    1.854    0.103    0.887
   5_adp:    1.854    0.103    0.887
   5_occ:    1.854    0.103    0.887
   5_bss:    1.854    0.103    0.887
------------------------------------------------------------------------

CPU time actual refinement: 386.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1200/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_1200/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1200/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1200/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1200/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 386.55 
  Macro-tasks:
    bulk solvent and scale       = 45.05  
    individual site refinement   = 169.74 
    weights calculation          = 31.09  
    collect and process          = 6.26   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 252.25 
  Micro-tasks:
    mask                            = 3.20   
    f_calc                          = 128.00 
    alpha_beta                      = 8.38   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 138.01 
    fmodel                         = 7.40   
    r_factors                      = 0.31   
    phase_errors                   = 9.67   
    foms                           = 0.21   
    TOTAL for micro-tasks          = 296.35 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.357 micro seconds
Total CPU time: 6.67 minutes
from_scatterers_fft:    662 calls, 127.72 s
gradients_fft:          607 calls, 123.99 s

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

# Date 2008-01-16 Time 06:41:43 PST -0800 (1200494503.11 s)
Start R-work = 0.4887, R-free = 0.4739 (no bulk solvent and anisotropic scale)
Final R-work = 0.1695, R-free = 0.2181 (no bulk solvent and anisotropic scale)

Start R-work = 0.4826, R-free = 0.4664
Final R-work = 0.1511, R-free = 0.1999