# Date 2008-01-16 Time 06:10:48 PST -0800 (1200492648.52 s)
#phil __OFF__

Command line arguments: "../1034.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10956
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1034

-------------------------------------------------------------------------------
  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: (71.3037, 47.1647, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95139
Completeness in resolution range: 0.921142
Completeness with d_max=infinity: 0.918421

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0490
                             d_min =   1.9514

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: (71.3037, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95139
Completeness in resolution range: 0.921142
Completeness with d_max=infinity: 0.918421

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0495 -  4.1770 [2231/2260]  2011   220   9.9%
  bin  2:  4.1770 -  3.3272 [2136/2159]  1921   215  10.1%
  bin  3:  3.3272 -  2.9101 [2109/2134]  1893   216  10.2%
  bin  4:  2.9101 -  2.6456 [2105/2121]  1900   205   9.7%
  bin  5:  2.6456 -  2.4568 [2066/2105]  1860   206  10.0%
  bin  6:  2.4568 -  2.3125 [2086/2119]  1874   212  10.2%
  bin  7:  2.3125 -  2.1971 [2052/2088]  1844   208  10.1%
  bin  8:  2.1971 -  2.1017 [2042/2084]  1842   200   9.8%
  bin  9:  2.1017 -  2.0210 [2044/2103]  1837   207  10.1%
  bin 10:  2.0210 -  1.9514 [ 718/2093]   648    70   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1034/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: 0.15 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:
        1.52 -     2.19: 23
        2.19 -     2.87: 1211
        2.87 -     3.55: 4476
        3.55 -     4.22: 9243
        4.22 -     4.90: 13490
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.516 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.524 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.810 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  17 " - " O   HOH Z 333 "  1.877 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28438 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_1034/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1034/model_refine_001.geo

CPU time processing inputs: 9.27


============================ 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 = 71.30375 47.16465 84.23025 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: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4110   r_free= 0.4178   ksol= 0.00   Bsol= 0.00   scale= 0.930    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.209892                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6595 0.99   1448  165 0.3241 0.3253      6.4552      6.4627|
|  2:  4.6595 -  3.7167 0.99   1392  149 0.3308 0.3151      6.6582      6.6564|
|  3:  3.7167 -  3.2523 0.99   1362  153 0.3721 0.3841      6.5483      6.6287|
|  4:  3.2523 -  2.9574 0.99   1366  150 0.3980 0.3960      6.4079      6.4187|
|  5:  2.9574 -  2.7468 0.98   1338  151 0.4232 0.4081      6.2708      6.2669|
|  6:  2.7468 -  2.5857 0.99   1347  150 0.4474 0.4573      6.2021      6.1568|
|  7:  2.5857 -  2.4568 0.99   1332  144 0.4431 0.4027      6.1763      6.1329|
|  8:  2.4568 -  2.3503 0.99   1332  152 0.4506 0.4775      6.0964      6.1398|
|  9:  2.3503 -  2.2601 0.99   1327  152 0.4625 0.4573      6.0942      6.0311|
| 10:  2.2601 -  2.1824 0.98   1326  147 0.4740 0.5207      6.0363      6.1213|
| 11:  2.1824 -  2.1143 0.98   1333  134 0.4774 0.5814      5.9918      6.0235|
| 12:  2.1143 -  2.0540 1.00   1310  155 0.4737 0.4915      5.9133      5.9578|
| 13:  2.0540 -  2.0001 0.83   1110  132 0.4903 0.4878      5.8458      5.8196|
| 14:  2.0001 -  1.9514 0.22    307   25 0.5747 0.5205      5.8234      5.8344|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6595  1448   165  0.76  29.07   0.85     0.78      51480.73|
|  2:  4.6595 -  3.7167  1392   149  0.77  28.79   0.95     0.86      74033.62|
|  3:  3.7167 -  3.2523  1362   153  0.69  36.41   0.94     0.86      81326.15|
|  4:  3.2523 -  2.9574  1366   150  0.60  43.60   0.96     0.81      75714.11|
|  5:  2.9574 -  2.7468  1338   151  0.54  48.41   0.92     0.74      61373.62|
|  6:  2.7468 -  2.5857  1347   150  0.53  49.54   0.94     0.73      52745.45|
|  7:  2.5857 -  2.4568  1332   144  0.54  49.13   0.96     0.71      46627.54|
|  8:  2.4568 -  2.3503  1332   152  0.51  51.05   0.93     0.73      45023.74|
|  9:  2.3503 -  2.2601  1327   152  0.49  53.06   0.98     0.69      42349.06|
| 10:  2.2601 -  2.1824  1326   147  0.43  57.99   0.98     0.63      44822.19|
| 11:  2.1824 -  2.1143  1333   134  0.37  62.25   0.98     0.55      43448.35|
| 12:  2.1143 -  2.0540  1310   155  0.33  65.31   0.96     0.54      42730.96|
| 13:  2.0540 -  2.0001  1110   132  0.34  64.97   0.95     0.53      35727.53|
| 14:  2.0001 -  1.9514   307    25  0.33  65.26   0.91     0.50      29223.48|
|alpha:            min =        0.50 max =            0.86 mean =         0.71|
|beta:             min =    29223.48 max =        81326.15 mean =     53612.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.94 mean =        49.02|
|phase err.(test): min =        0.00 max =           89.85 mean =        49.09|
|-----------------------------------------------------------------------------|

============================== 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 = 6.403716              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.895   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.707581              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.366   (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 |  1.516 -  1.854:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.854 -  2.193:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.193 -  2.531:       27 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.531 -  2.870:     1184 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.870 -  3.208:     1959 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.208 -  3.546:     2517 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.546 -  3.885:     4637 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.885 -  4.223:     4606 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.223 -  4.562:     6138 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.562 -  4.900:     7352 |
|-----------------------------------------------------------------------------|
|-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 |        0.180 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.516 |       0.443 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.835)------------------------------------------|
|    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: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4110   r_free= 0.4178   ksol= 0.00   Bsol= 0.00   scale= 0.930    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.209892                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4008   r_free= 0.4094   ksol= 0.30   Bsol= 50.00   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-2.01,2.88,-0.00,0.00,0.00); trace/3= 0.13                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.202054                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.007301              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.119   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.795486              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.140   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4008      final r-factor (work) = 0.2932          |
| start r-factor (free) = 0.4094      final r-factor (free) = 0.3279          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6974 = 5.01 * 0.50 * 6.1980 + 1.00 * 0.1798                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2295 = 5.01 * 0.50 * 6.0455 + 1.00 * 0.0937                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2932      final r-factor (work) = 0.2671          |
| start r-factor (free) = 0.3279      final r-factor (free) = 0.3328          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8154 = 0.80 * 1.00 * 6.0455 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7145 = 0.80 * 1.00 * 5.9089 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.835)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.66   18.19    None  None   None       |
|    all(noH): 2823   0      0.00    86.66   18.19    None  None   None       |
|    Sol.    : 438    0      2.24    85.79   40.74    None  None   None       |
|    Mac.    : 2385   0      0.00    86.66   14.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.666:  775   |   5:    43.330 -  51.996:   99        |
|      1:     8.666 -  17.332: 1018   |   6:    51.996 -  60.661:   66        |
|      2:    17.332 -  25.998:  446   |   7:    60.661 -  69.327:   38        |
|      3:    25.998 -  34.664:  200   |   8:    69.327 -  77.993:   23        |
|      4:    34.664 -  43.330:  151   |   9:    77.993 -  86.659:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2671 r_free = 0.3328             target_work(ml) = 5.916         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2668 r_free = 0.3328             target_work(ml) = 5.915         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2668   r_free= 0.3328   ksol= 0.30   Bsol= 50.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-2.01,2.88,-0.00,0.00,0.00); trace/3= 0.13                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.914783                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2659   r_free= 0.3309   ksol= 0.33   Bsol= 59.09   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-1.80,0.58,-0.00,0.00,0.00); trace/3= -0.88                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.912990                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.398830              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.470   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.486015              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.000  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2659      final r-factor (work) = 0.1914          |
| start r-factor (free) = 0.3309      final r-factor (free) = 0.2496          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0476 = 5.40 * 0.50 * 5.9101 + 1.00 * 0.0937                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6998 = 5.40 * 0.50 * 5.7906 + 1.00 * 0.0685                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1914      final r-factor (work) = 0.1742          |
| start r-factor (free) = 0.2496      final r-factor (free) = 0.2299          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8283 = 0.49 * 1.00 * 5.7906 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7216 = 0.49 * 1.00 * 5.5790 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.835)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.44    88.39   18.06    None  None   None       |
|    all(noH): 2823   0      0.44    88.39   18.06    None  None   None       |
|    Sol.    : 438    0      5.55    88.39   42.32    None  None   None       |
|    Mac.    : 2385   0      0.44    83.19   13.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.438 -   9.233:  823   |   5:    44.413 -  53.208:  122        |
|      1:     9.233 -  18.028: 1171   |   6:    53.208 -  62.003:   67        |
|      2:    18.028 -  26.823:  316   |   7:    62.003 -  70.798:   40        |
|      3:    26.823 -  35.618:  141   |   8:    70.798 -  79.593:   21        |
|      4:    35.618 -  44.413:  117   |   9:    79.593 -  88.388:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1742 r_free = 0.2299             target_work(ml) = 5.538         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1741 r_free = 0.2298             target_work(ml) = 5.538         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1741   r_free= 0.2298   ksol= 0.33   Bsol= 59.09   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-1.80,0.58,-0.00,0.00,0.00); trace/3= -0.88                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.537647                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1737   r_free= 0.2283   ksol= 0.33   Bsol= 55.76   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.31,-1.28,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.533944                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.758214              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.388   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.283601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.922  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1737      final r-factor (work) = 0.1400          |
| start r-factor (free) = 0.2283      final r-factor (free) = 0.1860          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7683 = 2.76 * 0.50 * 5.5832 + 1.00 * 0.0685                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5699 = 2.76 * 0.50 * 5.4501 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1400      final r-factor (work) = 0.1316          |
| start r-factor (free) = 0.1860      final r-factor (free) = 0.1779          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5557 = 0.28 * 1.00 * 5.4501 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5292 = 0.28 * 1.00 * 5.3106 + 1.00 * 0.0231                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.835)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.97   17.71    None  None   None       |
|    all(noH): 2823   0      0.00    86.97   17.71    None  None   None       |
|    Sol.    : 438    0      5.66    86.97   41.80    None  None   None       |
|    Mac.    : 2385   0      0.00    84.91   13.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.697:  652   |   5:    43.486 -  52.183:  122        |
|      1:     8.697 -  17.394: 1371   |   6:    52.183 -  60.880:   66        |
|      2:    17.394 -  26.092:  294   |   7:    60.880 -  69.577:   33        |
|      3:    26.092 -  34.789:  127   |   8:    69.577 -  78.275:   28        |
|      4:    34.789 -  43.486:  125   |   9:    78.275 -  86.972:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1316 r_free = 0.1779             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1315 r_free = 0.1777             target_work(ml) = 5.283         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1315   r_free= 0.1777   ksol= 0.33   Bsol= 55.76   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.31,-1.28,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.283259                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1315   r_free= 0.1771   ksol= 0.32   Bsol= 49.78   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.49,-2.03,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.283697                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.586933              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.417  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.808978              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.236   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1315      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1771      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2688 = 1.59 * 0.50 * 5.3123 + 1.00 * 0.0537                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2183 = 1.59 * 0.50 * 5.2532 + 1.00 * 0.0501                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1225      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1659      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2626 = 0.81 * 1.00 * 5.2532 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2213 = 0.81 * 1.00 * 5.2060 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.835)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.41    97.78   17.82    None  None   None       |
|    all(noH): 2823   0      1.41    97.78   17.82    None  None   None       |
|    Sol.    : 438    0      5.81    86.51   42.45    None  None   None       |
|    Mac.    : 2385   0      1.41    97.78   13.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.410 -  11.047: 1211   |   5:    49.595 -  59.232:   99        |
|      1:    11.047 -  20.684:  981   |   6:    59.232 -  68.869:   48        |
|      2:    20.684 -  30.321:  203   |   7:    68.869 -  78.506:   29        |
|      3:    30.321 -  39.958:  122   |   8:    78.506 -  88.143:   12        |
|      4:    39.958 -  49.595:  114   |   9:    88.143 -  97.779:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1194 r_free = 0.1653             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1194 r_free = 0.1653             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1653   ksol= 0.32   Bsol= 49.78   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.49,-2.03,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.202411                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1652   ksol= 0.32   Bsol= 49.78   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.41,-2.14,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.202221                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.695204              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.063  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.458024              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.057  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4624 = 1.70 * 0.50 * 5.2057 + 1.00 * 0.0501                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4481 = 1.70 * 0.50 * 5.1849 + 1.00 * 0.0534                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3846 = 0.46 * 1.00 * 5.1849 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3786 = 0.46 * 1.00 * 5.1731 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.835)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.44    101.06  17.46    None  None   None       |
|    all(noH): 2823   0      1.44    101.06  17.46    None  None   None       |
|    Sol.    : 438    0      5.77    86.87   41.11    None  None   None       |
|    Mac.    : 2385   0      1.44    101.06  13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.439 -  11.401: 1325   |   5:    51.249 -  61.211:   85        |
|      1:    11.401 -  21.363:  904   |   6:    61.211 -  71.173:   32        |
|      2:    21.363 -  31.325:  195   |   7:    71.173 -  81.135:   23        |
|      3:    31.325 -  41.287:  127   |   8:    81.135 -  91.097:    5        |
|      4:    41.287 -  51.249:  123   |   9:    91.097 - 101.059:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1137 r_free = 0.1606             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1136 r_free = 0.1607             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1607   ksol= 0.32   Bsol= 49.78   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.41,-2.14,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170191                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6595 0.99   1448  165 0.0981 0.1290      5.3808      5.5522|
|  2:  4.6595 -  3.7167 0.99   1392  149 0.0845 0.1037      5.4192      5.6196|
|  3:  3.7167 -  3.2523 0.99   1362  153 0.1053 0.1676      5.4616      5.8912|
|  4:  3.2523 -  2.9574 0.99   1366  150 0.1274 0.1567      5.4724      5.6035|
|  5:  2.9574 -  2.7468 0.98   1338  151 0.1346 0.1793      5.3405      5.5107|
|  6:  2.7468 -  2.5857 0.99   1347  150 0.1268 0.1866       5.227      5.4597|
|  7:  2.5857 -  2.4568 0.99   1332  144 0.1259 0.1738      5.1787      5.4024|
|  8:  2.4568 -  2.3503 0.99   1332  152 0.1199 0.1709      5.0683      5.2698|
|  9:  2.3503 -  2.2601 0.99   1327  152 0.1190 0.1954      5.0334      5.3223|
| 10:  2.2601 -  2.1824 0.98   1326  147 0.1159 0.1652       4.987      5.2344|
| 11:  2.1824 -  2.1143 0.98   1333  134 0.1168 0.1970      4.9552       5.309|
| 12:  2.1143 -  2.0540 1.00   1310  155 0.1159 0.1800      4.8909      5.1268|
| 13:  2.0540 -  2.0001 0.83   1110  132 0.1197 0.1743      4.7965      5.0163|
| 14:  2.0001 -  1.9514 0.22    307   25 0.1144 0.1591      4.6828      4.9185|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6595  1448   165  0.94   9.01   0.97     0.95       7045.90|
|  2:  4.6595 -  3.7167  1392   149  0.96   7.69   1.01     1.00       8643.32|
|  3:  3.7167 -  3.2523  1362   153  0.93  11.34   1.03     1.03      10153.44|
|  4:  3.2523 -  2.9574  1366   150  0.91  14.89   1.01     0.98      10801.70|
|  5:  2.9574 -  2.7468  1338   151  0.90  16.40   0.99     0.97       8611.97|
|  6:  2.7468 -  2.5857  1347   150  0.90  16.44   0.98     0.95       7242.39|
|  7:  2.5857 -  2.4568  1332   144  0.90  15.80   0.99     0.97       6459.32|
|  8:  2.4568 -  2.3503  1332   152  0.90  15.88   0.99     0.95       5376.08|
|  9:  2.3503 -  2.2601  1327   152  0.90  16.45   1.00     0.97       5085.77|
| 10:  2.2601 -  2.1824  1326   147  0.90  15.76   0.99     0.96       4682.65|
| 11:  2.1824 -  2.1143  1333   134  0.89  16.98   0.98     0.95       4598.60|
| 12:  2.1143 -  2.0540  1310   155  0.90  16.71   0.99     0.99       4223.13|
| 13:  2.0540 -  2.0001  1110   132  0.89  16.96   0.99     0.97       3409.15|
| 14:  2.0001 -  1.9514   307    25  0.90  16.23   0.98     0.94       2671.68|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2671.68 max =        10801.70 mean =      6641.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.57|
|phase err.(test): min =        0.00 max =           89.59 mean =        13.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1606   ksol= 0.32   Bsol= 49.73   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.19,-1.99,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170251                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1606   ksol= 0.32   Bsol= 49.73   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.19,-1.99,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170251                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6595 0.99   1448  165 0.0982 0.1291      5.3815      5.5531|
|  2:  4.6595 -  3.7167 0.99   1392  149 0.0845 0.1037      5.4194      5.6194|
|  3:  3.7167 -  3.2523 0.99   1362  153 0.1053 0.1676      5.4614      5.8912|
|  4:  3.2523 -  2.9574 0.99   1366  150 0.1274 0.1567      5.4723      5.6036|
|  5:  2.9574 -  2.7468 0.98   1338  151 0.1346 0.1793      5.3406      5.5106|
|  6:  2.7468 -  2.5857 0.99   1347  150 0.1268 0.1867      5.2272      5.4601|
|  7:  2.5857 -  2.4568 0.99   1332  144 0.1259 0.1737      5.1789      5.4025|
|  8:  2.4568 -  2.3503 0.99   1332  152 0.1199 0.1709      5.0684        5.27|
|  9:  2.3503 -  2.2601 0.99   1327  152 0.1190 0.1953      5.0335      5.3219|
| 10:  2.2601 -  2.1824 0.98   1326  147 0.1159 0.1652       4.987       5.234|
| 11:  2.1824 -  2.1143 0.98   1333  134 0.1168 0.1971      4.9552      5.3091|
| 12:  2.1143 -  2.0540 1.00   1310  155 0.1159 0.1799      4.8905      5.1262|
| 13:  2.0540 -  2.0001 0.83   1110  132 0.1196 0.1742      4.7964      5.0161|
| 14:  2.0001 -  1.9514 0.22    307   25 0.1144 0.1592      4.6828      4.9196|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6595  1448   165  0.94   9.02   0.98     0.95       7056.32|
|  2:  4.6595 -  3.7167  1392   149  0.96   7.69   1.01     1.00       8647.64|
|  3:  3.7167 -  3.2523  1362   153  0.93  11.34   1.03     1.03      10149.82|
|  4:  3.2523 -  2.9574  1366   150  0.91  14.89   1.01     0.98      10800.07|
|  5:  2.9574 -  2.7468  1338   151  0.90  16.40   1.00     0.97       8614.10|
|  6:  2.7468 -  2.5857  1347   150  0.90  16.45   0.99     0.96       7246.56|
|  7:  2.5857 -  2.4568  1332   144  0.90  15.81   0.99     0.97       6463.09|
|  8:  2.4568 -  2.3503  1332   152  0.90  15.88   0.99     0.96       5376.59|
|  9:  2.3503 -  2.2601  1327   152  0.90  16.45   1.00     0.97       5084.19|
| 10:  2.2601 -  2.1824  1326   147  0.90  15.75   0.99     0.96       4681.10|
| 11:  2.1824 -  2.1143  1333   134  0.89  16.98   0.99     0.96       4596.56|
| 12:  2.1143 -  2.0540  1310   155  0.90  16.71   1.00     1.00       4219.21|
| 13:  2.0540 -  2.0001  1110   132  0.89  16.96   0.99     0.98       3408.87|
| 14:  2.0001 -  1.9514   307    25  0.90  16.23   0.98     0.95       2674.20|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2674.20 max =        10800.07 mean =      6642.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.57|
|phase err.(test): min =        0.00 max =           89.59 mean =        13.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.835)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.39    101.01  17.40    None  None   None       |
|    all(noH): 2823   0      1.39    101.01  17.40    None  None   None       |
|    Sol.    : 438    0      5.72    86.82   41.06    None  None   None       |
|    Mac.    : 2385   0      1.39    101.01  13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.388 -  11.350: 1325   |   5:    51.198 -  61.160:   85        |
|      1:    11.350 -  21.312:  904   |   6:    61.160 -  71.122:   32        |
|      2:    21.312 -  31.274:  195   |   7:    71.122 -  81.084:   23        |
|      3:    31.274 -  41.236:  127   |   8:    81.084 -  91.046:    5        |
|      4:    41.236 -  51.198:  123   |   9:    91.046 - 101.008:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.652 - 5.819
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 318 from: 324
   mapped sites are within: 0.719 - 5.819

peak=    5.724 closest distance to " NH2 ARG A  56 " =    2.171
peak=    5.715 closest distance to " CB  GLN A 223 " =    1.478
peak=    5.659 closest distance to " CG  PRO A  54 " =    1.216
peak=    5.493 closest distance to " CB  SER A  63 " =    1.322
peak=    5.437 closest distance to " NH2BARG A 102 " =    1.025
peak=    5.026 closest distance to " CG  PRO A  90 " =    1.089
peak=    5.008 closest distance to " CG  PRO A 213 " =    1.205
peak=    4.997 closest distance to " CG  PRO A 198 " =    1.332
peak=    4.944 closest distance to " CB  PRO A  54 " =    0.878
peak=    4.898 closest distance to " CB  ARG A 275 " =    0.918
peak=    4.843 closest distance to " O   HOH Z  15 " =    2.115
peak=    4.647 closest distance to " CB  GLN A 183 " =    1.232
peak=    4.646 closest distance to " CB  GLU A 128 " =    1.142
peak=    4.627 closest distance to " O   HOH Z 193 " =    1.900
peak=    4.598 closest distance to " O   HOH Z 232 " =    2.164
peak=    4.586 closest distance to " CB  SER A   3 " =    1.347
peak=    4.556 closest distance to " O   HOH Z 126 " =    1.880
peak=    4.548 closest distance to " O   HOH Z 207 " =    1.770
peak=    4.516 closest distance to " C   PRO A 198 " =    1.534
peak=    4.485 closest distance to " OD2 ASP A 286 " =    2.903
peak=    4.479 closest distance to " CB  ASN A 148 " =    1.376
peak=    4.471 closest distance to " O   HOH Z 260 " =    1.200
peak=    4.466 closest distance to " CB  LEU A 228 " =    1.121
peak=    4.445 closest distance to " O   HOH Z 368 " =    1.983
peak=    4.441 closest distance to " OD1 ASN A  69 " =    2.512
peak=    4.427 closest distance to " O   HOH Z 247 " =    1.346
peak=    4.404 closest distance to " NE2 GLN A  11 " =    1.082
peak=    4.362 closest distance to " CB  TYR A 169 " =    0.811
peak=    4.359 closest distance to " O   HOH Z 298 " =    1.822
peak=    4.346 closest distance to " CA  TYR A  30 " =    0.957
peak=    4.332 closest distance to " O   HOH Z 108 " =    1.576
peak=    4.313 closest distance to " CA  ALA A  21 " =    1.159
peak=    4.308 closest distance to " O   HOH Z 134 " =    1.487
peak=    4.265 closest distance to " O   HOH Z 316 " =    3.040
peak=    4.259 closest distance to " O   HOH Z  78 " =    2.045
peak=    4.239 closest distance to " CB  GLU A 152 " =    1.179
peak=    4.203 closest distance to " O   HOH Z 144 " =    1.642
peak=    4.200 closest distance to " CB  VAL A 202 " =    1.684
peak=    4.174 closest distance to " O   HOH Z 344 " =    3.071
peak=    4.160 closest distance to " CA  THR A 221 " =    1.003
peak=    4.157 closest distance to " CD BLYS A 290 " =    1.021
peak=    4.152 closest distance to " O   HOH Z 234 " =    3.797
peak=    4.144 closest distance to " O   HOH Z 369 " =    1.997
peak=    4.138 closest distance to " O   HOH Z 135 " =    1.848
peak=    4.125 closest distance to " O   HOH Z 236 " =    2.034
peak=    4.092 closest distance to " CB  TRP A 179 " =    1.408
peak=    4.082 closest distance to " O   HOH Z 156 " =    3.424
peak=    4.029 closest distance to " O   HOH Z  20 " =    1.773
peak=    4.018 closest distance to " O   SER A  87 " =    2.203
peak=    4.018 closest distance to " O   HOH Z  48 " =    1.474
peak=    4.017 closest distance to " O   HOH Z 214 " =    0.991
peak=    4.007 closest distance to " O   HOH Z 180 " =    2.169
peak=    3.989 closest distance to " O   HOH Z 126 " =    1.557
peak=    3.989 closest distance to " O   HOH Z  88 " =    3.583
peak=    3.978 closest distance to " CA  MET A  40 " =    1.068
peak=    3.977 closest distance to " O   HOH Z 427 " =    2.929
peak=    3.976 closest distance to " CG  PRO A 280 " =    0.756
peak=    3.973 closest distance to " CD1 LEU A 300 " =    1.211
peak=    3.971 closest distance to " O   HOH Z  68 " =    1.682
peak=    3.969 closest distance to " CG  PRO A 243 " =    1.096
peak=    3.964 closest distance to " CD  LYS A 119 " =    1.169
peak=    3.963 closest distance to " O   HOH Z 284 " =    2.999
peak=    3.948 closest distance to " CB  TRP A 266 " =    0.966
peak=    3.945 closest distance to " O   HOH Z 389 " =    1.905
peak=    3.944 closest distance to " O   HOH Z 108 " =    1.870
peak=    3.937 closest distance to " O   HOH Z  54 " =    1.685
peak=    3.937 closest distance to " NH1AARG A 145 " =    0.953
peak=    3.931 closest distance to " NH2 ARG A 156 " =    1.240
peak=    3.924 closest distance to " CB  GLU A 277 " =    3.626
peak=    3.908 closest distance to " O   HOH Z 282 " =    1.486
peak=    3.889 closest distance to " O   HOH Z 278 " =    0.944
peak=    3.870 closest distance to " O   HOH Z  49 " =    2.187
peak=    3.867 closest distance to " O   HOH Z  61 " =    1.634
peak=    3.862 closest distance to " O   HOH Z 426 " =    1.489
peak=    3.839 closest distance to " O   HOH Z 295 " =    1.487
peak=    3.834 closest distance to " O   ALA A 165 " =    1.376
peak=    3.830 closest distance to " CG1 ILE A  33 " =    1.235
peak=    3.809 closest distance to " NH2BARG A 145 " =    2.084
peak=    3.809 closest distance to " O   HOH Z 203 " =    1.918
peak=    3.804 closest distance to " O   HOH Z 425 " =    1.434
peak=    3.800 closest distance to " CA  THR A 264 " =    0.860
peak=    3.800 closest distance to " O   HOH Z 261 " =    1.941
peak=    3.799 closest distance to " O   HOH Z 411 " =    3.719
peak=    3.798 closest distance to " CB  VAL A 265 " =    1.195
peak=    3.798 closest distance to " O   HOH Z 189 " =    2.126
peak=    3.797 closest distance to " O   HOH Z 132 " =    0.957
peak=    3.782 closest distance to " O   HOH Z 209 " =    2.374
peak=    3.780 closest distance to " O   HOH Z 279 " =    2.363
peak=    3.771 closest distance to " O   HOH Z 128 " =    2.245
peak=    3.769 closest distance to " O   HOH Z 272 " =    1.891
peak=    3.753 closest distance to " ND2 ASN A 187 " =    1.585
peak=    3.752 closest distance to " O   HOH Z  93 " =    2.473
peak=    3.741 closest distance to " O   HOH Z  21 " =    1.685
peak=    3.721 closest distance to " O   HOH Z 132 " =    2.511
peak=    3.721 closest distance to " O   HOH Z 227 " =    1.632
peak=    3.720 closest distance to " CB  MET A  47 " =    1.059
peak=    3.711 closest distance to " CB  GLU A 152 " =    1.541
peak=    3.711 closest distance to " N   ASN A 127 " =    1.235
peak=    3.710 closest distance to " N   ASN A  39 " =    1.337
peak=    3.702 closest distance to " O   HOH Z 183 " =    1.531
peak=    3.700 closest distance to " CB  PRO A 198 " =    1.000
peak=    3.689 closest distance to " O   HOH Z 133 " =    2.191
peak=    3.686 closest distance to " CG2 THR A 221 " =    1.010
peak=    3.683 closest distance to " O   HOH Z 133 " =    1.660
peak=    3.681 closest distance to " O   MET A 105 " =    1.820
peak=    3.676 closest distance to " CA  ASP A 191 " =    0.797
peak=    3.673 closest distance to " O   HOH Z 193 " =    2.091
peak=    3.666 closest distance to " CD  LYS A 166 " =    1.348
peak=    3.664 closest distance to " CA  ALA A  51 " =    0.928
peak=    3.662 closest distance to " O   HOH Z 374 " =    2.565
peak=    3.657 closest distance to " CD  ARG A 159 " =    0.846
peak=    3.653 closest distance to " CD2 LEU A 255 " =    1.403
peak=    3.644 closest distance to " O   HOH Z 193 " =    1.587
peak=    3.641 closest distance to " O   HOH Z  80 " =    1.643
peak=    3.637 closest distance to " CA  ASN A 215 " =    1.245
peak=    3.627 closest distance to " O   HOH Z 313 " =    1.816
peak=    3.624 closest distance to " CB  ARG A  79 " =    1.315
peak=    3.622 closest distance to " NZ  LYS A 117 " =    3.282
peak=    3.615 closest distance to " O   HOH Z 346 " =    1.586
peak=    3.615 closest distance to " CB  SER A 216 " =    0.835
peak=    3.608 closest distance to " O   HOH Z   6 " =    2.221
peak=    3.603 closest distance to " CA  ASP A 140 " =    1.137
peak=    3.602 closest distance to " CA  ASP A 124 " =    0.719
peak=    3.599 closest distance to " O   HOH Z  59 " =    2.314
peak=    3.590 closest distance to " O   HOH Z 124 " =    1.370
peak=    3.583 closest distance to " CB  SER A 141 " =    1.028
peak=    3.579 closest distance to " CG2 ILE A 120 " =    1.208
peak=    3.579 closest distance to " O   HOH Z 199 " =    0.984
peak=    3.572 closest distance to " O   HOH Z  97 " =    1.939
peak=    3.570 closest distance to " N   ARG A 156 " =    1.378
peak=    3.550 closest distance to " O   HOH Z 281 " =    4.186
peak=    3.533 closest distance to " CB  ALA A 248 " =    0.949
peak=    3.528 closest distance to " O   HOH Z 263 " =    2.252
peak=    3.522 closest distance to " O   HOH Z 128 " =    2.217
peak=    3.519 closest distance to " CE  LYS A  76 " =    0.865
peak=    3.515 closest distance to " CG  GLN A  88 " =    1.038
peak=    3.513 closest distance to " CB  MET A  40 " =    0.814
peak=    3.510 closest distance to " O   HOH Z 303 " =    2.151
peak=    3.510 closest distance to " O   HOH Z  43 " =    1.963
peak=    3.501 closest distance to " O   HOH Z 214 " =    2.298
peak=    3.500 closest distance to " ND1 HIS A  86 " =    1.817
peak=    3.499 closest distance to " O   THR A 220 " =    1.382
peak=    3.497 closest distance to " O   THR A 251 " =    1.223
peak=    3.497 closest distance to " CB  ALA A 291 " =    1.373
peak=    3.496 closest distance to " O   HOH Z  98 " =    2.224
peak=    3.494 closest distance to " CB  PHE A  16 " =    0.985
peak=    3.485 closest distance to " NH2AARG A 190 " =    1.477
peak=    3.483 closest distance to " O   ALA A   1 " =    1.525
peak=    3.482 closest distance to " CG  LEU A 167 " =    1.167
peak=    3.480 closest distance to " OG BSER A 164 " =    2.551
peak=    3.478 closest distance to " CA  LEU A 282 " =    1.108
peak=    3.476 closest distance to " O   HOH Z 118 " =    1.601
peak=    3.473 closest distance to " CD  ARG A 269 " =    0.885
peak=    3.470 closest distance to " CG1BVAL A  72 " =    1.617
peak=    3.468 closest distance to " O   HOH Z  40 " =    1.584
peak=    3.459 closest distance to " O   HOH Z 172 " =    3.975
peak=    3.457 closest distance to " O   HOH Z 276 " =    1.297
peak=    3.456 closest distance to " CB  LEU A 143 " =    1.107
peak=    3.455 closest distance to " CD  PRO A 280 " =    0.913
peak=    3.455 closest distance to " OD1 ASN A 217 " =    1.729
peak=    3.445 closest distance to " CG  ARG A  66 " =    2.497
peak=    3.442 closest distance to " O   HOH Z 171 " =    3.793
peak=    3.441 closest distance to " O   HOH Z 116 " =    1.856
peak=    3.437 closest distance to " O   HOH Z 403 " =    1.664
peak=    3.437 closest distance to " CA  ALA A 160 " =    0.827
peak=    3.437 closest distance to " O   HOH Z  10 " =    1.863
peak=    3.434 closest distance to " O   HOH Z 214 " =    2.017
peak=    3.429 closest distance to " CB  ARG A 139 " =    0.942
peak=    3.429 closest distance to " CA  ARG A  36 " =    1.166
peak=    3.427 closest distance to " CG2 THR A 220 " =    1.093
peak=    3.423 closest distance to " ND1 HIS A  81 " =    1.540
peak=    3.423 closest distance to " CB  ARG A 190 " =    1.725
peak=    3.419 closest distance to " CB  SER A 212 " =    1.048
peak=    3.418 closest distance to " O   HOH Z 197 " =    2.557
peak=    3.412 closest distance to " CZ  PHE A 208 " =    1.132
peak=    3.403 closest distance to " CZ  PHE A 218 " =    1.019
peak=    3.402 closest distance to " O   HOH Z 423 " =    1.890
peak=    3.399 closest distance to " O   HOH Z 326 " =    1.464
peak=    3.397 closest distance to " CA  ALA A 158 " =    1.078
peak=    3.396 closest distance to " O   HOH Z 215 " =    1.569
peak=    3.393 closest distance to " NZ  LYS A  76 " =    1.209
peak=    3.392 closest distance to " O   HOH Z  54 " =    2.271
peak=    3.387 closest distance to " NH1BARG A 145 " =    0.968
peak=    3.383 closest distance to " NE AARG A 275 " =    1.463
peak=    3.382 closest distance to " O   HOH Z 345 " =    3.384
peak=    3.373 closest distance to " O   HOH Z 173 " =    1.872
peak=    3.371 closest distance to " O   HOH Z 334 " =    1.400
peak=    3.370 closest distance to " O   HOH Z 112 " =    1.422
peak=    3.369 closest distance to " CG1 VAL A 202 " =    2.103
peak=    3.362 closest distance to " OE1 GLN A  11 " =    1.902
peak=    3.361 closest distance to " O   TRP A 274 " =    1.760
peak=    3.356 closest distance to " CD1 TRP A 266 " =    1.153
peak=    3.352 closest distance to " CD2 HIS A  81 " =    1.098
peak=    3.350 closest distance to " OD1 ASP A 231 " =    1.856
peak=    3.347 closest distance to " CA  GLU A 152 " =    0.897
peak=    3.346 closest distance to " OD1 ASP A 238 " =    0.838
peak=    3.346 closest distance to " CA  GLY A 267 " =    1.160
peak=    3.343 closest distance to " CB  ASP A 140 " =    0.743
peak=    3.340 closest distance to " O   HOH Z 409 " =    3.134
peak=    3.340 closest distance to " CG BARG A 102 " =    1.906
peak=    3.333 closest distance to " CB  HIS A 108 " =    0.912
peak=    3.330 closest distance to " O   HOH Z 411 " =    1.810
peak=    3.329 closest distance to " CA  LYS A 117 " =    1.224
peak=    3.326 closest distance to " O   HOH Z 271 " =    2.175
peak=    3.326 closest distance to " O   HOH Z 163 " =    1.830
peak=    3.325 closest distance to " O   HOH Z 437 " =    1.601
peak=    3.325 closest distance to " OE1 GLN A  58 " =    1.317
peak=    3.317 closest distance to " C   LYS A 290 " =    1.292
peak=    3.303 closest distance to " O   HOH Z 387 " =    2.937
peak=    3.302 closest distance to " CG  GLN A  58 " =    2.493
peak=    3.301 closest distance to " NE BARG A 102 " =    1.286
peak=    3.293 closest distance to " O   HOH Z 215 " =    1.501
peak=    3.292 closest distance to " O   HOH Z  20 " =    3.749
peak=    3.284 closest distance to " O   HOH Z  44 " =    1.780
peak=    3.280 closest distance to " CD2 LEU A 297 " =    0.862
peak=    3.273 closest distance to " O   HOH Z 422 " =    2.684
peak=    3.273 closest distance to " OE1 GLN A  58 " =    5.819
peak=    3.270 closest distance to " CB  TYR A  30 " =    1.426
peak=    3.267 closest distance to " CG1 ILE A 151 " =    0.903
peak=    3.266 closest distance to " O   HOH Z 250 " =    1.460
peak=    3.263 closest distance to " CG  MET A 113 " =    1.393
peak=    3.263 closest distance to " O   HOH Z 327 " =    2.278
peak=    3.261 closest distance to " OH  TYR A  30 " =    1.279
peak=    3.261 closest distance to " CG  GLN A  77 " =    2.073
peak=    3.259 closest distance to " OG1 THR A 294 " =    1.604
peak=    3.257 closest distance to " CG  MET A  93 " =    0.976
peak=    3.255 closest distance to " CB  ILE A 199 " =    0.971
peak=    3.250 closest distance to " O   HOH Z   4 " =    1.962
peak=    3.248 closest distance to " O   HOH Z  53 " =    2.506
peak=    3.247 closest distance to " O   HOH Z 287 " =    1.776
peak=    3.244 closest distance to " CA  ALA A 248 " =    1.186
peak=    3.244 closest distance to " O   HOH Z 211 " =    2.220
peak=    3.244 closest distance to " O   HOH Z 287 " =    2.279
peak=    3.244 closest distance to " O   HOH Z 106 " =    2.343
peak=    3.243 closest distance to " O   HOH Z 114 " =    1.568
peak=    3.242 closest distance to " O   SER A  26 " =    1.697
peak=    3.240 closest distance to " OG  SER A  22 " =    2.788
peak=    3.238 closest distance to " CA  ALA A 154 " =    1.008
peak=    3.238 closest distance to " CG2 VAL A  78 " =    0.946
peak=    3.237 closest distance to " OG  SER A  97 " =    3.534
peak=    3.234 closest distance to " CG1 VAL A 153 " =    0.991
peak=    3.233 closest distance to " NH1 ARG A  14 " =    1.178
peak=    3.232 closest distance to " CG2BVAL A  41 " =    0.841
peak=    3.231 closest distance to " O   HOH Z 273 " =    2.831
peak=    3.230 closest distance to " O   HOH Z 388 " =    1.869
peak=    3.228 closest distance to " O   HOH Z 158 " =    2.841
peak=    3.227 closest distance to " O   HOH Z 345 " =    1.651
peak=    3.222 closest distance to " NZ ALYS A 290 " =    1.137
peak=    3.222 closest distance to " O   GLY A  57 " =    2.554
peak=    3.222 closest distance to " CG AARG A 275 " =    0.947
peak=    3.220 closest distance to " CE1 TYR A 186 " =    1.175
peak=    3.220 closest distance to " CD  ARG A 219 " =    0.965
peak=    3.219 closest distance to " O   HOH Z 427 " =    3.068
peak=    3.218 closest distance to " O   HOH Z 156 " =    2.865
peak=    3.217 closest distance to " O   HOH Z 286 " =    2.152
peak=    3.215 closest distance to " OE1 GLU A 152 " =    0.893
peak=    3.212 closest distance to " C   GLY A  80 " =    1.113
peak=    3.199 closest distance to " O   HOH Z 236 " =    1.564
peak=    3.198 closest distance to " O   HOH Z 368 " =    2.616
peak=    3.194 closest distance to " CB  LEU A 237 " =    1.019
peak=    3.190 closest distance to " CG2 VAL A 257 " =    0.872
peak=    3.184 closest distance to " O   HOH Z 139 " =    3.112
peak=    3.182 closest distance to " O   HOH Z 261 " =    1.485
peak=    3.182 closest distance to " O   HOH Z 174 " =    2.552
peak=    3.182 closest distance to " O   HOH Z 152 " =    1.312
peak=    3.181 closest distance to " O   HOH Z 368 " =    3.634
peak=    3.179 closest distance to " O   PRO A 213 " =    1.562
peak=    3.174 closest distance to " CG  MET A 185 " =    1.136
peak=    3.172 closest distance to " OE1 GLU A 277 " =    1.790
peak=    3.170 closest distance to " O   HOH Z 291 " =    1.942
peak=    3.165 closest distance to " O   HOH Z  66 " =    2.052
peak=    3.160 closest distance to " O   HOH Z  44 " =    3.426
peak=    3.160 closest distance to " SD AMET A  47 " =    1.238
peak=    3.157 closest distance to " O   HOH Z 329 " =    3.399
peak=    3.157 closest distance to " O   ALA A 158 " =    1.282
peak=    3.157 closest distance to " O   HOH Z  30 " =    1.281
peak=    3.155 closest distance to " O   HOH Z 147 " =    1.650
peak=    3.155 closest distance to " NH1 ARG A  56 " =    1.075
peak=    3.154 closest distance to " CZ  PHE A 192 " =    0.907
peak=    3.152 closest distance to " CA  SER A  87 " =    0.935
peak=    3.149 closest distance to " O   HOH Z 166 " =    3.397
peak=    3.148 closest distance to " O   HOH Z 425 " =    2.125
peak=    3.147 closest distance to " O   HOH Z 277 " =    2.458
peak=    3.142 closest distance to " O   HOH Z  38 " =    2.016
peak=    3.138 closest distance to " O   HOH Z 426 " =    3.247
peak=    3.137 closest distance to " O   HOH Z 248 " =    1.535
peak=    3.136 closest distance to " O   HOH Z 337 " =    3.790
peak=    3.135 closest distance to " CA  GLN A 223 " =    0.984
peak=    3.132 closest distance to " CB  SER A  62 " =    1.222
peak=    3.131 closest distance to " O   HOH Z 395 " =    1.458
peak=    3.130 closest distance to " O   HOH Z 217 " =    1.224
peak=    3.127 closest distance to " O   HOH Z  71 " =    1.052
peak=    3.127 closest distance to " CA  TYR A 186 " =    1.397
peak=    3.126 closest distance to " CA  GLY A 211 " =    1.207
peak=    3.124 closest distance to " O   HOH Z 273 " =    3.379
peak=    3.120 closest distance to " O   HOH Z  50 " =    3.486
peak=    3.117 closest distance to " O   HOH Z 334 " =    1.560
peak=    3.117 closest distance to " C   ALA A 299 " =    0.955
peak=    3.116 closest distance to " CD1AILE A 234 " =    1.018
peak=    3.115 closest distance to " O   HOH Z 163 " =    1.481
peak=    3.100 closest distance to " O   HOH Z  63 " =    2.213
peak=    3.100 closest distance to " O   HOH Z 305 " =    3.725
peak=    3.099 closest distance to " O   HOH Z  43 " =    2.747
peak=    3.098 closest distance to " O   HOH Z 367 " =    3.579
peak=    3.095 closest distance to " NH2 ARG A 219 " =    1.836
peak=    3.092 closest distance to " O   HOH Z 329 " =    2.635
peak=    3.084 closest distance to " CA  LEU A 101 " =    1.503
peak=    3.081 closest distance to " CA  LYS A  48 " =    1.351
peak=    3.079 closest distance to " O   HOH Z 106 " =    2.249
peak=    3.072 closest distance to " CB  PRO A 243 " =    1.216
peak=    3.068 closest distance to " O   HOH Z 266 " =    1.516
peak=    3.067 closest distance to " NE1 TRP A 266 " =    1.275
peak=    3.060 closest distance to " CD2 HIS A  81 " =    1.092
peak=    3.060 closest distance to " O   HOH Z 285 " =    1.883
peak=    3.055 closest distance to " CA  ILE A  33 " =    1.670
peak=    3.034 closest distance to " OG ASER A  99 " =    1.982
peak=    3.029 closest distance to " O   HOH Z  73 " =    1.447
peak=    3.012 closest distance to " NZ  LYS A 119 " =    1.274

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.833 - 5.476
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.833 - 5.476

peak=   -4.581 closest distance to " O   HOH Z 266 " =    4.261
peak=   -4.507 closest distance to " O   HOH Z 377 " =    1.740
peak=   -4.441 closest distance to " O   HOH Z 290 " =    1.035
peak=   -4.396 closest distance to " O   HOH Z 198 " =    2.446
peak=   -4.165 closest distance to " C   ASN A 187 " =    1.869
peak=   -4.096 closest distance to " O   ILE A 109 " =    2.628
peak=   -4.094 closest distance to " O   HOH Z  98 " =    1.824
peak=   -4.093 closest distance to " CG  LYS A 193 " =    2.468
peak=   -4.087 closest distance to " CB  PRO A 243 " =    2.646
peak=   -4.079 closest distance to " O   HOH Z 388 " =    1.889
peak=   -4.043 closest distance to " C   ALA A 158 " =    1.204
peak=   -4.008 closest distance to " O   HOH Z  93 " =    1.749
peak=   -4.006 closest distance to " CD  ARG A 156 " =    1.896
peak=   -3.997 closest distance to " N   ALA A  43 " =    2.440
peak=   -3.989 closest distance to " O   HOH Z 231 " =    1.873
peak=   -3.988 closest distance to " O   HOH Z  43 " =    1.422
peak=   -3.982 closest distance to " O   HOH Z  19 " =    2.211
peak=   -3.980 closest distance to " O   HOH Z 407 " =    3.369
peak=   -3.935 closest distance to " O   HOH Z  13 " =    1.290
peak=   -3.934 closest distance to " OXT GLY A 302 " =    2.927
peak=   -3.930 closest distance to " O   HOH Z  52 " =    1.408
peak=   -3.928 closest distance to " ND2 ASN A  45 " =    0.938
peak=   -3.917 closest distance to " O   VAL A  67 " =    2.830
peak=   -3.915 closest distance to " O   HOH Z  92 " =    1.523
peak=   -3.901 closest distance to " C   ASN A 285 " =    2.552
peak=   -3.882 closest distance to " CB  TYR A  15 " =    2.199
peak=   -3.864 closest distance to " NH2 ARG A  66 " =    1.919
peak=   -3.845 closest distance to " CE  MET A  93 " =    1.316
peak=   -3.839 closest distance to " OG ASER A 134 " =    1.257
peak=   -3.835 closest distance to " O   PRO A 163 " =    2.034
peak=   -3.826 closest distance to " CD  LYS A 289 " =    2.556
peak=   -3.825 closest distance to " CD2 LEU A 237 " =    2.432
peak=   -3.816 closest distance to " OG  SER A  97 " =    2.166
peak=   -3.806 closest distance to " CD1 LEU A 228 " =    2.344
peak=   -3.806 closest distance to " CD  GLN A  88 " =    2.130
peak=   -3.805 closest distance to " CE2 TYR A  30 " =    2.890
peak=   -3.805 closest distance to " O   HOH Z  11 " =    1.787
peak=   -3.795 closest distance to " O   HOH Z  97 " =    1.748
peak=   -3.777 closest distance to " CG  GLU A  53 " =    1.388
peak=   -3.762 closest distance to " O   HOH Z 292 " =    4.476
peak=   -3.760 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.758 closest distance to " N   GLN A  58 " =    1.726
peak=   -3.734 closest distance to " O   HOH Z  10 " =    1.589
peak=   -3.719 closest distance to " CD2 LEU A 300 " =    2.933
peak=   -3.714 closest distance to " CZ  PHE A  59 " =    1.705
peak=   -3.681 closest distance to " CG  MET A 105 " =    0.951
peak=   -3.673 closest distance to " O   HOH Z  38 " =    1.435
peak=   -3.673 closest distance to " OG  SER A  62 " =    1.564
peak=   -3.671 closest distance to " CB  CYS A 254 " =    2.337
peak=   -3.662 closest distance to " O   HOH Z 166 " =    1.824
peak=   -3.656 closest distance to " CG  ASP A 231 " =    0.873
peak=   -3.654 closest distance to " O   HOH Z 185 " =    2.191
peak=   -3.648 closest distance to " O   HOH Z 283 " =    1.804
peak=   -3.643 closest distance to " CG2 THR A   4 " =    1.964
peak=   -3.634 closest distance to " CD  ARG A 139 " =    1.668
peak=   -3.633 closest distance to " CB  ALA A 291 " =    2.383
peak=   -3.629 closest distance to " CZ3 TRP A 179 " =    1.265
peak=   -3.628 closest distance to " O   HOH Z 436 " =    1.525
peak=   -3.620 closest distance to " OE2 GLU A   2 " =    1.741
peak=   -3.615 closest distance to " O   HOH Z 350 " =    1.686
peak=   -3.611 closest distance to " O   GLY A 211 " =    1.448
peak=   -3.604 closest distance to " OE1 GLN A 223 " =    2.002
peak=   -3.589 closest distance to " CD2 PHE A  59 " =    2.556
peak=   -3.585 closest distance to " CB  ASN A  39 " =    2.129
peak=   -3.584 closest distance to " NH1 ARG A 195 " =    2.633
peak=   -3.580 closest distance to " CD  GLN A  88 " =    0.833
peak=   -3.567 closest distance to " O   HOH Z 266 " =    4.629
peak=   -3.567 closest distance to " CG  GLN A  58 " =    1.424
peak=   -3.565 closest distance to " O   HOH Z  98 " =    1.326
peak=   -3.564 closest distance to " OE1 GLN A  88 " =    1.095
peak=   -3.563 closest distance to " N   SER A 276 " =    1.303
peak=   -3.563 closest distance to " CD  ARG A  14 " =    3.344
peak=   -3.559 closest distance to " SG  CYS A 254 " =    3.099
peak=   -3.553 closest distance to " CD  ARG A 195 " =    5.137
peak=   -3.551 closest distance to " O   HOH Z 353 " =    2.186
peak=   -3.544 closest distance to " O   GLY A 196 " =    1.113
peak=   -3.542 closest distance to " CA  VAL A 232 " =    2.522
peak=   -3.535 closest distance to " O   HOH Z  71 " =    1.103
peak=   -3.531 closest distance to " CB  ALA A  43 " =    2.454
peak=   -3.520 closest distance to " OG  SER A  87 " =    1.391
peak=   -3.518 closest distance to " CZ  TYR A 169 " =    1.809
peak=   -3.510 closest distance to " N   ALA A 226 " =    2.147
peak=   -3.484 closest distance to " O   HOH Z 166 " =    1.436
peak=   -3.475 closest distance to " O   HOH Z 213 " =    1.243
peak=   -3.473 closest distance to " O   HOH Z 275 " =    1.588
peak=   -3.473 closest distance to " C   HIS A 108 " =    1.127
peak=   -3.472 closest distance to " CB  ALA A 291 " =    2.262
peak=   -3.468 closest distance to " CB  SER A 245 " =    2.415
peak=   -3.464 closest distance to " N   SER A 212 " =    2.017
peak=   -3.458 closest distance to " OD1 ASP A 191 " =    1.665
peak=   -3.448 closest distance to " CG  GLU A 277 " =    1.134
peak=   -3.445 closest distance to " O   VAL A 174 " =    2.007
peak=   -3.430 closest distance to " OD1 ASP A 200 " =    1.370
peak=   -3.428 closest distance to " CE  MET A 105 " =    2.085
peak=   -3.427 closest distance to " C   GLN A 240 " =    2.280
peak=   -3.425 closest distance to " OD1 ASN A 176 " =    1.031
peak=   -3.423 closest distance to " O   HOH Z  76 " =    1.842
peak=   -3.420 closest distance to " O   ASN A 301 " =    1.584
peak=   -3.404 closest distance to " C   LEU A 143 " =    1.480
peak=   -3.402 closest distance to " O   HOH Z 385 " =    2.092
peak=   -3.395 closest distance to " CE3 TRP A 150 " =    1.891
peak=   -3.389 closest distance to " CG  LEU A  83 " =    1.918
peak=   -3.389 closest distance to " OD1 ASN A 148 " =    1.731
peak=   -3.387 closest distance to " N   THR A 157 " =    1.619
peak=   -3.380 closest distance to " O   HOH Z  15 " =    2.129
peak=   -3.366 closest distance to " O   HOH Z  88 " =    2.352
peak=   -3.365 closest distance to " N   GLN A 122 " =    1.637
peak=   -3.357 closest distance to " O   HOH Z 396 " =    1.672
peak=   -3.353 closest distance to " O   HOH Z 128 " =    2.534
peak=   -3.351 closest distance to " OE1 GLN A  77 " =    1.968
peak=   -3.340 closest distance to " O   GLY A 118 " =    2.229
peak=   -3.335 closest distance to " CD  GLU A 236 " =    1.059
peak=   -3.330 closest distance to " O   ALA A 161 " =    1.577
peak=   -3.317 closest distance to " CD1 PHE A  59 " =    1.781
peak=   -3.317 closest distance to " O   HOH Z  15 " =    1.701
peak=   -3.316 closest distance to " CB  SER A 134 " =    1.822
peak=   -3.296 closest distance to " CA  ASP A 298 " =    1.061
peak=   -3.294 closest distance to " O   HOH Z  60 " =    1.907
peak=   -3.288 closest distance to " CD1 ILE A 263 " =    2.428
peak=   -3.285 closest distance to " SG ACYS A 201 " =    2.260
peak=   -3.284 closest distance to " O   HOH Z 389 " =    1.786
peak=   -3.283 closest distance to " CG  ASP A  50 " =    2.363
peak=   -3.279 closest distance to " NH2AARG A 275 " =    5.476
peak=   -3.278 closest distance to " O   HOH Z 234 " =    4.198
peak=   -3.277 closest distance to " O   HOH Z 184 " =    1.643
peak=   -3.270 closest distance to " O   HOH Z  63 " =    1.226
peak=   -3.267 closest distance to " O   HOH Z 118 " =    2.664
peak=   -3.264 closest distance to " CD1 LEU A 101 " =    2.631
peak=   -3.263 closest distance to " O   HOH Z 387 " =    3.667
peak=   -3.257 closest distance to " CD  LYS A 119 " =    1.064
peak=   -3.256 closest distance to " OD2 ASP A 171 " =    1.779
peak=   -3.255 closest distance to " CB  ALA A  51 " =    1.857
peak=   -3.254 closest distance to " OG  SER A 245 " =    0.944
peak=   -3.253 closest distance to " CD  PRO A 198 " =    1.429
peak=   -3.249 closest distance to " ND2 ASN A 187 " =    1.592
peak=   -3.249 closest distance to " CB  SER A 258 " =    2.099
peak=   -3.246 closest distance to " CG  TRP A 266 " =    1.631
peak=   -3.241 closest distance to " OD2 ASP A 171 " =    2.259
peak=   -3.236 closest distance to " O   HOH Z 148 " =    3.336
peak=   -3.236 closest distance to " CB  LEU A 167 " =    2.113
peak=   -3.233 closest distance to " CE  LYS A  76 " =    2.963
peak=   -3.230 closest distance to " O   HOH Z 148 " =    1.866
peak=   -3.224 closest distance to " NH2 ARG A  79 " =    1.820
peak=   -3.221 closest distance to " O   HOH Z 281 " =    2.687
peak=   -3.215 closest distance to " CB  PHE A 283 " =    2.762
peak=   -3.213 closest distance to " O   HOH Z 252 " =    4.361
peak=   -3.212 closest distance to " O   HOH Z 409 " =    4.595
peak=   -3.209 closest distance to " O   HOH Z 243 " =    2.017
peak=   -3.205 closest distance to " N   GLY A 133 " =    1.855
peak=   -3.201 closest distance to " CA  VAL A 197 " =    1.064
peak=   -3.197 closest distance to " CB  ASP A 132 " =    2.233
peak=   -3.195 closest distance to " CG  ARG A  66 " =    2.399
peak=   -3.194 closest distance to " O   HOH Z 399 " =    2.242
peak=   -3.194 closest distance to " CA  TRP A 274 " =    1.689
peak=   -3.188 closest distance to " OH  TYR A 169 " =    0.969
peak=   -3.186 closest distance to " CG2AVAL A  41 " =    2.787
peak=   -3.185 closest distance to " N   THR A 264 " =    1.321
peak=   -3.183 closest distance to " CB  ALA A 248 " =    1.941
peak=   -3.183 closest distance to " ND2 ASN A 249 " =    1.939
peak=   -3.183 closest distance to " O   VAL A 153 " =    2.290
peak=   -3.179 closest distance to " O   HOH Z 377 " =    1.122
peak=   -3.179 closest distance to " CD2 TYR A 293 " =    2.100
peak=   -3.178 closest distance to " O   HOH Z 411 " =    3.406
peak=   -3.174 closest distance to " CD1 ILE A 239 " =    2.015
peak=   -3.169 closest distance to " O   PHE A 218 " =    1.411
peak=   -3.168 closest distance to " O   HOH Z   9 " =    2.002
peak=   -3.164 closest distance to " O   HOH Z 361 " =    3.363
peak=   -3.163 closest distance to " NE2 GLN A  58 " =    1.025
peak=   -3.163 closest distance to " OG BSER A 134 " =    1.166
peak=   -3.152 closest distance to " CB  PHE A  16 " =    2.563
peak=   -3.148 closest distance to " CD  ARG A 159 " =    1.185
peak=   -3.147 closest distance to " CG  ARG A 269 " =    2.388
peak=   -3.137 closest distance to " O   HOH Z  61 " =    1.580
peak=   -3.133 closest distance to " O   ALA A 256 " =    1.561
peak=   -3.130 closest distance to " CE  MET A 105 " =    1.932
peak=   -3.127 closest distance to " O   HOH Z 222 " =    1.221
peak=   -3.126 closest distance to " SD BMET A  47 " =    0.999
peak=   -3.125 closest distance to " O   SER A 135 " =    1.547
peak=   -3.121 closest distance to " CE3 TRP A  70 " =    1.756
peak=   -3.120 closest distance to " NH2 ARG A 159 " =    2.435
peak=   -3.116 closest distance to " O   LEU A 167 " =    1.518
peak=   -3.111 closest distance to " CE3 TRP A 274 " =    2.488
peak=   -3.108 closest distance to " CB  SER A  63 " =    3.300
peak=   -3.105 closest distance to " CG  ARG A 259 " =    2.865
peak=   -3.101 closest distance to " OD2 ASP A 270 " =    1.389
peak=   -3.097 closest distance to " CD1 TRP A 179 " =    1.066
peak=   -3.093 closest distance to " CB  CYS A 201 " =    2.256
peak=   -3.086 closest distance to " O   HOH Z 310 " =    3.559
peak=   -3.083 closest distance to " O   HOH Z 113 " =    2.515
peak=   -3.078 closest distance to " OXT GLY A 302 " =    3.127
peak=   -3.052 closest distance to " O   PRO A 198 " =    1.334
peak=   -3.051 closest distance to " CD  GLN A  88 " =    0.996
peak=   -3.038 closest distance to " CB  PHE A 192 " =    1.869

================= 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    :  0.4110 0.4178   6.209892e+00   6.218764e+00
   1_bss:  0.4008 0.4094   6.202054e+00   6.205408e+00
   1_xyz:  0.2932 0.3279   5.964904e+00   6.051244e+00
   1_adp:  0.2671 0.3328   5.916005e+00   6.065848e+00
   1_occ:  0.2668 0.3328   5.914783e+00   6.064979e+00
   2_bss:  0.2659 0.3309   5.912990e+00   6.060501e+00
   2_xyz:  0.1914 0.2496   5.619505e+00   5.821828e+00
   2_adp:  0.1742 0.2299   5.538062e+00   5.748770e+00
   2_occ:  0.1741 0.2298   5.537647e+00   5.748378e+00
   3_bss:  0.1737 0.2283   5.533944e+00   5.743235e+00
   3_xyz:  0.1400 0.1860   5.335471e+00   5.556126e+00
   3_adp:  0.1316 0.1779   5.284075e+00   5.504846e+00
   3_occ:  0.1315 0.1777   5.283259e+00   5.504088e+00
   4_bss:  0.1315 0.1771   5.283697e+00   5.504594e+00
   4_xyz:  0.1225 0.1659   5.216528e+00   5.437369e+00
   4_adp:  0.1194 0.1653   5.202737e+00   5.431221e+00
   4_occ:  0.1194 0.1653   5.202411e+00   5.431182e+00
   5_bss:  0.1193 0.1652   5.202221e+00   5.431035e+00
   5_xyz:  0.1143 0.1618   5.175028e+00   5.413245e+00
   5_adp:  0.1137 0.1606   5.170430e+00   5.408176e+00
   5_occ:  0.1136 0.1607   5.170191e+00   5.408342e+00
   5_bss:  0.1136 0.1606   5.170251e+00   5.408365e+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:  0.300  50.000  -0.483  -2.015   2.876  -0.000   0.000   0.000
   1_xyz:  0.300  50.000  -0.483  -2.015   2.876  -0.000   0.000   0.000
   1_adp:  0.300  50.000  -0.483  -2.015   2.876  -0.000   0.000   0.000
   1_occ:  0.300  50.000  -0.483  -2.015   2.876  -0.000   0.000   0.000
   2_bss:  0.329  59.085  -1.412  -1.804   0.583  -0.000   0.000   0.000
   2_xyz:  0.329  59.085  -1.412  -1.804   0.583  -0.000   0.000   0.000
   2_adp:  0.329  59.085  -1.412  -1.804   0.583  -0.000   0.000   0.000
   2_occ:  0.329  59.085  -1.412  -1.804   0.583  -0.000   0.000   0.000
   3_bss:  0.327  55.757  -2.045  -2.312  -1.279  -0.000  -0.000  -0.000
   3_xyz:  0.327  55.757  -2.045  -2.312  -1.279  -0.000  -0.000  -0.000
   3_adp:  0.327  55.757  -2.045  -2.312  -1.279  -0.000  -0.000  -0.000
   3_occ:  0.327  55.757  -2.045  -2.312  -1.279  -0.000  -0.000  -0.000
   4_bss:  0.321  49.781  -2.429  -2.491  -2.030  -0.000  -0.000  -0.000
   4_xyz:  0.321  49.781  -2.429  -2.491  -2.030  -0.000  -0.000  -0.000
   4_adp:  0.321  49.781  -2.429  -2.491  -2.030  -0.000  -0.000  -0.000
   4_occ:  0.321  49.781  -2.429  -2.491  -2.030  -0.000  -0.000  -0.000
   5_bss:  0.320  49.781  -2.345  -2.408  -2.142  -0.000  -0.000  -0.000
   5_xyz:  0.320  49.781  -2.345  -2.408  -2.142  -0.000  -0.000  -0.000
   5_adp:  0.320  49.781  -2.345  -2.408  -2.142  -0.000  -0.000  -0.000
   5_occ:  0.320  49.781  -2.345  -2.408  -2.142  -0.000  -0.000  -0.000
   5_bss:  0.320  49.730  -2.158  -2.189  -1.993  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.027 0.5325  0.7050    53610.260
   1_bss:  47.572 0.5485  0.7336    49913.498
   1_xyz:  35.139 0.6997  0.9079    30320.639
   1_adp:  36.399 0.6840  0.8958    31908.189
   1_occ:  36.372 0.6842  0.8960    31824.337
   2_bss:  36.044 0.6880  0.8702    31410.672
   2_xyz:  25.486 0.8053  0.9810    16581.089
   2_adp:  22.871 0.8332  0.9968    14019.520
   2_occ:  22.871 0.8332  0.9966    14010.422
   3_bss:  22.667 0.8352  0.9626    13795.848
   3_xyz:  17.884 0.8808  0.9854     8999.501
   3_adp:  16.604 0.8930  0.9875     8201.021
   3_occ:  16.576 0.8933  0.9874     8183.265
   4_bss:  16.578 0.8933  0.9717     8203.731
   4_xyz:  15.164 0.9054  0.9775     7104.056
   4_adp:  14.977 0.9072  0.9744     7007.643
   4_occ:  14.968 0.9073  0.9743     7004.120
   5_bss:  14.967 0.9073  0.9748     7005.191
   5_xyz:  14.650 0.9097  0.9748     6707.255
   5_adp:  14.517 0.9109  0.9705     6639.811
   5_occ:  14.511 0.9110  0.9703     6641.123
   5_bss:  14.513 0.9110  0.9749     6642.061
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7984e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7984e-01
   1_xyz:   1.291  0.010  0.082 15.435  0.005  4.112   9.3711e-02
   1_adp:   1.291  0.010  0.082 15.435  0.005  4.112   9.3711e-02
   1_occ:   1.291  0.010  0.082 15.435  0.005  4.112   9.3711e-02
   2_bss:   1.291  0.010  0.082 15.435  0.005  4.112   9.3711e-02
   2_xyz:   1.134  0.008  0.073 14.233  0.004  4.126   6.8469e-02
   2_adp:   1.134  0.008  0.073 14.233  0.004  4.126   6.8469e-02
   2_occ:   1.134  0.008  0.073 14.233  0.004  4.126   6.8469e-02
   3_bss:   1.134  0.008  0.073 14.233  0.004  4.126   6.8469e-02
   3_xyz:   0.947  0.006  0.066 14.186  0.003  4.112   5.3689e-02
   3_adp:   0.947  0.006  0.066 14.186  0.003  4.112   5.3689e-02
   3_occ:   0.947  0.006  0.066 14.186  0.003  4.112   5.3689e-02
   4_bss:   0.947  0.006  0.066 14.186  0.003  4.112   5.3689e-02
   4_xyz:   0.927  0.005  0.067 14.130  0.003  4.115   5.0126e-02
   4_adp:   0.927  0.005  0.067 14.130  0.003  4.115   5.0126e-02
   4_occ:   0.927  0.005  0.067 14.130  0.003  4.115   5.0126e-02
   5_bss:   0.927  0.005  0.067 14.130  0.003  4.115   5.0126e-02
   5_xyz:   0.965  0.006  0.069 14.243  0.003  4.116   5.3370e-02
   5_adp:   0.965  0.006  0.069 14.243  0.003  4.116   5.3370e-02
   5_occ:   0.965  0.006  0.069 14.243  0.003  4.116   5.3370e-02
   5_bss:   0.965  0.006  0.069 14.243  0.003  4.116   5.3370e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.516   2.4085e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.516   2.4085e-01
   1_xyz:   8.111  0.055  0.278 86.700  0.032  2.176   8.7767e-02
   1_adp:   8.111  0.055  0.278 86.700  0.032  2.176   8.7767e-02
   1_occ:   8.111  0.055  0.278 86.700  0.032  2.176   8.7767e-02
   2_bss:   8.111  0.055  0.278 86.700  0.032  2.176   8.7767e-02
   2_xyz:   8.056  0.043  0.247 89.003  0.027  2.321   9.1141e-02
   2_adp:   8.056  0.043  0.247 89.003  0.027  2.321   9.1141e-02
   2_occ:   8.056  0.043  0.247 89.003  0.027  2.321   9.1141e-02
   3_bss:   8.056  0.043  0.247 89.003  0.027  2.321   9.1141e-02
   3_xyz:   8.097  0.040  0.263 84.793  0.032  2.347   4.1871e-02
   3_adp:   8.097  0.040  0.263 84.793  0.032  2.347   4.1871e-02
   3_occ:   8.097  0.040  0.263 84.793  0.032  2.347   4.1871e-02
   4_bss:   8.097  0.040  0.263 84.793  0.032  2.347   4.1871e-02
   4_xyz:   6.872  0.044  0.219 82.841  0.027  2.371   3.0958e-02
   4_adp:   6.872  0.044  0.219 82.841  0.027  2.371   3.0958e-02
   4_occ:   6.872  0.044  0.219 82.841  0.027  2.371   3.0958e-02
   5_bss:   6.872  0.044  0.219 82.841  0.027  2.371   3.0958e-02
   5_xyz:   7.579  0.046  0.210 82.925  0.028  2.323   3.5759e-02
   5_adp:   7.579  0.046  0.210 82.925  0.028  2.323   3.5759e-02
   5_occ:   7.579  0.046  0.210 82.925  0.028  2.323   3.5759e-02
   5_bss:   7.579  0.046  0.210 82.925  0.028  2.323   3.5759e-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:  86.66   0.00  18.19  86.66   0.00  14.05  85.79   2.24  40.74
   1_occ:  86.66   0.00  18.19  86.66   0.00  14.05  85.79   2.24  40.74
   2_bss:  86.66   0.00  18.19  86.66   0.00  14.05  85.79   2.24  40.74
   2_xyz:  86.66   0.00  18.19  86.66   0.00  14.05  85.79   2.24  40.74
   2_adp:  88.39   0.44  18.06  83.19   0.44  13.61  88.39   5.55  42.32
   2_occ:  88.39   0.44  18.06  83.19   0.44  13.61  88.39   5.55  42.32
   3_bss:  88.39   0.44  18.06  83.19   0.44  13.61  88.39   5.55  42.32
   3_xyz:  88.39   0.44  18.06  83.19   0.44  13.61  88.39   5.55  42.32
   3_adp:  86.97   0.00  17.71  84.91   0.00  13.28  86.97   5.66  41.80
   3_occ:  86.97   0.00  17.71  84.91   0.00  13.28  86.97   5.66  41.80
   4_bss:  86.97   0.00  17.71  84.91   0.00  13.28  86.97   5.66  41.80
   4_xyz:  86.97   0.00  17.71  84.91   0.00  13.28  86.97   5.66  41.80
   4_adp:  97.78   1.41  17.82  97.78   1.41  13.29  86.51   5.81  42.45
   4_occ:  97.78   1.41  17.82  97.78   1.41  13.29  86.51   5.81  42.45
   5_bss:  97.78   1.41  17.82  97.78   1.41  13.29  86.51   5.81  42.45
   5_xyz:  97.78   1.41  17.82  97.78   1.41  13.29  86.51   5.81  42.45
   5_adp: 101.06   1.44  17.46 101.06   1.44  13.11  86.87   5.77  41.11
   5_occ: 101.06   1.44  17.46 101.06   1.44  13.11  86.87   5.77  41.11
   5_bss: 101.01   1.39  17.40 101.01   1.39  13.06  86.82   5.72  41.06
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.884    0.007    0.297
   1_adp:    1.884    0.007    0.297
   1_occ:    1.884    0.007    0.297
   2_bss:    1.884    0.007    0.297
   2_xyz:    1.448    0.052    0.469
   2_adp:    1.448    0.052    0.469
   2_occ:    1.448    0.052    0.469
   3_bss:    1.448    0.052    0.469
   3_xyz:    1.452    0.039    0.551
   3_adp:    1.452    0.039    0.551
   3_occ:    1.452    0.039    0.551
   4_bss:    1.452    0.039    0.551
   4_xyz:    1.478    0.033    0.574
   4_adp:    1.478    0.033    0.574
   4_occ:    1.478    0.033    0.574
   5_bss:    1.478    0.033    0.574
   5_xyz:    1.561    0.052    0.592
   5_adp:    1.561    0.052    0.592
   5_occ:    1.561    0.052    0.592
   5_bss:    1.561    0.052    0.592
------------------------------------------------------------------------

CPU time actual refinement: 353.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1034/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_1034/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1034/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1034/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1034/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.32 
  Macro-tasks:
    bulk solvent and scale       = 38.10  
    individual site refinement   = 150.09 
    weights calculation          = 30.29  
    collect and process          = 6.58   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 225.15 
  Micro-tasks:
    mask                            = 1.89   
    f_calc                          = 117.90 
    alpha_beta                      = 8.15   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 125.53 
    fmodel                         = 6.32   
    r_factors                      = 0.17   
    phase_errors                   = 10.86  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 272.23 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.987 micro seconds
Total CPU time: 6.12 minutes
from_scatterers_fft:    644 calls, 117.56 s
gradients_fft:          589 calls, 111.92 s

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

# Date 2008-01-16 Time 06:16:55 PST -0800 (1200493015.89 s)
Start R-work = 0.4110, R-free = 0.4178 (no bulk solvent and anisotropic scale)
Final R-work = 0.1381, R-free = 0.1817 (no bulk solvent and anisotropic scale)

Start R-work = 0.4008, R-free = 0.4094
Final R-work = 0.1136, R-free = 0.1606